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Topic Editors

School of Cancer and Pharmaceutical Sciences, King's College London, London SE1 9NH, UK
Department of Chemistry, the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, UK
Department of Chemistry, University of Oxford, Oxford, UK
1. I.P – National Institute for Agrarian and Veterinarian Research (INIAV), Vairão, Portugal
2. Centre of Biological Engineering (CEB), Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
3. LABBELS–Associate Laboratory, Braga/Guimarães, Portugal

Novel Antimicrobial Agents: Discovery, Design and New Therapeutic Strategies

Abstract submission deadline
closed (31 December 2021)
Manuscript submission deadline
closed (31 March 2022)
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215950

Topic Information

Dear Colleagues,

The increase in antibiotic resistance raises concerns that, at least in some regions (especially developing countries), we are returning to a pre-antibiotic era, in particular for Gram-negative infections. The CV-19 outbreak exemplifies that resistance originating from some parts of the world has global effects, hence we need to act now to eradicate antimicrobial resistance worldwide. There are few novel anti-Gram-negative/positive drugs entering clinical trials, therefore, novel drugs, but also development of novel techniques and methods that lead to new drugs, are needed. Overcoming resistance to restore the activity of existing drugs and repurposing with an excellent safety record are also important topics. This Special Issue is seeking original research articles and synopses (reviews) that make substantial advances within this field and we are inviting researchers from different fields (chemistry, biology, biochemistry, medicinal chemistry, PK PD modellers) to contribute to this editorial project. We aim to cover not only traditional but also non-traditional products, with both broad range and single target antibiotics both for human and animal use.

Dr. Daniele Castagnolo
Dr. Jürgen Brem
Prof. Dr. Mark G. Moloney
Dr. Sónia Silva
Topic Editors

Keywords

  • antibiotic resistance
  • antimicrobial agents
  • novel anti-Gram-negative drugs
  • novel anti-Gram-positive drugs
  • antibiotics use

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Antibiotics
antibiotics
4.3 7.3 2012 14.7 Days CHF 2900
Chemistry
chemistry
2.4 3.2 2019 13.4 Days CHF 1800
Molecules
molecules
4.2 7.4 1996 15.1 Days CHF 2700

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Published Papers (61 papers)

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21 pages, 3266 KiB  
Article
Antiplasmodial Cyclodecapeptides from Tyrothricin Share a Target with Chloroquine
by Adrienne N.-N. Leussa and Marina Rautenbach
Antibiotics 2022, 11(6), 801; https://doi.org/10.3390/antibiotics11060801 - 14 Jun 2022
Cited by 3 | Viewed by 2485
Abstract
Previous research found that the six major cyclodecapeptides from the tyrothricin complex, produced by Brevibacillus parabrevis, showed potent activity against chloroquine sensitive (CQS) Plasmodium falciparum. The identity of the aromatic residues in the aromatic dipeptide unit in cyclo-(D-Phe1-Pro2 [...] Read more.
Previous research found that the six major cyclodecapeptides from the tyrothricin complex, produced by Brevibacillus parabrevis, showed potent activity against chloroquine sensitive (CQS) Plasmodium falciparum. The identity of the aromatic residues in the aromatic dipeptide unit in cyclo-(D-Phe1-Pro2-(Phe3/Trp3)-D-Phe4/D-Trp4)-Asn5-Gln6-(Tyr7/Phe7/Trp7)-Val8-(Orn9/Lys9)-Leu10 was proposed to have an important role in activity. CQS and resistant (CQR) P. falciparum strains were challenged with three representative cyclodecapeptides. Our results confirmed that cyclodecapeptides from tyrothricin had significantly higher antiplasmodial activity than the analogous gramicidin S, rivaling that of CQ. However, the previously hypothesized size and hydrophobicity dependent activity for these peptides did not hold true for P. falciparum strains, other than for the CQS 3D7 strain. The Tyr7 in tyrocidine A (TrcA) with Phe3-D-Phe4 seem to be related with loss in activity correlating with CQ antagonism and resistance, indicating a shared target and/or resistance mechanism in which the phenolic groups play a role. Phe7 in phenycidine A, the second peptide containing Phe3-D-Phe4, also showed CQ antagonism. Conversely, Trp7 in tryptocidine C (TpcC) with Trp3-D-Trp4 showed improved peptide selectivity and activity towards the more resistant strains, without overt antagonism towards CQ. However, TpcC lead to similar parasite stage inhibition and parasite morphology changes than previously observed for TrcA. The disorganization of chromatin packing and neutral lipid structures, combined with amorphous hemozoin crystals, could account for halted growth in late trophozoite/early schizont stage and the nanomolar non-lytic activity of these peptides. These targets related to CQ antagonism, changes in neural lipid distribution, leading to hemozoin malformation, indicate that the tyrothricin cyclodecapeptides and CQ share a target in the malaria parasite. The differing activities of these cyclic peptides towards CQS and CQR P. falciparum strains could be due to variable target interaction in multiple modes of activity. This indicated that the cyclodecapeptide activity and parasite resistance response depended on the aromatic residues in positions 3, 4 and 7. This new insight on these natural cyclic decapeptides could also benefit the design of unique small peptidomimetics in which activity and resistance can be modulated. Full article
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Graphical abstract

Graphical abstract
Full article ">Figure 1
<p>The chemical structures of gramicidin S (GS), tyrocidine A (TrcA), phenycidine A (PhcA), tryptocidine C (TpcC), and chloroquine (CQ).</p>
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<p>Distribution of trophozoite, schizont and ring parasite stages over time from 0 to 48 h following treatment of synchronized <span class="html-italic">P. falciparum</span> D10 cultures at trophozoite stage incubated without (control) (<b>A</b>), with 200 nM of TpcC (<b>B</b>) or 200 ng/mL Trc mixture (<b>C</b>). Each data point represents the mean ± SEM of parasite counts made within 8–13 regions on the microscope slide from two cultures of each treatment.</p>
Full article ">Figure 3
<p>Super-resolution structured illumination fluorescence microscopy images of late intra-erythrocytic stages of <span class="html-italic">P. falciparum</span> D10 stained with the membrane impermeable fluorescent dye trypan blue (red) and the permeable nucleic acid fluorescent dye SYTO9 (green). Images (<b>A</b>–<b>D</b>) show untreated normal trophozoites and (<b>D</b>) a normal schizont. Images (<b>E</b>–<b>I</b>) show TpcC-treated trophozoites (post 6 h treatment) and (<b>J</b>–<b>L</b>) show TpcC-treated schizonts (post 6 h treatment). The arrows in (<b>I</b>,<b>H</b>) highlights the of dark irregular elongated structures, which could indicate hemozoin crystals, within or close to the nuclear material mass. Each image shows a single erythrocyte, with an average diameter of 7.5 μm. Refer to <a href="#antibiotics-11-00801-f004" class="html-fig">Figure 4</a> more detailed magnification scales.</p>
Full article ">Figure 4
<p>Super-resolution structured illumination fluorescence microscopy images of late intra-erythrocytic stages of <span class="html-italic">P. falciparum</span> D10 stained with trypan blue (red) and neutral lipid binding fluorescent dye LipidTOX (green). The large panels are compiled images from super position of both dye images, with four selected enlarged infected cell images are shown on the right. Images (<b>A</b>–<b>E</b>) show the control cultures (no peptide added) and images (<b>F</b>–<b>J</b>) show trophozoite stage cultures treated with TpcC after 5 h in culture.</p>
Full article ">
17 pages, 3390 KiB  
Article
TXH11106: A Third-Generation MreB Inhibitor with Enhanced Activity against a Broad Range of Gram-Negative Bacterial Pathogens
by Eric J. Bryan, Hye Yeon Sagong, Ajit K. Parhi, Mark C. Grier, Jacques Y. Roberge, Edmond J. LaVoie and Daniel S. Pilch
Antibiotics 2022, 11(5), 693; https://doi.org/10.3390/antibiotics11050693 - 20 May 2022
Cited by 2 | Viewed by 2460
Abstract
The emergence of multi-drug-resistant Gram-negative pathogens highlights an urgent clinical need to explore and develop new antibiotics with novel antibacterial targets. MreB is a promising antibacterial target that functions as an essential elongasome protein in most Gram-negative bacterial rods. Here, we describe a [...] Read more.
The emergence of multi-drug-resistant Gram-negative pathogens highlights an urgent clinical need to explore and develop new antibiotics with novel antibacterial targets. MreB is a promising antibacterial target that functions as an essential elongasome protein in most Gram-negative bacterial rods. Here, we describe a third-generation MreB inhibitor (TXH11106) with enhanced bactericidal activity versus the Gram-negative pathogens Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa compared to the first- and second-generation compounds A22 and CBR-4830, respectively. Large inocula of these four pathogens are associated with a low frequency of resistance (FOR) to TXH11106. The enhanced bactericidal activity of TXH11106 relative to A22 and CBR-4830 correlates with a correspondingly enhanced capacity to inhibit E. coli MreB ATPase activity via a noncompetitive mechanism. Morphological changes induced by TXH11106 in E. coli, K. pneumoniae, A. baumannii, and P. aeruginosa provide further evidence supporting MreB as the bactericidal target of the compound. Taken together, our results highlight the potential of TXH11106 as an MreB inhibitor with activity against a broad spectrum of Gram-negative bacterial pathogens of acute clinical importance. Full article
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Figure 1

Figure 1
<p>Chemical structures A22, CBR-4830, and TXH11106, with the lettering and atomic numbering of the rings being as indicated. The basic functionalities of each compound are highlighted in blue and the halogen substituents on ring A of each compound are highlighted in red.</p>
Full article ">Figure 2
<p>Time–kill curves for <span class="html-italic">E. coli</span> 25922 (<b>A</b>), <span class="html-italic">K. pneumoniae</span> 13883 (<b>B</b>), <span class="html-italic">A. baumannii</span> 19606 (<b>C</b>), and <span class="html-italic">P. aeruginosa</span> 27853 (<b>D</b>) treated with DMSO vehicle or TXH11106 at the indicated concentrations. Each experimental data point represents the average of two replicates, with the error bars reflecting the standard deviation from the mean.</p>
Full article ">Figure 3
<p>Differential interference contrast (DIC) micrographs of <span class="html-italic">E. coli</span> 25922 (<b>A</b>,<b>B</b>), <span class="html-italic">K. pneumoniae</span> 13883 (<b>C</b>,<b>D</b>), <span class="html-italic">A. baumannii</span> 19606 (<b>E</b>,<b>F</b>), and <span class="html-italic">P. aeruginosa</span> 27853 (<b>G</b>,<b>H</b>) treated for 3 h with DMSO vehicle (<b>A</b>,<b>C</b>,<b>E</b>,<b>G</b>) or TXH11106 at 1× MIC (<b>B</b>,<b>D</b>,<b>F</b>,<b>H</b>). The scale bars reflect 2 µm in length.</p>
Full article ">Figure 4
<p>Quantification of the cell morphology results from the DIC microscopy experiments depicted in <a href="#antibiotics-11-00693-f003" class="html-fig">Figure 3</a>. The bar graphs show the prevalence (in %) of the various cell morphologies (rod, spherical, and reniform) observed in the vehicle-treated groups (<span class="html-italic">n</span> ranging from 349 to 1277) and TXH11106-treated groups (<span class="html-italic">n</span> ranging from 550 to 1291) for <span class="html-italic">E. coli</span> 25922 (<b>A</b>), <span class="html-italic">K. pneumoniae</span> 13883 (<b>B</b>), <span class="html-italic">A. baumannii</span> 19606 (<b>C</b>), and <span class="html-italic">P. aeruginosa</span> 27853 (<b>D</b>). Each percentage reflects an average of 5 different fields of view, with the average number of cells in each field of view ranging from 70 to 255 in the vehicle-treated groups and 110 to 258 for TXH11106-treated groups. The indicated error bars reflect the standard deviation from the mean. The statistical significance of differences in cell morphology were analyzed using a one-way ANOVA test. **** reflects a <span class="html-italic">p</span>-value &lt; 0.0001. n.o. = none observed.</p>
Full article ">Figure 5
<p>(<b>A</b>) Impact of increasing concentrations of TXH11106, CBR-4830, or A22 on the velocity of the ATPase reaction of wild-type (WT) <span class="html-italic">E. coli</span> MreB (EcMreB). Each experimental data point represents an average of two replicates, with the indicated error bars reflecting the standard deviation from the mean. The solid curves represent nonlinear least squares fits of the experimental data points with Equation (1). (<b>B</b>) Eadie–Hofstee plots of the ATP-dependent catalytic activity of WT EcMreB in the presence of DMSO vehicle or 30 µM inhibitor (TXH11106, CBR-4830, or A22). Each experimental data point represents an average of 3 replicates, with the indicated error bars reflecting the standard deviation from the mean. The solid lines represent linear fits of the experimental data points.</p>
Full article ">Figure 6
<p>(<b>A</b>) Alignment of a portion of the amino acid sequence from <span class="html-italic">C. crescentus</span> MreB (CcMreB), <span class="html-italic">E. coli</span> MreB (EcMreB), <span class="html-italic">K. pneumoniae</span> MreB (KpMreB), <span class="html-italic">A. baumannii</span> MreB (AbMreB), and <span class="html-italic">P. aeruginosa</span> MreB (PaMreB). As revealed by the previously reported crystal structure of the CcMreB-A22 complex (PDB: 4CZG) [<a href="#B23-antibiotics-11-00693" class="html-bibr">23</a>], this portion of the MreB amino acid sequence includes residues that form key contacts with the inhibitor. The E140 residue in CcMreB (highlighted in yellow) that forms electrostatic and hydrogen bonding contacts with the amidine functionality of A22 is conserved in the EcMreB, KpMreB, AbMreB, and PaMreB proteins. The hydrophobic residues of CcMreB (indicated by the arrows) that form Van der Waals contacts with ring A of A22 are also conserved in the other four MreB proteins. (<b>B</b>) Overlay of the gas-phase models of A22 (red) and TXH11106 (green). The contacts observed between the E140 residue of CcMreB and the amidine substituent of A22 are depicted by the black dashed lines, with the proposed corresponding contacts between the E143 residue of EcMreB and the amino functionality on ring C of TXH11106 being depicted by the blue dashed lines. The gas-phase models were generated using the Jaguar application of the Schrodinger Maestro version 12.9.123 software package. Compound geometries were optimized in the functional B3LYP-D3 gas phase. (<b>C</b>) Eadie–Hofstee plots of the ATP-dependent catalytic activity of E143G mutant EcMreB in the presence of DMSO vehicle or 30 µM TXH11106. Each experimental data point represents an average of three replicates, with the indicated error bars reflecting the standard deviation from the mean. The solid lines represent linear fits of the experimental data points. The inset depicts the impact of increasing concentrations of TXH11106 on the velocity of the ATPase reaction of E143G mutant EcMreB. Each experimental data point represents an average of two replicates, with the indicated error bars reflecting the standard deviation from the mean.</p>
Full article ">Scheme 1
<p>General scheme for the synthesis of TXH11106 (<b>4</b>).</p>
Full article ">
15 pages, 1598 KiB  
Article
Synergism between the Synthetic Antibacterial and Antibiofilm Peptide (SAAP)-148 and Halicin
by Miriam E. van Gent, Tanny J. K. van der Reijden, Patrick R. Lennard, Adriëtte W. de Visser, Bep Schonkeren-Ravensbergen, Natasja Dolezal, Robert A. Cordfunke, Jan Wouter Drijfhout and Peter H. Nibbering
Antibiotics 2022, 11(5), 673; https://doi.org/10.3390/antibiotics11050673 - 17 May 2022
Cited by 10 | Viewed by 3754
Abstract
Recently, using a deep learning approach, the novel antibiotic halicin was discovered. We compared the antibacterial activities of two novel bactericidal antimicrobial agents, i.e., the synthetic antibacterial and antibiofilm peptide (SAAP)-148 with this antibiotic halicin. Results revealed that SAAP-148 was more effective than [...] Read more.
Recently, using a deep learning approach, the novel antibiotic halicin was discovered. We compared the antibacterial activities of two novel bactericidal antimicrobial agents, i.e., the synthetic antibacterial and antibiofilm peptide (SAAP)-148 with this antibiotic halicin. Results revealed that SAAP-148 was more effective than halicin in killing planktonic bacteria of antimicrobial-resistant (AMR) Escherichia coli, Acinetobacter baumannii and Staphylococcus aureus, especially in biologically relevant media, such as plasma and urine, and in 3D human infection models. Surprisingly, SAAP-148 and halicin were equally effective against these bacteria residing in immature and mature biofilms. As their modes of action differ, potential favorable interactions between SAAP-148 and halicin were investigated. For some specific strains of AMR E. coli and S. aureus synergism between these agents was observed, whereas for other strains, additive interactions were noted. These favorable interactions were confirmed for AMR E. coli in a 3D human bladder infection model and AMR S. aureus in a 3D human epidermal infection model. Together, combinations of these two novel antimicrobial agents hold promise as an innovative treatment for infections not effectively treatable with current antibiotics. Full article
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Figure 1
<p><b>Hemolytic and cytotoxic activities of SAAP-148 and halicin.</b> (<b>A</b>) Values presented are cytotoxicity values of (i) 2% human erythrocytes in PBS or 50% plasma after 1 h exposure to SAAP-148 or halicin, (ii) a monolayer of human primary skin fibroblasts in DMEM medium with 0.5% human serum after 4 h and 24 h exposure to SAAP-148 or halicin and (iii) a monolayer of RT-4 urothelial cells in McCoy’s medium with 10% fetal calf serum after 4 h and 24 h exposure to SAAP-148 or halicin. Results are depicted as the medians (bold) and ranges of the IC<sub>50</sub>, i.e., the calculated concentration of the agents resulting in 50% cytotoxicity, of three independent experiments performed in triplicate. (<b>B</b>) Metabolic activity and cytotoxicity (determined by LDH release) of human primary skin fibroblasts upon exposure to SAAP-148 and halicin in DMEM medium with 0.5% human serum for 4 h (solid) and 24 h (dashed). Results are depicted as medians of three independent experiments performed in triplicate.</p>
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<p><b>Synergistic and additive interactions between SAAP-148 and halicin.</b> (<b>A</b>) fractional inhibitory concentration index (FICI) scores for exposure of planktonic cells of several bacterial strains to SAAP-148, halicin and combinations thereof. Interactions are considered synergistic or additive with a FICI score &lt;0.5 or between 0.5 and 1, respectively, while interactions are considered indifferent or antagonistic with a FICI score between 1 and 4 or &gt;4, respectively. Results are depicted as median and ranges of two to three (when additive effect) or three to four (when synergism) independent experiments. (<b>B</b>) Bacterial load of <span class="html-italic">S. aureus</span> (LUH14616) biofilms adhered to silicone disks after 4 h exposure to SAAP-148, halicin or combinations thereof. Results are shown as individual values and medians of at least two independent experiments performed in quadruplicate. Statistical differences between the two groups are depicted as * for <span class="html-italic">p</span> ≤ 0.1 and **** for <span class="html-italic">p</span> ≤ 0.0001 as calculated by the Mann-Whitney U-test.</p>
Full article ">Figure 3
<p><b>Bactericidal effects of SAAP-148 and halicin and combinations thereof on <span class="html-italic">E. coli</span> in the luminal and cellular compartments of 3D bladder infection models.</b> Bacterial load of <span class="html-italic">E. coli</span> (LUH15108) in (<b>A</b>) the supernatant (luminal compartment) and (<b>B</b>) the model (cellular compartment) of 3D bladder models composed of RT-4 cells after 4 h exposure to SAAP-148, halicin or combinations thereof. Results are shown as individual values and medians of three to seven independent experiments performed in duplicate. Statistical differences between the two groups are depicted as ** for <span class="html-italic">p</span> ≤ 0.01 and **** for <span class="html-italic">p</span> ≤ 0.0001 as calculated by the Mann–Whitney U-test.</p>
Full article ">Figure 4
<p><b>Bactericidal effects of SAAP-148 and halicin and combinations thereof on <span class="html-italic">S. aureus</span> in the adherent fraction of 3D epidermal infection model.</b> Bacterial load of adherent bacteria of MRSA (LUH14616) infected 3D human epidermal models after 4-h exposure to SAAP-148, halicin or combinations thereof. Results are shown as individual values and medians of three independent experiments performed in duplicate or triplicate. Statistical differences between the two groups are depicted as * for <span class="html-italic">p</span> ≤ 0.1 and *** for <span class="html-italic">p</span> ≤ 0.001 as calculated by the Mann–Whitney U-test.</p>
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13 pages, 1793 KiB  
Article
Derivatives of Esculentin-1 Peptides as Promising Candidates for Fighting Infections from Escherichia coli O157:H7
by Raffaella Scotti, Bruno Casciaro, Annarita Stringaro, Fabrizio Morgia, Maria Luisa Mangoni and Roberta Gabbianelli
Antibiotics 2022, 11(5), 656; https://doi.org/10.3390/antibiotics11050656 - 13 May 2022
Cited by 7 | Viewed by 2215
Abstract
New strategies are needed to fight the emergence of multidrug-resistant bacteria caused by an overuse of antibiotics in medical and veterinary fields. Due to the importance of biofilms in clinical infections, antibiofilm peptides have a great potential to treat infections. In recent years, [...] Read more.
New strategies are needed to fight the emergence of multidrug-resistant bacteria caused by an overuse of antibiotics in medical and veterinary fields. Due to the importance of biofilms in clinical infections, antibiofilm peptides have a great potential to treat infections. In recent years, an increased interest has emerged in antimicrobial peptides (AMPs). One of the richest sources of AMPs is represented by amphibian skin. In the present work, we investigated the effects of two peptides derived from the frog skin AMP esculentin-1, namely, Esc(1-21) and Esc(1-18), on the growth, biofilm formation, and gene expression of the non-pathogenic Escherichia coli strain K12 and of enterohemorrhagic E. coli O157:H7. Both peptides showed minimal bactericidal concentrations ranging from 4 to 8 µM for Esc(1-21) and from 32 to 64 µM for Esc(1-18). They also, at sub-MIC doses, reduced the formation of biofilm, as supported by both microbiological assays and scanning electron microscopy, while they displayed no marked activity against the planktonic form of the bacteria. Transcriptional analysis in E. coli O157:H7 showed that both AMPs induced the expression of several genes involved in the regulation of formation and dispersal of biofilm, as well as in the stress response. In conclusion, we demonstrated that these AMPs affect E. coli O157:H7 growth and biofilm formation, thus suggesting a great potential to be developed as novel therapeutics against infections caused by bacterial biofilms. Full article
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Figure 1

Figure 1
<p>Primary structure and net charge of the two parent peptides from frog skin (esculentin-1a and esculentin-1b) and the two respective derivatives under investigation [i.e., Esc(1-21) and Esc(1-18)]. Basic and acidic residues are in red and light blue, respectively.</p>
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<p>Time-kill assay of the <span class="html-italic">E. coli</span> O157:H7 EDL933 strain in the presence of Esc(1-18) (<b>A</b>), Esc(1-21) (<b>B</b>), and kanamycin (<b>C</b>). Concentrations of antimicrobial compounds were 2 × and 4 × Mic: 64 and 128 μM for Esc(1-18), 8 and 16 μM for Esc(1-21), and 32 and 64 μM for kanamycin. CTR indicates the controls. The dotted line represents a 2-log reduction (99%) of the initial inoculum. The data are the means ± standard deviations (SDs) of at least three independent experiments (although they are not visible).</p>
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<p>Membrane perturbation assay performed with Sytox Green dye in the presence of Esc(1-18) and Esc(1-21) on the EDL933 strain. Time 0 indicates the addition of the peptide. Data points are taken from a single experiment representative of three independent experiments. Controls (Ctrl) are cells not treated with peptides.</p>
Full article ">Figure 4
<p>Antibacterial and antibiofilm activity of the peptides on <span class="html-italic">E. coli</span> strains. Planktonic growth (white bars) and biofilm formation (black bars) were quantified in modM9 (CTR) and in modM9 in the presence of 2 or 1 μM for Esc(1-21) and 16 or 8 μM for Esc(1-18) on the EDL933 (<b>A</b>) and K12 (<b>B</b>) strains, respectively. The bacterial culture was grown for 24 h in 96-well plates at 28 °C. The optical density (OD) of the planktonic cell suspension was measured at 595 nm to evaluate the bacterial turbidity before its removal from each well of the microtiter, while the OD of the biofilm was measured after CV staining of adherent cells at the same wavelength of 595 nm (see <a href="#sec4-antibiotics-11-00656" class="html-sec">Section 4</a>). Data are presented as mean ± SD.</p>
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<p>Expression levels of selected genes related to biofilm formation and stress conditions in the <span class="html-italic">E. coli</span> O157:H7 EDL933 strain treated with the peptides at sub-inhibitory concentrations of 2 and 16 μM for Esc(1-21) and Esc(1-18), respectively, compared to the untreated control samples (CTR). Transcriptional profiles were measured with qRT-PCR. <span class="html-italic">p</span> &lt; 0.01 for all bars with respect to CTR.</p>
Full article ">Figure 6
<p>Effects of Esc(1-18) and Esc(1-21) on biofilm formation by <span class="html-italic">E. coli</span> strains. SEM was used to examine biofilm cells grown on glass coverslips in modM9 in the presence or absence of peptides at the concentration of ½ MIC for 24 h (magnification 30,000×).</p>
Full article ">
19 pages, 2091 KiB  
Review
Phytochemical Profile of Antibacterial Agents from Red Betel Leaf (Piper crocatum Ruiz and Pav) against Bacteria in Dental Caries
by Leny Heliawati, Seftiana Lestari, Uswatun Hasanah, Dwipa Ajiati and Dikdik Kurnia
Molecules 2022, 27(9), 2861; https://doi.org/10.3390/molecules27092861 - 30 Apr 2022
Cited by 17 | Viewed by 4390
Abstract
Based on data from The Global Burden of Disease Study in 2016, dental and oral health problems, especially dental caries, are a disease experienced by almost half of the world’s population (3.58 billion people). One of the main causes of dental caries is [...] Read more.
Based on data from The Global Burden of Disease Study in 2016, dental and oral health problems, especially dental caries, are a disease experienced by almost half of the world’s population (3.58 billion people). One of the main causes of dental caries is the pathogenesis of Streptococcus mutans. Prevention can be achieved by controlling S. mutans using an antibacterial agent. The most commonly used antibacterial for the treatment of dental caries is chlorhexidine. However, long-term use of chlorhexidine has been reported to cause resistance and some side effects. Therefore, the discovery of a natural antibacterial agent is an urgent need. A natural antibacterial agent that can be used are herbal medicines derived from medicinal plants. Piper crocatum Ruiz and Pav has the potential to be used as a natural antibacterial agent for treating dental and oral health problems. Several studies reported that the leaves of P. crocatum Ruiz and Pav contain secondary metabolites such as essential oils, flavonoids, alkaloids, terpenoids, tannins, and phenolic compounds that are active against S. mutans. This review summarizes some information about P. crocatum Ruiz and Pav, various isolation methods, bioactivity, S. mutans bacteria that cause dental caries, biofilm formation mechanism, antibacterial properties, and the antibacterial mechanism of secondary metabolites in P. crocatum Ruiz and Pav. Full article
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Figure 1

Figure 1
<p>(<b>A</b>) Co-aggregation between <span class="html-italic">S. mutans</span> and filaments in developing dental biofilm; (<b>B</b>) typical corncob formation [<a href="#B30-molecules-27-02861" class="html-bibr">30</a>].</p>
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<p>Contribution of <span class="html-italic">S. mutans</span> in the process of biofilm formation [<a href="#B39-molecules-27-02861" class="html-bibr">39</a>].</p>
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<p>Pathway of inhibition of bacteria by antibacterial agents [<a href="#B73-molecules-27-02861" class="html-bibr">73</a>].</p>
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<p>Catalytic reaction on the MurA enzyme [<a href="#B106-molecules-27-02861" class="html-bibr">106</a>].</p>
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<p>Compounds obtained from the methanol extract of red betel leaf. (<b>1</b>) (8<span class="html-italic">R</span>)-8-(4-hydroxy-3,5-dimethoxy)-propane-8-ol-4-<span class="html-italic">O</span>-β-D-glucopyranoside; (<b>2</b>) 4-Allyl-2,6-dimethoxy-3-hydroxy-1-D-glucopyranoside; (<b>3</b>) 3-[(1<span class="html-italic">E</span>)-3-hydroxy-1-propen-1-yl]-2,5-dimethoxyphenyl-D-glucopyranoside; (<b>4</b>) Cimidahurinin; (<b>5</b>) Erigeside II; (<b>6</b>) Syringe; (<b>7</b>) β-phenylethyl-β-D-glucoside; (<b>8</b>) Methylsalicylate-2-<span class="html-italic">O</span>-β-D-glucopyranoside; (<b>9</b>) Icariside D1; (<b>10</b>) 4-Hydroxybenzoic acid-D-glucosylester; (<b>11</b>) Benzyl-β-D-glucoside; (<b>12</b>) Phenylmethyl-6-<span class="html-italic">O</span>-α-L-arabinofuranosyl-β-D-glucopyranoside; (<b>13</b>) Hydroxytyrosol-1glucopyranoside (<b>14</b>) Gentisic acid; (<b>15</b>) Catechaldehyde; (<b>16</b>) (<span class="html-italic">S</span>)-Menthiafolic acid; (<b>17</b>) Ioliolide; (<b>18</b>) 5β,6β-dihydroxy-3α-(β-D-glucopyranosyloxy)-7<span class="html-italic">E</span>-Megastigmen-9-one; (<b>19</b>) (3<span class="html-italic">E</span>)-4-[(1<span class="html-italic">S</span>,2<span class="html-italic">S</span>,4<span class="html-italic">S</span>)-4-(β-D-glucopyranosyloxy)-1,2-dihydroxy-2,6,6-tri-methylcyclohexyl]3-buten-2-one; (<b>20</b>) (6<span class="html-italic">S</span>,9<span class="html-italic">S</span>)-roseoside; (<b>21</b>) Cuneataside E (<b>22</b>) <span class="html-italic">N</span>-trans-feruloyltyramine-4′-<span class="html-italic">O</span>-β-D-glucopyranoside; (<b>23</b>) Syringaresinol-β-D-glucoside; and (<b>24</b>) Vitexin 2″-<span class="html-italic">O</span>-rhamnoside.</p>
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<p>Compounds obtained from the methanol extract of red betel leaf. (<b>1</b>) (8<span class="html-italic">R</span>)-8-(4-hydroxy-3,5-dimethoxy)-propane-8-ol-4-<span class="html-italic">O</span>-β-D-glucopyranoside; (<b>2</b>) 4-Allyl-2,6-dimethoxy-3-hydroxy-1-D-glucopyranoside; (<b>3</b>) 3-[(1<span class="html-italic">E</span>)-3-hydroxy-1-propen-1-yl]-2,5-dimethoxyphenyl-D-glucopyranoside; (<b>4</b>) Cimidahurinin; (<b>5</b>) Erigeside II; (<b>6</b>) Syringe; (<b>7</b>) β-phenylethyl-β-D-glucoside; (<b>8</b>) Methylsalicylate-2-<span class="html-italic">O</span>-β-D-glucopyranoside; (<b>9</b>) Icariside D1; (<b>10</b>) 4-Hydroxybenzoic acid-D-glucosylester; (<b>11</b>) Benzyl-β-D-glucoside; (<b>12</b>) Phenylmethyl-6-<span class="html-italic">O</span>-α-L-arabinofuranosyl-β-D-glucopyranoside; (<b>13</b>) Hydroxytyrosol-1glucopyranoside (<b>14</b>) Gentisic acid; (<b>15</b>) Catechaldehyde; (<b>16</b>) (<span class="html-italic">S</span>)-Menthiafolic acid; (<b>17</b>) Ioliolide; (<b>18</b>) 5β,6β-dihydroxy-3α-(β-D-glucopyranosyloxy)-7<span class="html-italic">E</span>-Megastigmen-9-one; (<b>19</b>) (3<span class="html-italic">E</span>)-4-[(1<span class="html-italic">S</span>,2<span class="html-italic">S</span>,4<span class="html-italic">S</span>)-4-(β-D-glucopyranosyloxy)-1,2-dihydroxy-2,6,6-tri-methylcyclohexyl]3-buten-2-one; (<b>20</b>) (6<span class="html-italic">S</span>,9<span class="html-italic">S</span>)-roseoside; (<b>21</b>) Cuneataside E (<b>22</b>) <span class="html-italic">N</span>-trans-feruloyltyramine-4′-<span class="html-italic">O</span>-β-D-glucopyranoside; (<b>23</b>) Syringaresinol-β-D-glucoside; and (<b>24</b>) Vitexin 2″-<span class="html-italic">O</span>-rhamnoside.</p>
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<p>Compounds obtained from the methanolic extract of red betel leaf (<span class="html-italic">P. crocatum</span> Ruiz and Pav). (<b>25</b>) β-sitosterol and (<b>26</b>) 2-(5′,6′-dimethoxy-3′,4′-methylenedioxyphenyl)-6-(3″,4″,5-trimethoxyphenyl)-dioxabiclo [3,3,0] octane.</p>
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<p>Compounds obtained from the methanolic extract of red betel leaf (<span class="html-italic">P. crocatum</span> Ruiz and Pav). (<b>27</b>) Crocatin A; (<b>28</b>) Crocatin B; (<b>29</b>) Pachypodol [4′,5-dihydroxy-3,3′,7-trimethoxyflavone]; and (<b>30</b>) 1-Triacontanol.</p>
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<p>Compounds obtained from the methanolic extract of red betel leaf. (<b>31</b>) Pipcroside A; (<b>32</b>) Pipcroside B; (<b>33</b>) Pipcroside C; and (<b>34</b>) Bicyclo [3.2.1] octanoid neolignans.</p>
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<p>Structure of compounds of isolated red betel leaf oil. (<b>35</b>) Camphene and (<b>36</b>) Myrcene [<a href="#B13-molecules-27-02861" class="html-bibr">13</a>].</p>
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22 pages, 7764 KiB  
Article
Rhamnolipid Nano-Micelles versus Alcohol-Based Hand Sanitizer: A Comparative Study for Antibacterial Activity against Hospital-Acquired Infections and Toxicity Concerns
by Yasmin Abo-zeid, Marwa Reda Bakkar, Gehad E. Elkhouly, Nermeen R. Raya and Dalia Zaafar
Antibiotics 2022, 11(5), 605; https://doi.org/10.3390/antibiotics11050605 - 29 Apr 2022
Cited by 12 | Viewed by 3896
Abstract
Hospital-acquired infections (HAIs) are considered to be a major global healthcare challenge, in large part because of the development of microbial resistance to currently approved antimicrobial drugs. HAIs are frequently preventable through infection prevention and control measures, with hand hygiene as a key [...] Read more.
Hospital-acquired infections (HAIs) are considered to be a major global healthcare challenge, in large part because of the development of microbial resistance to currently approved antimicrobial drugs. HAIs are frequently preventable through infection prevention and control measures, with hand hygiene as a key activity. Improving hand hygiene was reported to reduce the transmission of healthcare-associated pathogens and HAIs. Alcohol-based hand sanitizers are commonly used due to their rapid action and broad spectrum of microbicidal activity, offering protection against bacteria and viruses. However, their frequent administration has been reported to be associated with many side effects, such as skin sensitivity, skin drying, and cracks, which promote further skin infections. Thus, there is an essential need to find alternative approaches to hand sanitation. Rhamnolipids are glycolipids produced by Pseudomonas aeruginosa, and were shown to have broad antimicrobial activity as biosurfactants. We have previously demonstrated the antimicrobial activity of rhamnolipid nano-micelles against selected drug-resistant Gram-negative (Salmonella Montevideo and Salmonella Typhimurium) and Gram-positive bacteria (Staphylococcus aureus, Streptococcus pneumoniae). To the best of our knowledge, the antimicrobial activity of rhamnolipid nano-micelles in comparison to alcohol-based hand sanitizers against microorganisms commonly causing HAIs in Egypt—such as Acinetobacter baumannii and Staphylococcus aureus—has not yet been studied. In the present work, a comparative study of the antibacterial activity of rhamnolipid nano-micelles versus alcohol-based hand sanitizers was performed, and their safety profiles were also assessed. It was demonstrated that rhamnolipid nano-micelles had a comparable antibacterial activity to alcohol-based hand sanitizer, with a better safety profile, i.e., rhamnolipid nano-micelles are unlikely to cause any harmful effects on the skin. Thus, rhamnolipid nano-micelles could be recommended to replace alcohol-based hand sanitizers; however, they must still be tested by healthcare workers in healthcare settings to ascertain their antimicrobial activity and safety. Full article
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<p>TEM images of rhamnolipid nano-micelles in (<b>A</b>) solution and (<b>B</b>) gel prepared at a concentration 10 mg/mL of rhamnolipids.</p>
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<p>Percentage of bacterial growth inhibition of <span class="html-italic">A. baumannii</span> and <span class="html-italic">S. aureus</span> recorded by microdilution assay at different concentrations of rhamnolipid nano-micelles formulations (solution and gel). Data are expressed as the mean ± SD. Data were analyzed by two-way ANOVA followed by Bonferroni’s test for multiple comparisons. Significant differences in the antibacterial potency of the rhamnolipid nano-micelles formulations (solution and gel) against <span class="html-italic">A. baumannii</span> and <span class="html-italic">S. aureus</span> are denoted by * and # at <span class="html-italic">p</span> &lt; 0.05, respectively.</p>
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<p>Time–kill curve of antibacterial activity of the rhamnolipid nano-micelles solution at its MIC value against (<b>A</b>) <span class="html-italic">S. aureus</span> and (<b>B</b>) <span class="html-italic">A. baumannii</span>; each time point is the average of two independent experiments with three replicates each.</p>
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<p>TEM images presenting the structural changes in <span class="html-italic">Staphylococcus aureus</span> after treatment with rhamnolipid nano-micelles at concentrations less than the MIC. Images (<b>A</b>,<b>B</b>) show a normal cell wall outline without any itching or degradation, and with a normal central plane of division and complete cellular components. Image (<b>C</b>) shows abnormal cell morphologies. Images (<b>D</b>–<b>F</b>) show the possible antibacterial mechanisms recorded for the rhamnolipid nano-micelle solution: (<b>D</b>) abnormal cell division as revealed by an incomplete central plane of division (white arrow); (<b>E</b>) abnormal, degraded, itched, and permeabilized cell wall (striped arrow); and (<b>F</b>) bleaching of intracellular components (black arrow).</p>
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<p>TEM images presenting the structural changes in <span class="html-italic">Acinetobacter baumannii</span> after treatment with rhamnolipid nano-micelles at concentrations less than the MIC. Images (<b>A</b>,<b>B</b>) show a normal cell wall outline without any itching or degradation, and with normal intracellular components. Image (<b>C</b>) is an overview of the field showing abnormal cell morphology. Images (<b>D</b>–<b>F</b>) present the possible antibacterial mechanisms of the rhamnolipid nano-micelles solution: (<b>D</b>) abnormal, degraded, itched, and permeabilized cell wall (stripped arrow); (<b>E</b>) ghost cell showing loss of intracellular components (black arrow); and (<b>F</b>) the presence of amorphous electron-dense materials (white arrow).</p>
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<p>MTT cytotoxicity study of rhamnolipid nano-micelles and ethyl alcohol formulations on normal human dermal fibroblasts (HDFa): (<b>A</b>) Cell viability percentage of HDFa after treatment with different concentrations (0.0195 to 1.25 mg/mL) of rhamnolipid nano-micelle solution and gel. (<b>B</b>) Cell viability percentage of HDFa after treatment with different concentrations (1.09 to 35%) of ethyl alcohol solution and gel. Significant differences in the cytotoxic effects of rhamnolipid nano-micelles and ethyl alcohol formulations on HDFa cells are denoted with asterisks * at <span class="html-italic">p</span> &lt; 0.05. (<b>C</b>) Phase-contrast microscopy images of rhamnolipid nano-micelle formulations at concentrations of 0.019 and 0.156 mg/mL, and of ethyl alcohol formulations at concentrations of 1.09% and 8.75%. Determination of the cytotoxic concentration responsible for the death of 50% of HDFa cells (CC50) for (<b>D</b>) rhamnolipid nano-micelle solution (0.625 mg/mL) and gel (0.2654 mg/mL), and (<b>E</b>) ethyl alcohol solution (41.76%) and gel (14.44%). Results are an average of three independent experiments with three replicates each.</p>
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19 pages, 3531 KiB  
Article
Design, Synthesis and Biological Evaluation of N-phenylindole Derivatives as Pks13 Inhibitors againstMycobacterium tuberculosis
by Yanpeng Cai, Wei Zhang, Shichun Lun, Tongtong Zhu, Weijun Xu, Fan Yang, Jie Tang, William R. Bishai and Lifang Yu
Molecules 2022, 27(9), 2844; https://doi.org/10.3390/molecules27092844 - 29 Apr 2022
Cited by 6 | Viewed by 2695
Abstract
Polyketide synthase 13 (Pks13), an essential enzyme for the survival of Mycobacterium tuberculosis (Mtb), is an attractive target for new anti-TB agents. In our previous work, we have identified 2-phenylindole derivatives against Mtb. The crystallography studies demonstrated that the two-position [...] Read more.
Polyketide synthase 13 (Pks13), an essential enzyme for the survival of Mycobacterium tuberculosis (Mtb), is an attractive target for new anti-TB agents. In our previous work, we have identified 2-phenylindole derivatives against Mtb. The crystallography studies demonstrated that the two-position phenol was solvent-exposed in the Pks13-TE crystal structure and a crucial hydrogen bond was lost while introducing bulkier hydrophobic groups at indole N moieties. Thirty-six N-phenylindole derivatives were synthesized and evaluated for antitubercular activity using a structure-guided approach. The structure–activity relationship (SAR) studies resulted in the discovery of the potent Compounds 45 and 58 against Mtb H37Rv, with an MIC value of 0.0625 μg/mL and 0.125 μg/mL, respectively. The thermal stability analysis showed that they bind with high affinity to the Pks13-TE domain. Preliminary ADME evaluation showed that Compound 58 displayed modest human microsomal stability. This report further validates that targeting Pks13 is a valid strategy for the inhibition of Mtb and provides a novel scaffold for developing leading anti-TB compounds. Full article
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<p>Anti-TB drugs: bedaquiline (<b>1</b>), delamanid (<b>2</b>), pretomanid (<b>3</b>), and selected Pks13 inhibitors (<b>4–8</b>).</p>
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<p>Design strategies of <span class="html-italic">N</span>-phenylindole derivatives.</p>
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<p>Crystal structures of Pks13-TE with TAM16 (PDB ID 5V3Y) (<b>A</b>) and proposed binding modes of Compound <b>18</b> (<b>B</b>). The key amino acid residues are colored green in the active site of Pks13-TE, and compounds are colored cyan.</p>
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<p>Synthesis of Compounds <b>13–20</b> and <b>22–25</b>. Reagents and conditions: (a) ammonium formate or aniline, CH<sub>3</sub>COOH, EtOH, reflux, 6–10 h; (b) benzoquinone, ZnBr<sub>2</sub>, rt, THF, 8–10 h; (c) formaldehyde (37% aq), piperidine, EtOH, reflux, 8–12 h; (d) BBr<sub>3</sub> in CH<sub>2</sub>Cl<sub>2</sub>(1 M), CH<sub>2</sub>Cl<sub>2</sub>, rt, overnight; (e) NaOH(1N), EtOH, 90 °C, 2–6 h; (f) EDCI·HCl, HOBt, corresponding amines, DIPEA, DMF, rt, 5–8 h.</p>
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<p>Synthesis of Compounds <b>28–39.</b> Reagents and conditions: (a) benzoquinone, aniline, montmorillonite, 1,2-dichloroethane, reflux, 7–12 h; (b) formaldehyde (37% aq), piperidine, EtOH, reflux, 8–12 h.</p>
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<p>Synthesis of Compounds <b>45</b>, <b>48–58</b>. Reagents and conditions: (a) CH<sub>3</sub>COOH, EtOH, reflux, 6–10 h; (b) benzoquinone, ZnBr<sub>2</sub>, rt, THF, 8–10 h; (c) Pd(PPh<sub>3</sub>)<sub>4</sub>, Phenylboronic acid, K<sub>2</sub>CO<sub>3</sub>, toluene/EtOH/H<sub>2</sub>O = 3/2/1, 100 °C, 12 h; (d) formaldehyde (37% aq), piperidine, EtOH, reflux, 8–12 h; (e) K<sub>2</sub>CO<sub>3</sub>, piperidine, DMSO, 90 °C, 5 h; (f) Pd/C, H<sub>2</sub>, CH<sub>3</sub>OH, rt, 3 h.</p>
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14 pages, 1729 KiB  
Article
Hydroxyapatite/TiO2 Nanomaterial with Defined Microstructural and Good Antimicrobial Properties
by Miljana Mirković, Suzana Filipović, Ana Kalijadis, Pavle Mašković, Jelena Mašković, Branislav Vlahović and Vladimir Pavlović
Antibiotics 2022, 11(5), 592; https://doi.org/10.3390/antibiotics11050592 - 28 Apr 2022
Cited by 11 | Viewed by 2253
Abstract
Due to the growing number of people infected with the new coronavirus globally, which weakens immunity, there has been an increase in bacterial infections. Hence, knowledge about simple and low-cost synthesis methods of materials with good structural and antimicrobial properties is of great [...] Read more.
Due to the growing number of people infected with the new coronavirus globally, which weakens immunity, there has been an increase in bacterial infections. Hence, knowledge about simple and low-cost synthesis methods of materials with good structural and antimicrobial properties is of great importance. A material obtained through the combination of a nanoscale hydroxyapatite material (with good biocompatibility) and titanium dioxide (with good degradation properties of organic molecules) can absorb and decompose bacteria. In this investigation, three different synthesis routes used to prepare hydroxyapatite/titanium dioxide nanomaterials are examined. The morphology and semiquantitative chemical composition are characterized by scanning electron microscopy with energy dispersive X-ray analysis (SEM-EDX). The obtained materials’ phase and structural characterization are determined using the X-ray powder diffraction method (XRD). The crystallite sizes of the obtained materials are in the range of 8 nm to 15 nm. Based on XRD peak positions, the hexagonal hydroxyapatite phases are formed in all samples along with TiO2 anatase and rutile phases. According to SEM and TEM analyses, the morphology of the prepared samples differs depending on the synthesis route. The EDX analysis confirmed the presence of Ti, Ca, P, and O in the obtained materials. The IR spectroscopy verified the vibration bands characteristic for HAp and titanium. The investigated materials show excellent antimicrobial and photocatalytic properties. Full article
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<p>XRD results of TiO<sub>2</sub>/HAp-01 (black line), TiO<sub>2</sub>/HAp-02 (blue line), and TiO<sub>2</sub>/HAp-03 (red line).</p>
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<p>FTIR spectra of TiO<sub>2</sub>/HAp-01, TiO<sub>2</sub>/HAp-02, and TiO<sub>2</sub>/HAp-03.</p>
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<p>PSD distribution in TiO<sub>2</sub>/Hap-01, TiO<sub>2</sub>/Hap-02, and TiO<sub>2</sub>/HAp-03 samples.</p>
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<p>SEM results with inserted EDS spectra TiO<sub>2</sub>/HAp-01, TiO<sub>2</sub>/HAp-02, and TiO<sub>2</sub>/HAp-03.</p>
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<p>TEM images of (<b>a</b>) TiO<sub>2</sub>/HAp-01, (<b>b</b>) TiO<sub>2</sub>/HAp-02, and (<b>c</b>) TiO<sub>2</sub>/HAp-03.</p>
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<p>(<b>a</b>) MIC properties of TiO<sub>2</sub>/HAp-01, TiO<sub>2</sub>/HAp-02, and TiO<sub>2</sub>/HAp-03 in relation to Amracin; (<b>b</b>) MIC properties of TiO<sub>2</sub>/HAp-01, TiO<sub>2</sub>/HAp-02, and TiO<sub>2</sub>/HAp-03 materials in relation to Ketoconazole.</p>
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<p>(<b>a</b>) Photocatalytic efficiency of the TiO<sub>2</sub>/HAp-01; (<b>b</b>) possible mechanism of the MB photocatalytic degradation in the presence of TiO<sub>2</sub>/HAp-01.</p>
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17 pages, 5325 KiB  
Article
Identification of Mtb GlmU Uridyltransferase Domain Inhibitors by Ligand-Based and Structure-Based Drug Design Approaches
by Manvi Singh, Priya Kempanna and Kavitha Bharatham
Molecules 2022, 27(9), 2805; https://doi.org/10.3390/molecules27092805 - 28 Apr 2022
Cited by 2 | Viewed by 2323
Abstract
Targeting enzymes that play a role in the biosynthesis of the bacterial cell wall has long been a strategy for antibacterial discovery. In particular, the cell wall of Mycobacterium tuberculosis (Mtb) is a complex of three layers, one of which is Peptidoglycan, an [...] Read more.
Targeting enzymes that play a role in the biosynthesis of the bacterial cell wall has long been a strategy for antibacterial discovery. In particular, the cell wall of Mycobacterium tuberculosis (Mtb) is a complex of three layers, one of which is Peptidoglycan, an essential component providing rigidity and strength. UDP-GlcNAc, a precursor for the synthesis of peptidoglycan, is formed by GlmU, a bi-functional enzyme. Inhibiting GlmU Uridyltransferase activity has been proven to be an effective anti-bacterial, but its similarity with human enzymes has been a deterrent to drug development. To develop Mtb selective hits, the Mtb GlmU substrate binding pocket was compared with structurally similar human enzymes to identify selectivity determining factors. Substrate binding pockets and conformational changes upon substrate binding were analyzed and MD simulations with substrates were performed to quantify crucial interactions to develop critical pharmacophore features. Thereafter, two strategies were applied to propose potent and selective bacterial GlmU Uridyltransferase domain inhibitors: (i) optimization of existing inhibitors, and (ii) identification by virtual screening. The binding modes of hits identified from virtual screening and ligand growing approaches were evaluated further for their ability to retain stable contacts within the pocket during 20 ns MD simulations. Hits that are predicted to be more potent than existing inhibitors and selective against human homologues could be of great interest for rejuvenating drug discovery efforts towards targeting the Mtb cell wall for antibacterial discovery. Full article
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<p>GlmU structure and its reactions. Acetyltransferase reaction catalyzed by C-terminal acetyltransferase domain. Uridyl transferase reaction catalyzed by N-terminal uridyltransferase domain.</p>
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<p>(<b>A</b>) Comparison of MtbGlmU with Human AGX1. (<b>B</b>) Structural alignment of apo forms of Mtb (PDB ID: 3D98), HI (PDB ID: 2V0H) and <span class="html-italic">E. coli</span> (PDB ID: 1FXJ). (<b>C</b>) Structural comparison of apo, UD1 and inhibitor bound HI structures. (<b>D</b>) Alignment of Mtb GlmU structures; the three forms apo (PDB ID: 3D98), closed (PDB ID: 4G3Q) and GlcNAc-1-P bound (PDB ID: 4HCQ) structures are aligned (<b>E</b>) Structure based sequence alignment of pocket residues of N-terminal GlmUMtb with HI and <span class="html-italic">E. coli</span>. (<b>F</b>) The pocket volume of closed forms of Mtb, HI and <span class="html-italic">E. coli</span> generated using CASTp server [<a href="#B17-molecules-27-02805" class="html-bibr">17</a>] visualised by MSMS package of Chimera [<a href="#B18-molecules-27-02805" class="html-bibr">18</a>]. (<b>G</b>) Pocket residues alignment between Mtb and human AGX1. Differing pocket residues of Mtb and human AGX1 could be used in exploring selectivity.</p>
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<p>(<b>A</b>) The two compounds which were tested on all three organisms Mtb, HI and <span class="html-italic">E. coli</span> [<a href="#B2-molecules-27-02805" class="html-bibr">2</a>,<a href="#B19-molecules-27-02805" class="html-bibr">19</a>]. Compound 1 superposed on to <span class="html-italic">E. coli</span> and MtbGlmU pocket. The pocket volumes of apo forms of three organisms generated using CASTp server [<a href="#B17-molecules-27-02805" class="html-bibr">17</a>] visualised by MSMS package of Chimera [<a href="#B18-molecules-27-02805" class="html-bibr">18</a>]. (<b>B</b>) Binding poses of compound A and compound E. (<b>C</b>) MD simulation analysis of compound A and E.</p>
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<p>(<b>A</b>) Optimization and Virtual screening workflow followed in the present study. (<b>B</b>) Generation of merged pharmacophore. The merged hypothesis from all three PDBs:ADAADD. (<b>C</b>) Five hits obtained from virtual screening.</p>
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<p>(<b>A</b>) Putative binding poses of vs. hits ZINC000002684513 and ZINC000012422035 (<b>B</b>) MD simulation of ZINC000002684513 and ZINC000012422035 for 20ns. (<b>C</b>) Overlay of Fragment and the three vs. hits ZINC000002684513, and ZINC000012422035 in human AGX1 (PDB ID: 1JV1). Ugly clashes are shown in red color.</p>
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6 pages, 537 KiB  
Communication
Cefiderocol Protects against Cytokine- and Endotoxin-Induced Disruption of Vascular Endothelial Cell Integrity in an In Vitro Experimental Model
by Dagmar Hildebrand, Jana Böhringer, Eva Körner, Ute Chiriac, Sandra Förmer, Aline Sähr, Torsten Hoppe-Tichy, Klaus Heeg and Dennis Nurjadi
Antibiotics 2022, 11(5), 581; https://doi.org/10.3390/antibiotics11050581 - 26 Apr 2022
Cited by 2 | Viewed by 5579
Abstract
The severe course of bloodstream infections with Gram-negative bacilli can lead to organ dysfunctions and compromise the integrity of the vascular barrier, which are the hallmarks of sepsis. This study aimed to investigate the potential effect of cefiderocol on the barrier function of [...] Read more.
The severe course of bloodstream infections with Gram-negative bacilli can lead to organ dysfunctions and compromise the integrity of the vascular barrier, which are the hallmarks of sepsis. This study aimed to investigate the potential effect of cefiderocol on the barrier function of vascular endothelial cells (vECs) in an in vitro experimental set-up. Human umbilical vein cells (HUVECs), co-cultured with erythrocyte-depleted whole blood for up to 48 h, were activated with tumor necrosis factor-alpha (TNF-α) or lipopolysaccharide (LPS) to induce endothelial damage in the absence or presence of cefiderocol (concentrations of 10, 40 and 70 mg/L). The endothelial integrity was quantified using transendothelial electrical resistance (TEER) measurement, performed at 0, 3, 24 and 48 h after stimulation. Stimulation with TNF-α and LPS increased the endothelial permeability assessed by TEER at 24 and 48 h of co-culture. Furthermore, cefiderocol reduces interleukin-6 (IL-6), interleukin-1β (IL-1β) and TNF-α release in peripheral blood mononuclear cells (PBMCs) following LPS stimulation in a dose-dependent manner. Collectively, the data suggest that cefiderocol may have an influence on the cellular immune response and might support the maintenance of vEC integrity during inflammation associated with infection with Gram-negative bacteria, which warrants further investigations. Full article
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<p><b>Cefiderocol dampens LPS-stimulated production of pro-inflammatory cytokines.</b> PBMCs were stimulated with 100 ng/mL LPS with or without cefiderocol (FDC 10 mg/L, 40 mg/L, 70 mg/L) for 3 days. Unstimulated PBMCs were incubated with 70 mg/L FDC as negative controls. Supernatant was used for ELISA analysis of IL-1β (<b>A</b>), IL-6 (<b>B</b>) and TNF-α (<b>C</b>). Shown are mean and standard deviation of three biological replicates (<span class="html-italic">n</span> = 3). Statistical significance was calculated using a one-sided Mann–Whitney U test (<span class="html-italic">p</span> &lt; 0.05 = *). Abbreviations: FDC = cefiderocol, LPS = lipopolysaccharide, TNF-α = tumor necrosis factor-α.</p>
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<p><b>Cefiderocol dampens LPS and TNF-α induced decrease in endothelial cell integrity.</b> HUVEC/edWB coculture was stimulated with 100 ng/mL LPS or 100 ng/mL TNF-α with or without cefiderocol (concentrations: (<b>A</b>): 70 mg/L, (<b>B</b>): 10 mg/L, 40 mg/L, 70 mg/L). TEER was measured with the EVOM3 volt/ohmmeter (timepoints: (<b>A</b>): after 0 h, 3 h, 24 h and 48 h, (<b>B</b>): after 48 h). Shown are mean and standard deviation of three biological replicates (<span class="html-italic">n</span> = 3). Statistical significance was calculated using a one-sided Mann–Whitney U test (<span class="html-italic">p</span> &lt; 0.05 = * and was considered statistically significant, ns = statistically not significant). Abbreviations: TEER = transendothelial electrical resistance, FDC = cefiderocol, TNF-α = tumor necrosis factor-α, LPS = lipopolysaccharide.</p>
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13 pages, 3137 KiB  
Article
Investigating the Antibacterial Characteristics of Japanese Bamboo
by Raviduth Ramful, Thefye P. M. Sunthar, Kaeko Kamei and Giuseppe Pezzotti
Antibiotics 2022, 11(5), 569; https://doi.org/10.3390/antibiotics11050569 - 24 Apr 2022
Cited by 3 | Viewed by 3214
Abstract
Natural materials, such as bamboo, is able to withstand the rough conditions posed by its environment, such as resistance to degradation by microorganisms, due to notable antibacterial characteristics. The methods of extraction exert a significant influence on the effectiveness of bamboo-derived antibacterial agents. [...] Read more.
Natural materials, such as bamboo, is able to withstand the rough conditions posed by its environment, such as resistance to degradation by microorganisms, due to notable antibacterial characteristics. The methods of extraction exert a significant influence on the effectiveness of bamboo-derived antibacterial agents. In this study, the antibacterial characteristics of various types of Japanese bamboo, namely, Kyoto-Moso, Kyushu-Moso and Kyushu-Madake were investigated by considering an extraction and a non-extraction method. The characterization of the efficacy of antibacterial agents of various bamboo samples derived from both methods of extractions was conducted using an in vitro cultured bacteria technique consisting of E. coli and S. aureus. Antibacterial test results based on colony-forming units showed that antibacterial agents derived from the non-extraction method yielded better efficacy when tested against E. coli and S. aureus. Most specimens displayed maximum antibacterial efficacy following a 48-h period. The antibacterial agents derived from thermally modified bamboo powder via the non-extraction method showed improved antibacterial activity against S. aureus specifically. In contrast, absorbance results indicated that antibacterial agents derived from the extraction method yielded poor efficacy when tested against both E. coli and S. aureus. From FTIR analysis, characteristic bands assigned to the C-O and C-H functional groups in lignin were recognized as responsible for the antibacterial trait observed in both natural and thermally modified Japanese bamboo powder. Techniques to exploit the antibacterial characteristics present in bamboo by identification of antibacterial source and adoption of adequate methods of extraction are key steps in taking advantage of this attribute in numerous applications involving bamboo-derived products such as laminates and textile fabrics. Full article
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<p>Schematic illustration of methodology of specimen preparation in this study. (<b>a</b>) Stage I of the treatment involving grinding, coarse sieving and preparatory heat treatment, and (<b>b</b>) Stage II of the treatment involving fine sieving, thermal treatment and sealed storage.</p>
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<p>Microbial growth curves of <span class="html-italic">E. coli</span> and <span class="html-italic">S. aureus</span> indicating the three main periods of microbial activity, namely, the lag phase, log phase and stationary phase, based on optical density values collected by the miniphoto 518R photometer.</p>
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<p>Absorbance results of various types of antibacterial agents of bamboo specimens of differing concentrations, C1 and C2, after in vitro testing with <span class="html-italic">E. coli</span> for a 24- and 48-h periods (NS = no significant difference).</p>
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<p>Absorbance results of various types of antibacterial agents of bamboo specimens of differing concentrations, C1 and C2, after in vitro testing with <span class="html-italic">S. aureus</span> for 24 h and 48 h periods (* statistically significant difference, NS = no significant difference).</p>
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<p>Colony-forming units (CFU) of various types of antibacterial agents of bamboo specimens of varying treatment modifications after in vitro testing with <span class="html-italic">E. coli</span> for a 24 h and 48 h periods (* statistically significant difference, NS = no significant difference).</p>
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<p>Colony-forming units (CFU) of various types of antibacterial agents of bamboo specimens of varying treatment modifications after in vitro testing with <span class="html-italic">S. aureus</span> for 24 h and 48 h periods (* statistically significant difference, NS = no significant difference).</p>
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<p>FTIR spectra in the range 400–1800 cm<sup>−1</sup> of three different types of untreated and thermally modified bamboo specimens, namely, Kyoto Moso, Kyushu Moso and Kyushu Madake bamboo.</p>
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12 pages, 4827 KiB  
Article
In Silico and In Vitro Antimalarial Screening and Validation Targeting Plasmodium falciparum Plasmepsin V
by Xin Ji, Zhensheng Wang, Qianqian Chen, Jingzhong Li, Heng Wang, Zenglei Wang and Lan Yang
Molecules 2022, 27(9), 2670; https://doi.org/10.3390/molecules27092670 - 21 Apr 2022
Cited by 4 | Viewed by 2236
Abstract
Malaria chemotherapy is greatly threatened by the recent emergence and spread of resistance in the Plasmodium falciparum parasite against artemisinins and their partner drugs. Therefore, it is an urgent priority to develop new antimalarials. Plasmepsin V (PMV) is regarded as a superior drug [...] Read more.
Malaria chemotherapy is greatly threatened by the recent emergence and spread of resistance in the Plasmodium falciparum parasite against artemisinins and their partner drugs. Therefore, it is an urgent priority to develop new antimalarials. Plasmepsin V (PMV) is regarded as a superior drug target for its essential role in protein export. In this study, we performed virtual screening based on homology modeling of PMV structure, molecular docking and pharmacophore model analysis against a library with 1,535,478 compounds, which yielded 233 hits. Their antimalarial activities were assessed amongst four non-peptidomimetic compounds that demonstrated the promising inhibition of parasite growth, with mean IC50 values of 6.67 μM, 5.10 μM, 12.55 μM and 8.31 μM. No significant affection to the viability of L929 cells was detected in these candidates. These four compounds displayed strong binding activities with the PfPMV model through H-bond, hydrophobic, halogen bond or π-π interactions in molecular docking, with binding scores under −9.0 kcal/mol. The experimental validation of molecule-protein interaction identified the binding of four compounds with multiple plasmepsins; however, only compound 47 showed interaction with plasmepsin V, which exhibited the potential to be developed as an active PfPMV inhibitor. Full article
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Graphical abstract

Graphical abstract
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<p>Homology modeling of <span class="html-italic">Pf</span>PMV 3D structure. (<b>a</b>) Sequence comparison of plasmepsin V in <span class="html-italic">Plasmodium vivax</span> and <span class="html-italic">Plasmodium falciparum</span>. (<b>b</b>) Superposition of homology 3D structure of <span class="html-italic">Pf</span>PMV (M09, in purple) and the crystal structure of <span class="html-italic">Pv</span>PMV (PDB: 4ZL4, in green). (<b>c</b>) The Ramachandran plot of model M09.</p>
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<p>Pharmacophore model construction. (<b>a</b>) Protein–ligand interactions of WEHI-842 with <span class="html-italic">Pv</span>PMV. S1, S2 and S3 represent three subpockets. WEHI-842 is colored green. Dashed line in red indicates H-bond interactions, grey represents hydrophobic interaction, yellow illustrates pi–pi interaction, and orange implies salt bridge interaction. (<b>b</b>) Protein–ligand interactions of WEHI-842 with <span class="html-italic">Pf</span>PMV (M09). (<b>c</b>) Superposition of <span class="html-italic">Pf</span>PMV (in grey) and <span class="html-italic">Pv</span>PMV (in light blue) interacted with WEHI-842. (<b>d</b>) The pharmacophore model of <span class="html-italic">Pf</span>PMV.</p>
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<p>Dose–response curves of candidate compounds. (<b>a</b>–<b>d</b>) represent the dose–response curve of compounds <b>17</b>, <b>47</b>, <b>62</b> and <b>147</b>.</p>
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<p>Comparison of LD<sub>50</sub> and IC<sub>50</sub> values of the candidate compounds. (<b>a</b>–<b>d</b>) indicate the comparison for compounds <b>17</b>, <b>47</b>, <b>62</b> and <b>147</b>.</p>
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<p>Proteinligand interactions of candidate compounds with <span class="html-italic">Pf</span>PMV. (<b>a</b>–<b>d</b>) illustrate the binding of residues with compounds <b>17</b>, <b>47</b>, <b>62</b> and <b>147</b>. Candidate compounds were shown in green color. S1, S2 and S3 represent three subpockets. Dashed line in red indicates H-bonds interactions, grey represents t hydrophobic interaction, yellow illustrates pi–pi interaction and blue implies halogen bond interaction.</p>
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<p>Target validation of candidate compounds by DARTS strategy. (<b>a</b>) SDS−PAGE gel of the compound−protein complexes. (<b>b</b>) Identification of the plasmepsin V based on the label−free LC−MS/MS analysis.</p>
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18 pages, 3314 KiB  
Article
Computational Insights and In Vitro Validation of Antibacterial Potential of Shikimate Pathway-Derived Phenolic Acids as NorA Efflux Pump Inhibitors
by Karishma Singh, Roger M. Coopoosamy, Njabulo J. Gumede and Saheed Sabiu
Molecules 2022, 27(8), 2601; https://doi.org/10.3390/molecules27082601 - 18 Apr 2022
Cited by 10 | Viewed by 2328
Abstract
The expression of the efflux pump systems is the most important mechanism of antibiotic resistance in bacteria, as it contributes to reduced concentration and the subsequent inactivity of administered antibiotics. NorA is one of the most studied antibacterial targets used as a model [...] Read more.
The expression of the efflux pump systems is the most important mechanism of antibiotic resistance in bacteria, as it contributes to reduced concentration and the subsequent inactivity of administered antibiotics. NorA is one of the most studied antibacterial targets used as a model for efflux-mediated resistance. The present study evaluated shikimate pathway-derived phenolic acids against NorA (PDB ID: 1PW4) as a druggable target in antibacterial therapy using in silico modelling and in vitro methods. Of the 22 compounds evaluated, sinapic acid (−9.0 kcal/mol) and p-coumaric acid (−6.3 kcal/mol) had the best and most prominent affinity for NorA relative to ciprofloxacin, a reference standard (−4.9 kcal/mol). A further probe into the structural stability and flexibility of the resulting NorA-phenolic acids complexes through molecular dynamic simulations over a 100 ns period revealed p-coumaric acid as the best inhibitor of NorA relative to the reference standard. In addition, both phenolic acids formed H-bonds with TYR 76, a crucial residue implicated in NorA efflux pump inhibition. Furthermore, the phenolic acids demonstrated favourable drug likeliness and conformed to Lipinski’s rule of five for ADME properties. For the in vitro evaluation, the phenolic acids had MIC values in the range 31.2 to 62.5 μg/mL against S. aureus, and E. coli, and there was an overall reduction in MIC following their combination with ciprofloxacin. Taken together, the findings from both the in silico and in vitro evaluations in this study have demonstrated high affinity of p-coumaric acid towards NorA and could be suggestive of its exploration as a novel NorA efflux pump inhibitor. Full article
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<p>The binding mode of (<b>a</b>) sinapic acid (<b>c</b>) p-coumaric acid, and (<b>e</b>) ciprofloxacin in the active site cavity of NorA. The ligand interaction diagram of (<b>b</b>) sinapic acid, (<b>d</b>) p-coumaric acid, and (<b>f</b>) ciprofloxacin.</p>
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<p>The binding mode of (<b>a</b>) sinapic acid (<b>c</b>) p-coumaric acid, and (<b>e</b>) ciprofloxacin in the active site cavity of NorA. The ligand interaction diagram of (<b>b</b>) sinapic acid, (<b>d</b>) p-coumaric acid, and (<b>f</b>) ciprofloxacin.</p>
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<p>Protein-ligand root mean square deviation for NorA with (<b>a</b>) sinapic acid, (<b>b</b>) p-coumaric acid and (<b>c</b>) ciprofloxacin in a simulation trajectory of 100 ns.</p>
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<p>Protein root mean square fluctuation plot for NorA in the presence of (<b>a</b>) Sinapic acid, (<b>b</b>) p-Coumaric acid, and (<b>c</b>) Ciprofloxacin as complexes.</p>
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<p>(<b>a</b>) Bar chart plot detailing protein-ligand interactions of sinapic acid-NorA complex with the key amino acid residues at NorA active site. (<b>b</b>) Simulation interaction diagram detailing the interaction of sinapic acid with NorA that occur in 30% of simulation time from 0–100 ns.</p>
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<p>(<b>a</b>) Bar chart plot detailing protein-ligand interactions of p-coumaric acid-NorA complex with the key amino acid residues at NorA active site. (<b>b</b>) Simulation interaction diagram detailing the interaction of p-coumaric acid with NorA from 0–100 ns.</p>
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<p>(<b>a</b>) Bar chart plot detailing protein-ligand interactions of ciprofloxacin-NorA complex with the key amino acid residues in the active site cavity. (<b>b</b>) Simulation interaction diagram detailing the interaction of ciprofloxacin with NorA that occur in 30% of simulation time from 0–100 ns.</p>
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<p>Time-kill kinetics of (<b>a</b>) sinapic acid and <span class="html-italic">Staphylococcus aureus</span>, (<b>b</b>) p-coumaric acid and <span class="html-italic">S. aureus</span>, (<b>c</b>) ciprofloxacin and <span class="html-italic">S. aureus</span>, (<b>d</b>) sinapic acid and <span class="html-italic">Escherichia coli</span>, (<b>e</b>) p-coumaric acid and <span class="html-italic">E. coli</span>, (<b>f</b>) ciprofloxacin and <span class="html-italic">E. coli.</span></p>
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14 pages, 1849 KiB  
Article
The Isolation and Characterization of Antagonist Trichoderma spp. from the Soil of Abha, Saudi Arabia
by Aisha Saleh Alwadai, Kahkashan Perveen and Mona Alwahaibi
Molecules 2022, 27(8), 2525; https://doi.org/10.3390/molecules27082525 - 14 Apr 2022
Cited by 9 | Viewed by 3378
Abstract
Background: The genus Trichoderma is widely spread in the environment, mainly in soils. Trichoderma are filamentous fungi and are used in a wide range of fields to manage plant patho-genic fungi. They have proven to be effective biocontrol agents due to their [...] Read more.
Background: The genus Trichoderma is widely spread in the environment, mainly in soils. Trichoderma are filamentous fungi and are used in a wide range of fields to manage plant patho-genic fungi. They have proven to be effective biocontrol agents due to their high reproducibility, adaptability, efficient nutrient mobilization, ability to colonize the rhizosphere, significant inhibitory effects against phytopathogenic fungi, and efficacy in promoting plant growth. In the present study, the antagonist Trichoderma isolates were characterized from the soil of Abha region, Saudi Arabia. Methodology: Soil samples were collected from six locations of Abha, Saudi Arabia to isolate Trichoderma having the antagonistic potential against plant pathogenic fungi. The soil dilution plate method was used to isolate Trichoderma (Trichoderma Specific Medium (TSM)). Isolated Trichoderma were evaluated for their antagonistic potential against Fusarium oxysporum, Alternaria alternata and Helminthosporium rostratum. The antagonist activity was assessed by dual culture assay, and the effect of volatile metabolites and culture filtrate of Trichoderma. In addition, the effect of different temperature and salt concentrations on the growth of Trichoderma isolates were also evaluated. Results: The most potent Trichoderma species were identified by using ITS4 and ITS 5 primers. Total 48 Trichoderma isolates were isolated on (TSM) from the soil samples out of those six isolates were found to have antagonist potential against the tested plant pathogenic fungi. In general, Trichoderma strains A (1) 2.1 T, A (3) 3.1 T and A (6) 2.2 T were found to be highly effective in reducing the growth of tested plant pathogenic fungi. Trichoderma A (1) 2.1 T was highly effective against F. oxysporum (82%), whereas Trichoderma A (6) 2.2 T prevented the maximal growth of H. rostratum (77%) according to the dual culture data. Furthermore, Trichoderma A (1) 2.1 T volatile metabolites hindered F. oxysporum growth. The volatile metabolite of Trichoderma A (6) 2.2 T, on the other hand, had the strongest activity against A. alternata (45%). The Trichoderma A (1) 2.1 T culture filtrate was proven to be effective in suppressing the growth of H. rostratum (47%). The temperature range of 26 °C to 30 °C was observed to be optimum for Trichoderma growth. Trichoderma isolates grew well at salt concentrations (NaCl) of 2%, and with the increasing salt concentration the growth of isolates decreased. The molecular analysis of potent fungi by ITS4 and ITS5 primers confirmed that the Trichoderma isolates A (1) 2.1 T, A (3) 3.1 and A (6) 2.2 T were T. harzianum, T. brevicompactum, and T. velutinum, respectively. Conclusions: The study concludes that the soil of the Abha region contains a large population of diverse fungi including Trichoderma, which can be explored further to be used as biocontrol agents. Full article
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<p>Effect of volatile metabolites of <span class="html-italic">Trichoderma</span> on the growth of plant pathogenic fungi.</p>
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<p>Inhibitory effect of the culture filtrate of <span class="html-italic">Trichoderma</span> isolates.</p>
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<p><span class="html-italic">Trichoderma</span> isolate (A (1) 2.1 T) (analysis of 18S rDNA of the <span class="html-italic">T. harzianum</span> (MF871551.1), with primers ITS4 and ITS5 in NCBI GenBank respectively).</p>
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<p><span class="html-italic">Trichoderma</span> isolate (A (3) 3.1 T) (analysis of 18S rDNA of the <span class="html-italic">T. brevicompactum</span> (KR094463.1), with primers ITS4 and ITS5 in NCBI GenBank respectively).</p>
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<p><span class="html-italic">Trichoderma</span> isolate (A (6) 2.2 T) (analysis of 18S rDNA of the <span class="html-italic">T. velutinum</span> (EU280080.1), with primers ITS4 and ITS5 in NCBI GenBank respectively).</p>
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<p>Location of soil samples collections sites, Abha, Saudi Arabia.</p>
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19 pages, 4690 KiB  
Article
New Organic Salt from Levofloxacin-Citric Acid: What Is the Impact on the Stability and Antibiotic Potency?
by Ilma Nugrahani, Agnesya Namira Laksana, Hidehiro Uekusa and Hironaga Oyama
Molecules 2022, 27(7), 2166; https://doi.org/10.3390/molecules27072166 - 27 Mar 2022
Cited by 8 | Viewed by 3604
Abstract
This research dealt with the composition, structure determination, stability, and antibiotic potency of a novel organic salt composed of levofloxacin (LF) and citric acid (CA), named levofloxacin-citrate (LC). After a stoichiometric proportion screening, the antibiotic-antioxidant reaction was conducted by slow and fast evaporation [...] Read more.
This research dealt with the composition, structure determination, stability, and antibiotic potency of a novel organic salt composed of levofloxacin (LF) and citric acid (CA), named levofloxacin-citrate (LC). After a stoichiometric proportion screening, the antibiotic-antioxidant reaction was conducted by slow and fast evaporation methods. A series of characterizations using thermal analysis, powder X-ray diffractometry, vibrational spectroscopy, and nuclear magnetic resonance confirmed LC formation. The new organic salt showed a distinct thermogram and diffractogram. Next, Fourier transform infrared indicated the change in N-methylamine and carboxylic stretching, confirmed by 1H nuclear magnetic resonance spectra to elucidate the 2D structure. Finally, single-crystal diffractometry determined LC as a new salt structure three-dimensionally. The attributive improvements were demonstrated on the stability toward the humidity and lighting of LC compared to LF alone. Moreover, the antibiotic potency of LF against Staphylococcus aureus (Gram-positive) and Escherichia coli (Gram-negative) enhanced ~1.5–2-fold by LC. Hereafter, LC is a potential salt antibiotic-antioxidant combination for dosage formulas development. Full article
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<p>Molecular structure of parent compounds: (<b>A</b>) levofloxacin (LF) [<a href="#B13-molecules-27-02166" class="html-bibr">13</a>] and (<b>B</b>) citric acid (CA) [<a href="#B14-molecules-27-02166" class="html-bibr">14</a>].</p>
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<p>Phase diagram of LF-CA binary system.</p>
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<p>DSC thermogram of LC (1:1) compared to the starting materials, levofloxacin (hemihydrate), citric acid (dihydrate), and their physical mixture (PM).</p>
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<p>Powder X-ray diffractogram of levofloxacin citrate (LC) compared to the starting materials, levofloxacin (LF)—hemihydrate, and citric acid (CA)—dihydrate, and a physical mixture (PM) of LF and CA.</p>
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<p>FTIR spectra of levofloxacin-citrate (LC) compared to levofloxacin (LF), citric acid (CA), and physical mixture (PM) of levofloxacin and citric acid. The new bands are depicted in the orange marks.</p>
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<p><sup>1</sup>H NMR spectra of levofloxacin (LF) and citric acid (CA) in CDCl<sub>3</sub> solution, and levofloxacin-citrate (LC) in D<sub>2</sub>O.</p>
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<p>Numbering molecule structure of (<b>A</b>) levofloxacin/LF, (<b>B</b>) citric acid/CA, and (<b>C</b>) levofloxacin citrate/LC.</p>
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<p>Empirical structure of levofloxacin-citrate/LC (<b>A</b>); the different C-O distance of ionized citric acid in the LC structure (<b>B</b>); ORTEP-3D structural drawing of LC with the hydrogen bonds in blue (<b>C</b>); and the calculated compared to the measured diffractogram of LC (<b>D</b>).</p>
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<p>The curves of hygroscopicity test data (<b>A</b>) and photo-degradation curve (<b>B</b>) of levofloxacin (LF) and levofloxacin citrate (LC).</p>
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<p>Crystal packing of levofloxacin citrate from a, b, and c view-sites compared to LF-hemihydrate as the parent compound.</p>
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<p>Antibiotic potency comparison against <span class="html-italic">Staphylococcus aureus</span> (<b>A</b>) and <span class="html-italic">Escherichia coli</span> (<b>B</b>). Note: levofloxacin (LF), citric acid (CA), levofloxacin-citrate (LC), and physical mixture (PM) of levofloxacin and citric acid.</p>
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13 pages, 1913 KiB  
Article
In Silico Screen Identifies a New Family of Agonists for the Bacterial Mechanosensitive Channel MscL
by Robin Wray, Paul Blount, Junmei Wang and Irene Iscla
Antibiotics 2022, 11(4), 433; https://doi.org/10.3390/antibiotics11040433 - 24 Mar 2022
Cited by 4 | Viewed by 2620
Abstract
MscL is a highly conserved mechanosensitive channel found in the majority of bacterial species, including pathogens. It functions as a biological emergency release valve, jettisoning solutes from the cytoplasm upon acute hypoosmotic stress. It opens the largest known gated pore and has been [...] Read more.
MscL is a highly conserved mechanosensitive channel found in the majority of bacterial species, including pathogens. It functions as a biological emergency release valve, jettisoning solutes from the cytoplasm upon acute hypoosmotic stress. It opens the largest known gated pore and has been heralded as an antibacterial target. Although there are no known endogenous ligands, small compounds have recently been shown to specifically bind to and open the channel, leading to decreased cell growth and viability. Their binding site is at the cytoplasmic/membrane and subunit interfaces of the protein, which has been recently been proposed to play an essential role in channel gating. Here, we have targeted this pocket using in silico screening, resulting in the discovery of a new family of compounds, distinct from other known MscL-specific agonists. Our findings extended the study of this functional region, the progression of MscL as a viable drug target, and demonstrated the power of in silico screening for identifying and improving the design of MscL agonists. Full article
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<p>The binding site of compound 262 within the MscL structure as determined by docking and molecular dynamics (MD) simulations. (<b>A</b>) The docking pose of the compound, shown in green within the red circle at the cytoplasmic–membrane interface. The boundaries of the lipid bilayer are marked by the grey rectangles on the left. (<b>B</b>) Representative conformation of the ligand, in brown, within the pocket after MD simulation. Note that 262 resides in the binding pocket with little conformational change. (<b>C</b>) Root-mean-square deviation (RMSD) analysis over time shows that compound 262 underwent some translational or rotational movement (blue curve), but the overall conformations are very similar to the docking pose. “MscL” (black curve) is for all residues, while “SS” (red curve) is for residues in secondary structures. The green and blue curves represent the RMSDs of the ligand with and without least square fitting, respectively.</p>
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<p>Compound 262 affects both the growth and viability of <span class="html-italic">E. coli</span> cultures in an MscL-dependent manner. <span class="html-italic">E. coli</span> MJF455 (ΔMscL and ΔMscS) bacterial strain are shown. For the expression of MscL (red) and MscS (blue), the pb10d expression vector (black) was used. (<b>A</b>) Growth inhibition in the presence of increasing concentrations of compound 262 is shown as the percentage of growth (OD<sub>600</sub>), normalized to untreated cultures. The structure of compound 262 is shown as an insert. Error bars show the standard error of the mean (SEM) (n = 3). (<b>B</b>) The percent reduction in CFU’s normalized to untreated samples after overnight treatment with 40 µM compound 262 (n = 4). ** <span class="html-italic">p</span> &lt; 0.005 by a 2-tailed, homoscedastic <span class="html-italic">t</span>-test.</p>
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<p>Compound 262 affects cultures with endogenous levels of expression of <span class="html-italic">E. coli</span> MscL. Cell lines used were indicated with endogenous levels of expression of MscL or MscL expressed in trans (EXP MscL), treated with compound 262 overnight at either 20 µM (blue) or 40 µM (red). The percent changes in OD<sub>600</sub> normalized to untreated cultures are shown (n = 3). ** <span class="html-italic">p</span> &lt; 0.005 by a 2-tailed, homoscedastic <span class="html-italic">t</span>-test when compared to MJF455 (ΔMscL and ΔMscS) at the same concentration.</p>
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<p>Compound 262 increases MscL activity in a patch clamp of native bacterial membranes. (<b>A</b>) Representative traces of MscL activity in an excised patch from bacterial giant cells, held at a pressure of −110 mmHg, before (control) and after 10 min of the addition of 40 μM compound 262 to the bath. (<b>B</b>) Quantification of MscL channel activity measured as the open probability (NPo) of the channels in a patch held at the same pressure, before and after curcumin treatment. * <span class="html-italic">p</span> &lt; 0.05 Student paired <span class="html-italic">t</span>-test (n = 5).</p>
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<p>Two views of compound 262 in the binding pocket after MD simulations. Interactions with specific residues are shown.</p>
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<p>Mutational analysis provides additional evidence for the binding site of compound 262. The inhibition of growth after treatment of compound 262 at 40 µM is shown as OD<sub>600</sub> normalized to untreated cultures. The MJF455 (ΔMscL and ΔMscS) cell lines carrying pB10d empty plasmid (Null) and expressing wild type <span class="html-italic">E. coli</span> MscL (WT) or mutations of <span class="html-italic">E. coli</span> MscL are indicated (n = 3–10). * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.005, *** <span class="html-italic">p</span> &lt; 0.0005, **** <span class="html-italic">p</span> &lt; 0.00005, mutations vs. WT for the <span class="html-italic">E. coli</span> MscL 2-tailed, homoscedastic <span class="html-italic">t</span>-test.</p>
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<p>Compound 262 efficacies for cells expressing MscL orthologues and mutants of <span class="html-italic">Bacillus subtilis</span> and <span class="html-italic">Haemophilus influenza</span> (<span class="html-italic">H. inf</span>), which are consistent with its docking profile. <span class="html-italic">E. coli</span> strain MJF455 cultures was in the presence of 40 µM compound 262. (<b>A</b>) The percent changes in OD<sub>600</sub> normalized to untreated cultures. Note that changing the <span class="html-italic">E. coli</span> MscL K97 to R decreased compound 262 sensitivity, whereas changing <span class="html-italic">B. sub</span>-MscL R88 to K increased compound 262 sensitivity, consistent with the canonical sequence in the proposed binding pocket. (<b>B</b>) <span class="html-italic">E. coli</span> expressing <span class="html-italic">E. coli</span> MscL (<span class="html-italic">E. coli</span>) or the orthologue <span class="html-italic">H. inf</span>. Note that changing the <span class="html-italic">E. coli</span> MscL L19 to M or <span class="html-italic">H. inf</span> M19 to L did not change compound 262 sensitivity, demonstrating compound 262 did not share the canonical binding pocket in the pore, where dihydrostreptomycin is known to bind. n = 3–6. * <span class="html-italic">p</span> &lt; 0.05, mutations vs. WT for either <span class="html-italic">E. coli</span>-, <span class="html-italic">B. sub</span>-, or <span class="html-italic">H. inf</span>-MscL, 2-tailed, homoscedastic <span class="html-italic">t</span>-test.</p>
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<p>Compound 262 increases the potency of the common antibiotic kanamycin, only when MscL is present. Values are expressed as a percentage of growth (OD<sub>600</sub>), relative to non-treated samples. MJF455 (ΔMscL, ΔMscS) cultures carrying empty plasmid (Null) or expressing <span class="html-italic">E. coli</span> MscL (MscL) were treated with varying concentrations of compound 262 and grown in the presence or the absence of 0.5 μM kanamycin as indicated (n = 3–4). Error bars show the standard errors of the means (SEMs).</p>
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20 pages, 4023 KiB  
Article
Identification of Putative Vaccine and Drug Targets against the Methicillin-Resistant Staphylococcus aureus by Reverse Vaccinology and Subtractive Genomics Approaches
by Romen Singh Naorem, Bandana Devi Pangabam, Sudipta Sankar Bora, Gunajit Goswami, Madhumita Barooah, Dibya Jyoti Hazarika and Csaba Fekete
Molecules 2022, 27(7), 2083; https://doi.org/10.3390/molecules27072083 - 24 Mar 2022
Cited by 20 | Viewed by 4142
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen and responsible for causing life-threatening infections. The emergence of hypervirulent and multidrug-resistant (MDR) S. aureus strains led to challenging issues in antibiotic therapy. Consequently, the morbidity and mortality rates caused by S. aureus infections have [...] Read more.
Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen and responsible for causing life-threatening infections. The emergence of hypervirulent and multidrug-resistant (MDR) S. aureus strains led to challenging issues in antibiotic therapy. Consequently, the morbidity and mortality rates caused by S. aureus infections have a substantial impact on health concerns. The current worldwide prevalence of MRSA infections highlights the need for long-lasting preventive measures and strategies. Unfortunately, effective measures are limited. In this study, we focus on the identification of vaccine candidates and drug target proteins against the 16 strains of MRSA using reverse vaccinology and subtractive genomics approaches. Using the reverse vaccinology approach, 4 putative antigenic proteins were identified; among these, PrsA and EssA proteins were found to be more promising vaccine candidates. We applied a molecular docking approach of selected 8 drug target proteins with the drug-like molecules, revealing that the ZINC4235426 as potential drug molecule with favorable interactions with the target active site residues of 5 drug target proteins viz., biotin protein ligase, HPr kinase/phosphorylase, thymidylate kinase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase, and pantothenate synthetase. Thus, the identified proteins can be used for further rational drug or vaccine design to identify novel therapeutic agents for the treatment of multidrug-resistant staphylococcal infection. Full article
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<p>Systemic workflow of vaccine and drug targets identification using subtractive genome analysis.</p>
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<p>The molecular docking analysis of BPL (WP_000049913.1) with compound ZINC4235426. (<b>a</b>) 3D surface representation of ZINC4235426 (red) and BPL interactions with hydrogen bonding sites (blue), and hydrophobic interactions (cyan). (<b>b</b>) Residues (cyan) involved in the H-bond interaction (green dashed lines) with the compound (scaled ball and stick).</p>
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<p>The molecular docking analysis of HPr kinase (WP_000958224.1) with compounds ZINC4235426 and ZINC4235924, respectively. (<b>a</b>,<b>c</b>) 3D surface representation of ZINC4235426 (red), ZINC4235924 (red), and HPr kinase interactions with hydrogen bonding sites (blue), and hydrophobic interactions (cyan). (<b>b</b>,<b>d</b>) Residues (cyan) involved in the H-bond interaction (green dashed lines) with the compound (scaled ball and stick).</p>
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<p>The molecular docking analysis of TMK (WP_001272126.1) with compound ZINC4259578. (<b>a</b>) 3D surface representation of ZINC4259578 (red) and TMK interactions with hydrogen bonding sites (blue), and hydrophobic interactions (cyan). (<b>b</b>) Residues (cyan) involved in the H-bond interaction (green dashed lines) with the compound (scaled ball and stick).</p>
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<p>The molecular docking analysis of Pta (WP_000774281.1) with compound ZINC4270981. (<b>a</b>) 3D surface representation of ZINC4270981 (red) and Pta interactions with hydrogen bonding sites (blue), and hydrophobic interactions (cyan). (<b>b</b>) Residues (cyan) involved in the H-bond interaction (green dashed lines) with the compound (scaled ball and stick).</p>
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<p>The molecular docking analysis of MurE (WP_000340119.1) with compound ZINC4235426. (<b>a</b>) 3D surface representation of ZINC4235426 (red) and MurE interactions with hydrogen bonding sites (blue), and hydrophobic interactions (cyan). (<b>b</b>) Residues (cyan) involved in the H-bond interaction (green dashed lines) with the compound (scaled ball and stick).</p>
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<p>The molecular docking analysis of UGPase (WP_000721337.1) with compound ZINC428871. (<b>a</b>) 3D surface representation of ZINC428871 (red) and MurE interactions with hydrogen bonding sites (blue), and hydrophobic interactions (cyan). (<b>b</b>) Residue (cyan) involved in the H-bond interaction (green dashed lines) with the compound (scaled ball and stick).</p>
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<p>The molecular docking analysis of PlsX (WP_000239744.1) with compound ZINC4237105. (<b>a</b>) 3D surface representation of ZINC4237105 (red) and PlsX interactions with hydrogen bonding sites (blue), and hydrophobic interactions (cyan). (<b>b</b>) Residue (cyan) involved in the H-bond interaction (green dashed lines) with the compound (scaled ball and stick).</p>
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<p>The molecular docking analysis of PanC (WP_000163742.1) with compound ZINC4235426. (<b>a</b>) 3D surface representation of ZINC4235426 (red) and PanC interactions with hydrogen bonding sites (blue), and hydrophobic interactions (cyan). (<b>b</b>) Residues (cyan) involved in the H-bond interaction (green dashed lines) with the compound (scaled ball and stick).</p>
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13 pages, 850 KiB  
Article
Antimicrobial Activity and 70S Ribosome Binding of Apidaecin-Derived Api805 with Increased Bacterial Uptake Rate
by Tobias Ludwig, Andor Krizsan, Gubran Khalil Mohammed and Ralf Hoffmann
Antibiotics 2022, 11(4), 430; https://doi.org/10.3390/antibiotics11040430 - 23 Mar 2022
Cited by 6 | Viewed by 3373
Abstract
In view of the global spread of multiresistant bacteria and the occurrence of panresistant bacteria, there is an urgent need for antimicrobials with novel modes of action. A promising class is antimicrobial peptides (AMPs), including them proline-rich AMPs (PrAMPs), which target the 70S [...] Read more.
In view of the global spread of multiresistant bacteria and the occurrence of panresistant bacteria, there is an urgent need for antimicrobials with novel modes of action. A promising class is antimicrobial peptides (AMPs), including them proline-rich AMPs (PrAMPs), which target the 70S ribosome to inhibit protein translation. Here, we present a new designer peptide, Api805, combining the N- and C-terminal sequences of PrAMPs Api137 and drosocin, respectively. Api805 was similarly active against two Escherichia coli B strains but was inactive against E. coli K12 strain BW25113. These different activities could not be explained by the dissociation constants measured for 70S ribosome preparations from E. coli K12 and B strains. Mutations in the SbmA transporter that PrAMPs use to pass the inner membrane or proteolytic degradation of Api805 by lysate proteases could not explain this either. Interestingly, Api805 seems not to bind to the known binding sites of PrAMPs at the 70S ribosome and inhibited in vitro protein translation, independent of release factors, most likely using a “multimodal effect”. Interestingly, Api805 entered the E. coli B strain Rosetta faster and at larger quantities than the E. coli K-12 strain BW25113, which may be related to the different LPS core structure. In conclusion, slight structural changes in PrAMPs significantly altered their binding sites and mechanisms of action, allowing for the design of different antibiotic classes. Full article
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Figure 1
<p>Fluorescence polarization assay testing of Api805 (orange), Api801 (red), Api137 (blue), and Onc112 (black) in competition with cf-Api137 (left) and cf-Onc112 (right) for the ribosomal binding sites of Api137 and Onc112. Experiments were performed twice in triplicate. Error bars indicate the standard deviation of all six replicates. The horizontal dotted line separates positive and negative ranges on the <span class="html-italic">y</span>-axis.</p>
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<p>In vitro translation of GFP in the presence of PrAMPs Onc112, Api137, Api805, drosocin, and Api88 with (dark grey) or without (light grey) added release factor RF1. Presented is the measured GFP fluorescence relative to the control experiment without the addition of a PrAMP (=100%). Experiments were performed twice in duplicate. Error bars indicate the standard deviation of all four replicates. Significant differences were determined using <span class="html-italic">t</span>-test (<a href="#app1-antibiotics-11-00430" class="html-app">Tables S4 and S5</a>).</p>
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<p>Uptake assay of <span class="html-italic">E. coli</span> BW25113 and Rosetta cultures incubated in the absence of PrAMP (black, negative control) or in the presence of cf-labeled Api137 (blue), Api88 (gray), and Api805 (orange) for 0, 90, and 180 min. Presented is the fluorescence remaining in the <span class="html-italic">E. coli</span> cells after washing them twice with PBS normalized to the OD<sub>600</sub> of the corresponding cell culture. The peptide concentration was 23 µmol/L. Experiments were performed twice in triplicate. Error bars indicate the standard deviation of all six replicates. Significant differences were determined using <span class="html-italic">t</span>-test (<a href="#app1-antibiotics-11-00430" class="html-app">Table S6</a>).</p>
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25 pages, 7034 KiB  
Article
Morphing Natural Product Platensimycin via Heck, Sonogashira, and One-Pot Sonogashira/Cycloaddition Reactions to Produce Antibiotics with In Vivo Activity
by Youchao Deng, Yuling Li, Zhongqing Wen, Claudia H. Ruiz, Xiang Weng, Michael D. Cameron, Yanwen Duan and Yong Huang
Antibiotics 2022, 11(4), 425; https://doi.org/10.3390/antibiotics11040425 - 23 Mar 2022
Cited by 1 | Viewed by 2341
Abstract
Type II fatty acid synthases are promising drug targets against major bacterial pathogens. Platensimycin (PTM) is a potent inhibitor against β-ketoacyl-[acyl carrier protein] synthase II (FabF) and β-ketoacyl-[acyl carrier protein] synthase I (FabB), while the poor pharmacokinetics has prevented its further [...] Read more.
Type II fatty acid synthases are promising drug targets against major bacterial pathogens. Platensimycin (PTM) is a potent inhibitor against β-ketoacyl-[acyl carrier protein] synthase II (FabF) and β-ketoacyl-[acyl carrier protein] synthase I (FabB), while the poor pharmacokinetics has prevented its further development. In this work, thirty-two PTM derivatives were rapidly prepared via Heck, Sonogashira, and one-pot Sonogashira/cycloaddition cascade reactions based on the Gram-scale synthesis of 6-iodo PTM (4). About half of the synthesized compounds were approximately equipotent to PTM against the tested Staphylococcus aureus strains. Among them, the representative compounds 4, A4, and B8 exhibited different plasma protein binding affinity or stability in the human hepatic microsome assay and showed improved in vivo efficacy over PTM in a mouse peritonitis model. In addition, A4 was also effective in an S. aureus-infected skin mouse model. Our study not only significantly expands the known PTM derivatives with improved antibacterial activities in vivo, but showcased that C–C cross-coupling reactions are useful tools to functionalize natural product drug leads. Full article
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<p>The strategy to modify PTM terpene cage. (<b>A</b>) The structure–activity relationships of PTM. (<b>B</b>) The retrosynthetic analysis for preparation of 6-acrylyl or alkynyl PTM (<b>A1</b>–<b>A10</b>, <b>B1</b>–<b>15</b>) through Heck and Sonogashira reactions and cyclized analogues through a Sonogashira/cycloaddition cascade reaction (<b>C1</b>–<b>C7</b>).</p>
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<p>The predicted docking mode of <b>A4</b>, <b>B8</b>, and <b>C5</b> with ecFabF. (<b>A</b>) <b>A4</b> (yellow) overlaps with PTM (green). (<b>B</b>) The interaction map of <b>A4</b> with FabF shown in a two-dimensional mode. (<b>C</b>–<b>F</b>) The docking mode of <b>B8</b> and <b>C5</b> with ecFabF.</p>
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<p>Molecular dynamics simulation. (<b>A</b>) The RMSD values of the FabF backbone and (<b>B</b>) the nonbond interaction energies between protein and ligand in the complexes between 2 and 50 ns. <b>A4</b> was in red and PTM was in black.</p>
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<p>In vivo antimicrobial activity of PTM derivatives. (<b>A</b>) The general procedures of the mouse peritonitis model. (<b>B</b>) Therapeutic efficacy of compound <b>4</b>, <b>A4</b>, <b>B8</b>, and PTM on MRSA infected mice. Saline was used as the negative control and vancomycin as the antibiotic control. There were five mice in each group. The infected mice were inspected two times and their survival was tracked for 7 days. (<b>C</b>) The average weights of each group were recorded once a day. (<b>D</b>,<b>F</b>,<b>H</b>) Therapeutic efficacy of <b>A4</b> in different dosages, using the same procedures. (<b>E</b>,<b>G</b>,<b>I</b>) The average weights of each group.</p>
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<p>The antibacterial activity of PTM and <b>A4</b> in MRSA-induced mice skin infection. (<b>A</b>) General procedures for evaluating the therapeutic efficacy of <b>A4</b> in a mouse skin infection model. Mupirocin was used as the positive control. The infected mice were treated twice a day for 7 days. (<b>B</b>) The total bacterial loads in the skin lesions were determined. Statistical analysis was calculated by the Mann–Whitney test. **** <span class="html-italic">p</span> &lt; 0.0001. (<b>C</b>) Wounds of BALB/c mice treated and untreated with compounds after 7 days. (<b>D</b>–<b>F</b>) HE staining histological appearance of <span class="html-italic">S. aureus</span>-infected skin lesion on day 10. Biopsy specimens were taken immediately after the termination of the experiment, fixed in formalin, and embedded in paraffin. The biopsy specimens were stained with hematoxylin and eosin. Each point represents data from a single mouse. Mean values are presented; n = 5.</p>
Full article ">Scheme 1
<p>The synthesis of 6-iodo-PTM (<b>4</b>). (<b>a</b>) LiOH (2 M, 3.0 eq. in MeOH and water, rt; &gt;95%; (<b>b</b>) <b>3</b>, PyBOP 1.0 eq., Et<sub>3</sub>N 3.0 eq. in the mixture solvent of DMF and DCM, stirred under rt, &gt;80%.</p>
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<p>Synthesis of PTM derivatives. Compounds <b>A1</b>–<b>A10</b>, <b>B1</b>–<b>B15</b> were prepared in classical Heck and Sonogashira reaction conditions. <b>C1</b>–<b>C7</b> were prepared via a one-pot synthesis strategy from <b>4</b>.</p>
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<p>The mechanistic study for the one-pot synthesis of <b>C1</b>–<b>C7</b>. (<b>A</b>) The proposed mechanism for the formation of <b>C1</b>–<b>C7</b>. (<b>B</b>) Density functional theory-based calculation for the asymmetric Michael reaction of the deprotonated acetylacetone to PTM surrogate <b>3a</b>, followed by cyclization en route to the formation of <b>3g</b>. M06-2X/6-31 + G(d,p)/CPCM (DMSO). All energies in kcal mol<span class="html-italic"><sup>−</sup></span><sup>1</sup> and bond distances in Å.</p>
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13 pages, 12614 KiB  
Article
Novel Antimicrobial Peptides Designed Using a Recurrent Neural Network Reduce Mortality in Experimental Sepsis
by Albert Bolatchiev, Vladimir Baturin, Evgeny Shchetinin and Elizaveta Bolatchieva
Antibiotics 2022, 11(3), 411; https://doi.org/10.3390/antibiotics11030411 - 18 Mar 2022
Cited by 11 | Viewed by 3704
Abstract
The search and development of new antibiotics is relevant due to widespread antibiotic resistance. One of the promising strategies is the de novo design of novel antimicrobial peptides. The amino acid sequences of 198 novel peptides were obtained using a generative long short-term [...] Read more.
The search and development of new antibiotics is relevant due to widespread antibiotic resistance. One of the promising strategies is the de novo design of novel antimicrobial peptides. The amino acid sequences of 198 novel peptides were obtained using a generative long short-term memory recurrent neural network (LSTM RNN). To assess their antimicrobial effect, we synthesized five out of 198 generated peptides. The PEP-38 and PEP-137 peptides were active in vitro against carbapenem-resistant isolates of Klebsiella aerogenes and K. pneumoniae. PEP-137 was also active against Pseudomonas aeruginosa. The remaining three peptides (PEP-36, PEP-136 and PEP-174) showed no antibacterial effect. Then the effect of PEP-38 and PEP-137 (a single intraperitoneal administration of a 100 μg dose 30 min after infection) on animal survival in an experimental murine model of K. pneumoniae-induced sepsis was investigated. As a control, two groups of mice were used: one received sterile saline, and the other received inactive in vitro PEP-36 (a single 100 μg dose). The PEP-36 peptide was shown to provide the highest survival rate (66.7%). PEP-137 showed a survival rate of 50%. PEP-38 was found to be ineffective. The data obtained can be used to develop new antibacterial peptide drugs to combat antibiotic resistance. Full article
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Figure 1
<p>Comparison of peptide characteristics between the training data (Training, orange), the generated sequences (Sampled, blue), the pseudo-random sequences with the same amino acid distribution as in the training set (Ran, purple), and the manually created hypothetical amphipathic helices (Hel, green). The horizontal dashed lines represent the mean (violin plots) and median (box plots) values; the whiskers extend to the outermost non-outlier data points. Graphs from left to right: Eisenberg hydrophobicity, Eisenberg hydrophobic moment, and sequence length. The figure was generated using the modlAMP’s GlobalAnalysis.plot_summary method in Python [<a href="#B16-antibiotics-11-00411" class="html-bibr">16</a>].</p>
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<p>Comparison of probability of survival (%) in each group: control (sterile saline), PEP-36, PEP-38 and PEP-137. The peptides were injected once in a dose of 100 μg 30 min after infection of mice with 6.75 × 10<sup>8</sup> CFU suspension of a carbapenem-resistant isolate of <span class="html-italic">K. pneumoniae</span>. *—significant differences from the control group using the Kaplan-Meier method and Log-rank (Mantel-Cox) test.</p>
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<p>Visual comparison of the structures of LL-37 (yellow; PDB ID: 2K6O) and synthesized peptides: PEP-137—blue, PEP-38—red, PEP-36—green (by AlphaFold).</p>
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<p>Initial and final snapshot of peptide-membrane system before and after 225 ns of MD simulation. The membrane is shown in lines (cyan) and the peptides are shown in helical structure (colored according to the type of amino acids). Phosphate atoms of the membrane are shown in gray color.</p>
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<p>Top view of the peptide-membrane system (<b>left</b>) at 225 ns of MD simulation showing the unravelling of the helical structure. Phosphate atoms of the membrane are shown in gray color. Side view (<b>right</b>) showing the penetration of peptide at 225 ns.</p>
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21 pages, 8115 KiB  
Article
Inhibition of Filamentous Thermosensitive Mutant-Z Protein in Bacillus subtilis by Cyanobacterial Bioactive Compounds
by Manisha Gurnani, Prangya Rath, Abhishek Chauhan, Anuj Ranjan, Arabinda Ghosh, Rup Lal, Nobendu Mukerjee, Nada H. Aljarba, Saad Alkahtani, Vishnu D. Rajput, Svetlana Sushkova, Evgenya V. Prazdnova, Tatiana Minkina and Tanu Jindal
Molecules 2022, 27(6), 1907; https://doi.org/10.3390/molecules27061907 - 15 Mar 2022
Cited by 2 | Viewed by 3750
Abstract
Antibiotic resistance is one of the major growing concerns for public health. Conventional antibiotics act on a few predefined targets and, with time, several bacteria have developed resistance against a large number of antibiotics. The WHO has suggested that antibiotic resistance is at [...] Read more.
Antibiotic resistance is one of the major growing concerns for public health. Conventional antibiotics act on a few predefined targets and, with time, several bacteria have developed resistance against a large number of antibiotics. The WHO has suggested that antibiotic resistance is at a crisis stage and identification of new antibiotics and targets could be the only approach to bridge the gap. Filamentous Temperature Sensitive-Mutant Z (Fts-Z) is one of the promising and less explored antibiotic targets. It is a highly conserved protein and plays a key role in bacterial cell division by introducing a cytokinetic Z-ring formation. In the present article, the potential of over 165 cyanobacterial compounds with reported antibiotic activity against the catalytic core domain in the Fts-Z protein of the Bacillus subtilis was studied. The identified cyanobacterial compounds were screened using the GLIDE module of Maestro v-2019-2 followed by 100-ns molecular dynamics (MD) simulation. Ranking of the potential compound was performed using dock score and MMGBSA based free energy. The study reported that the docking score of aphanorphine (−6.010 Kcalmol−1) and alpha-dimorphecolic acid (ADMA) (−6.574 Kcalmol−1) showed significant role with respect to the reported potential inhibitor PC190723 (−4.135 Kcalmol−1). A 100 ns MD simulation infers that Fts-Z ADMA complex has a stable conformation throughout the progress of the simulation. Both the compounds, i.e., ADMA and Aphanorphine, were further considered for In-vitro validation by performing anti-bacterial studies against B. subtilis by agar well diffusion method. The results obtained through In-vitro studies confirm that ADMA, a small molecule of cyanobacterial origin, is a potential compound with an antibacterial activity that may act by inhibiting the novel target Fts-Z and could be a great drug candidate for antibiotic development. Full article
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Figure 1
<p>(<b>A</b>) An illustration representing the role of Fts-Z in the Z-ring assembly pathway, emphasizing normal and interrupted cell division in bacteria; (<b>B</b>) Structure of Fts-Z protein from S. aureus (PDB ID-2VXY) in ribbons bound to GDP (in brown CPK). The T7 loop is in pink and α-H7 helix is in green. The blue-colored portion is the N-terminal and the green portion is the C-terminal. The figure was visualized in BIOVIA Discovery studio visualizer v21.1; (<b>C</b>) The binding sites present on the Fts-Z protein. (Figure generated through PDBSUM) [<a href="#B37-molecules-27-01907" class="html-bibr">37</a>].</p>
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<p>The figure shows the grid formed around the receptor Fts-Z (PDB ID 2VXY), taking the site map tool’s predictions. Site points (presented on grey surface) for the potential binding site (site-1). The site score was 0.911 with a size of 791. Dscore- was 1.028, Volume—558.061, HB don./acc.—1.401, Hydrophilic—0.185, Hydrophobic—0.464.</p>
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<p>Schematic figure showing steps followed during virtual screening of compounds.</p>
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<p>The 2D and 3D diagrams of docking poses. (<b>A-I</b>) 3D interaction diagram of Alpha dimorphecolic acid (5312830) with Fts-Z protein.; (<b>A-II</b>) 2D interaction diagram of Alpha dimorphecolic acid (5312830) with Fts-Z protein.; (<b>B-I</b>) 3D interaction diagram of Aphanorphine (189594) with Fts-Z protein. (<b>B-II</b>) 2D interaction diagram of Aphanorphine (189594) with Fts-Z protein.; (<b>C-I</b>) 3D interaction diagram of Circinamide (21601944) with Fts-Z protein. (<b>C-II</b>) 2D interaction diagram of Circinamide (21601944) with Fts-Z protein.; (<b>D-I</b>) 3D interaction diagram of Aeruginosin 102 A (10101474) with Fts-Z protein. (<b>D-II</b>) 2D interaction diagram of Aeruginosin 102 A (10101474) with Fts-Z protein.; (<b>E-I</b>) 3D interaction diagram of PC190723 (25016417) with Fts-Z protein. (<b>E-II</b>) interaction diagram of PC190723 (25016417) with Fts-Z protein.</p>
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<p>The 2D and 3D diagrams of docking poses. (<b>A-I</b>) 3D interaction diagram of Alpha dimorphecolic acid (5312830) with Fts-Z protein.; (<b>A-II</b>) 2D interaction diagram of Alpha dimorphecolic acid (5312830) with Fts-Z protein.; (<b>B-I</b>) 3D interaction diagram of Aphanorphine (189594) with Fts-Z protein. (<b>B-II</b>) 2D interaction diagram of Aphanorphine (189594) with Fts-Z protein.; (<b>C-I</b>) 3D interaction diagram of Circinamide (21601944) with Fts-Z protein. (<b>C-II</b>) 2D interaction diagram of Circinamide (21601944) with Fts-Z protein.; (<b>D-I</b>) 3D interaction diagram of Aeruginosin 102 A (10101474) with Fts-Z protein. (<b>D-II</b>) 2D interaction diagram of Aeruginosin 102 A (10101474) with Fts-Z protein.; (<b>E-I</b>) 3D interaction diagram of PC190723 (25016417) with Fts-Z protein. (<b>E-II</b>) interaction diagram of PC190723 (25016417) with Fts-Z protein.</p>
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<p>Surface is added to Fts-Z protein (PDB ID-2VXY) on the basis of hydrophobicity, and ADMA compound (in green) is shown to be docked in the binding cavity and another zoom in figure is shown for interacting residues of the protein with ligand. Further Zoom in view of the ADMA compound and interacting residues from binding cavity. The visualization was done through Biovia Discovery Studio Visualizer.</p>
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<p>The RMSD (in Å) of Fts-Z protein (PDB ID- 2VXY) with ADMA (ligand) compound during 100 ns MD trajectory. The fluctuations of both the ligand and the receptor were in an acceptable range. Fts-Z protein (in green) fluctuation was within 2 Å, achieving stability towards the end of the simulation, and that of ligand (in maroon) with respect to protein and its binding pocket was also not fluctuating significantly showing a stabler confirmation.</p>
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<p>The Root Mean Square Fluctuation (RMSF) of Fts-Z protein (PDB ID-2VXY) throughout 100 ns molecular dynamic simulations showing local fluctuations along with the receptor.</p>
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<p>(<b>A</b>) Two-dimensional diagram of contacts made more than 9% of simulation time between ADMA (ligand) and Fts-Z (PDB ID-2VXY) (receptor) in 100-ns molecular dynamics. Gln 192 showed a contact time of 110% because it had multiple interactions of a single type with ADMA atoms. (<b>B</b>) The plot represents the interaction of the ADMA with 2VXY residues in simulation. (<b>C</b>) A timeline representation of residues interacting with the ligand along with density in each trajectory frame.</p>
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<p>Ligand properties—Root mean square deviation (RMSD) of the ligand with respect to the reference conformation; rGyr (Measure of Extendedness of ligand); intraHB; MolSA; SASA; PSA.2.5. In-vitro Validation of Lead Compound.</p>
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<p>Zone of inhibition against <span class="html-italic">Bacillus subtilis</span> (MTCC 441): Muller Hinton Agar plate, (<b>A</b>) well size: 16.14 mm for Methanolic extract of <span class="html-italic">Oscillatoria</span> biomass (100 µgmL<sup>−1</sup>). (<b>B</b>) 23.12 mm for Alpha dimorphecolic acid (5 µgmL<sup>−1</sup>) 21.33 mm for Polymyxin B-sulphate (5 µgmL<sup>−1</sup>). Zone size in mm was recorded after 24 h of incubation time at 37 °C.</p>
Full article ">Figure 11
<p>Minimum inhibitory concentration of Methanolic extract of <span class="html-italic">Oscillatoria</span> against <span class="html-italic">Bacillus subtilis</span> (MTCC 441) Muller Hinton agar broth tubes A to K dilution range from 1024 to 1 µgmL<sup>−1</sup>. A—1024 µgmL<sup>−1</sup>, B—512 µgmL<sup>−1</sup>, C—256 µgmL<sup>−1</sup>, D—128 µgmL<sup>−1</sup>, E—64 µgmL<sup>−1</sup>, F—32 µgmL<sup>−1</sup>, G—16 µgmL<sup>−1</sup>, H—8 µgmL<sup>−1</sup>, I—4 µgmL<sup>−1</sup>, J—2 µgmL<sup>−1</sup>, K—1 µgmL<sup>−1</sup>.</p>
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<p>Minimum inhibitory concentration of Alpha dimorphecolic acid against <span class="html-italic">Bacillus subtilis</span> (MTCC 441) Muller Hinton agar broth tubes A to K dilution range from 1024 to 1 µgmL<sup>−1</sup>. A—1024 µgmL<sup>−1</sup>, B—512 µgmL<sup>−1</sup>, C—256 µgmL<sup>−1</sup>, D—128 µgmL<sup>−1</sup>, E—64 µgmL<sup>−1</sup>, F—32 µgmL<sup>−1</sup>, G—16 µgmL<sup>−1</sup>, H—8 µgmL<sup>−1</sup>, I—4 µgmL<sup>−1</sup>, J—2 µgmL<sup>−1</sup>, K—1 µgmL<sup>−1</sup>.</p>
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<p>Minimum inhibitory concentration of Polymyxin B sulphate against <span class="html-italic">Bacillus subtilis</span> (MTCC 441) Muller Hinton agar broth tubes A to K dilution range from 1024 to 1 µgmL<sup>−1</sup>. A—1024 µgmL<sup>−1</sup>, B—512 µgmL<sup>−1</sup>, C—256 µgmL<sup>−1</sup>, D—128 µgmL<sup>−1</sup>, E—64 µgmL<sup>−1</sup>, F—32 µgmL<sup>−1</sup>, G—16 µgmL<sup>−1</sup>, H—8 µgmL<sup>−1</sup>, I—4 µgmL<sup>−1</sup>, J—2 µgmL<sup>−1</sup>, K—1 µgmL<sup>−1</sup>.</p>
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14 pages, 3822 KiB  
Article
Biological Activity of Pulcherrimin from the Meschnikowia pulcherrima Clade
by Dorota Kregiel, Maria Nowacka, Anna Rygala and Renáta Vadkertiová
Molecules 2022, 27(6), 1855; https://doi.org/10.3390/molecules27061855 - 12 Mar 2022
Cited by 17 | Viewed by 3151
Abstract
Pulcherrimin is a secondary metabolite of yeasts belonging to the Metschnikowia pulcherrima clade, and pulcherrimin formation is responsible for the antimicrobial action of its producers. Understanding the environmental function of this metabolite can provide insight into various microbial interactions and enables the efficient [...] Read more.
Pulcherrimin is a secondary metabolite of yeasts belonging to the Metschnikowia pulcherrima clade, and pulcherrimin formation is responsible for the antimicrobial action of its producers. Understanding the environmental function of this metabolite can provide insight into various microbial interactions and enables the efficient development of new effective bioproducts and methods. In this study, we evaluated the antimicrobial and antiadhesive action of yeast pulcherrimin, as well as its protective properties under selected stressful conditions. Classical microbiological plate methods, microscopy, and physico-chemical testing were used. The results show that pure pulcherrimin does not have antimicrobial properties, but its unique hydrophilic nature may hinder the adhesion of hydrophilic bacterial cells to abiotic surfaces. Pulcherrimin also proved to be a good cell protectant against UV–C radiation at both high and low temperatures. Full article
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Figure 1

Figure 1
<p>Comparison of antimicrobial activity of <span class="html-italic">Metschnikowia</span> sp. LOCK1144 cells and pure pulcherrimin suspension (~3% <span class="html-italic">w</span>/<span class="html-italic">v</span>) against tested microorganisms. Samples with pure pulcherrimine were taken as controls. Values show the mean ± standard deviation (SD, n = 3). Values with different letters are statistically different: <sup>a</sup>: <span class="html-italic">p</span> ≥ 0.05; <sup>c</sup>: <span class="html-italic">p</span> &lt; 0.005.</p>
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<p>Surface free energy of glass and glass with yeast pulcherrimin evaluated for two solvents: a dispersive solvent (glycerol), and a polar solvent (water). Glass surface and its SFE components were taken as references. Values show the mean ± standard deviation (SD, n = 3). Values with different letters are statistically different: <sup>b</sup>: 0.005 &lt; <span class="html-italic">p</span> &lt; 0.05; <sup>c</sup>: <span class="html-italic">p</span> &lt; 0.005.</p>
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<p>Adhesion coefficient A evaluated for microbial cultures incubated in culture media with and without pulcherrimin supplementation. Values show the mean ± standard deviation (SD, n = 3). Results obtained in minimal medium with pulcherrimin were compared with those for minimal medium without supplementation (control). Values with different letters are statistically different: <sup>a</sup>: <span class="html-italic">p</span> ≥ 0.05; <sup>b</sup>: 0.005 &lt; <span class="html-italic">p</span> &lt; 0.05.</p>
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<p>Attachment of microbial cells to glass surface. Yeast cells of W. anomalus cultivated without pulcherrimin (<b>a</b>) and with pulcherrimin (<b>b</b>). Bacterial cells of A. lannensis FMW2 cultivated without pulcherrimin (<b>c</b>) and with pulcherrimin (<b>d</b>). Bars represent 20 μm.</p>
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<p>Decimal reduction times determined for three strains of <span class="html-italic">M. pulcherrima</span> clade: <span class="html-italic">M. pulcherrima</span> CCY 29-2-145, <span class="html-italic">Metschnikowia</span> sp. LOCK1135, and <span class="html-italic">Metschnikowia</span> sp. LOCK1144. Values show the mean ± standard deviation (SD, n = 3). Results obtained for minimal medium (control samples) were compared with those for minimal medium with Fe(III) ions (pulcherrimin production). Values with different letters are statistically different: <sup>c</sup>: <span class="html-italic">p</span> &lt; 0.005.</p>
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<p>Comparison of the number of viable yeast cells after 6 months of storage at −196 °C in the presence of different cryoprotectants: DMSO (control) and DMSO with pulcherrimin (<b>a</b>); DMSO with glycoprotein (control) and DMSO with pulcherrimin (<b>b</b>). Yeast strains: 1—<span class="html-italic">C. macerans</span> CCY 10-1-17; 2—<span class="html-italic">G. candidum</span> CCY 16-1-25; 3—<span class="html-italic">P. flavescens</span> CCY 17-3-34; 4—<span class="html-italic">S. metaroseus</span> CCY 19-6-22; 5—<span class="html-italic">R. dairenensis</span> CCY 20-2-25; 6—<span class="html-italic">F. capsuligenum</span> CCY 29-143-1; 7—<span class="html-italic">C. zemplinina</span> CCY 20-178-1; 8—<span class="html-italic">A. porosum</span> CCY 30-18-5; 9—<span class="html-italic">S. pombe</span> CCY 44-1-3. Values with different letters are statistically different: <sup>a</sup>: <span class="html-italic">p</span> ≥ 0.05; <sup>b</sup>: 0.005 &lt; <span class="html-italic">p</span> &lt; 0.05; <sup>c</sup>: <span class="html-italic">p</span> &lt; 0.005.</p>
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<p>Morphology and division of <span class="html-italic">S. pombe</span> cells during cultivation in a culture medium: without pulcherrimin (<b>a</b>), with pulcherrimin (<b>b</b>). <span class="html-italic">S. pombe</span> cells show abnormal multiple divisions in the presence of pulcherrimin (white circles).</p>
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16 pages, 4843 KiB  
Article
Screening Repurposed Antiviral Small Molecules as Antimycobacterial Compounds by a Lux-Based phoP Promoter-Reporter Platform
by Li Zhu, Annie Wing-Tung Lee, Kelvin Ka-Lok Wu, Peng Gao, Kingsley King-Gee Tam, Rahim Rajwani, Galata Chala Chaburte, Timothy Ting-Leung Ng, Chloe Toi-Mei Chan, Hiu Yin Lao, Wing Cheong Yam, Richard Yi-Tsun Kao and Gilman Kit Hang Siu
Antibiotics 2022, 11(3), 369; https://doi.org/10.3390/antibiotics11030369 - 9 Mar 2022
Cited by 3 | Viewed by 2756
Abstract
The emergence of multidrug-resistant strains and hyper-virulent strains of Mycobacterium tuberculosis are big therapeutic challenges for tuberculosis (TB) control. Repurposing bioactive small-molecule compounds has recently become a new therapeutic approach against TB. This study aimed to identify novel anti-TB agents from a library [...] Read more.
The emergence of multidrug-resistant strains and hyper-virulent strains of Mycobacterium tuberculosis are big therapeutic challenges for tuberculosis (TB) control. Repurposing bioactive small-molecule compounds has recently become a new therapeutic approach against TB. This study aimed to identify novel anti-TB agents from a library of small-molecule compounds via a rapid screening system. A total of 320 small-molecule compounds were used to screen for their ability to suppress the expression of a key virulence gene, phop, of the M. tuberculosis complex using luminescence (lux)-based promoter-reporter platforms. The minimum inhibitory and bactericidal concentrations on drug-resistant M. tuberculosis and cytotoxicity to human macrophages were determined. RNA sequencing (RNA-seq) was conducted to determine the drug mechanisms of the selected compounds as novel antibiotics or anti-virulent agents against the M. tuberculosis complex. The results showed that six compounds displayed bactericidal activity against M. bovis BCG, of which Ebselen demonstrated the lowest cytotoxicity to macrophages and was considered as a potential antibiotic for TB. Another ten compounds did not inhibit the in vitro growth of the M. tuberculosis complex and six of them downregulated the expression of phoP/R significantly. Of these, ST-193 and ST-193 (hydrochloride) showed low cytotoxicity and were suggested to be potential anti-virulence agents for M. tuberculosis. Full article
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Figure 1

Figure 1
<p>Construction and validation of the <span class="html-italic">lux</span>-based promoter-reporter platform. (<b>A</b>) pMV306G13+Lux. (<b>B</b>) pMV306PhoP+Lux. (<b>C</b>) Mean (± SD, <span class="html-italic">n</span> = 3) <span class="html-italic">lux</span> signal (in log lux) and OD<sub>600</sub> in <span class="html-italic">M. bovis</span> BCG with and without (control) ETZ treatment at time 0 h and 24 h. (<b>D</b>) <span class="html-italic">LuxA</span> and <span class="html-italic">phoP</span> expression of <span class="html-italic">M. bovis</span> BCG with and without (control) ETZ treatment. Data are presented as means ± SD (<span class="html-italic">n</span> = 3) and analyzed using an unpaired <span class="html-italic">t</span>-test, *** <span class="html-italic">p</span> &lt; 0.001 vs. BCG without ETZ treatment.</p>
Full article ">Figure 1 Cont.
<p>Construction and validation of the <span class="html-italic">lux</span>-based promoter-reporter platform. (<b>A</b>) pMV306G13+Lux. (<b>B</b>) pMV306PhoP+Lux. (<b>C</b>) Mean (± SD, <span class="html-italic">n</span> = 3) <span class="html-italic">lux</span> signal (in log lux) and OD<sub>600</sub> in <span class="html-italic">M. bovis</span> BCG with and without (control) ETZ treatment at time 0 h and 24 h. (<b>D</b>) <span class="html-italic">LuxA</span> and <span class="html-italic">phoP</span> expression of <span class="html-italic">M. bovis</span> BCG with and without (control) ETZ treatment. Data are presented as means ± SD (<span class="html-italic">n</span> = 3) and analyzed using an unpaired <span class="html-italic">t</span>-test, *** <span class="html-italic">p</span> &lt; 0.001 vs. BCG without ETZ treatment.</p>
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<p>Screening of 320 antiviral compounds and 3 anti-TB drugs. (<b>A</b>) OD<sub>600</sub> and LUX of all samples with/without 4 h compound treatment in negative control platform of <span class="html-italic">M. bovis</span> BCG. (<b>B</b>) OD<sub>600</sub> and LUX of all samples in the <span class="html-italic">phoP</span> promoter-reporter platform. Green dots represent BCG samples (including pMV306Adaptor+Lux) without any compound treatment. Red dots represent samples treated with the three anti-TB drugs. Blue dots represent samples treated with the 16 selected compounds, while black dots represent samples treated with other compounds. (<b>C</b>) Comparison of lux signals between the compound treatment and control samples. ** <span class="html-italic">p</span> &lt; 0.01.</p>
Full article ">Figure 2 Cont.
<p>Screening of 320 antiviral compounds and 3 anti-TB drugs. (<b>A</b>) OD<sub>600</sub> and LUX of all samples with/without 4 h compound treatment in negative control platform of <span class="html-italic">M. bovis</span> BCG. (<b>B</b>) OD<sub>600</sub> and LUX of all samples in the <span class="html-italic">phoP</span> promoter-reporter platform. Green dots represent BCG samples (including pMV306Adaptor+Lux) without any compound treatment. Red dots represent samples treated with the three anti-TB drugs. Blue dots represent samples treated with the 16 selected compounds, while black dots represent samples treated with other compounds. (<b>C</b>) Comparison of lux signals between the compound treatment and control samples. ** <span class="html-italic">p</span> &lt; 0.01.</p>
Full article ">Figure 3
<p>RNA-Seq transcriptome analysis and representative genes involved in the phoP- pathway. (<b>A</b>) Principal component analysis (PCA) of BCGs after treatment with 16 compounds in 3 groups based on the gene expression detected in all samples. (<b>B</b>) Heatmap showing a clustering analysis of gene expression levels for the three groups of BCGs (<span class="html-italic">p</span> &lt; 0.05, FC &gt; 2 or &lt; 0.5). (<b>C</b>) Expression of <span class="html-italic">phoP</span> and <span class="html-italic">phoR</span> in S1, S2, D, and the control groups. Data are presented as means ± SD (<span class="html-italic">n</span> = 6 for S1 and D, <span class="html-italic">n</span> = 4 for S2, and <span class="html-italic">n</span> = 1 for the control group) and were analyzed using a two-way ANOVA, * <span class="html-italic">p</span> &lt; 0.05, *** <span class="html-italic">p</span> &lt; 0.001, while those without a label have no significances. (<b>D</b>) The expression of genes regulated by phoP/R in BCGs after treatment with the 16 compounds.</p>
Full article ">Figure 3 Cont.
<p>RNA-Seq transcriptome analysis and representative genes involved in the phoP- pathway. (<b>A</b>) Principal component analysis (PCA) of BCGs after treatment with 16 compounds in 3 groups based on the gene expression detected in all samples. (<b>B</b>) Heatmap showing a clustering analysis of gene expression levels for the three groups of BCGs (<span class="html-italic">p</span> &lt; 0.05, FC &gt; 2 or &lt; 0.5). (<b>C</b>) Expression of <span class="html-italic">phoP</span> and <span class="html-italic">phoR</span> in S1, S2, D, and the control groups. Data are presented as means ± SD (<span class="html-italic">n</span> = 6 for S1 and D, <span class="html-italic">n</span> = 4 for S2, and <span class="html-italic">n</span> = 1 for the control group) and were analyzed using a two-way ANOVA, * <span class="html-italic">p</span> &lt; 0.05, *** <span class="html-italic">p</span> &lt; 0.001, while those without a label have no significances. (<b>D</b>) The expression of genes regulated by phoP/R in BCGs after treatment with the 16 compounds.</p>
Full article ">Figure 4
<p>Molecular regulation associated with the anti-virulence process. (<b>A</b>) Volcano plot of the DEGs between D and S. (<b>B</b>) Volcano plot of the DEGs between D and S2. (<b>C</b>) Molecular functions and biological processes enriched in the DEGs for the survival groups.</p>
Full article ">Figure 5
<p>LDH results in 16 compounds in THP-1 cells. (<b>A</b>) Cell viability after being treated with drugs in the S1 group. (<b>B</b>) Cell viability after being treated with drugs in the S2 group. (<b>C</b>) Cell viability after being treated with drugs in the D group. Data are presented as means ± SD (<span class="html-italic">n</span> = 3).</p>
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20 pages, 2992 KiB  
Article
Synthesis of Novel Tritopic Hydrazone Ligands: Spectroscopy, Biological Activity, DFT, and Molecular Docking Studies
by Sharmin Akther Rupa, Md. Rassel Moni, Md. Abdul Majed Patwary, Md. Mayez Mahmud, Md. Aminul Haque, Jamal Uddin and S. M. Tareque Abedin
Molecules 2022, 27(5), 1656; https://doi.org/10.3390/molecules27051656 - 2 Mar 2022
Cited by 17 | Viewed by 3544
Abstract
Polytopic organic ligands with hydrazone moiety are at the forefront of new drug research among many others due to their unique and versatile functionality and ease of strategic ligand design. Quantum chemical calculations of these polyfunctional ligands can be carried out in silico [...] Read more.
Polytopic organic ligands with hydrazone moiety are at the forefront of new drug research among many others due to their unique and versatile functionality and ease of strategic ligand design. Quantum chemical calculations of these polyfunctional ligands can be carried out in silico to determine the thermodynamic parameters. In this study two new tritopic dihydrazide ligands, N’2, N’6-bis[(1E)-1-(thiophen-2-yl) ethylidene] pyridine-2,6-dicarbohydrazide (L1) and N’2, N’6-bis[(1E)-1-(1H-pyrrol-2-yl) ethylidene] pyridine-2,6-dicarbohydrazide (L2) were successfully prepared by the condensation reaction of pyridine-2,6-dicarboxylic hydrazide with 2-acetylthiophene and 2-acetylpyrrole. The FT-IR, 1H, and 13C NMR, as well as mass spectra of both L1 and L2, were recorded and analyzed. Quantum chemical calculations were performed at the DFT/B3LYP/cc-pvdz/6-311G+(d,p) level of theory to study the molecular geometry, vibrational frequencies, and thermodynamic properties including changes of ∆H, ∆S, and ∆G for both the ligands. The optimized vibrational frequency and (1H and 13C) NMR obtained by B3LYP/cc-pvdz/6-311G+(d,p) showed good agreement with experimental FT-IR and NMR data. Frontier molecular orbital (FMO) calculations were also conducted to find the HOMO, LUMO, and HOMO–LUMO gaps of the two synthesized compounds. To investigate the biological activities of the ligands, L1 and L2 were tested using in vitro bioassays against some Gram-negative and Gram-positive bacteria and fungus strains. In addition, molecular docking was used to study the molecular behavior of L1 and L2 against tyrosinase from Bacillus megaterium. The outcomes revealed that both L1 and L2 can suppress microbial growth of bacteria and fungi with variable potency. The antibacterial activity results demonstrated the compound L2 to be potentially effective against Bacillus megaterium with inhibition zones of 12 mm while the molecular docking study showed the binding energies for L1 and L2 to be −7.7 and −8.8 kcal mol−1, respectively, with tyrosinase from Bacillus megaterium. Full article
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Graphical abstract

Graphical abstract
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<p>Optimized structures of L1 and L2 generated at the B3LYP/6-311G+(d,p) level of theory.</p>
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<p>Optimized structures of L1 and L2 generated at the B3LYP/6-311G+(d,p) level of theory.</p>
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<p>Experimental <sup>1</sup>H and <sup>13</sup>C-NMR of (<b>a</b>) L1 and (<b>b</b>) L2 in DMSO-d<sub>6</sub> solvent.</p>
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<p>The optimized geometries of the reactants and products involved in chemical reactions calculated at the B3LYP/6-311G+(d,p) level.</p>
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<p>Frontier molecular orbitals (HOMO, HOMO-1, LUMO, and LUMO+1) of L1 and L2.</p>
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<p>Calculated electrostatic potential surfaces of L1 and L2 generated by B3LYP/6-311G+(d,p). Molecular surfaces were plotted at an electron density of 0.002 e<sup>−</sup>/bohr<sup>3</sup>.</p>
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<p>Picture showing interaction between ligands and amino acids of tyrosinase from <span class="html-italic">Bacillus megaterium</span> (PDB ID: 4j6u). The most important interaction distances (bold) are given in angstrom (Å).</p>
Full article ">Scheme 1
<p>Synthesis of L1 and L2.</p>
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16 pages, 7015 KiB  
Article
Synthesis and Antibacterial Properties of Oligomeric Dehydrogenation Polymer from Lignin Precursors
by Xin Wei, Sheng Cui and Yimin Xie
Molecules 2022, 27(5), 1466; https://doi.org/10.3390/molecules27051466 - 22 Feb 2022
Cited by 9 | Viewed by 2116
Abstract
The lignin precursors of coniferin and syringin were synthesised, and guaiacyl-type and guaiacyl-syringyl-type oligomeric lignin dehydrogenation polymers (DHP and DHP-GS) were prepared with the bulk method. The carbon-13 nuclear magnetic resonance spectroscopy showed that both DHP-G and DHP-GS contained β-O-4, β-5, β-β, β-1, [...] Read more.
The lignin precursors of coniferin and syringin were synthesised, and guaiacyl-type and guaiacyl-syringyl-type oligomeric lignin dehydrogenation polymers (DHP and DHP-GS) were prepared with the bulk method. The carbon-13 nuclear magnetic resonance spectroscopy showed that both DHP-G and DHP-GS contained β-O-4, β-5, β-β, β-1, and 5-5 substructures. Extraction with petroleum ether, ether, ethanol, and acetone resulted in four fractions for each of DHP-G (C11–C14) and DHP-GS (C21–C24). The antibacterial experiments showed that the fractions with lower molecular weight had relatively strong antibacterial activity. The ether-soluble fractions (C12 of DHP-G and C22 of DHP-GS) had strong antibacterial activities against E. coli and S. aureus. The C12 and C22 fractions were further separated by preparative chromatography, and 10 bioactive compounds (G1–G5 and GS1–GS5) were obtained. The overall antibacterial activities of these 10 compounds was stronger against E. coli than S. aureus. Compounds G1, G2, G3, and GS1, which had the most significant antibacterial activities, contained β-5 substructures. Of these, G1 had the best antibacterial activity. Its inhibition zone diameter was 19.81 ± 0.82 mm, and the minimum inhibition concentration was 56.3 ± 6.20 μg/mL. Atmospheric pressure chemical ionisation mass spectrometry (APCI-MS) showed that the antibacterial activity of G1 was attributable to a phenylcoumarin dimer, while the introduction of syringyl units reduced antibacterial activity. Full article
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Figure 1

Figure 1
<p><sup>13</sup>C-NMR spectrum of DHP-G.</p>
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<p><sup>13</sup>C-NMR spectrum of DHP-GS.</p>
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<p>Effect of DHP fractions on growth inhibition of <span class="html-italic">E. coli</span>. Legend: The red circle area is the inhibition zone; coniferin and syringin: precursors of DHP; DMSO: No sample was added, only DMSO was added; control: control group without sample and solvent.</p>
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<p>Inhibitory effect of DHP fractions on the growth of <span class="html-italic">S. aureus</span>. Legend: The red circle area is the inhibition zone; coniferin and syringin: precursors of DHP; DMSO: No sample was added, only DMSO was added; control: control group without sample and solvent.</p>
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<p>Inhibition zone diameter of DHP fractions on <span class="html-italic">E. coli</span> and <span class="html-italic">S. aureus</span>.</p>
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<p>MIC of DHP fractions against <span class="html-italic">E. coli</span> and <span class="html-italic">S. aureus</span>. Legend: MIC: the minimum inhibitory concentration.</p>
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<p>Inhibitory effect of purified compounds from DHP on the growth of <span class="html-italic">E. coli</span>. Legend: G<sub>1</sub>–G<sub>5</sub>: compounds purified from the ether fraction of DHP-G by preparative chromatography; GS<sub>1</sub>–GS<sub>5</sub>: compounds purified from the ether fraction of DHP-GS by preparative chromatography.</p>
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<p>Inhibitory effect of purified components from DHP on the growth of <span class="html-italic">S. aureus</span>. Legend: G<sub>1</sub>–G<sub>5</sub>: compounds purified from the ether fraction of DHP-G by preparative chromatography; GS<sub>1</sub>–GS<sub>5</sub>: compounds purified from the ether fraction of DHP-GS by preparative chromatography.</p>
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<p>Inhibition zone diameter of purified compounds from DHP on <span class="html-italic">E. coli</span> and <span class="html-italic">S. aureus</span>.</p>
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<p>MIC of purified compounds from DHP against <span class="html-italic">E. coli</span> and <span class="html-italic">S. aureus</span>. Legend: MIC: the minimum inhibitory concentration.</p>
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<p>Mass spectrum of the compound G<sub>1</sub>.</p>
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<p>Mass spectrum of the compound G<sub>2</sub>.</p>
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<p>Mass spectrum of the compound G<sub>3</sub>.</p>
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<p>Mass spectrum of the compound GS<sub>1</sub>.</p>
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<p>Chemical structure of the compound G<sub>1</sub>, G<sub>2</sub>, G<sub>3</sub>, and GS<sub>1</sub> with significant antibacterial effects.</p>
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<p>Chemical structure of coniferin and syringin.</p>
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<p>Chemical structure diagrams of DHP-G formation.</p>
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<p>Classification flow chart of DHP-G and DHP-GS.</p>
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<p>Purification process of DHP ether component.</p>
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16 pages, 1579 KiB  
Article
Stapling of Peptides Potentiates the Antibiotic Treatment of Acinetobacter baumannii In Vivo
by Gina K. Schouten, Felix M. Paulussen, Oscar P. Kuipers, Wilbert Bitter, Tom N. Grossmann and Peter van Ulsen
Antibiotics 2022, 11(2), 273; https://doi.org/10.3390/antibiotics11020273 - 19 Feb 2022
Cited by 11 | Viewed by 4208
Abstract
The rising incidence of multidrug resistance in Gram-negative bacteria underlines the urgency for novel treatment options. One promising new approach is the synergistic combination of antibiotics with antimicrobial peptides. However, the use of such peptides is not straightforward; they are often sensitive to [...] Read more.
The rising incidence of multidrug resistance in Gram-negative bacteria underlines the urgency for novel treatment options. One promising new approach is the synergistic combination of antibiotics with antimicrobial peptides. However, the use of such peptides is not straightforward; they are often sensitive to proteolytic degradation, which greatly limits their clinical potential. One approach to increase stability is to apply a hydrocarbon staple to the antimicrobial peptide, thereby fixing them in an α-helical conformation, which renders them less exposed to proteolytic activity. In this work we applied several different hydrocarbon staples to two previously described peptides shown to act on the outer membrane, L6 and L8, and tested their activity in a zebrafish embryo infection model using a clinical isolate of Acinetobacter baumannii as a pathogen. We show that the introduction of such a hydrocarbon staple to the peptide L8 improves its in vivo potentiating activity on antibiotic treatment, without increasing its in vivo antimicrobial activity, toxicity or hemolytic activity. Full article
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<p>Peptides L6 and L8 are active in vitro against Gram-negative clinical isolates and interact with LPS but have limited activity in vivo. In vitro MIC values of peptides or vancomycin alone and MIC values of peptides combined with vancomycin or vancomycin in combination with peptides against Gram-negative bacteria were determined via checkerboard assays either in medium containing no LPS (<b>A</b>) or in medium containing smooth (Sm) LPS, rough (Ra) LPS or deep rough (Rd) LPS (<b>B</b>). The FIC values were defined as the ratio of either the MIC value of the peptide in combination with vancomycin over the MIC value of the peptide alone (FIC<sub>L6</sub> and FIC<sub>L8</sub>) or the ratio of the MIC value of vancomycin combined with peptide over the MIC value of vancomycin alone (FIC<sub>Vancomycin</sub>). The degree of α-helicity of L6 and L8 either in medium containing no LPS, Sm-LPS, Ra-LPS or Rd-LPS was determined with CD spectroscopy. Relative helicity was calculated using circular dichroism analysis using neural networks (CDNN) software (<b>C</b>). Zebrafish larvae survival rates after infection with <span class="html-italic">A. baumannii</span> 1757 and treatment with peptides, vancomycin or combinations of peptide and vancomycin via caudal vein injection (<b>D</b>). The data are presented as mean ± standard deviation from three independent experiments.</p>
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<p>Design and properties of L6 and L8 as well as stapled versions. <span class="html-italic">Design</span> and structure of stapled L6 and stapled L8 (<b>A</b>). The degree of α-helicity of L6, L8 and the stapled variants of the peptides was determined with CD spectroscopy. Relative helicity was calculated using circular dichroism analysis using neural networks (CDNN) software (<b>B</b>). Stability of L6, L8 and the stapled variants of the peptides in human serum were analyzed by LCMS and quantified using total ion count (TIC) of selected molecular ions (<b>C</b>). MIC values of the stapled peptides or vancomycin alone and MIC values of the stapled peptides combined with vancomycin or vancomycin in combination with the stapled peptides against Gram-negative bacteria were determined via checkerboard assay. The FIC values were defined as the ratio of either the MIC value of the stapled peptide in combination with vancomycin over the MIC value of the stapled peptide alone (FIC<sub>L6</sub> and FIC<sub>L8</sub>), or the ratio of the MIC value of vancomycin combined with the stapled peptide over the MIC value of vancomycin alone (FIC<sub>Vancomycin</sub>) (<b>D</b>). The data are presented as mean ± standard deviation from three independent experiments.</p>
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<p>Peptide L8S1 is active in combination with vancomycin or rifampicin against <span class="html-italic">A. baumannii</span> in vivo. Zebrafish larvae survival rates were tracked over time following <span class="html-italic">A. baumannii</span> infection and treatment with stapled peptides, vancomycin or combinations of stapled peptide and vancomycin via caudal vein injection (<b>A</b>). MIC values of L8S1, rifampicin or erythromycin, MIC values of L8S1 combined with either rifampicin or erythromycin and MIC values of rifampicin or erythromycin combined with L8S1 were determined via checkerboard assay. The FIC values were defined as either the ratio of L8S1 in combination with rifampicin or erythromycin over the MIC value of L8S1 alone (FIC<sub>L8S1</sub>), or the ratio of the MIC value of rifampicin or erythromycin combined with L8S1 over the MIC value of rifampicin or erythromycin alone (FIC<sub>antibiotic</sub>) (<b>B</b>). Survival rates of <span class="html-italic">A. baumannii</span> infected zebrafish larvae were additionally followed upon treatment with peptide L11S1, rifampicin or a combination of L11S1 and rifampicin (<b>C</b>). The data are presented as mean ± standard deviation from three independent experiments.</p>
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8 pages, 920 KiB  
Article
Factors Associated with Daptomycin-Induced Eosinophilic Pneumonia
by Kazuhiro Ishikawa, Takahiro Matsuo, Yasumasa Tsuda, Mahbubur Rahman, Yuki Uehara and Nobuyoshi Mori
Antibiotics 2022, 11(2), 254; https://doi.org/10.3390/antibiotics11020254 - 16 Feb 2022
Cited by 3 | Viewed by 1926
Abstract
The risk factors for eosinophilic pneumonia (EP) remain unclear. We investigate the characteristics of patients with daptomycin (DAP)-induced EP and conducted a retrospective observational study. A total of 450 patients aged ≥ 18 years who received DAP (25 DAP with EP, 425 DAP [...] Read more.
The risk factors for eosinophilic pneumonia (EP) remain unclear. We investigate the characteristics of patients with daptomycin (DAP)-induced EP and conducted a retrospective observational study. A total of 450 patients aged ≥ 18 years who received DAP (25 DAP with EP, 425 DAP without EP) were included. The median duration from the first DAP administration to EP onset was 18.0 days. Definite, probable, and possible DAP-induced EP were diagnosed in 0, 9, and 16 patients, respectively. The median age (DAP with EP, 72.0 years; DAP without EP, 64.0 years), DAP dosage/body weight (BW) (9.00 vs. 7.50 mg/kg), blood eosinophil count (cells/μL) (419 vs. 96), and the percentage of hemodialyzed patients (40.0% vs. 13.4%) were significantly higher in patients with EP than in patients without EP in the univariate analysis. In separate multivariate logistic regression analyses, age (odds ratio (OR), 1.03; 95% confidence interval (CI), 1.00–1.05), DAP dosage/BW (OR, 1.61; 95% CI, 1.25–2.07), and hemodialysis (OR, 4.42; 95% CI, 1.86–10.5) were significantly associated with DAP-induced EP. Clinicians may need to consider the potential factors associated with EP, especially in older patients, patients on hemodialysis, or patients who receive > 9.00 mg/kg of DAP. Full article
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<p>Patient selection flow chart. Abbreviations: DAP, daptomycin; EP, eosinophilic pneumonia.</p>
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<p>The distribution of DAP dosage /BW (mg/kg) in DAP with EP. Abbreviations: DAP, daptomycin; EP, eosinophilic pneumonia; BW, body weight.</p>
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17 pages, 21622 KiB  
Review
Pharmacological Activities of Soursop (Annona muricata Lin.)
by Mutakin Mutakin, Rizky Fauziati, Fahrina Nur Fadhilah, Ade Zuhrotun, Riezki Amalia and Yuni Elsa Hadisaputri
Molecules 2022, 27(4), 1201; https://doi.org/10.3390/molecules27041201 - 10 Feb 2022
Cited by 39 | Viewed by 15376
Abstract
Soursop (Annona muricata Lin.) is a plant belonging to the Annonaceae family that has been widely used globally as a traditional medicine for many diseases. In this review, we discuss the traditional use, chemical content, and pharmacological activities of A.muricata. From [...] Read more.
Soursop (Annona muricata Lin.) is a plant belonging to the Annonaceae family that has been widely used globally as a traditional medicine for many diseases. In this review, we discuss the traditional use, chemical content, and pharmacological activities of A.muricata. From 49 research articles that were obtained from 1981 to 2021, A.muricata’s activities were shown to include anticancer (25%), antiulcer (17%), antidiabetic (14%), antiprotozoal (10%), antidiarrhea (8%), antibacterial (8%), antiviral (8%), antihypertensive (6%), and wound healing (4%). Several biological activities and the general mechanisms underlying the effects of A.muricata have been tested both in vitro and in vivo. A.muricata contains chemicals such as acetogenins (annomuricins and annonacin), alkaloids (coreximine and reticuline), flavonoids (quercetin), and vitamins, which are predicted to be responsible for the biological activity of A.muricata. Full article
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<p>(<b>a</b>) Leaves of <span class="html-italic">A. muricata</span> with an obovate, oblate, and acuminate shape. The leaf surface is dark green, with a thick and glossy upper surface. (<b>b</b>) The fruits are dark green and prickly. (<b>c</b>) The flower petals are thick and yellowish. The outer petals meet at the edges without overlapping and are broadly ovate, tapering to a point with a heart-shaped base. The inner petals are oval-shaped and overlap.</p>
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<p>Acetogenin compounds in <span class="html-italic">A. muricata</span>. (<b>a</b>) Linear structure, (<b>b</b>) epoxy acetogenin, (<b>c</b>) mono THF, (<b>d</b>) mono tetrahydrofuran, mono tetrahydropyran acetogenin, (<b>e</b>) bis THF-nonadjacent acetogenin, (<b>f</b>) and bis THF-adjacent acetogenin [<a href="#B4-molecules-27-01201" class="html-bibr">4</a>].</p>
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<p>The most abundant alkaloids in <span class="html-italic">A. muricata</span>: (<b>a</b>) coreximine and (<b>b</b>) reticuline.</p>
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<p>The most abundant flavonoid in <span class="html-italic">A. muricata</span>: (<b>a</b>) kaempferol (<b>b</b>) quercetin, and (<b>c</b>) rutin.</p>
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<p>Anticancer mechanism of <span class="html-italic">A. muricata</span>.</p>
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<p>Antiulcer mechanisms of <span class="html-italic">A. muricata</span>.</p>
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<p>Distribution of pharmacological activities of <span class="html-italic">A. muricata</span>.</p>
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<p>Proportions of phytochemical compounds in <span class="html-italic">A. muricata</span>.</p>
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17 pages, 1915 KiB  
Article
Preliminary Studies of Antimicrobial Activity of New Synthesized Hybrids of 2-Thiohydantoin and 2-Quinolone Derivatives Activated with Blue Light
by Agnieszka Kania, Waldemar Tejchman, Anna M. Pawlak, Krystian Mokrzyński, Bartosz Różanowski, Bogdan M. Musielak and Magdalena Greczek-Stachura
Molecules 2022, 27(3), 1069; https://doi.org/10.3390/molecules27031069 - 5 Feb 2022
Cited by 22 | Viewed by 2412
Abstract
Thiohydantoin and quinolone derivatives have attracted researchers’ attention because of a broad spectrum of their medical applications. The aim of our research was to synthesize and analyze the antimicrobial properties of novel 2-thiohydantoin and 2-quinolone derivatives. For this purpose, two series of hybrid [...] Read more.
Thiohydantoin and quinolone derivatives have attracted researchers’ attention because of a broad spectrum of their medical applications. The aim of our research was to synthesize and analyze the antimicrobial properties of novel 2-thiohydantoin and 2-quinolone derivatives. For this purpose, two series of hybrid compounds were synthesized. Both series consisted of 2-thiohydantoin core and 2-quinolone derivative ring, however one of them was enriched with an acetic acid group at N3 atom in 2-thiohydantoin core. Antibacterial properties of these compounds were examined against bacteria: Staphylococcus aureus, Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. The antimicrobial assay was carried out using a serial dilution method to obtain the MIC. The influence of blue light irradiation on the tested compounds was investigated. The relative yield of singlet oxygen (1O2*, 1Δg) generation upon excitation with 420 nm was determined by a comparative method, employing perinaphthenone (PN) as a standard. Antimicrobial properties were also investigated after blue light irradiation of the suspensions of the hybrids and bacteria placed in microtitrate plates. Preliminary results confirmed that some of the hybrid compounds showed bacteriostatic activity to the reference Gram-positive bacterial strains and a few of them were bacteriostatic towards Gram-negative bacteria, as well. Blue light activation enhanced bacteriostatic effect of the tested compounds. Full article
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<p>(<b>A</b>) Time-resolved singlet oxygen (<sup>1</sup>O<sub>2</sub>, <sup>1</sup>Δ<sub>g</sub>) phosphorescence at 1270 nm detected in DMSO: ethanol solutions (1:1, <span class="html-italic">v</span>/<span class="html-italic">v</span>) of perinaphtenone (PN) and selected samples (<b>4a</b> and <b>5a</b>) upon excitation with 420 nm laser pulses at 35% and 100% of laser energy, respectively. (<b>B</b>) Dependence of the initial intensity of <sup>1</sup>O<sub>2</sub> (<sup>1</sup>Δ<sub>g</sub>) phosphorescence generated by PN and selected samples on relative excitation energy.</p>
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<p>Singlet oxygen (<sup>1</sup>O<sub>2</sub>, <sup>1</sup>Δ<sub>g</sub>) phosphorescence decay detected at 1270 nm after laser excitation of selected samples: <b>4b</b> (<b>A</b>) and <b>4d</b> (<b>B</b>) in DMSO: ethanol solution (1:1, <span class="html-italic">v</span>/<span class="html-italic">v</span>) with 420 nm. Studied samples solutions were equilibrated with air (black) or saturated with argon (grey).</p>
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<p>Atom-numbering scheme of the tested compounds.</p>
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<p>Synthesis of 1-acetyl-2-thiohydantoin and its condensation with 2-chloroquinoline-3-carbaldehyde derivatives.</p>
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<p>Synthesis of 2-thiohydantoin-3-acetic acid its condensation with 2-chloro-3-quinolinecarboxaldehyde derivatives.</p>
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11 pages, 1131 KiB  
Article
Antileishmanial Effects of Acetylene Acetogenins from Seeds of Porcelia macrocarpa (Warm.) R.E. Fries (Annonaceae) and Semisynthetic Derivatives
by Ivanildo A. Brito, Fernanda Thevenard, Thais A. Costa-Silva, Samuel S. Oliveira, Rodrigo L. O. R. Cunha, Emerson A. de Oliveira, Patricia Sartorelli, Rafael C. Guadagnin, Maiara M. Romanelli, Andre G. Tempone and João Henrique G. Lago
Molecules 2022, 27(3), 893; https://doi.org/10.3390/molecules27030893 - 28 Jan 2022
Cited by 2 | Viewed by 2027
Abstract
As part of our continuous studies involving the prospection of natural products from Brazilian flora aiming at the discovery of prototypes for the development of new antiparasitic drugs, the present study describes the isolation of two natural acetylene acetogenins, (2S,3R [...] Read more.
As part of our continuous studies involving the prospection of natural products from Brazilian flora aiming at the discovery of prototypes for the development of new antiparasitic drugs, the present study describes the isolation of two natural acetylene acetogenins, (2S,3R,4R)-3-hydroxy-4-methyl-2-(n-eicos-11′-yn-19′-enyl)butanolide (1) and (2S,3R,4R)-3-hydroxy-4-methyl-2-(n-eicos-11′-ynyl)butanolide (2), from the seeds of Porcelia macrocarpa (Warm.) R.E. Fries (Annonaceae). Using an ex-vivo assay, compound 1 showed an IC50 value of 29.9 μM against the intracellular amastigote forms of Leishmania (L.) infantum, whereas compound 2 was inactive. These results suggested that the terminal double bond plays an important role in the activity. This effect was also observed for the semisynthetic acetylated (1a and 2a) and eliminated (1b and 2b) derivatives, since only compounds containing a double bond at C-19 displayed activity, resulting in IC50 values of 43.3 μM (1a) and 23.1 μM (1b). In order to evaluate the effect of the triple bond in the antileishmanial potential, the mixture of compounds 1 + 2 was subjected to catalytic hydrogenation to afford a compound 3 containing a saturated side chain. The antiparasitic assays performed with compound 3, acetylated (3a), and eliminated (3b) derivatives confirmed the lack of activity. Furthermore, an in-silico study using the SwissADME online platform was performed to bioactive compounds 1, 1a, and 1b in order to investigate their physicochemical parameters, pharmacokinetics, and drug-likeness. Despite the reduced effect against amastigote forms of the parasite to the purified compounds, different mixtures of compounds 1 + 2, 1a + 2a, and 1b + 2b were prepared and exhibited IC50 values ranging from 7.9 to 38.4 μM, with no toxicity for NCTC mammalian cells (CC50 > 200 μM). Selectivity indexes to these mixtures ranged from >5.2 to >25.3. The obtained results indicate that seeds of Porcelia macrocarpa are a promising source of interesting prototypes for further modifications aiming at the discovery of new antileishmanial drugs. Full article
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<p>Adult tree and dried seeds obtained from fresh fruits of <span class="html-italic">P. macrocarpa</span>.</p>
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<p>Chemical structures of natural acetogenins (<b>1</b> and <b>2</b>) and semisynthetic derivatives (<b>1a</b>, <b>1b</b>, <b>2a</b>, <b>2b</b>, <b>3, 3a</b>, and <b>3b</b>).</p>
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<p>Bioavailability radar for bioactive compounds (<b>1)</b>, (<b>1a</b>), and (<b>1b</b>). The pink zone indicates the physicochemical space for oral bioavailability, and the red line indicates the oral bioavailability properties.</p>
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7 pages, 968 KiB  
Article
The Chemical Property Position of Bedaquiline Construed by a Chemical Global Positioning System-Natural Product
by Muaaz Mutaz Alajlani
Molecules 2022, 27(3), 753; https://doi.org/10.3390/molecules27030753 - 24 Jan 2022
Cited by 4 | Viewed by 3077
Abstract
Bedaquiline is a novel adenosine triphosphate synthase inhibitor anti-tuberculosis drug. Bedaquiline belongs to the class of diarylquinolines, which are antituberculosis drugs that are quite different mechanistically from quinolines and flouroquinolines. The fact that relatively similar chemical drugs produce different mechanisms of action is [...] Read more.
Bedaquiline is a novel adenosine triphosphate synthase inhibitor anti-tuberculosis drug. Bedaquiline belongs to the class of diarylquinolines, which are antituberculosis drugs that are quite different mechanistically from quinolines and flouroquinolines. The fact that relatively similar chemical drugs produce different mechanisms of action is still not widely understood. To enhance discrimination in favor of bedaquiline, a new approach using eight-score principal component analysis (PCA), provided by a ChemGPS-NP model, is proposed. PCA scores were calculated based on 35 + 1 different physicochemical properties and demonstrated clear differences when compared with other quinolines. The ChemGPS-NP model provided an exceptional 100 compounds nearest to bedaquiline from antituberculosis screening sets (with a cumulative Euclidian distance of 196.83), compared with the different 2Dsimilarity provided by Tanimoto methods (extended connective fingerprints and the Molecular ACCess System, showing 30% and 182% increases in cumulative Euclidian distance, respectively). Potentially similar compounds from publicly available antituberculosis compounds and Maybridge sets, based on bedaquiline’s eight-dimensional similarity and different filtrations, were identified too. Full article
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<p>Chemical structures of bedaquiline and different typical antituberculosis quinoline compounds.</p>
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<p>Position of bedaquiline (large pink sphere), the 100 closest antituberculosis compounds (small spheres), and quinoline compounds (green spheres), using ChemGPS-NP scores, where PC1 (x = red), PC2 (y = yellow), and PC3 (green).</p>
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<p>Three sets of 50 antituberculosis compounds classified as closest to bedaquiline (large pink sphere): ChemGPS-NP (pink), Tanimoto ecfp (turquoise), and Tanimoto maccos (orange), projected on a three-dimension space.</p>
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<p>Red and green speckles represent mycobacterium permeability and impermeability, respectively. The large pink sphere represents the bedaquiline position in the chemical property space constructed by ChemGPS-NP for natural compounds.</p>
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17 pages, 5573 KiB  
Article
In Silico Drug Repurposing Approach: Investigation of Mycobacterium tuberculosis FadD32 Targeted by FDA-Approved Drugs
by Nolwazi Thobeka Portia Ngidi, Kgothatso Eugene Machaba and Ndumiso Nhlakanipho Mhlongo
Molecules 2022, 27(3), 668; https://doi.org/10.3390/molecules27030668 - 20 Jan 2022
Cited by 9 | Viewed by 2747
Abstract
Background: Despite the enormous efforts made towards combating tuberculosis (TB), the disease remains a major global threat. Hence, new drugs with novel mechanisms against TB are urgently needed. Fatty acid degradation protein D32 (FadD32) has been identified as a promising drug target [...] Read more.
Background: Despite the enormous efforts made towards combating tuberculosis (TB), the disease remains a major global threat. Hence, new drugs with novel mechanisms against TB are urgently needed. Fatty acid degradation protein D32 (FadD32) has been identified as a promising drug target against TB, the protein is required for the biosynthesis of mycolic acids, hence, essential for the growth and multiplication of the mycobacterium. However, the FadD32 mechanism upon the binding of FDA-approved drugs is not well established. Herein, we applied virtual screening (VS), molecular docking, and molecular dynamic (MD) simulation to identify potential FDA-approved drugs against FadD32. Methodology/Results: VS technique was found promising to identify four FDA-approved drugs (accolate, sorafenib, mefloquine, and loperamide) with higher molecular docking scores, ranging from −8.0 to −10.0 kcal/mol. Post-MD analysis showed that the accolate hit displayed the highest total binding energy of −45.13 kcal/mol. Results also showed that the accolate hit formed more interactions with FadD32 active site residues and all active site residues displayed an increase in total binding contribution. RMSD, RMSF, Rg, and DCCM analysis further supported that the presence of accolate exhibited more structural stability, lower bimolecular flexibility, and more compactness into the FadD32 protein. Conclusions: Our study revealed accolate as the best potential drug against FadD32, hence a prospective anti-TB drug in TB therapy. In addition, we believe that the approach presented in the current study will serve as a cornerstone to identifying new potential inhibitors against a wide range of biological targets. Full article
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<p>Three-dimensional (3D) structure of FadD32, showing the C-terminal domain (green) and the N-terminal domain (cyan), with the natural substrate, ATP (orange) [<a href="#B10-molecules-27-00668" class="html-bibr">10</a>].</p>
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<p>Chemical structures of accolate (<b>A</b>), sorafenib (<b>B</b>), mefloquine (<b>C</b>), and loperamide (<b>D</b>).</p>
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<p>Interaction profile of FadD32-Accolate (<b>A</b>), FadD32-Sorafenib (<b>B</b>), FadD32-Mefloquine (<b>C</b>), and FadD32-Loperamide (<b>D</b>).</p>
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<p>Per-residue decomposition analysis of FadD32-Accolate (<b>A</b>), FadD32-Sorafenib (<b>B</b>), FadD32-Mefloquine, (<b>C</b>) and FadD32-Loperamide (<b>D</b>).</p>
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<p>RMSD Plot of FadD32-Apo, FadD32-Accolate, FadD32-Sorafenib, FadD32-Mefloquine, and FadD32-Loperamide.</p>
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<p>RMSF Plot of FadD32-Apo, FadD32-Accolate, FadD32-Sorafenib, FadD32-Mefloquine, and FadD32-Loperamide.</p>
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<p>Radius of gyration plot of the FadD32-Apo, FadD32-Accolate, FadD32-Sorafenib, FadD32-Mefloquine, and FadD32-Loperamide.</p>
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<p>DCCM analysis graphs of the FadD32-Apo, FadD32-Accolate, FadD32-Sorafenib, FadD32-Mefloquine, and FadD32-Loperamide.</p>
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<p>PCA analysis graph projecting the eigenvalues of FadD32-Apo, FadD32-Accolate, FadD32-Sorafenib, FadD32-Mefloquine, and FadD32-Loperamide along PC1 and PC2.</p>
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<p>Aligned structures of <span class="html-italic">Mtb</span>FadD32 (green) and <span class="html-italic">Msm</span>FadD32 (red) proteins.</p>
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13 pages, 1274 KiB  
Article
Comparative Transcriptome Analysis Reveals Differentially Expressed Genes Related to Antimicrobial Properties of Lysostaphin in Staphylococcus aureus
by Xianghe Yan, Yanping Xie, Charles Li, David M. Donovan, Andrew Gehring, Peter Irwin and Yiping He
Antibiotics 2022, 11(2), 125; https://doi.org/10.3390/antibiotics11020125 - 18 Jan 2022
Cited by 3 | Viewed by 3012
Abstract
Comparative transcriptome analysis and de novo short-read assembly of S. aureus Newman strains revealed significant transcriptional changes in response to the exposure to triple-acting staphylolytic peptidoglycan hydrolase (PGH) 1801. Most altered transcriptions were associated with the membrane, cell wall, and related genes, including [...] Read more.
Comparative transcriptome analysis and de novo short-read assembly of S. aureus Newman strains revealed significant transcriptional changes in response to the exposure to triple-acting staphylolytic peptidoglycan hydrolase (PGH) 1801. Most altered transcriptions were associated with the membrane, cell wall, and related genes, including amidase, peptidase, holin, and phospholipase D/transphosphatidylase. The differential expression of genes obtained from RNA-seq was confirmed by reverse transcription quantitative PCR. Moreover, some of these gene expression changes were consistent with the observed structural perturbations at the DNA and RNA levels. These structural changes in the genes encoding membrane/cell surface proteins and altered gene expressions are the candidates for resistance to these novel antimicrobials. The findings in this study could provide insight into the design of new antimicrobial agents. Full article
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<p>WGS and RNA-seq polymorphism comparison. Ring 1 (outer circle) shows the chromosomal map positions; ring 2 lists chromosome genes; rings 3 and 4 represent the SNP differences between <span class="html-italic">S. aureus</span> mutant 1801_2010 to Newman_WT and Newman_2010 to Newman_WT; rings 5 and 6 represent the <span class="html-italic">InDel</span> differences between <span class="html-italic">S. aureus</span> mutant 1801_2010 to Newman_WT and Newman_2010 to Newman_WT.</p>
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<p>Summary statistics for the <span class="html-italic">InDel</span> and SNP data of <span class="html-italic">S. aureus</span> Newman_2010 and mutant 1801_2010 by comparing to Newman_WT (NC_009641).</p>
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<p>KEGG pathway classification of the DEGs between <span class="html-italic">S. aureus</span> mutant 1801_2010 and WT Newman_2010.</p>
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<p>Validation of RNA-seq analysis by RT-qPCR. Relative gene expression levels of <span class="html-italic">S. aureus</span> mutant 1801_2010 and WT Newman_2010 were quantified by RT-qPCR, and data were analyzed using the comparative critical threshold (ΔΔCT) method. The ratios (log2) of relative gene expression from RT-qPCR and RNA-seq are shown in grey and black bars, respectively. A ratio greater than zero (&gt;0) indicates up regulation of gene expression and a ratio below zero (&lt;0) indicates down regulation in mutant 1801_2010. Error bars indicate standard deviations of three replicates.</p>
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<p>Validation of RNA-seq analysis by RT-qPCR. Relative gene expression levels of <span class="html-italic">S. aureus</span> mutant 1801_2010 and WT Newman_2010 were quantified by RT-qPCR, and data were analyzed using the comparative critical threshold (ΔΔCT) method. The ratios (log2) of relative gene expression from RT-qPCR and RNA-seq are shown in grey and black bars, respectively. A ratio greater than zero (&gt;0) indicates up regulation of gene expression and a ratio below zero (&lt;0) indicates down regulation in mutant 1801_2010. Error bars indicate standard deviations of three replicates.</p>
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17 pages, 2476 KiB  
Article
In Vitro Evaluation of the Cytotoxic Effect of Streptococcus pyogenes Strains, Protegrin PG-1, Cathelicidin LL-37, Nerve Growth Factor and Chemotherapy on the C6 Glioma Cell Line
by Alexandr N. Chernov, Anna Tsapieva, Diana A. Alaverdian, Tatiana A. Filatenkova, Elvira S. Galimova, Mariia Suvorova, Olga V. Shamova and Alexander N. Suvorov
Molecules 2022, 27(2), 569; https://doi.org/10.3390/molecules27020569 - 17 Jan 2022
Cited by 6 | Viewed by 2766
Abstract
Brain cancer treatment, where glioblastoma represents up to 50% of all CNS malignancies, is one of the most challenging calls for neurooncologists. The major driver of this study was a search for new approaches for the treatment of glioblastoma. We tested live S. [...] Read more.
Brain cancer treatment, where glioblastoma represents up to 50% of all CNS malignancies, is one of the most challenging calls for neurooncologists. The major driver of this study was a search for new approaches for the treatment of glioblastoma. We tested live S. pyogenes, cathelicidin family peptides and NGF, assessing the oncolytic activity of these compounds as monotherapy or in combination with chemotherapeutics. For cytotoxicity evaluation, we used the MTT assay, trypan blue assay and the xCELLigence system. To evaluate the safety of the studied therapeutic approaches, we performed experiments on normal human fibroblasts. Streptococci and peptides demonstrated high antitumor efficiency against glioma C6 cells in all assays applied, surpassing the effect of chemotherapeutics (doxorubicin, carboplatin, cisplatin, etoposide). A real-time cytotoxicity analysis showed that the cell viability index dropped to 21% 2–5 h after S. pyogenes strain exposure. It was shown that LL-37, PG-1 and NGF also exhibited strong antitumor effects on C6 glioma cells when applied at less than 10−4 M. Synergistic effects for combinations of PG-1 with carboplatin and LL-37 with etoposide were shown. Combinations of S. pyogenes strain #7 with NGF or LL-37 demonstrated a cytotoxic effect (56.7% and 57.3%, accordingly) on C6 glioma cells after 3 h of exposure. Full article
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<p>The effect of GAS strains on C6 cells in real time.</p>
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<p>The effect of LL-37 (1 μM), PG-1 (10 μM), NGF (2.3 × 10<sup>−4</sup> μM) and TMZ (1.55 μM) on C6 cells in real time.</p>
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<p>The effect of doxorubicin (50 μM), carboplatin (500 μM), cisplatin (125 μM), etoposide (2.5 μM) and temozolomide (1.55 μM) on C6 cells in real time.</p>
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<p>The effects <span class="html-italic">S. pyogenes</span> 7 (<b>a</b>) and <span class="html-italic">S. pyogenes</span> 21 (<b>b</b>) in combination with LL-37 (1 μM), PG-1 (10 μM), NGF (2.3 × 10<sup>−4</sup> μM) and TMZ (1.55 mkM) on C6 cells in real time.</p>
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<p>IC of the combinations of peptides LL-37 (1 μM), PG-1 (10 μM) with NGF (2.3 × 10<sup>−4</sup> μM) on C6 glioma cells according to the results of the MTT assay; * <span class="html-italic">p</span> &lt; 0.05 for the IC of the combinations and the IC of PG-1; # <span class="html-italic">p</span> &lt; 0.05 for the IC of the combinations and the IC of NGF.</p>
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<p>IC of the combinations of peptides LL-37 (1 μM) and PG-1 (10 μM) with NGF (2.3 × 10<sup>−4</sup> μM) on C6 glioma cells according to the results of the trypan blue staining; * <span class="html-italic">p</span> &lt; 0.05 for the IC of the combinations and the IC of PG-1; # <span class="html-italic">p</span> &lt; 0.05 for the IC of the combinations and the IC of NGF; × <span class="html-italic">p</span> &lt; 0.05 for the IC of combinations and the IC of LL-37.</p>
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<p>The effects of NGF (2.3 × 10<sup>−4</sup> μM), LL-37 (1 μM), and PG-1 (10 μM) on human fibroblasts in real time.</p>
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<p>The effects of <span class="html-italic">S. pyogenes</span> 7, <span class="html-italic">S. pyogenes</span> 21, <span class="html-italic">S. pyogenes</span> GUR and <span class="html-italic">S. pyogenes</span> GURSA1 on human fibroblasts in real time.</p>
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16 pages, 46951 KiB  
Article
In Silico and In Vitro Structure–Activity Relationship of Mastoparan and Its Analogs
by Prapenpuksiri Rungsa, Steve Peigneur, Nisachon Jangpromma, Sompong Klaynongsruang, Jan Tytgat and Sakda Daduang
Molecules 2022, 27(2), 561; https://doi.org/10.3390/molecules27020561 - 16 Jan 2022
Cited by 9 | Viewed by 2513
Abstract
Antimicrobial peptides are an important class of therapeutic agent used against a wide range of pathogens such as Gram-negative and Gram-positive bacteria, fungi, and viruses. Mastoparan (MpVT) is an α-helix and amphipathic tetradecapeptide obtained from Vespa tropica venom. This peptide exhibits antibacterial activity. [...] Read more.
Antimicrobial peptides are an important class of therapeutic agent used against a wide range of pathogens such as Gram-negative and Gram-positive bacteria, fungi, and viruses. Mastoparan (MpVT) is an α-helix and amphipathic tetradecapeptide obtained from Vespa tropica venom. This peptide exhibits antibacterial activity. In this work, we investigate the effect of amino acid substitutions and deletion of the first three C-terminal residues on the structure–activity relationship. In this in silico study, the predicted structure of MpVT and its analog have characteristic features of linear cationic peptides rich in hydrophobic and basic amino acids without disulfide bonds. The secondary structure and the biological activity of six designed analogs are studied. The biological activity assays show that the substitution of phenylalanine (MpVT1) results in a higher antibacterial activity than that of MpVT without increasing toxicity. The analogs with the first three deleted C-terminal residues showed decreased antibacterial and hemolytic activity. The CD (circular dichroism) spectra of these peptides show a high content α-helical conformation in the presence of 40% 2,2,2-trifluoroethanol (TFE). In conclusion, the first three C-terminal deletions reduced the length of the α-helix, explaining the decreased biological activity. MpVTs show that the hemolytic activity of mastoparan is correlated to mean hydrophobicity and mean hydrophobic moment. The position and spatial arrangement of specific hydrophobic residues on the non-polar face of α-helical AMPs may be crucial for the interaction of AMPs with cell membranes. Full article
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<p>The partial nucleotide sequence and deduced amino acid sequence of <span class="html-italic">V. tropica</span> mastoparans (MpVT): (<b>A</b>) The nucleotide sequence of MpVT. The stop codon of the sequences marks as -. The mature sequences are shown in red letters and italic type, which were obtained by Edman degradation. (<b>B</b>) The deduced MpVT amino acid sequences of prosequences and mature sequences.</p>
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<p>Helical wheel diagram of MpVT and its analogs (<b>A</b>–<b>G</b>). Helical wheel projection was performed using the Netwheels: Peptides Helical Wheel and Net projections maker. Red, green, and yellow circles represent polar/basic amino acids, polar/uncharged amino acids, and non-polar amino acids, respectively.</p>
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<p>Circular dichroism (CD) spectra of MpVT and its analogs obtained at 100 μg/mL peptide concentration at 25 °C (<b>A</b>–<b>G</b>). All MpVTs showed unordered conformation in water (blue line) and characteristic α-helical spectra in the presence of 40% TFE (red line).</p>
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<p>Circular dichroism (CD) spectra of MpVT and its analogs obtained at 100 μg/mL peptide concentration at 25 °C (<b>A</b>–<b>G</b>). All MpVTs showed unordered conformation in water (blue line) and characteristic α-helical spectra in the presence of 40% TFE (red line).</p>
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<p>Structural models of MpVT and its analogs: (<b>A</b>) MpVT; (<b>B</b>) MpVT1; (<b>C</b>) MpVT3; (<b>D</b>) MpVT4; (<b>E</b>) MpVT5; (<b>F</b>) MpVT6; and (<b>G</b>) MpVT7. The models present the secondary structure in ribbon structure and the amino acid in sticky residues. Cationic residues (Lys amino acid) are labeled in white letters and the amino acid substitution is labeled in yellow letters.</p>
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<p>Antibacterial activities assay of <span class="html-italic">E. coli</span> (0157:H7) and <span class="html-italic">S. aureus</span> (ATCC 25923) treated with MpVT (<b>A</b>,<b>B</b>), MpVT1 (<b>C</b>,<b>D</b>), and MpVT3 (<b>E</b>,<b>F</b>) by disk diffusion method.</p>
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<p>Scanning electron micrographs of <span class="html-italic">E. coli</span> treated with peptides: (<b>A</b>) control bacteria after treatment with 0.01% acetic acid for 1 h; (<b>B</b>,<b>C</b>) bacteria after treatment with MpVT at 2× MIC for 1 h.</p>
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<p>Time–kill kinetics of MpVT, MpVT1, MpVT3 and Control against <span class="html-italic">E. coli</span> 0157:H7 (open triangles) at a concentration two-fold above the MIC (100 μg/mL). Controls correspond to bacteria incubated in PBS without peptide. Data are the means ± S.E.M. of one experiment performed in triplicate; *** <span class="html-italic">p</span> &lt; 0.001 versus control, **** <span class="html-italic">p</span> &lt; 0.0001 versus control.</p>
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<p>Hemolytic activity of MpVT and its analogs on human erythrocytes. Triton-X 100 was used as a positive control. These concentrations represent the mean values of three independent experiments performed in duplicate. Data are the means ± S.E.M. of one experiment performed in triplicate; * <span class="html-italic">p</span> &lt; 0.3 versus control, ** <span class="html-italic">p</span> &lt; 0.02 versus control, *** <span class="html-italic">p</span> &lt; 0.07 versus control. **** <span class="html-italic">p</span> &lt; 0.0001 versus control.</p>
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15 pages, 872 KiB  
Article
Development of New Antimicrobial Oleanonic Acid Polyamine Conjugates
by Elmira F. Khusnutdinova, Véronique Sinou, Denis A. Babkov, Oxana Kazakova and Jean Michel Brunel
Antibiotics 2022, 11(1), 94; https://doi.org/10.3390/antibiotics11010094 - 12 Jan 2022
Cited by 11 | Viewed by 2209
Abstract
A series of oleanolic acid derivatives holding oxo- or 3-N-polyamino-3-deoxy-substituents at C3 as well as carboxamide function at C17 with different long chain polyamines have been synthesized and evaluated for antimicrobial activities. Almost all series presented good to moderate activity against [...] Read more.
A series of oleanolic acid derivatives holding oxo- or 3-N-polyamino-3-deoxy-substituents at C3 as well as carboxamide function at C17 with different long chain polyamines have been synthesized and evaluated for antimicrobial activities. Almost all series presented good to moderate activity against Gram-positive S. aureus, S. faecalis and B. cereus bacteria with minimum inhibitory concentration (MIC) values from 3.125 to 200 µg/mL. Moreover, compounds possess important antimicrobial activities against Gram-negative E. coli, P. aeruginosa, S. enterica, and EA289 bacteria with MICs ranging from 6.25 to 200 µg/mL. The testing of ability to restore antibiotic activity of doxycycline and erythromycin at a 2 µg/mL concentration in a synergistic assay showed that oleanonic acid conjugate with spermine spacered through propargylamide led to a moderate improvement in terms of antimicrobial activities of the different selected combinations against both P. aeruginosa and E. coli. The study of mechanism of action of the lead conjugate 2i presenting a N-methyl norspermidine moiety showed the effect of disruption of the outer bacterial membrane of P. aeruginosa PA01 cells. Computational ADMET profiling renders this compound as a suitable starting point for pharmacokinetic optimization. These results give confidence to the successful outcome of bioconjugation of polyamines and oleanane-type triterpenoids in the development of antimicrobial agents. Full article
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Graphical abstract

Graphical abstract
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<p>Nitrocefin hydrolysis kinetics in presence of compounds <b>2i</b> at 18 µg/mL and compared to PMB and PMBn.</p>
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<p>Synthesis of olenonic diamine and polyamine conjugates <b>2a</b>–<b>2n</b>. Reagents and conditions: R-NH<sub>2</sub>, BOP, DIPEA, DCM, 20 °C, 12 h.</p>
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<p>Synthesis of C3 and C28 oleanolic acid polyamine conjugates. Reagents and conditions: a. i. R-NH<sub>2</sub>, Ti(O<span class="html-italic">i</span>-Pr)<sub>4</sub>, MeOH, 20 °C, 12 h; ii. NaBH<sub>4</sub>, −78 °C, 2 h. b. i. CrO<sub>3</sub>, H<sub>2</sub>SO<sub>4</sub>, 20 °C, 2 h; ii. (COCl)<sub>2</sub>, CH<sub>2</sub>Cl<sub>2</sub>, 20 °C, 2 h; iii. NH<sub>2</sub>CH<sub>2</sub>CCH, Et<sub>3</sub>N, CH<sub>2</sub>Cl<sub>2</sub>, 20 °C, 5 h. c. spermine, formalin, CuI (cat.), DMSO, 40 °C, 24 h. d. R-NH<sub>2</sub>, BOP, DIPEA, DCM, 20 °C, 12 h.</p>
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16 pages, 3558 KiB  
Article
Impact of a Novel Anticoccidial Analogue on Systemic Staphylococcus aureus Infection in a Bioluminescent Mouse Model
by Hang Thi Nguyen, Henrietta Venter, Lucy Woolford, Kelly Young, Adam McCluskey, Sanjay Garg, Stephen W. Page, Darren J. Trott and Abiodun David Ogunniyi
Antibiotics 2022, 11(1), 65; https://doi.org/10.3390/antibiotics11010065 - 6 Jan 2022
Cited by 2 | Viewed by 2776
Abstract
In this study, we investigated the potential of an analogue of robenidine (NCL179) to expand its chemical diversity for the treatment of multidrug-resistant (MDR) bacterial infections. We show that NCL179 exhibits potent bactericidal activity, returning minimum inhibitory concentration/minimum bactericidal concentrations (MICs/MBCs) of 1–2 [...] Read more.
In this study, we investigated the potential of an analogue of robenidine (NCL179) to expand its chemical diversity for the treatment of multidrug-resistant (MDR) bacterial infections. We show that NCL179 exhibits potent bactericidal activity, returning minimum inhibitory concentration/minimum bactericidal concentrations (MICs/MBCs) of 1–2 µg/mL against methicillin-resistant Staphylococcus aureus, MICs/MBCs of 1–2 µg/mL against methicillin-resistant S. pseudintermedius and MICs/MBCs of 2–4 µg/mL against vancomycin-resistant enterococci. NCL179 showed synergistic activity against clinical isolates and reference strains of Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa in the presence of sub-inhibitory concentrations of colistin, whereas NCL179 alone had no activity. Mice given oral NCL179 at 10 mg/kg and 50 mg/kg (4 × doses, 4 h apart) showed no adverse clinical effects and no observable histological effects in any of the organs examined. In a bioluminescent S. aureus sepsis challenge model, mice that received four oral doses of NCL179 at 50 mg/kg at 4 h intervals exhibited significantly reduced bacterial loads, longer survival times and higher overall survival rates than the vehicle-only treated mice. These results support NCL179 as a valid candidate for further development to treat MDR bacterial infections as a stand-alone antibiotic or in combination with existing antibiotic classes. Full article
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<p>Chemical structures of NCL812 (Robenidine), NCL179 and NCL195. Red colouration highlights the structural changes in NCL179 and NCL195 relative to NCL812. The guanidine to triaminopyrimidine novel bioisosteric modification of NCL812 yielded NCL179 (2,2′-<span class="html-italic">bis</span>[(4-chlorophenyl)methylene] carbonimidic dihydrazide) and NCL195 (4,6-bis(2-((E)-4-methylbenzylidene)hydrazinyl)pyrimidin-2-amine). NCL179 contains a halogen (chlorine) that distinguishes it from NCL195.</p>
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<p>Time- and concentration-dependent kill kinetics of NCL179 against Gram-positive bacteria. (<b>A</b>), against MRSA QLDpvl+; (<b>C</b>), against VRE 49R; and (<b>E</b>), against MRSP (VDL1290) using daptomycin (<b>B</b>,<b>D</b>) and amikacin (<b>F</b>) as control drugs.</p>
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<p>Time-and-concentration-dependent kill kinetics of NCL179 alone and in combination with colistin against Gram-negative bacteria. (<b>A</b>), NCL179 alone or in combination with colistin against <span class="html-italic">A. baumannii</span> ATCC 19606; (<b>B</b>), clinical colistin-resistant <span class="html-italic">A. baumannii</span> 246-53D; (<b>C</b>), <span class="html-italic">E. coli</span> Xen14; and (<b>D</b>), colistin-resistant <span class="html-italic">E. coli</span> Xen14. The concentrations of NCL179 and colistin for each combination were chosen based on data presented in <a href="#antibiotics-11-00065-t002" class="html-table">Table 2</a>. Assays were performed on a Cytation 5 Multi-Mode Reader (BioTek, Winooski, VT, USA) by optical density (<span class="html-italic">A</span><sub>600nm</sub>) measurements; Col, colistin.</p>
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<p>In vitro toxicity assessment of NCL179 alone and in combination with colistin. Real-time cell viability measurement for Hep G2 (<b>A</b>) and HEK293 (<b>B</b>) cells after treatment with different concentrations of NCL179 alone and in combination with 0.5 µg/mL of colistin. The cell viability was determined using the RealTime-Glo<sup>TM</sup> MT Cell Viability Assay reagent (Promega, Madison, WI, USA) and measured every hour for 20 h at 37 °C in 5% CO<sub>2</sub> on a Cytation 5 Cell Imaging Multi-Mode Reader (BioTek, BioTek, Winooski, VT, USA). Data are relative light units (RLU) for each treatment per time point; col, colistin; Amp, ampicillin.</p>
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<p>Selected well diffusion of NCL179 used in the efficacy trial. (<b>A</b>), to each well, 30 µL of either NCL179 formulation or vehicle only was added; (<b>B</b>), 30 µL of moxifloxacin (BovaVet, Caringbah, NSW, Australia). Concentrations of NCL179 in formulations were prepared as a 50 mg/mL solution to achieve 50 mg/kg in mice (30 g); moxifloxacin is a drug control and was prepared as a 6 mg/mL solution to achieve 6 mg/kg in mice (30 g); Xen29, <span class="html-italic">S. aureus</span> Xen29.</p>
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<p>Representative histological images of heart, lung, liver, stomach, spleen, kidneys and small and large intestines from NCL179-treated and vehicle-treated mice. No histopathological changes were observed in mice treated orally with (<b>A</b>), 10 mg/kg, 50 mg/kg (2 × doses, 8 h apart), or (<b>B</b>), with 10 mg/kg, 50 mg/kg (4 × doses, 4 h apart) of NCL179 in comparison with vehicle. S-intestine, small intestine; L-intestine, large intestine. Scale bars: 200 µm.</p>
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<p>Oral efficacy of 4 doses of NCL179 given 4 h apart in a bioluminescent <span class="html-italic">S. aureus</span> Xen29 sepsis mouse model. (<b>A</b>), Comparison of luminescence signals between groups of CD1 mice (<span class="html-italic">n</span> = 6) challenged IP with Xen29 and treated with NCL179, moxifloxacin and vehicle at 0 h, 4 h, 8 h and 12 h post-infection. Mice were subjected to bioluminescence imaging on IVIS Lumina XRMS Series III system at the indicated times (ns, no significant; *, <span class="html-italic">p</span> &lt; 0.05; **, <span class="html-italic">p</span> &lt; 0.01; ***, <span class="html-italic">p</span> &lt; 0.0002, ****, <span class="html-italic">p</span> &lt;0.0001, Mann-Whitney <span class="html-italic">U</span>-test, two-tailed). (<b>B</b>), Survival analysis for mice treated with NCL179, moxifloxacin and vehicle (ns, no significant; *, <span class="html-italic">p</span> &lt; 0.05; ***, <span class="html-italic">p</span> &lt; 0.0002; Log-rank (Mantel-Cox test)). (<b>C</b>), Ventral and dorsal images of representative CD1 mice challenged with approx. 3 × 10<sup>7</sup> CFU of bioluminescent <span class="html-italic">S. aureus</span> ATCC 12600 (Xen29). Moxifloxacin used as a control drug was prepared in almond oil at 6 mg/mL by BovaVet, Australia.</p>
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15 pages, 13795 KiB  
Article
Solvent-Free Synthesis, In Vitro and In Silico Studies of Novel Potential 1,3,4-Thiadiazole-Based Molecules against Microbial Pathogens
by Ihsan A. Shehadi, Mohamad T. Abdelrahman, Mohamed Abdelraof and Huda R. M. Rashdan
Molecules 2022, 27(2), 342; https://doi.org/10.3390/molecules27020342 - 6 Jan 2022
Cited by 19 | Viewed by 2305
Abstract
A new series of 1,3,4-thiadiazoles was synthesized by the reaction of methyl 2-(4-hydroxy-3-methoxybenzylidene) hydrazine-1-carbodithioate (2) with selected derivatives of hydrazonoyl halide by grinding method at room temperature. The chemical structures of the newly synthesized derivatives were resolved from correct spectral and [...] Read more.
A new series of 1,3,4-thiadiazoles was synthesized by the reaction of methyl 2-(4-hydroxy-3-methoxybenzylidene) hydrazine-1-carbodithioate (2) with selected derivatives of hydrazonoyl halide by grinding method at room temperature. The chemical structures of the newly synthesized derivatives were resolved from correct spectral and microanalytical data. Moreover, all synthesized compounds were screened for their antimicrobial activities using Escherichia coli, Pseudomonas aeruginosa, Proteus vulgaris, Bacillus subtilis, Staphylococcus aureus, and Candida albicans. However, compounds 3 and 5 showed significant antimicrobial activity against all tested microorganisms. The other prepared compounds exhibited either only antimicrobial activity against Gram-positive bacteria like compounds 4 and 6, or only antifungal activity like compound 7. A molecular docking study of the compounds was performed against two important microbial enzymes: tyrosyl-tRNA synthetase (TyrRS) and N-myristoyl transferase (Nmt). The tested compounds showed variety in binding poses and interactions. However, compound 3 showed the best interactions in terms of number of hydrogen bonds, and the lowest affinity binding energy (−8.4 and −9.1 kcal/mol, respectively). From the in vitro and in silico studies, compound 3 is a good candidate for the next steps of the drug development process as an antimicrobial drug. Full article
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Figure 1
<p>Chemical structures of drugs containing 1,3,4-thiadiazole moiety.</p>
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<p>2D (<b>B</b>) and 3D (<b>A</b>) representation of compound <b>3</b> docking with TyrRS.</p>
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<p>2D (<b>B</b>) and 3D (<b>A</b>) representation of compound <b>4</b> docking with TyrRS.</p>
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<p>2D (<b>B</b>) and 3D (<b>A</b>) representation of compound <b>5</b> docking with TyrRS.</p>
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<p>2D (<b>B</b>) and 3D (<b>A</b>) representation of compound <b>6</b> docking with TyrRS.</p>
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<p>2D (<b>B</b>) and 3D (<b>A</b>) representation of TyrRS docked with its cocrystalized inhibitor.</p>
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<p>2D (<b>B</b>) and 3D (<b>A</b>) representation of compound <b>3</b> docking with Nmt.</p>
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<p>2D (<b>B</b>) and 3D (<b>A</b>) representation of compound <b>5</b> docking with Nmt.</p>
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<p>2D (<b>B</b>) and 3D (<b>A</b>) representation of compound <b>7</b> docking with Nmt.</p>
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<p>2D (<b>B</b>) and 3D (<b>A</b>) representation of Nmt docked with its cocrystalized inhibitor.</p>
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<p>Root-mean-square deviation (RMSD) plot of both backbone proteins in simulated complex system with compound <b>3</b>.</p>
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<p>Solvent-free synthesis of 1,3,4-thiadiazole derivatives <b>3</b>–<b>7</b>.</p>
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10 pages, 2129 KiB  
Article
Dictamnine Inhibits the Adhesion to and Invasion of Uropathogenic Escherichia Coli (UPEC) to Urothelial Cells
by Wenbo Yang, Peng Liu, Ying Chen, Qingyu Lv, Zhongtian Wang, Wenhua Huang, Hua Jiang, Yuling Zheng, Yongqiang Jiang and Liping Sun
Molecules 2022, 27(1), 272; https://doi.org/10.3390/molecules27010272 - 2 Jan 2022
Cited by 10 | Viewed by 2666
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common pathogenic bacteria associated with urinary tract infection (UTI). UPEC can cause UTI by adhering to and invading uroepithelial cells. Fimbriae is the most important virulence factor of UPEC, and a potentially promising target in developing [...] Read more.
Uropathogenic Escherichia coli (UPEC) is the most common pathogenic bacteria associated with urinary tract infection (UTI). UPEC can cause UTI by adhering to and invading uroepithelial cells. Fimbriae is the most important virulence factor of UPEC, and a potentially promising target in developing novel antibacterial treatments. In this study, the antibacterial properties and effects of the compound dictamnine, extracted from the traditional Chinese medicine Cortex Dictamni, on the bacterial morphology, cell adhesion, and invasion of UPEC were studied. Dictamnine exhibited no obvious antibacterial activity against UPEC, but significantly impeded the ability of UPEC to adhere to and invade uroepithelial cells. RT-qPCR analysis showed that treatment downregulated the expression of type 1 fimbriae, P fimbriae, and curli fimbriae adhesion genes, and also downregulated adhesion-related receptor genes of uroepithelial cells. Transmission electron microscopy showed that dictamnine destroyed the structure of the fimbriae and the surface of the bacteria became smooth. These results suggest that dictamnine may help to prevent UTI by simultaneously targeting UPEC fimbriae and urothelial adhesin receptors, and may have a potential use as a new anti-UPEC drug. Full article
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<p>Chemical structure of dictamnine.</p>
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<p>Influence of dictamnine, at concentrations ranging from 0 to 200 µg/mL, on the cell viability (CCK-8 assay) of T24 cells after 24 h incubation. Values represent the mean ± SD from three independent experiments containing 18 technical replicates. *** <span class="html-italic">p</span> &lt; 0.001, **** <span class="html-italic">p</span> &lt; 0.0001.</p>
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<p>Effects of dictamnine on the in vitro growth of UPEC307. (<b>A</b>) Absorbance of bacteria at 600 nm at different time points; (<b>B</b>) number of viable bacteria at different time points. CFU: colony-forming unit.</p>
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<p>Effect of dictamnine on cellular adhesion and invasion by UPEC. The relative adhesion rate (<b>A</b>) and relative invasion rate (<b>B</b>) of UPEC to T24 cells after co-incubation of UPEC with T24 cells for 2 h. The relative adhesion rate (<b>C</b>) and relative invasion rate (<b>D</b>) of UPEC to T24 cells after 2 h of pre-incubation of dictamnine with T24 cells. Values represent the mean ± SD from three independent experiments with three technical replicates. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001, **** <span class="html-italic">p</span> &lt; 0.0001.</p>
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<p>Effects of dictamnine on fimbriae production. Evaluation of expression levels of fimbriae-associated genes by RT-qPCR: (<b>A</b>) type 1 fimbriae, (<b>B</b>) curli fimbriae and P fimbriae. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01.</p>
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<p>Expression of integrin and uroplakin genes in T24 bladder epithelial cells treated with dictamnine determined by RT-qPCR. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01.</p>
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<p>Transmission electron microscopy images of growing UPEC fimbriae. (<b>A</b>)Untreated UPEC fimbriae and (<b>B</b>) dictamnine-treated UPEC fimbriae.</p>
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14 pages, 1455 KiB  
Article
Lacticaseicin 30 and Colistin as a Promising Antibiotic Formulation against Gram-Negative β-Lactamase-Producing Strains and Colistin-Resistant Strains
by Désiré Madi-Moussa, Yanath Belguesmia, Audrey Charlet, Djamel Drider and Françoise Coucheney
Antibiotics 2022, 11(1), 20; https://doi.org/10.3390/antibiotics11010020 - 24 Dec 2021
Cited by 5 | Viewed by 2700
Abstract
Antimicrobial resistance is a global health concern across the world and it is foreseen to swell if no actions are taken now. To help curbing this well announced crisis different strategies are announced, and these include the use of antimicrobial peptides (AMP), which [...] Read more.
Antimicrobial resistance is a global health concern across the world and it is foreseen to swell if no actions are taken now. To help curbing this well announced crisis different strategies are announced, and these include the use of antimicrobial peptides (AMP), which are remarkable molecules known for their killing activities towards pathogenic bacteria. Bacteriocins are ribosomally synthesized AMP produced by almost all prokaryotic lineages. Bacteriocins, unlike antibiotics, offer a set of advantages in terms of cytotoxicity towards eukaryotic cells, their mode of action, cross-resistance and impact of microbiota content. Most known bacteriocins are produced by Gram-positive bacteria, and specifically by lactic acid bacteria (LAB). LAB-bacteriocins were steadily reported and characterized for their activity against genetically related Gram-positive bacteria, and seldom against Gram-negative bacteria. The aim of this study is to show that lacticaseicin 30, which is one of the bacteriocins produced by Lacticaseibacillus paracasei CNCM I-5369, is active against Gram-negative clinical strains (Salmonella enterica Enteritidis H10, S. enterica Typhimurium H97, Enterobacter cloacae H51, Escherichia coli H45, E. coli H51, E. coli H66, Klebsiella oxytoca H40, K. pneumoniae H71, K. variicola H77, K. pneumoniae H79, K. pneumoniae H79), whereas antibiotics failed. In addition, lacticaseicin 30 and colistin enabled synergistic interactions towards the aforementioned target Gram-negative clinical strains. Further, the combinations of lacticaseicin 30 and colistin prompted a drastic downregulation of mcr-1 and mcr-9 genes, which are associated with the colistin resistance phenotypes of these clinical strains. This report shows that lacticaseicin 30 is active against Gram-negative clinical strains carrying a rainbow of mcr genes, and the combination of these antimicrobials constitutes a promising therapeutic option that needs to be further exploited. Full article
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<p>RAPD analysis of clinical Gram-negative strains, using R1247 and R1283 primers for <span class="html-italic">E. coli</span> strains: <span class="html-italic">E coli</span> 184 (1), <span class="html-italic">E coli</span> H45 (2), <span class="html-italic">E. coli</span> H51 (3), <span class="html-italic">E. coli</span> H66 (4), RAPD4 primer for <span class="html-italic">Klebsiella</span> strains: <span class="html-italic">K. oxytoca</span> H40 (5), <span class="html-italic">K. pneumoniae</span> H71 (6), <span class="html-italic">K. variicola</span> H77 (7), <span class="html-italic">K. pneumoniae</span> H79 (8), <span class="html-italic">K. pneumoniae</span> H79 (9), OPP-11 and OPP-16 for <span class="html-italic">Salmonella</span> strains: <span class="html-italic">S. enterica</span> Enteritidis H10 (10), <span class="html-italic">S. enterica</span> Typhimurium H97 (11).</p>
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<p>(<b>A</b>) Purified lacticaseicin 30 with (1) and without (2) histidine-tag (SDS-PAGE, 12% acrylamide), M correspond to size of proteins markers (Dual Xtra Standards, Bio-Rad). (<b>B</b>) Agar diffusion test against <span class="html-italic">E. coli</span> ATCC 8739 of lacticaseicin 30 (400 AU/mL) without histidine-tag.</p>
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<p>Expression of <span class="html-italic">mcr-1</span> or <span class="html-italic">mcr-9</span> gene (<span class="html-italic">mcr-1</span> or <span class="html-italic">mcr-9</span>) following bacterial treatment with colistin, lacticaseicin 30 or their combination at sub-inhibitory concentrations (MIC/2). qPCR assays performed in strains for which a synergetic interaction between lacticaseicin 30-colistin has been evidenced. Furthermore, the 16S rRNA gene was used as internal control as house-keeping gene. Three biological and technical replicates of each reaction were performed. The error bars represent a standard deviation of these replicates.</p>
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10 pages, 1237 KiB  
Article
Evaluation of the Antiviral Activity against Infectious Pancreatic Necrosis Virus (IPNV) of a Copper (I) Homoleptic Complex with a Coumarin as Ligand
by Daniela Gutiérrez, Almendra Benavides, Beatriz Valenzuela, Carolina Mascayano, Maialen Aldabaldetrecu, Angel Olguín, Juan Guerrero and Brenda Modak
Molecules 2022, 27(1), 32; https://doi.org/10.3390/molecules27010032 - 22 Dec 2021
Cited by 6 | Viewed by 2389
Abstract
The aquatic infectious pancreatic necrosis virus (IPNV) causes a severe disease in farmed salmonid fish that generates great economic losses in the aquaculture industry. In the search for new tools to control the disease, in this paper we show the results obtained from [...] Read more.
The aquatic infectious pancreatic necrosis virus (IPNV) causes a severe disease in farmed salmonid fish that generates great economic losses in the aquaculture industry. In the search for new tools to control the disease, in this paper we show the results obtained from the evaluation of the antiviral effect of [Cu(NN1)2](ClO4) Cu(I) complex, synthesized in our laboratory, where the NN1 ligand is a synthetic derivate of the natural compound coumarin. This complex demonstrated antiviral activity against IPNV at 5.0 and 15.0 µg/mL causing a decrease viral load 99.0% and 99.5%, respectively. The Molecular Docking studies carried out showed that the copper complex would interact with the VP2 protein, specifically in the S domain, altering the process of entry of the virus into the host cell. Full article
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Graphical abstract

Graphical abstract
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<p>Chemistry Structure of Copper (I) Complex [Cu(NN<sub>1</sub>)<sub>2</sub>]ClO<sub>4</sub>. Where NN<sub>1</sub> is 6-((quinolin-2-ylmethylene)amine)-2H-chromen-2-one.</p>
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<p>Determination of cytotoxicity of test compounds on CHSE-214 cells. CHSE-214 cells were treated with 0.5, 15.0, 50.0 and 250.0 µg/mL of (<b>a</b>) coumarin, (<b>b</b>) ([Cu(CH<sub>3</sub>CN)<sub>4</sub>]ClO<sub>4</sub>) and (<b>c</b>) copper(I) complex [Cu(NN<sub>1</sub>)<sub>2</sub>]ClO<sub>4</sub> and viability was determined by flow cytometry.</p>
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<p>Antiviral activity against IPNV of test compounds in CHSE-214 cells. IPNV was incubated for 24 h with 0.5, 5.0, and 15.0 µg/mL of (<b>a</b>) coumarin, (<b>b</b>) [Cu(CH<sub>3</sub>CN)<sub>4</sub>]ClO<sub>4</sub>, (<b>c</b>) [Cu(NN<sub>1</sub>)<sub>2</sub>]ClO<sub>4</sub> complex, after that CHSE-214 cells were treated for 24 h with IPNV. RNA total extraction was performed from the cell cultures and viral load was determined by quantitative real-time PCR with three technical replicates. Statistical differences were determined by one-way ANOVA test (* <span class="html-italic">p</span> &lt; 0.05; ns = non-significant).</p>
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<p>(<b>A</b>) 3D representation of the chains (colored) and S domain (red) affected by ligand binding (colored); (<b>B</b>) binding interaction between complex and protein; (<b>C</b>) RMSF profile between initial state (fuchsia) and final state (blue light) and their corresponding residues.</p>
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12 pages, 3717 KiB  
Article
Suppressing Alpha-Hemolysin as Potential Target to Screen of Flavonoids to Combat Bacterial Coinfection
by Shangwen He, Qian Deng, Bingbing Liang, Feike Yu, Xiaohan Yu, Dawei Guo, Xiaoye Liu and Hong Dong
Molecules 2021, 26(24), 7577; https://doi.org/10.3390/molecules26247577 - 14 Dec 2021
Cited by 7 | Viewed by 2564
Abstract
The rapid emergence of bacterial coinfection caused by cytosolic bacteria has become a huge threat to public health worldwide. Past efforts have been devoted to discover the broad-spectrum antibiotics, while the emergence of antibiotic resistance encourages the development of antibacterial agents. In essence, [...] Read more.
The rapid emergence of bacterial coinfection caused by cytosolic bacteria has become a huge threat to public health worldwide. Past efforts have been devoted to discover the broad-spectrum antibiotics, while the emergence of antibiotic resistance encourages the development of antibacterial agents. In essence, bacterial virulence is a factor in antibiotic tolerance. However, the discovery and development of new antibacterial drugs and special antitoxin drugs is much more difficult in the antibiotic resistance era. Herein, we hypothesize that antitoxin hemolytic activity can serve as a screening principle to select antibacterial drugs to combat coinfection from natural products. Being the most abundant natural drug of plant origins, flavonoids were selected to assess the ability of antibacterial coinfections in this paper. Firstly, we note that four flavonoids, namely, baicalin, catechin, kaempferol, and quercetin, have previously exhibited antibacterial abilities. Then, we found that baicalin, kaempferol, and quercetin have better inhibitions of hemolytic activity of Hla than catechin. In addition, kaempferol and quercetin, have therapeutic effectivity for the coinfections of Staphylococcus aureus and Pseudomonas aeruginosa in vitro and in vivo. Finally, our results indicated that kaempferol and quercetin therapied the bacterial coinfection by inhibiting S. aureus α-hemolysin (Hla) and reduced the host inflammatory response. These results suggest that antitoxins may play a promising role as a potential target for screening flavonoids to combat bacterial coinfection. Full article
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<p>Flavonoids inhibit <span class="html-italic">Staphylococcus aureus</span> growth at the initial period: (<b>A</b>) Flavonoids inhibited <span class="html-italic">S. aureus</span> in both time- and dose dependent manners. Chessboard method was employed to detect the antibacterial effect of flavonoids. Different concentrations of flavonoids including baicalin, catechin, kaempferol, and quercetin (0 to 2048 μg/mL) were treated with <span class="html-italic">S. aureus</span> at different time points (0, 4, 8, 12, 16, and 18 h). Bacterial growth was quantified based on the absorbance by a plate reader at wavelength of 600 nm. (<b>B</b>) Quantification of <span class="html-italic">S. aureus</span> absorbance at 8 h under flavonoid treatment at the final concentrations of 0, 64, 128, and 256 μg/mL. Data were shown as Mean ± SED (n = 6).</p>
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<p>Screening of flavonoids on the hemolytic activity of <span class="html-italic">S. aureus</span> Hla: (<b>A</b>) Detection of hemolytic activity workflow. (<b>B</b>) Images of flavonoids treated with <span class="html-italic">S. aureus</span> Hla in blood cell suspension. The supernatants of <span class="html-italic">S. aureus</span> treated with different concentrations of flavonoids (0–128 μg/mL) incubated with the rabbit blood cell suspension for 20 min. (<b>C</b>) Quantification of hemolytic activation of flavonoids. (<b>D</b>) Detection of Hla levels by ELISA. Experiments were performed with at least 3 independent repeats. <span class="html-italic">ns</span> indicates <span class="html-italic">p</span> &gt; 0.05 showed no significant differences.</p>
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<p>Detection of flavonoids on the growth of <span class="html-italic">S. aureus</span> and <span class="html-italic">P. aeruginosa</span> in vitro: (<b>A</b>) The antibacterial function of flavonoids against the coinfection of <span class="html-italic">S. aureus</span> and <span class="html-italic">P. aeruginosa.</span> Pulmonary microvascular endothelial cells (PMVECs) were infected with the mixture of <span class="html-italic">S. aureus</span> and <span class="html-italic">P. aeruginosa</span> at different CFUs (10<sup>4</sup> to 10<sup>8</sup> CFU/mL) and treated with flavonoids including baicalin, catechin, kaempferol, and quercetin (at the concentration of 128 μg/mL) for 10 h. (<b>B</b>) Images of the hemolytic activity of bacterial mixtures of <span class="html-italic">S. aureus</span> (1 × 10<sup>8</sup> CFUs) and <span class="html-italic">P. aeruginosa</span> (1 × 10<sup>8</sup> CFUs) treated with flavonoids for 10 h. (<b>C</b>) The hemolysis detections of the mixtures of <span class="html-italic">S. aureus</span> and <span class="html-italic">P. aeruginosa</span> after the flavonoid treatment.</p>
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<p>Clinical validation of flavonoids on the mouse lung coinfection of <span class="html-italic">S. aureus</span> and <span class="html-italic">P. aeruginosa</span>: (<b>A</b>) Scheme of the pre-treatment and treatment of flavonoids on mouse lung coinfection. Briefly, mice were coinfected with <span class="html-italic">S. aureus</span> (1 × 10<sup>9</sup> CFUs) and <span class="html-italic">P. aeruginosa</span> (1 × 10<sup>9</sup> CFUs) and flavonoids were pre-treated or treated with infected mice for further determine the therapeutic effects. (<b>B</b>,<b>C</b>) Kaempferol had the better antibacterial effects on the lung coinfection of <span class="html-italic">S. aureus</span> and <span class="html-italic">P. aeruginosa</span> compared to quercetin on both pre-treatment (<b>B</b>) and treatment (<b>C</b>).</p>
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<p>Flavonoids have a better therapeutic effect on lung coinfections of <span class="html-italic">S. aureus</span> and <span class="html-italic">P. aeruginosa</span> in vivo: (<b>A</b>) H&amp;E staining of the lung tissue. Mice were infected with <span class="html-italic">S. aureus</span>, <span class="html-italic">P. aeruginosa</span> or the mixture of <span class="html-italic">S. aureus</span> and <span class="html-italic">P. aeruginosa.</span> Then, infected mice were treated with flavonoids. The black arrows show inflammatory cell infiltration. The blue arrows indicate the structure of the alveolar cavity. Scar bar = 200 μm. (<b>B</b>–<b>E</b>) Quantitative analysis of inflammatory cells number and pulmonary alveolar area (PAA) in mouse lung tissues. (<b>B</b>,<b>C</b>) Quantification of the number of inflammatory cells and the PAA in the lung tissues of infected mice. (<b>D</b>,<b>E</b>) Quantitative analysis of pulmonary inflammatory cells and PAA after prevention or treatment with kaempferol or quercetin. Three independent experiments were performed to obtain stable results. <span class="html-italic">ns</span> indicated no significant difference when compared with the non-treated controls.</p>
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<p>Flavonoids decreased the inflammatory levels caused by Hla in vitro detection: Pulmonary microvascular endothelial cells (PMVECs) were treated Hla with 4 h (<b>A</b>) ASC, Caspase-1 and NLRP3 expressions of Kaempferol and quercetin treatment were detected by Western Blot. (<b>B</b>) The corresponding proteins analyzed from A were normalized to the of levels of β-actin. (<b>C</b>) The IL-1β and IL-18 levels were determined by ELISA assay.</p>
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31 pages, 3229 KiB  
Review
Potential Therapeutic Targets for Combination Antibody Therapy against Pseudomonas aeruginosa Infections
by Luke L. Proctor, Whitney L. Ward, Conner S. Roggy, Alexandra G. Koontz, Katie M. Clark, Alyssa P. Quinn, Meredith Schroeder, Amanda E. Brooks, James M. Small, Francina D. Towne and Benjamin D. Brooks
Antibiotics 2021, 10(12), 1530; https://doi.org/10.3390/antibiotics10121530 - 14 Dec 2021
Cited by 8 | Viewed by 10317
Abstract
Despite advances in antimicrobial therapy and even the advent of some effective vaccines, Pseudomonas aeruginosa (P. aeruginosa) remains a significant cause of infectious disease, primarily due to antibiotic resistance. Although P. aeruginosa is commonly treatable with readily available therapeutics, these therapies are not [...] Read more.
Despite advances in antimicrobial therapy and even the advent of some effective vaccines, Pseudomonas aeruginosa (P. aeruginosa) remains a significant cause of infectious disease, primarily due to antibiotic resistance. Although P. aeruginosa is commonly treatable with readily available therapeutics, these therapies are not always efficacious, particularly for certain classes of patients (e.g., cystic fibrosis (CF)) and for drug-resistant strains. Multi-drug resistant P. aeruginosa infections are listed on both the CDC’s and WHO’s list of serious worldwide threats. This increasing emergence of drug resistance and prevalence of P. aeruginosa highlights the need to identify new therapeutic strategies. Combinations of monoclonal antibodies against different targets and epitopes have demonstrated synergistic efficacy with each other as well as in combination with antimicrobial agents typically used to treat these infections. Such a strategy has reduced the ability of infectious agents to develop resistance. This manuscript details the development of potential therapeutic targets for polyclonal antibody therapies to combat the emergence of multidrug-resistant P. aeruginosa infections. In particular, potential drug targets for combinational immunotherapy against P. aeruginosa are identified to combat current and future drug resistance. Full article
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<p>Types of Acute <span class="html-italic">P. Aeruginosa</span> Infections [<a href="#B5-antibiotics-10-01530" class="html-bibr">5</a>]. <span class="html-italic">P. aeruginosa</span> is prevalent in skin and soft tissue infections (top right) including trauma, burns, and dermatitis. It also commonly causes swimmer’s’ ear (external otitis), hot tub folliculitis, and ocular infections, bacteremia and septicemia, especially in immunocompromised patients, and endocarditis associated with IV drug users and prosthetic heart valves (bottom right). <span class="html-italic">P. aeruginosa</span> can also cause central nervous system (CNS) infections such as meningitis and brain abscess (top left), bone and joint infections, including osteomyelitis and osteochondritis, respiratory tract infections, and hospital-acquired urinary tract infections (UTIs; bottom left). <span class="html-italic">P. aeruginosa</span> is also resistant to many common antibiotics [<a href="#B5-antibiotics-10-01530" class="html-bibr">5</a>].</p>
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<p>Treatment strategy for carbapenem-resistant <span class="html-italic">P. aeruginosa</span> isolates including future treatment options based on combinatorial antibody therapies [<a href="#B21-antibiotics-10-01530" class="html-bibr">21</a>].</p>
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<p>Mechanisms of antibiotic resistance in <span class="html-italic">P. aeruginosa</span>. These include all of the mechanisms in blue and biofilms.</p>
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<p>Protein secretion systems in <span class="html-italic">P. aeruginosa</span> described further in the text.</p>
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<p>Effector function or mechanisms of killing by antibodies.</p>
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17 pages, 1958 KiB  
Review
How to Combat Gram-Negative Bacteria Using Antimicrobial Peptides: A Challenge or an Unattainable Goal?
by Adriana Barreto-Santamaría, Gabriela Arévalo-Pinzón, Manuel A. Patarroyo and Manuel E. Patarroyo
Antibiotics 2021, 10(12), 1499; https://doi.org/10.3390/antibiotics10121499 - 7 Dec 2021
Cited by 21 | Viewed by 5568
Abstract
Antimicrobial peptides (AMPs) represent a promising and effective alternative for combating pathogens, having some advantages compared to conventional antibiotics. However, AMPs must also contend with complex and specialised Gram-negative bacteria envelops. The variety of lipopolysaccharide and phospholipid composition in Gram-negative bacteria strains and [...] Read more.
Antimicrobial peptides (AMPs) represent a promising and effective alternative for combating pathogens, having some advantages compared to conventional antibiotics. However, AMPs must also contend with complex and specialised Gram-negative bacteria envelops. The variety of lipopolysaccharide and phospholipid composition in Gram-negative bacteria strains and species are decisive characteristics regarding their susceptibility or resistance to AMPs. Such biological and structural barriers have created delays in tuning AMPs to deal with Gram-negative bacteria. This becomes even more acute because little is known about the interaction AMP–Gram-negative bacteria and/or AMPs’ physicochemical characteristics, which could lead to obtaining selective molecules against Gram-negative bacteria. As a consequence, available AMPs usually have highly associated haemolytic and/or cytotoxic activity. Only one AMP has so far been FDA approved and another two are currently in clinical trials against Gram-negative bacteria. Such a pessimistic panorama suggests that efforts should be concentrated on the search for new molecules, designs and strategies for combating infection caused by this type of microorganism. This review has therefore been aimed at describing the currently available AMPs for combating Gram-negative bacteria, exploring the characteristics of these bacteria’s cell envelop hampering the development of new AMPs, and offers a perspective regarding the challenges for designing new AMPs against Gram-negative bacteria. Full article
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<p>FDA-approved AMP structure and that of antibacterial or immunomodulatory peptides in development against Gram-negative bacteria. Colistin, pexiganan and LL-37 are large molecules having direct antibacterial activity and a membranolytic mechanism of action. Peptides EA-230, AB-103 and SGX-942 do not have direct antibacterial activity; however, they do have an immunomodulator effect which helps resolve Gram-negative bacterial infection in vivo. A bond between Dab’s side chain and Thr’s carboxyl terminal forms the cycle. PerkinElmer ChemDraw Professional 16.0.1.4 molecule editor was used for drawing the structures.</p>
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<p>AMP-susceptible Gram-negative bacteria cell envelop compared to that of Gram-positive bacteria resistant ones. LPS-rich negatively charged outer membrane (OM) is prone to interact with cationic AMPs (left), whilst LPS altered by (1) ArnT-mediated 4′-phosphate (negatively charged) being replaced by 4-amino-4-deoxy-L-arabinopyranose (L-Arap4N) (positively charged), or (2) EptB-mediated ethanolamine molecules (positively charged) added to the diphosphates (negatively charged) lead to electrostatic repulsion with cationic AMP amino acids, making bacteria resistant to them. (3) LPS lipid A palmitoylation (i.e., adding palmitic acid, usually transferred from PG or PE) and (4) PG palmitoylation (i.e., adding palmitic acid, usually transferred from PE) leads to a better hydrophobic barrier for AMP penetration. Once AMPs reach the inner membrane (IM), negative charge density becomes a decisive factor for its membranolytic action, as bacteria having greater charge density are usually more susceptible to these AMPs.</p>
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<p>Gram-negative and Gram-positive bacterial membranes’ phospholipid composition. Phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and cardiolipin (CL) percentages are shown. Compiled from data reported in [<a href="#B78-antibiotics-10-01499" class="html-bibr">78</a>,<a href="#B83-antibiotics-10-01499" class="html-bibr">83</a>].</p>
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7 pages, 992 KiB  
Communication
Assessment of the Antibacterial Efficacy of Halicin against Pathogenic Bacteria
by Rayan Y. Booq, Essam A. Tawfik, Haya A. Alfassam, Ahmed J. Alfahad and Essam J. Alyamani
Antibiotics 2021, 10(12), 1480; https://doi.org/10.3390/antibiotics10121480 - 2 Dec 2021
Cited by 13 | Viewed by 4115
Abstract
Artificial intelligence (AI) is a new technology that has been employed to screen and discover new drugs. Using AI, an anti-diabetic treatment (Halicin) was nominated and proven to have a unique antibacterial activity against several harmful bacterial strains, including multidrug-resistant bacteria. This study [...] Read more.
Artificial intelligence (AI) is a new technology that has been employed to screen and discover new drugs. Using AI, an anti-diabetic treatment (Halicin) was nominated and proven to have a unique antibacterial activity against several harmful bacterial strains, including multidrug-resistant bacteria. This study aims to explore the antibacterial effect of halicin and microbial susceptibility using the zone of inhibition and the minimum inhibition concentration (MIC) values while assessing the stability of stored halicin over a period of time with cost-effective and straightforward methods. Linear regression graphs were constructed, and the correlation coefficient was calculated. The new antibacterial agent was able to inhibit all tested gram-positive and gram-negative bacterial strains, but in different concentrations—including the A. baumannii multidrug-resistant (MDR) isolate. The MIC of halicin was found to be 16 μg/mL for S. aureus (ATCC BAA-977), 32 μg/mL for E. coli (ATCC 25922), 128 μg/mL for A. baumannii (ATCC BAA-747), and 256 μg/mL for MDR A. baumannii. Upon storage, the MICs were increased, suggesting instability of the drug after approximately a week of storage at 4 °C. MICs and zones of inhibition were found to be high (R = 0.90 to 0.98), suggesting that halicin has a promising antimicrobial activity and may be used as a wide-spectrum antibacterial drug. However, the drug’s pharmacokinetics have not been investigated, and further elucidation is needed. Full article
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<p>The line charts for minimum inhibitory concentration (MIC) values of fresh and old halicin against four types of bacteria showing the efficiency of halicin. The MICs of freshly prepared halicin were measured at 16 μg/mL for <span class="html-italic">S. aureus</span> ATCC BAA-977 (<b>A</b>), 32 μg/mL for <span class="html-italic">E. coli</span> ATCC 25922 (<b>B</b>), 128 μg/mL for <span class="html-italic">A. baumannii</span> ATCC BAA-747 (<b>C</b>), and 256 μg/mL for MDR <span class="html-italic">A. baumannii</span> MDR 3086 (<b>D</b>). In comparison, they doubled for the old-prepared halicin, which increased to be 32 μg/mL for <span class="html-italic">S. aureus</span>, 64 μg/mL for <span class="html-italic">E. coli</span>, 128 μg/mL for <span class="html-italic">A. baumannii</span>, and ≥256 μg/mL for MDR <span class="html-italic">A. baumannii.</span></p>
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<p>The line charts for the coefficient of determination (R<sup>2</sup>) values show the efficiency of halicin against four types of bacterial strains. The R<sup>2</sup> of halicin was generally considered strong (R<sup>2</sup> ≥ 0.9) against <span class="html-italic">E. coli</span> ATCC 25922 (<b>B</b>; R<sup>2</sup> = 0.9544) and <span class="html-italic">A. baumannii</span> ATCC BAA-747 (<b>C</b>; R<sup>2</sup> = 0.9524), and fairly strong (R<sup>2</sup> ≥ 0.8 and &lt;0.9) against <span class="html-italic">S. aureus</span> ATCC BAA-977 (<b>A</b>; R<sup>2</sup>= 0.8087) and <span class="html-italic">A. baumannii</span> MDR 3086 (<b>D</b>; R<sup>2</sup> = 0.8717).</p>
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13 pages, 2803 KiB  
Article
Transporter Protein-Guided Genome Mining for Head-to-Tail Cyclized Bacteriocins
by Daniel Major, Lara Flanzbaum, Leah Lussier, Carly Davies, Kristian Mark P. Caldo and Jeella Z. Acedo
Molecules 2021, 26(23), 7218; https://doi.org/10.3390/molecules26237218 - 28 Nov 2021
Cited by 11 | Viewed by 2685
Abstract
Head-to-tail cyclized bacteriocins are ribosomally synthesized antimicrobial peptides that are defined by peptide backbone cyclization involving the N- and C- terminal amino acids. Their cyclic nature and overall three-dimensional fold confer superior stability against extreme pH and temperature conditions, and protease degradation. Most [...] Read more.
Head-to-tail cyclized bacteriocins are ribosomally synthesized antimicrobial peptides that are defined by peptide backbone cyclization involving the N- and C- terminal amino acids. Their cyclic nature and overall three-dimensional fold confer superior stability against extreme pH and temperature conditions, and protease degradation. Most of the characterized head-to-tail cyclized bacteriocins were discovered through a traditional approach that involved the screening of bacterial isolates for antimicrobial activity and subsequent isolation and characterization of the active molecule. In this study, we performed genome mining using transporter protein sequences associated with experimentally validated head-to-tail cyclized bacteriocins as driver sequences to search for novel bacteriocins. Biosynthetic gene cluster analysis was then performed to select the high probability functional gene clusters. A total of 387 producer strains that encode putative head-to-tail cyclized bacteriocins were identified. Sequence and phylogenetic analyses revealed that this class of bacteriocins is more diverse than previously thought. Furthermore, our genome mining strategy captured hits that were not identified in precursor-based bioprospecting, showcasing the utility of this approach to expanding the repertoire of head-to-tail cyclized bacteriocins. This work sets the stage for future isolation of novel head-to-tail cyclized bacteriocins to serve as possible alternatives to traditional antibiotics and potentially help address the increasing threat posed by resistant pathogens. Full article
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<p>Genera distribution of subgroup <b>i</b> and subgroup <b>ii</b> head-to-tail cyclized bacteriocin producer organisms identified in this study.</p>
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<p>Amino acid sequence similarity network of head-to-tail cyclized bacteriocin precursor peptides resulting in 12 groups and 12 singletons. The group numbers are indicated in bold. Putative novel head-to-tail cyclized bacteriocins are shown in gray, while characterized bacteriocins are shown in red and are labelled.</p>
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<p>Amino acid sequence logos for precursor peptides of head-to-tail cyclized bacteriocins belonging to groups 1 to 8 of the sequence similarity network in <a href="#molecules-26-07218-f002" class="html-fig">Figure 2</a>. Polar, neutral, basic, acidic, and hydrophobic amino acids are shown in green, purple, blue, red, and black, respectively [<a href="#B42-molecules-26-07218" class="html-bibr">42</a>]. The red broken lines indicate the predicted leader peptide cleavage site based on the characterized members of groups 1 to 5. Groups 6 to 8 do not have characterized members, and hence, the cleavage sites could not be proposed.</p>
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<p>Representative biosynthetic gene clusters of head-to-tail cyclized bacteriocins. Characterized bacteriocins are labelled in bold with the bacteriocin name, while the putative bacteriocins are indicated with their respective protein accession number.</p>
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<p>Phylogenetic relationships among putative head-to-tail cyclized bacteriocins identified using the transporter-guided genome mining. The maximum likelihood phylogenetic tree was generated using IQ-TREE [<a href="#B46-molecules-26-07218" class="html-bibr">46</a>] and annotated and visualized using iTOL [<a href="#B47-molecules-26-07218" class="html-bibr">47</a>]. Members of the five biggest groups in the sequence similarity network analysis are shown in different colors (Group 1—blue, 2—orange, 3—violet, 4—teal, 5—brown). The subgroup number of each accession number and their corresponding hydrophobicity based on GRAVY analysis are indicated in the annotation.</p>
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32 pages, 16513 KiB  
Review
Antimicrobial and Antiviral (SARS-CoV-2) Potential of Cannabinoids and Cannabis sativa: A Comprehensive Review
by Md Sultan Mahmud, Mohammad Sorowar Hossain, A. T. M. Faiz Ahmed, Md Zahidul Islam, Md Emdad Sarker and Md Reajul Islam
Molecules 2021, 26(23), 7216; https://doi.org/10.3390/molecules26237216 - 28 Nov 2021
Cited by 16 | Viewed by 8153
Abstract
Antimicrobial resistance has emerged as a global health crisis and, therefore, new drug discovery is a paramount need. Cannabis sativa contains hundreds of chemical constituents produced by secondary metabolism, exerting outstanding antimicrobial, antiviral, and therapeutic properties. This paper comprehensively reviews the antimicrobial and [...] Read more.
Antimicrobial resistance has emerged as a global health crisis and, therefore, new drug discovery is a paramount need. Cannabis sativa contains hundreds of chemical constituents produced by secondary metabolism, exerting outstanding antimicrobial, antiviral, and therapeutic properties. This paper comprehensively reviews the antimicrobial and antiviral (particularly against SARS-CoV-2) properties of C. sativa with the potential for new antibiotic drug and/or natural antimicrobial agents for industrial or agricultural use, and their therapeutic potential against the newly emerged coronavirus disease (COVID-19). Cannabis compounds have good potential as drug candidates for new antibiotics, even for some of the WHO’s current priority list of resistant pathogens. Recent studies revealed that cannabinoids seem to have stable conformations with the binding pocket of the Mpro enzyme of SARS-CoV-2, which has a pivotal role in viral replication and transcription. They are found to be suppressive of viral entry and viral activation by downregulating the ACE2 receptor and TMPRSS2 enzymes in the host cellular system. The therapeutic potential of cannabinoids as anti-inflammatory compounds is hypothesized for the treatment of COVID-19. However, more systemic investigations are warranted to establish the best efficacy and their toxic effects, followed by preclinical trials on a large number of participants. Full article
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<p>WHO global priority list of resistant bacteria [<a href="#B15-molecules-26-07216" class="html-bibr">15</a>].</p>
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<p>Location and distribution of main cannabinoids receptors in the human body (adapted from [<a href="#B129-molecules-26-07216" class="html-bibr">129</a>]).</p>
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<p>The impact of the cannabinoid system on the immune system in SARS-CoV-2 infection (adapted from [<a href="#B154-molecules-26-07216" class="html-bibr">154</a>]).</p>
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<p>Potential effects of cannabis compounds on SARS-CoV-2 entry and replications (adapted from [<a href="#B160-molecules-26-07216" class="html-bibr">160</a>]).</p>
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20 pages, 4532 KiB  
Article
An Antibacterial Peptide with High Resistance to Trypsin Obtained by Substituting d-Amino Acids for Trypsin Cleavage Sites
by Xiaoou Zhao, Mengna Zhang, Inam Muhammad, Qi Cui, Haipeng Zhang, Yu Jia, Qijun Xu, Lingcong Kong and Hongxia Ma
Antibiotics 2021, 10(12), 1465; https://doi.org/10.3390/antibiotics10121465 - 28 Nov 2021
Cited by 14 | Viewed by 2553
Abstract
The poor stability of antibacterial peptide to protease limits its clinical application. Among these limitations, trypsin mainly exists in digestive tract, which is an insurmountable obstacle to orally delivered peptides. OM19R is a random curly polyproline cationic antimicrobial peptide, which has high antibacterial [...] Read more.
The poor stability of antibacterial peptide to protease limits its clinical application. Among these limitations, trypsin mainly exists in digestive tract, which is an insurmountable obstacle to orally delivered peptides. OM19R is a random curly polyproline cationic antimicrobial peptide, which has high antibacterial activity against some gram-negative bacteria, but its stability against pancreatin is poor. According to the structure-activity relationship of OM19R, all cationic amino acid residues (l-arginine and l-lysine) at the trypsin cleavage sites were replaced with corresponding d-amino acid residues to obtain the designed peptide OM19D, which not only maintained its antibacterial activity but also enhanced the stability of trypsin. Proceeding high concentrations of trypsin and long-time (such as 10 mg/mL, 8 h) treatment, it still had high antibacterial activity (MIC = 16–32 µg/mL). In addition, OM19D also showed high stability to serum, plasma and other environmental factors. It is similar to its parent peptide in secondary structure and mechanism of action. Therefore, this strategy is beneficial to improve the protease stability of antibacterial peptides. Full article
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<p>Antibacterial activity of <span class="html-small-caps">l</span>-Alanine scanner derivatives of OM19R against <span class="html-italic">Escherichia coli</span> ATCC25922. The red dotted box is the sequence of the parent peptide OM19R.</p>
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<p>The circular dichroism (CD) spectra of OM19D and OM19R were dissolved in (<b>A</b>) 10 mM phosphate-buffered saline (PBS), (<b>B</b>) 30 mM sodium dodecyl sulfate (SDS), and (<b>C</b>) 50% trifluoroethanol (TFE). The average value after three scans of every sample is shown. The CD spectrum of the buffer was subtracted.</p>
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<p>(<b>A</b>) Cytotoxicity of peptides against RAW 264.7 cells. (<b>B</b>) Hemolytic activity of peptides against rabbit red blood cells. The peptide concentration range is 1–512 µg/mL, melittin and OM19R performed as controls.</p>
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<p>Time-killing curve (<b>A</b>) and Growth curves (<b>B</b>) for OM19D against <span class="html-italic">Escherichia coli</span> ATCC25922. Cells suspensions were incubated with a final concentration of peptides of 0.5 × MIC, MIC, 2 × MIC and controls were performed without the peptide.</p>
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<p>The AKP activity of <span class="html-italic">Escherichia coli</span> ATCC25922 was treated with MIC of OM19D and OM19R, the control group was bacteria treated without any peptide. All data are presented as mean ± SD and the significances were determined by nonparametric one-way ANOVA (*** <span class="html-italic">p</span> &lt; 0.001, ns represents insignificant).</p>
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<p>Outer membrane permeability of OM19D (<b>A</b>) and OM19R (<b>B</b>) at the concentrations from 0.5 × MIC to 2 × MIC. Inner membrane permeability of OM19D (<b>C</b>) and OM19R (<b>D</b>) at the concentrations from 0.5 × MIC to 2 × MIC. All data are presented as mean ± SD and the significances were determined by nonparametric one-way ANOVA *** <span class="html-italic">p</span> &lt; 0.001, ns represents insignificant).</p>
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<p>Outer membrane permeability of OM19D (<b>A</b>) and OM19R (<b>B</b>) at the concentrations from 0.5 × MIC to 2 × MIC. Inner membrane permeability of OM19D (<b>C</b>) and OM19R (<b>D</b>) at the concentrations from 0.5 × MIC to 2 × MIC. All data are presented as mean ± SD and the significances were determined by nonparametric one-way ANOVA *** <span class="html-italic">p</span> &lt; 0.001, ns represents insignificant).</p>
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<p>Effects of OM19D (<b>A</b>) and OM19R (<b>B</b>) on bacterial membrane potential (Δφ) in the concentration range of 0.5 × MIC to 4 × MIC, controls were performed without the peptide. Effect of OM19D (<b>C</b>) and OM19R (<b>D</b>) on bacterial intracellular pH (ΔpH) in the concentration range of 0.5 × MIC to 4 × MIC, PBS and glucose were the control groups. All data are presented as mean ± SD and the significances were determined by nonparametric one-way ANOVA (*** <span class="html-italic">p</span> &lt; 0.001, ns represents insignificant).</p>
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<p>Effects of different concentrations of OM19D (<b>A</b>) and OM19R (<b>B</b>) on intracellular ATP in <span class="html-italic">Escherichia coli</span> ATC25922. All data are presented as mean ± SD and the significances were determined by nonparametric one-way ANOVA (* <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001, ns represents insignificant).</p>
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<p>Effects of intracellular reactive oxygen species in <span class="html-italic">Escherichia coli</span> ATCC 25922 treated with OM19D (<b>A</b>) and OM19R (<b>B</b>) at concentrations ranging from 0.5 × MIC to 4 × MIC. The negative control was PBS, and the positive control was hydroperoxide. All data are presented as mean ± SD and the significances were determined by nonparametric one-way ANOVA *** <span class="html-italic">p</span> &lt; 0.001.</p>
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<p>Gel electrophoresis of OM19D (<b>A</b>) and OM19R (<b>B</b>) from 0–512 μg/mL binding to genomic DNA of <span class="html-italic">Escherichia coli</span> ATCC25922, Gel electrophoresis of OM19D (<b>C</b>) and OM19R (<b>D</b>) from 0–512 μg/mL binding to small DNA fragments of <span class="html-italic">Escherichia coli</span> ATCC25922, the letter M stands for individual gene markers, and the number stands for concentration values.</p>
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<p>The trend of intracellular protein concentration of bacteria treated with 0.5 × MIC of OM19D (<b>A</b>) and OM19R (<b>B</b>) followed by time. The trend of intracellular protein concentration of bacteria followed the concentration of OM19D (<b>C</b>) and OM19R (<b>D</b>). The concentration of peptides ranged from 0.5 × MIC to 2 × MIC. All data are presented as mean ± SD and the significances were determined by nonparametric one-way ANOVA (* <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, *** <span class="html-italic">p</span> &lt; 0.001, ns represents insignificant).</p>
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<p>Effects of different concentrations of OM19D (<b>A</b>)and OM19R (<b>B</b>) on the efflux pump of <span class="html-italic">Escherichia coli</span> ATCC 25922.</p>
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13 pages, 2928 KiB  
Article
Expression, Purification and Characterization of a Novel Hybrid Peptide CLP with Excellent Antibacterial Activity
by Junhao Cheng, Marhaba Ahmat, Henan Guo, Xubiao Wei, Lulu Zhang, Qiang Cheng, Jing Zhang, Junyong Wang, Dayong Si, Yueping Zhang and Rijun Zhang
Molecules 2021, 26(23), 7142; https://doi.org/10.3390/molecules26237142 - 25 Nov 2021
Cited by 7 | Viewed by 2878
Abstract
CLP is a novel hybrid peptide derived from CM4, LL37 and TP5, with significantly reduced hemolytic activity and increased antibacterial activity than parental antimicrobial peptides. To avoid host toxicity and obtain high-level bio-production of CLP, we established a His-tagged SUMO fusion expression system [...] Read more.
CLP is a novel hybrid peptide derived from CM4, LL37 and TP5, with significantly reduced hemolytic activity and increased antibacterial activity than parental antimicrobial peptides. To avoid host toxicity and obtain high-level bio-production of CLP, we established a His-tagged SUMO fusion expression system in Escherichia coli. The fusion protein can be purified using a Nickel column, cleaved by TEV protease, and further purified in flow-through of the Nickel column. As a result, the recombinant CLP with a yield of 27.56 mg/L and a purity of 93.6% was obtained. The purified CLP exhibits potent antimicrobial activity against gram+ and gram- bacteria. Furthermore, the result of propidium iodide staining and scanning electron microscopy (SEM) showed that CLP can induce the membrane permeabilization and cell death of Enterotoxigenic Escherichia coli (ETEC) K88. The analysis of thermal stability results showed that the antibacterial activity of CLP decreases slightly below 70 °C for 30 min. However, when the temperature was above 70 °C, the antibacterial activity was significantly decreased. In addition, the antibacterial activity of CLP was stable in the pH range from 4.0 to 9.0; however, when pH was below 4.0 and over 9.0, the activity of CLP decreased significantly. In the presence of various proteases, such as pepsin, papain, trypsin and proteinase K, the antibacterial activity of CLP remained above 46.2%. In summary, this study not only provides an effective strategy for high-level production of antimicrobial peptides and evaluates the interference factors that affect the biological activity of hybrid peptide CLP, but also paves the way for further exploration of the treatment of multidrug-resistant bacterial infections. Full article
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<p>The expression and purification of CLP. (<b>A</b>) Tris-Tricine-SDS-PAGE detection of cell lysate supernatant after IPTG induction for 1 to 5 h. (<b>B</b>) Tris-Tricine-SDS-PAGE detection of purified SUMO-TEV-CLP and its product cleaved by TEV protease. (<b>C</b>) Tris-Tricine-SDS-PAGE detection of purified CLP.</p>
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<p>Analysis of purified CLP using electrospray ionization–mass spectrometry.</p>
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<p>The antimicrobial activity of recombinant CLP against ETEC K88 at 37 °C for 12 h. (<b>A</b>) Inhibition zone of CLP and SUMO-TEV-CLP on ETEC K88. (<b>B</b>) Statistical analysis of the inhibition zone of ETEC K88 by CLP and SUMO-TEV-CLP. CLP represents recombinant CLP; SUMO-TEV-CLP represents the recombinant fusion protein SUMO-TEV-CLP; PBS represents sodium phosphate buffer was the negative control. One-way analysis of variance (ANOVA) and Dunnett’s multiple comparisons test were used for statistical analysis. *** <span class="html-italic">p</span> &lt; 0.01 indicates a significant difference compared with the PBS control. Finally, ns indicates no significant difference.</p>
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<p>The uptake of propidium iodide (PI) by ETEC K88 under the treatment of purified CLP. The reference fluorescence (100%) was samples treated with 0.05% SDS, and PBS treatment was as a negative control. 0.5 × MIC, 1 × MIC and 2 × MIC of purified CLP against ETEC K88 were at concentrations of 1, 2 and 4 µg/mL. Data shown are averages over 3 independent replicates. The standard deviation was shown by the error bars. One-way analysis of variance (ANOVA) and Dunnett’s multiple comparisons test was used for statistical analysis. *** <span class="html-italic">p</span> &lt; 0.01 and <sup>###</sup> <span class="html-italic">p</span> &lt; 0.01 indicate a significant difference compared with the PBS control at 50 minutes and 100 minutes, respectively.</p>
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<p>Scanning electron microscope micrographs of ETEC K88 treated by recombinant CLP. (<b>A</b>) No peptide (Control). (<b>B</b>) Treated with 1 × MIC recombinant CLP for 2 h. Scale bar, 1.0 µm.</p>
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<p>The influence of pH, temperature and protease treatment on the antibacterial activity of recombinant CLP (<b>A</b>–<b>C</b>) and synthesized CLP (<b>D</b>–<b>F</b>). (<b>C</b>) The effects of different protease treatments on the antibacterial activity of recombinant CLP. PBS was employed as a control. ETEC K88 was used as the reference strain. Data shown are averages over 3 independent replicates. The standard deviation was shown by the error bars.</p>
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<p>Hemolytic effects of purified hybrid peptide CLP against sheep RBCs. Data shown are averages over 3 independent replicates. The standard deviation was shown by the error bars.</p>
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16 pages, 2287 KiB  
Article
New Auranofin Analogs with Antibacterial Properties against Burkholderia Clinical Isolates
by Dustin Maydaniuk, Bin Wu, Dang Truong, Sajani H. Liyanage, Andrew M. Hogan, Zhong Ling Yap, Mingdi Yan and Silvia T. Cardona
Antibiotics 2021, 10(12), 1443; https://doi.org/10.3390/antibiotics10121443 - 24 Nov 2021
Cited by 7 | Viewed by 2305
Abstract
Bacteria of the genus Burkholderia include pathogenic Burkholderia mallei, Burkholderia pseudomallei and the Burkholderia cepacia complex (Bcc). These Gram-negative pathogens have intrinsic drug resistance, which makes treatment of infections difficult. Bcc affects individuals with cystic fibrosis (CF) and the species B. cenocepacia [...] Read more.
Bacteria of the genus Burkholderia include pathogenic Burkholderia mallei, Burkholderia pseudomallei and the Burkholderia cepacia complex (Bcc). These Gram-negative pathogens have intrinsic drug resistance, which makes treatment of infections difficult. Bcc affects individuals with cystic fibrosis (CF) and the species B. cenocepacia is associated with one of the worst clinical outcomes. Following the repurposing of auranofin as an antibacterial against Gram-positive bacteria, we previously synthetized auranofin analogs with activity against Gram-negatives. In this work, we show that two auranofin analogs, MS-40S and MS-40, have antibiotic activity against Burkholderia clinical isolates. The compounds are bactericidal against B. cenocepacia and kill stationary-phase cells and persisters without selecting for multistep resistance. Caenorhabditis elegans and Galleria mellonella tolerated high concentrations of MS-40S and MS-40, demonstrating that these compounds have low toxicity in these model organisms. In summary, we show that MS-40 and MS-40S have antimicrobial properties that warrant further investigations to determine their therapeutic potential against Burkholderia infections. Full article
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<p>Chemical structure of auranofin and auranofin analogs. (<b>Top left</b>) Auranofin. (<b>Top right</b>) Group one auranofin analogs containing modifications of the thioglucose and replacement of triethylphosphine (P(CH<sub>2</sub>CH<sub>3</sub>)<sub>3</sub>; PEt<sub>3</sub>) with trimethylphosphine (P(CH<sub>3</sub>)<sub>3</sub>; PMe<sub>3</sub>). (<b>Bottom</b>) Group two auranofin analogs, contains mercaptoethanol (OHCH<sub>2</sub>CH<sub>2</sub>SH) replacing the thioglucose, then further modifications of mercaptoethanol.</p>
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<p>Resistance is not generated to MS-40S. Repeated exposure of a continuously grown culture to sub-lethal concentrations of the antimicrobials were achieved by determining the MIC of the compound. Then, for each compound, 30 μL of bacteria from the well with growth with the highest concentration of compound was grown overnight and used in the next MIC test. This was repeated over 24 days, with the MIC tested every second day. MEM, meropenem; DOX, doxycycline.</p>
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<p>Exponential and stationary time kills of <span class="html-italic">Burkholderia cenocepacia</span> K56-2. The compounds used were MS-40, MS-40S, and ceftazidime–avibactam (CZA) at 1×, 2×, and 4× MIC, as well as doxycycline (DOX) at 4× MIC. The cultures were grown overnight for stationary phase cells or grown overnight, subcultured, and grown to early exponential phase. Samples were taken every hour for six hours to determine CFU/mL. No ATB; no antibiotic.</p>
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<p>MS-40S kills and inhibits the formation of persister cells. (<b>Top</b>) An exponential phase culture with approximately 1 × 10<sup>8</sup> CFU/mL was exposed to 5× MIC ciprofloxacin (CIP) to generate persister cells. At three hours post-exposure, persister cells were washed, resuspended in PBS and exposed to 0×, 2×, or 4× MIC of MS-40 (<b>top left</b>) and MS-40S (<b>top right</b>) for an additional three hours. No ATB; no antibiotic. (<b>Bottom</b>) An overnight culture of <span class="html-italic">B. cenocepacia</span> K56-2 was incubated with the corresponding antimicrobial, MS-40, MS-40S, meropenem (MEM), or ceftazidime–avibactam (CZA). Percent survival was calculated by the log<sub>10</sub> CFU/mL of the surviving population/log<sub>10</sub> CFU/mL of the initial population. N.C., no colonies.</p>
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<p>(<b>A</b>) Synthesis of MS-40S. (<b>B</b>) Synthesis of MS-40. Reagents and conditions: a: NaOCH<sub>3</sub>, CH<sub>3</sub>OH, room temperature, 2 h; b: dichloromethane, 0 °C, 23 h.</p>
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17 pages, 807 KiB  
Article
Effects of Bacillus amyloliquefaciens LFB112 on Growth Performance, Carcass Traits, Immune, and Serum Biochemical Response in Broiler Chickens
by Marhaba Ahmat, Junhao Cheng, Zaheer Abbas, Qiang Cheng, Zhen Fan, Baseer Ahmad, Min Hou, Ghenijan Osman, Henan Guo, Junyong Wang and Rijun Zhang
Antibiotics 2021, 10(11), 1427; https://doi.org/10.3390/antibiotics10111427 - 22 Nov 2021
Cited by 22 | Viewed by 2647
Abstract
This study aimed to investigate the effects of Bacillus amyloliquefaciens LFB112 on the growth performance, carcass traits, immune response, and serum biochemical parameters of broiler chickens. A total of 396 1 day old, mixed-sex commercial Ross 308 broilers with similar body weights were [...] Read more.
This study aimed to investigate the effects of Bacillus amyloliquefaciens LFB112 on the growth performance, carcass traits, immune response, and serum biochemical parameters of broiler chickens. A total of 396 1 day old, mixed-sex commercial Ross 308 broilers with similar body weights were allotted into six treatment groups. The assigned groups were the CON group (basal diet with no supplement), AB (antibiotics) group (basal diet + 150 mg of aureomycin/kg), C+M group (basal diet + 5 × 108 CFU/kg B. amyloliquefaciens LFB112 powder with vegetative cells + metabolites), C group (basal diet + 5 × 108 CFU/kg B. amyloliquefaciens LFB112 vegetative cell powder with removed metabolites), M group (basal diet + 5 × 108 CFU/kg B. amyloliquefaciens LFB112 metabolite powder with removed vegetative cells), and CICC group (basal diet + 5 × 108 CFU/kg Bacillus subtilis CICC 20179). Results indicated that chickens in the C+M, C, and M groups had higher body weight (BW) and average daily gain (ADG) (p < 0.05) and lower feed conversion ratio (FCR) (p = 0.02) compared to the CON group. The C+M group showed the lowest abdominal fat rate compared to those in the CON, AB, and CICC groups (p < 0.05). Compared to the CON group, serum IgA and IgG levels in the C+M, C, and M groups significantly increased while declining in the AB group (p < 0.05). B. amyloliquefaciens LFB112 supplementation significantly reduced the serum triglyceride, cholesterol, urea, and creatinine levels, while increasing the serum glucose and total protein (p < 0.05). In conclusion, B. amyloliquefaciens LFB112 significantly improved the growth performance, carcass traits, immunity, and blood chemical indices of broiler chickens and may be used as an efficient broiler feed supplement. Full article
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Graphical abstract
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<p>Effect of <span class="html-italic">Bacillus amyloliquefaciens</span> LFB112 on immune organ index (g/kg) of broilers. (<b>a</b>) Effect of <span class="html-italic">Bacillus amyloliquefaciens</span> LFB112 on thymus. (<b>b</b>) Effect of <span class="html-italic">Bacillus amyloliquefaciens</span> LFB112 on bursa of Fabricius. (<b>c</b>) Effect of <span class="html-italic">Bacillus amyloliquefaciens</span> LFB112 on spleen. Experimental groups assigned were as follows: CON = basal diet; AB (antibiotics) = basal diet + aureomycin 150 mg/kg; C + M = basal diet + LFB112 fermentation dry powder with <span class="html-italic">Bacillus</span> cells + metabolites (5 × 10<sup>8</sup> CFU/g); C = basal diet + LFB112 <span class="html-italic">Bacillus</span> cells powder with removed metabolites (5 × 10<sup>8</sup> CFU/g); M = basal diet + LFB112 metabolite powder with removed <span class="html-italic">Bacillus</span> cells (5 × 10<sup>8</sup> CFU/g); CICC = basal diet + <span class="html-italic">Bacillus subtilis</span> 20,179 (5 × 10<sup>8</sup> CFU/g). (<b>a</b>–<b>c</b>) Different letters on standard error bars indicate a significant difference (<span class="html-italic">p</span> &lt; 0.05). Data are shown as means and standard errors (<span class="html-italic">n</span> = 6).</p>
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<p>Effect of <span class="html-italic">Bacillus amyloliquefaciens</span> LFB112 on serum immune factors (g/L) of broiler. Ig = immunoglobulin. (<b>a</b>) Effect of <span class="html-italic">Bacillus amyloliquefaciens</span> LFB112 on IgA. (<b>b</b>) Effect of <span class="html-italic">Bacillus amyloliquefaciens</span> LFB112 on IgG. (<b>c</b>) Effect of <span class="html-italic">Bacillus amyloliquefaciens</span> LFB112 on IgM. Experimental groups assigned were as follows: CON = basal diet; AB (antibiotics) = basal diet + aureomycin 150 mg/kg; C + M = basal diet + LFB112 fermentation dry powder with <span class="html-italic">Bacillus</span> cells + metabolites (5 × 10<sup>8</sup> CFU/g); C = basal diet + LFB112 <span class="html-italic">Bacillus</span> cell powder with removed metabolites (5 × 10<sup>8</sup> CFU/g); M = basal diet + LFB112 metabolite powder with removed <span class="html-italic">Bacillus</span> cells (5 × 10<sup>8</sup> CFU/g); CICC = basal diet + <span class="html-italic">Bacillus subtilis</span> 20,179 (5 × 10<sup>8</sup> CFU/g). (<b>a</b>–<b>c</b>) Different letters on standard error bars indicate a significant difference (<span class="html-italic">p</span> &lt; 0.05). Data are shown as means and standard errors (<span class="html-italic">n</span> = 6).</p>
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19 pages, 4237 KiB  
Article
Improvement of the Antimicrobial Activity of Oregano Oil by Encapsulation in Chitosan—Alginate Nanoparticles
by Krassimira Yoncheva, Niko Benbassat, Maya M. Zaharieva, Lyudmila Dimitrova, Alexander Kroumov, Ivanka Spassova, Daniela Kovacheva and Hristo M. Najdenski
Molecules 2021, 26(22), 7017; https://doi.org/10.3390/molecules26227017 - 20 Nov 2021
Cited by 33 | Viewed by 6747
Abstract
Oregano oil (OrO) possesses well-pronounced antimicrobial properties but its application is limited due to low water solubility and possible instability. The aim of this study was to evaluate the possibility to incorporate OrO in an aqueous dispersion of chitosan—alginate nanoparticles and how this [...] Read more.
Oregano oil (OrO) possesses well-pronounced antimicrobial properties but its application is limited due to low water solubility and possible instability. The aim of this study was to evaluate the possibility to incorporate OrO in an aqueous dispersion of chitosan—alginate nanoparticles and how this will affect its antimicrobial activity. The encapsulation of OrO was performed by emulsification and consequent electrostatic gelation of both polysaccharides. OrO-loaded nanoparticles (OrO-NP) have small size (320 nm) and negative charge (−25 mV). The data from FTIR spectroscopy and XRD analyses reveal successful encapsulation of the oil into the nanoparticles. The results of thermogravimetry suggest improved thermal stability of the encapsulated oil. The minimal inhibitory concentrations of OrO-NP determined on a panel of Gram-positive and Gram-negative pathogens (ISO 20776-1:2006) are 4–32-fold lower than those of OrO. OrO-NP inhibit the respiratory activity of the bacteria (MTT assay) to a lower extent than OrO; however, the minimal bactericidal concentrations still remain significantly lower. OrO-NP exhibit significantly lower in vitro cytotoxicity than pure OrO on the HaCaT cell line as determined by ISO 10993-5:2009. The irritation test (ISO 10993-10) shows no signs of irritation or edema on the application site. In conclusion, the nanodelivery system of oregano oil possesses strong antimicrobial activity and is promising for development of food additives. Full article
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<p>XRD patterns of empty chitosan—alginate nanoparticles (<b>a</b>), oregano oil (<b>b</b>), and oregano oil-loaded chitosan—alginate nanoparticles (<b>c</b>).</p>
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<p>FTIR spectra of pure oregano oil (<b>a</b>), empty (<b>b</b>) and OrO—loaded chitosan—alginate nanoparticles (<b>c</b>).</p>
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<p>DTG curves of oregano oil (<b>a</b>), chitosan–alginate (<b>b</b>), and oregano oil–loaded chitosan–alginate (<b>c</b>).</p>
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<p>Minimal inhibitory concentrations and dehydrogenase activity at MIC of the oregano oil—comparison between OrO and OrO—NP. Legend: OrO—oregano oil; OrO—NP—OrO—loaded chitosan—alginate nanoparticles.</p>
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<p>Metabolic activity of the bacterial strains treated with oregano oil—comparison between pure oil and the nanoformulation based on chitosan and alginate. Legend: OrO = <span class="html-italic">Origanum vulgare</span> oil, OrO-NP = <span class="html-italic">Origanum vulgare</span> oil encapsulated in a chitosan nanodelivery system, P1 = coefficient of inhibition in the Lambert–Pearson model; P2 = hill slope (by realization of the model); R = correlation coefficient showing the descriptive power of the model for the specific experimental data; NMA = normalized metabolic activity.</p>
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<p>Median inhibitory concentrations, maximum nontoxic concentrations and RSA analysis of oregano oil, chitosan–alginate, and the nanodelivery system of chitosan–alginate loaded with oregano oil. Legend: OrO—<span class="html-italic">Origanum vulgare</span> oil, OrO-NP—<span class="html-italic">Origanum vulgare</span> oil encapsulated in a chitosan-alginate nanodelivery system.</p>
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<p>Skin irritation test for pure and encapsulated oregano oil. Legend: 1—administered concentration: 0.1% for pure oregano oil and 0.01% for encapsulated oregano oil; 2—positive control (10% sodium dodecyl sulphate); 3—negative control (sunflower oil); 4—administered concentration: 1% pure oregano oil, 0.1% encapsulated oregano oil.</p>
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21 pages, 5208 KiB  
Article
In Silico and In Vitro Evaluation of the Antimicrobial Potential of Bacillus cereus Isolated from Apis dorsata Gut against Neisseria gonorrhoeae
by Nurdjannah Jane Niode, Aryani Adji, Jimmy Rimbing, Max Tulung, Mohammed Alorabi, Ahmed M. El-Shehawi, Rinaldi Idroes, Ismail Celik, Fatimawali, Ahmad Akroman Adam, Kuldeep Dhama, Gomaa Mostafa-Hedeab, Amany Abdel-Rahman Mohamed, Trina Ekawati Tallei and Talha Bin Emran
Antibiotics 2021, 10(11), 1401; https://doi.org/10.3390/antibiotics10111401 - 15 Nov 2021
Cited by 15 | Viewed by 4045
Abstract
Antimicrobial resistance is a major public health and development concern on a global scale. The increasing resistance of the pathogenic bacteria Neisseria gonorrhoeae to antibiotics necessitates efforts to identify potential alternative antibiotics from nature, including insects, which are already recognized as a source [...] Read more.
Antimicrobial resistance is a major public health and development concern on a global scale. The increasing resistance of the pathogenic bacteria Neisseria gonorrhoeae to antibiotics necessitates efforts to identify potential alternative antibiotics from nature, including insects, which are already recognized as a source of natural antibiotics by the scientific community. This study aimed to determine the potential of components of gut-associated bacteria isolated from Apis dorsata, an Asian giant honeybee, as an antibacterial against N. gonorrhoeae by in vitro and in silico methods as an initial process in the stage of new drug discovery. The identified gut-associated bacteria of A. dorsata included Acinetobacter indicus and Bacillus cereus with 100% identity to referenced bacteria from GenBank. Cell-free culture supernatants (CFCS) of B. cereus had a very strong antibacterial activity against N. gonorrhoeae in an in vitro antibacterial testing. Meanwhile, molecular docking revealed that antimicrobial lipopeptides from B. cereus (surfactin, fengycin, and iturin A) had a comparable value of binding-free energy (BFE) with the target protein receptor for N. gonorrhoeae, namely penicillin-binding protein (PBP) 1 and PBP2 when compared with the ceftriaxone, cefixime, and doxycycline. The molecular dynamics simulation (MDS) study revealed that the surfactin remains stable at the active site of PBP2 despite the alteration of the H-bond and hydrophobic interactions. According to this finding, surfactin has the greatest antibacterial potential against PBP2 of N. gonorrhoeae. Full article
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Figure 1
<p>The 2D structures of the ligands: (<b>A</b>) Surfactin, (<b>B</b>) Fengycin, and (<b>C</b>) Iturin A.</p>
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<p>Molecular interaction between PBP1 with (<b>A</b>) fengycin, (<b>B</b>) surfactin, and (<b>C</b>) iturin A.</p>
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<p>Molecular interaction between PBP1 with (<b>A</b>) fengycin, (<b>B</b>) surfactin, and (<b>C</b>) iturin A.</p>
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<p>Molecular interaction between PBP2 with (<b>A</b>) fengycin, (<b>B</b>) surfactin, and (<b>C</b>) iturin A.</p>
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<p>Molecular interaction between PBP2 with (<b>A</b>) fengycin, (<b>B</b>) surfactin, and (<b>C</b>) iturin A.</p>
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<p>Molecular dynamics simulations of apoprotein (PBP2 and Apo), Surfactin (PBP2 and Surfactin) and Fengycin (PBP2 and Fengycin) complexes with penicillin-binding protein 2 (PBP2) (<b>A</b>) RMSD of apoprotein, Surfactin and Fengycin bound PBP2 complexes, (<b>B</b>) RMS fluctuation, and (<b>C</b>) Rg plots during the period of 100 ns simulation.</p>
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<p>Molecular interactions of surfactin at 50 ns and 100 ns at PBP2 active site (<b>A</b>) binding pose of surfactin at 50 ns and (<b>B</b>) schematic protein–ligand interaction diagram of the binding of surfactin and PBP2 active site at 50 ns simulation, (<b>C</b>) binding pose of surfactin at 100 ns and (<b>D</b>) schematic protein–ligand interaction diagram of the binding of surfactin and PBP2 active site at 100 ns simulation.</p>
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18 pages, 2438 KiB  
Article
Bis(Tryptophan) Amphiphiles Form Ion Conducting Pores and Enhance Antimicrobial Activity against Resistant Bacteria
by Mohit Patel, Saeedeh Negin, Joseph Meisel, Shanheng Yin, Michael Gokel, Hannah Gill and George Gokel
Antibiotics 2021, 10(11), 1391; https://doi.org/10.3390/antibiotics10111391 - 12 Nov 2021
Cited by 1 | Viewed by 1786
Abstract
The compounds referred to as bis(tryptophan)s (BTs) have shown activity as antimicrobials. The hypothesis that the activity of these novel amphiphiles results from insertion in bilayer membranes and transport of cations is supported by planar bilayer voltage-clamp studies reported herein. In addition, [...] Read more.
The compounds referred to as bis(tryptophan)s (BTs) have shown activity as antimicrobials. The hypothesis that the activity of these novel amphiphiles results from insertion in bilayer membranes and transport of cations is supported by planar bilayer voltage-clamp studies reported herein. In addition, fluorescence studies of propidium iodide penetration of vital bacteria confirmed enhanced permeability. It was also found that BTs having either meta-phenylene or n-dodecylene linkers function as effective adjuvants to enhance the properties of FDA-approved antimicrobials against organisms such as S. aureus. In one example, a BT-mediated synergistic effect enhanced the potency of norfloxacin against S. aureus by 128-fold. In order to determine if related compounds in which tryptophan was replaced by other common amino acids (H2N-Aaa-linker-Aaa-NH2) we active, a family of analogs have been prepared, characterized, and tested as controls for both antimicrobial activity and as adjuvants for other antimicrobials against both Gram-negative and Gram-positive bacteria. The most active of the compounds surveyed remain the bis(tryptophan) derivatives. Full article
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<p>Structures of <span class="html-italic">bis</span>(tryptophan) derivatives <b>1</b>–<b>6</b>.</p>
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<p>Planar bilayer voltage clamp trace for <b>2</b> in asolection bilayers, applied voltage = 30 mV, 10 mM HEPES buffer, [KCl] = 450 mM.</p>
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<p>Planar bilayer voltage clamp trace for W-<span class="html-italic">o</span>C<sub>6</sub>H<sub>4</sub>-W (<b>3</b>) in asolectin bilayers, applied voltage = 30 mV, 10 mM HEPES buffer, [KCl] = 450 mM.</p>
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<p>Planar bilayer results for W-C<sub>12</sub>-W (<b>6</b>). After some initial evidence of conductance, only spiking behavior (right of trace) could be observed.</p>
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<p>Structures of propidium iodide (<b>left</b>) and ethidium bromide (<b>right</b>), non-membrane permeable, fluorescent agents that stain by DNA intercalation.</p>
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<p>Fluorescence-based assay for propidium iodide penetration of <span class="html-italic">S. aureus</span> cells. RFU = relative fluorescence units. TX100 = Triton X-100. W = L-tryptophan; w = D-tryptophan. Each bar represents three independent determinations; error bars removed for clarity. The compound numbers corresponding to the structures are W-<span class="html-italic">m</span>Ph-W, <b>1</b>; w-<span class="html-italic">m</span>Ph-w, <b>2</b>; and W-C<sub>12</sub>-W, <b>6</b>.</p>
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<p>Checkerboard analysis of cooperative function of two different compounds assessed against <span class="html-italic">S. aureus</span>. The <span class="html-italic">y</span>-axis and <span class="html-italic">x</span>-axis compound concentrations (µM) respectively are identified for checkerboards A-H as follows. (<b>A</b>) W-C<sub>12</sub>-W (<b>6</b>), norfloxacin; (<b>B</b>) w-<span class="html-italic">m</span>C<sub>6</sub>H<sub>4</sub>-w (<b>2</b>), norfloxacin; (<b>C</b>) W-<span class="html-italic">m</span>C<sub>6</sub>H<sub>4</sub>-W, norfloxacin; (<b>D</b>) W-<span class="html-italic">n</span>C<sub>12</sub>-W (<b>6</b>), ethidium bromide; (<b>E</b>) w-<span class="html-italic">m</span>C<sub>6</sub>H<sub>4</sub>-w, ethidium bromide; (<b>F</b>) W-<span class="html-italic">m</span>C<sub>6</sub>H<sub>4</sub>-W (<b>1</b>), ethidium bromide; (<b>G</b>) CCCP, norfloxacin; (<b>H</b>) CCCP, ethidium bromide.</p>
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<p><span class="html-italic">Bis</span>(amino acid) compounds were prepared and used for the present study. All of the new <span class="html-italic">bis</span>(amino acid) compounds or their salts were obtained as colorless solids. They were fully characterized by spectral methods that were found to be in agreement with their assigned structures.</p>
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<p>Synthetic approach to compounds <b>7</b>–<b>13</b>.</p>
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13 pages, 276 KiB  
Review
Artificial Intelligence and Antibiotic Discovery
by Liliana David, Anca Monica Brata, Cristina Mogosan, Cristina Pop, Zoltan Czako, Lucian Muresan, Abdulrahman Ismaiel, Dinu Iuliu Dumitrascu, Daniel Corneliu Leucuta, Mihaela Fadygas Stanculete, Irina Iaru and Stefan Lucian Popa
Antibiotics 2021, 10(11), 1376; https://doi.org/10.3390/antibiotics10111376 - 10 Nov 2021
Cited by 18 | Viewed by 4888
Abstract
Over recent decades, a new antibiotic crisis has been unfolding due to a decreased research in this domain, a low return of investment for the companies that developed the drug, a lengthy and difficult research process, a low success rate for candidate molecules, [...] Read more.
Over recent decades, a new antibiotic crisis has been unfolding due to a decreased research in this domain, a low return of investment for the companies that developed the drug, a lengthy and difficult research process, a low success rate for candidate molecules, an increased use of antibiotics in farms and an overall inappropriate use of antibiotics. This has led to a series of pathogens developing antibiotic resistance, which poses severe threats to public health systems while also driving up the costs of hospitalization and treatment. Moreover, without proper action and collaboration between academic and health institutions, a catastrophic trend might develop, with the possibility of returning to a pre-antibiotic era. Nevertheless, new emerging AI-based technologies have started to enter the field of antibiotic and drug development, offering a new perspective to an ever-growing problem. Cheaper and faster research can be achieved through algorithms that identify hit compounds, thereby further accelerating the development of new antibiotics, which represents a vital step in solving the current antibiotic crisis. The aim of this review is to provide an extended overview of the current artificial intelligence-based technologies that are used for antibiotic discovery, together with their technological and economic impact on the industrial sector. Full article
7 pages, 7209 KiB  
Communication
Facile Synthesis of 3-Substituted Thiazolo[2,3-α]tetrahydroisoquinolines
by Sheng-Han Huang, Wan-Yu Huang, Guo-Lun Zhang and Te-Fang Yang
Molecules 2021, 26(20), 6126; https://doi.org/10.3390/molecules26206126 - 11 Oct 2021
Cited by 1 | Viewed by 1678
Abstract
It was found that 4-hydroxy-2-butenoic ester (11) could not react with 3,4-dihydro-isoquinoline (4a). Individual addition reactions of γ-mercapto-α,β-unsaturated esters (18) and -unsaturated amide (19) with 3,4-dihydroisoquinolines (4) were carried out under appropriate conditions to provide the corresponding [...] Read more.
It was found that 4-hydroxy-2-butenoic ester (11) could not react with 3,4-dihydro-isoquinoline (4a). Individual addition reactions of γ-mercapto-α,β-unsaturated esters (18) and -unsaturated amide (19) with 3,4-dihydroisoquinolines (4) were carried out under appropriate conditions to provide the corresponding thiazolo[2,3-α]isoquinoline derivatives with good yields (up to 87%) and significant diastereomeric selectivity. The mechanism of the crucial reaction was discussed. Full article
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<p>Molecular structures of quinocarcin (<b>1</b>) and tetrazomine (<b>2</b>).</p>
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<p>Scope of the addition of 3,4-dihydroisoquinolines with γ-mercapto-α,β-unsaturated esters and-unsaturated amides.</p>
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<p>The plausible mechanism for the formation of 20 [<a href="#B12-molecules-26-06126" class="html-bibr">12</a>].</p>
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<p>Our Previous Work [<a href="#B10-molecules-26-06126" class="html-bibr">10</a>].</p>
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<p>Dimerization of 4-mercapto enones.</p>
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<p>The control experiment.</p>
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<p>Some synthetic methods for thiazolo[2,3-α]tetrahydroisoquinolines.</p>
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<p>Preparation of some (<span class="html-italic">E</span>)-mercapto-2-butenoic esters.</p>
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<p>Preparation of some (<span class="html-italic">E</span>)-mercaptoamide 19.</p>
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13 pages, 1364 KiB  
Article
Kinase Inhibitor Library Screening Identifies the Cancer Therapeutic Sorafenib and Structurally Similar Compounds as Strong Inhibitors of the Fungal Pathogen Histoplasma capsulatum
by Charlotte Berkes, Jimmy Franco, Maxx Lawson, Katelynn Brann, Jessica Mermelstein, Daniel Laverty and Allison Connors
Antibiotics 2021, 10(10), 1223; https://doi.org/10.3390/antibiotics10101223 - 8 Oct 2021
Cited by 3 | Viewed by 2686
Abstract
Histoplasma capsulatum is a dimorphic fungal pathogen endemic to the midwestern and southern United States. It causes mycoses ranging from subclinical respiratory infections to severe systemic disease, and is of particular concern for immunocompromised patients in endemic areas. Clinical management of histoplasmosis relies [...] Read more.
Histoplasma capsulatum is a dimorphic fungal pathogen endemic to the midwestern and southern United States. It causes mycoses ranging from subclinical respiratory infections to severe systemic disease, and is of particular concern for immunocompromised patients in endemic areas. Clinical management of histoplasmosis relies on protracted regimens of antifungal drugs whose effectiveness can be limited by toxicity. In this study, we hypothesize that conserved biochemical signaling pathways in the eukaryotic domain can be leveraged to repurpose kinase inhibitors as antifungal compounds. We conducted a screen of two kinase inhibitor libraries to identify compounds inhibiting the growth of Histoplasma capsulatum in the pathogenic yeast form. Our approach identified seven compounds with an elongated hydrophobic polyaromatic structure, five of which share a molecular motif including a urea unit linking a halogenated benzene ring and a para-substituted polyaromatic group. The top hits include the cancer therapeutic Sorafenib, which inhibits growth of Histoplasma in vitro and in a macrophage infection model with low host cell cytotoxicity. Our results reveal the possibility of repurposing Sorafenib or derivatives thereof as therapy for histoplasmosis, and suggest that repurposing of libraries developed for human cellular targets may be a fruitful source of antifungal discovery. Full article
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<p>Graphical representation of primary screen results of the Published Kinase Inhibitor Set (<b>A</b>) and the SelleckChem MAPK Inhibitor Library (<b>B</b>) against <span class="html-italic">Histoplasma capsulatum</span>. Each individual compound was tested, in duplicate, at a final concentration of 5 μM. Log phase <span class="html-italic">Hc</span> WU15 yeasts were seeded in 96 well plates at a density of 1 × 10<sup>6</sup> yeasts/mL in HMM/uracil. Compounds were diluted in DMSO and added to each well at a final DMSO concentration of 0.5%. Plates were incubated at 37 °C and 5% CO<sub>2</sub> with twice-daily shaking to improve aeration. OD<sub>595</sub> readings were taken on day 0 and day 4. The results for each compound are shown as average percent growth inhibition over the four day time period relative to the DMSO control. All compounds showing greater than 50% growth inhibition at day 4 are identified.</p>
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<p>Chemical structures of compounds strongly inhibiting <span class="html-italic">H. capsulatum</span> growth at MIC &lt; 2 μM. Sorafenib, Sorafenib tosylate, and GW5074 were identified in the SelleckChem library screen. SC−1 was included due to its structural similarity to Sorafenib. GW778894X, GW770249A, and GW795486X were identified in the PKIS library. (<b>A</b>) All seven of the compounds have an elongated hydrophobic polyaromatic structural motif. Five of the seven compounds contain highly similar molecular structures containing the chemical motif of a urea unit linking a halogenated benzene ring and a <span class="html-italic">para</span> substituted poly aromatic group, represented schematically in (<b>B</b>).</p>
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<p>Sorafenib and SC−1 are fungistatic to <span class="html-italic">H. capsulatum</span> yeasts. <span class="html-italic">Hc</span> WU15 yeasts were seeded in 96 well plates at a density of 4 × 10<sup>6</sup> yeasts/mL in HMM. Sorafenib tosylate (<b>a</b>) or SC−1 (<b>b</b>) were diluted in DMSO and added to each well at a final DMSO concentration of 0.5% with a two-fold dilution series of each compound. Growth of yeasts was monitored by measuring absorbance at 595 nm. IC<sub>50</sub> values were calculated using nonlinear regression of the data at the 4 day time point. (<b>c</b>) Fungistasis was demonstrated by plating serial dilutions of yeasts onto solid media at 2 and 48 h following addition of compounds to measure the number of viable CFU. The images shown are representative of four independent experiments.</p>
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<p>Sorafenib inhibits growth of intracellular <span class="html-italic">H. capsulatum</span> and macrophage lysis. Murine BMDM were seeded in 24 well tissue culture treated wells and infected with <span class="html-italic">Hc</span> WU15 at an MOI of 5. After two hours, extracellular yeasts were removed by washing and media containing Sorafenib-tosylate or DMSO only was added, with each condition in triplicate. Following 48 h incubation at 37 °C and 5% CO<sub>2</sub>, macrophage lysis was monitored by CytoTox LDH release assay. % lysis was calculated relative to a detergent-treated uninfected control. Data shown are representative of three independent experiments.</p>
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14 pages, 2319 KiB  
Article
Antiviral Effect of Nonfunctionalized Gold Nanoparticles against Herpes Simplex Virus Type-1 (HSV-1) and Possible Contribution of Near-Field Interaction Mechanism
by Edyta Paradowska, Mirosława Studzińska, Agnieszka Jabłońska, Valeri Lozovski, Natalia Rusinchuk, Iuliia Mukha, Nadiia Vitiuk and Zbigniew J. Leśnikowski
Molecules 2021, 26(19), 5960; https://doi.org/10.3390/molecules26195960 - 1 Oct 2021
Cited by 25 | Viewed by 3483
Abstract
The antiviral activity of nonfunctionalized gold nanoparticles (AuNPs) against herpes simplex virus type-1 (HSV-1) in vitro was revealed in this study. We found that AuNPs are capable of reducing the cytopathic effect (CPE) of HSV-1 in Vero cells in a dose- and time-dependent [...] Read more.
The antiviral activity of nonfunctionalized gold nanoparticles (AuNPs) against herpes simplex virus type-1 (HSV-1) in vitro was revealed in this study. We found that AuNPs are capable of reducing the cytopathic effect (CPE) of HSV-1 in Vero cells in a dose- and time-dependent manner when used in pretreatment mode. The demonstrated antiviral activity was within the nontoxic concentration range of AuNPs. Interestingly, we noted that nanoparticles with smaller sizes reduced the CPE of HSV-1 more effectively than larger ones. The observed phenomenon can be tentatively explained by the near-field action of nanoparticles at the virus envelope. These results show that AuNPs can be considered as potential candidates for the treatment of HSV-1 infections. Full article
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<p>Absorption spectra (<b>a</b>) and DLS size distribution (<b>b</b>) of gold nanoparticles in obtained colloids.</p>
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<p>Cytotoxicity of AuNPs in Vero cells. Number of viable cells to the untreated cell control (%) after incubation for 48 h. AuNPs of approximate diameters of 10 nm (AuNPs I) and 16 nm (AuNPs II) were used at concentrations of 0.295 and 5.9 μg/mL, respectively. The cell viability was measured using an MTT assay. The data are shown as means ± SD of three experiments performed six times. <span class="html-italic">P,</span> Student’s <span class="html-italic">t</span>-test.</p>
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<p>Sketch of the studied system. (<b>a</b>) is an idealized view of the virus surface with adsorbed nanoparticles; (<b>b</b>) is a model for calculations of adsorption potential for different sites of nanoparticles relative to virus spikes; (<b>c</b>) is the cross-section of ‘b’.</p>
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<p>Interaction potential between the nanoparticle and the virus depending on the nanoparticle location near the virus spike (curve 1 corresponds to site 1 in <a href="#molecules-26-05960-f003" class="html-fig">Figure 3</a>; curve 2 corresponds to site 2 in <a href="#molecules-26-05960-f003" class="html-fig">Figure 3</a>; curve 3 corresponds to site 3 in <a href="#molecules-26-05960-f003" class="html-fig">Figure 3</a>). All the results were normalized to the deepest energy minimum corresponding to case ‘1′ of 5 nm nanoparticles.</p>
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<p>(<b>a</b>): Hypothetical interaction of Au nanoparticles ● and HSV-1 virion (HSV-1 model adapted from [<a href="#B36-molecules-26-05960" class="html-bibr">36</a>]). (<b>b</b>): Cryo-TEM of HSV-1 treated with AuNP 10 nm particles (1 h incubation time), (<b>c</b>): AuNP 10 nm particles.</p>
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14 pages, 2492 KiB  
Article
Attempts to Access a Series of Pyrazoles Lead to New Hydrazones with Antifungal Potential against Candida species including Azole-Resistant Strains
by Georgiana Negru, Laure Kamus, Elena Bîcu, Sergiu Shova, Boualem Sendid, Faustine Dubar and Alina Ghinet
Molecules 2021, 26(19), 5861; https://doi.org/10.3390/molecules26195861 - 27 Sep 2021
Viewed by 1901
Abstract
The treatment of benzylidenemalononitriles with phenylhydrazines in refluxing ethanol did not provide pyrazole derivatives, but instead furnished hydrazones. The structure of hydrazones was secured by X-ray analysis. The chemical proof was also obtained by direct reaction of 3,4,5-trimethoxybenzaldehyde with 2,4-dichlorophenylhydrazine. Newly synthesized hydrazones [...] Read more.
The treatment of benzylidenemalononitriles with phenylhydrazines in refluxing ethanol did not provide pyrazole derivatives, but instead furnished hydrazones. The structure of hydrazones was secured by X-ray analysis. The chemical proof was also obtained by direct reaction of 3,4,5-trimethoxybenzaldehyde with 2,4-dichlorophenylhydrazine. Newly synthesized hydrazones were tested against eight Candida spp. strains in a dose response assay to determine the minimum inhibitory concentration (MIC99). Five compounds were identified as promising antifungal agents against Candida spp. (C. albicans SC5314, C. glabrata, C. tropicalis, C. parapsilosis and C. glabrata (R azoles)), with MIC99 values ranging from 16 to 32 µg/mL and selective antifungal activity over cytotoxicity. Full article
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<p>Structure of a selection of anti-Candida experimental drugs (<b>A</b>–<b>D</b>) and of target hydrazones <b>1a</b>–<b>o</b>.</p>
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<p>A view of the asymmetric part in the crystal structure of <b>1e</b> (<b>a</b>) and <b>1i</b> (<b>b</b>) with atom labeling and thermal ellipsoids at 50% level.</p>
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<p>1D supramolecular chain in the crystal structure of <b>1i</b>. Non-relevant hydrogen atoms are not shown. H-bonds are drawn as black-dashed lines. Symmetry code: <span class="html-italic">i</span>) −<span class="html-italic">x</span>, −0.5 + <span class="html-italic">y</span>, −1.5 − <span class="html-italic">z</span>. H-bond parameters: N2-H···O2 [N2-H 0.86 Å, H···O2 2.65 Å, N2···O2′ 3.432(2) Å, ∠N2HO2 151.4°]; C10-H···O2 [C10-H 0.93 Å, H···O2 2.59 Å, C10···O2′ 3.470(2) Å, ∠C10HO2 158.4°].</p>
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<p>Evaluation of the cytotoxicity of experimental antifungals on HEK293 cells at different concentrations (32 µg/mL to 0.06 µg/mL): (<b>a</b>) hydrazone <b>1c</b>; (<b>b</b>) hydrazone <b>1d</b>; (<b>c</b>) hydrazone <b>1i</b>; (<b>d</b>) hydrazone <b>1k</b>; (<b>e</b>) hydrazone <b>1l</b>. ns: no significance; ****: <span class="html-italic">p</span> value ≤ 0.0001.</p>
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<p>Reagents and conditions: (i) piperidine, EtOH, reflux, 6–8 h.</p>
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<p>Reagents and conditions: (i) EtOH, reflux, 4–8 h.</p>
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<p>Proposed mechanism for the formation of hydrazones <b>1a</b>–<b>o</b> from benzylidenemalononitriles <b>3a</b>–<b>c</b> upon reaction with hydrazines <b>4a</b>–<b>n</b>.</p>
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15 pages, 5841 KiB  
Article
Therapeutic Efficacy of Sesquiterpene Farnesol in Treatment of Cutibacterium acnes-Induced Dermal Disorders
by Guan-Xuan Wu, Yu-Wen Wang, Chun-Shien Wu, Yen-Hung Lin, Chih-Hsin Hung, Han-Hsiang Huang and Shyh-Ming Kuo
Molecules 2021, 26(18), 5723; https://doi.org/10.3390/molecules26185723 - 21 Sep 2021
Cited by 5 | Viewed by 2999
Abstract
Acne vulgaris is a highly prevalent skin disorder requiring treatment and management by dermatologists. Antibiotics such as clindamycin are commonly used to treat acne vulgaris. However, from both medical and public health perspectives, the development of alternative remedies has become essential due to [...] Read more.
Acne vulgaris is a highly prevalent skin disorder requiring treatment and management by dermatologists. Antibiotics such as clindamycin are commonly used to treat acne vulgaris. However, from both medical and public health perspectives, the development of alternative remedies has become essential due to the increase in antibiotic resistance. Topical therapy is useful as a single or combined treatment for mild and moderate acne and is often employed as maintenance therapy. Thus, the current study investigated the anti-inflammatory, antibacterial, and restorative effects of sesquiterpene farnesol on acne vulgaris induced by Cutibacterium acnes (C. acnes) in vitro and in a rat model. The minimum inhibitory concentration (MIC) of farnesol against C. acnes was 0.14 mM, and the IC50 of 24 h exposure to farnesol in HaCaT keratinocytes was approximately 1.4 mM. Moreover, 0.8 mM farnesol exhibited the strongest effects in terms of the alleviation of inflammatory responses and abscesses and necrotic tissue repair in C.acnes-induced acne lesions; 0.4 mM farnesol and clindamycin gel also exerted similar actions after a two-time treatment. By contrast, nearly doubling the tissue repair scores, 0.4 mM farnesol displayed great anti-inflammatory and the strongest reparative actions after a four-time treatment, followed by 0.8 mM farnesol and a commercial gel. Approximately 2–10-fold decreases in interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α, found by Western blot analysis, were predominantly consistent with the histopathological findings and tissue repair scores. The basal hydroxypropyl methylcellulose (HPMC) gel did not exert anti-inflammatory or reparative effects on rat acne lesions. Our results suggest that the topical application of a gel containing farnesol is a promising alternative remedy for acne vulgaris. Full article
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Figure 1
<p>(<b>A</b>) Schematic of the development and the time scale of treatment of <span class="html-italic">C. acnes</span>-induced rat skin acne. (<b>B</b>) The dorsal skin of a rat injected with 5 × 10<sup>8</sup> CFU/mL <span class="html-italic">C. acnes</span> at 96 h postinjection (<b>a</b>), 144 h postinjection (<b>b</b>), and 192 h postinjection (<b>c</b>).</p>
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<p>MIC test results for farnesol in the treatment of <span class="html-italic">C.</span> <span class="html-italic">acnes</span>-induced acne after 24 and 48 h incubations. The MIC was measured by assessing the effects of a series of farnesol concentrations (from 0.004 to 0.576 mM) on the absorbance at 600 nm (OD<sub>600</sub>). The MIC was determined as 0.14 mM.</p>
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<p>(<b>A</b>) Cell viability assay displaying the low cytotoxicity of farnesol on HaCaT keratinocytes. (<b>B</b>) Cell morphology images of keratinocytes after various treatments with the indicated the concentrations of farnesol, supporting the cell viability assay results (Bar, 50 μm). ** <span class="html-italic">p</span> &lt; 0.01; *** <span class="html-italic">p</span> &lt; 0.001 (through ANOVA).</p>
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<p>H&amp;E stains of the dorsal skin of rat after two-time (<b>A</b>) and four-time (<b>B</b>) treatment with 0.4 mM farnesol, 0.8 mM farnesol, HPMC, and commercial clindamycin gels.</p>
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<p>Masson’s trichrome staining of the dorsal skin of rats after two-time (<b>A</b>) and four-time (<b>B</b>) treatment with 0.4 mM farnesol, 0.8 mM farnesol, HPMC, and commercial clindamycin gels. Semiquantitative assessment of collagen from blue color stains in Masson’s trichrome images for (<b>C</b>) two-time and (<b>D</b>) four-time treatment groups (<span class="html-italic">n</span> = 3). ** <span class="html-italic">p</span> &lt; 0.01 (compared with the normal group); <sup>#</sup> <span class="html-italic">p</span> &lt; 0.05 (compared with the untreated group), <sup>##</sup> <span class="html-italic">p</span> &lt; 0.01.</p>
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<p>Masson’s trichrome staining of the dorsal skin of rats after two-time (<b>A</b>) and four-time (<b>B</b>) treatment with 0.4 mM farnesol, 0.8 mM farnesol, HPMC, and commercial clindamycin gels. Semiquantitative assessment of collagen from blue color stains in Masson’s trichrome images for (<b>C</b>) two-time and (<b>D</b>) four-time treatment groups (<span class="html-italic">n</span> = 3). ** <span class="html-italic">p</span> &lt; 0.01 (compared with the normal group); <sup>#</sup> <span class="html-italic">p</span> &lt; 0.05 (compared with the untreated group), <sup>##</sup> <span class="html-italic">p</span> &lt; 0.01.</p>
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<p>Western blot of the dorsal skin of rats after two-time (<b>A</b>) and four-time (<b>B</b>) treatment with 0.4 mM farnesol, 0.8 mM farnesol, HPMC, and commercial clindamycin gels. (<b>C</b>) Semiquantitative analyses of Western blot of proinflammatory cytokines, using the ImageJ software. * <span class="html-italic">p</span> &lt; 0.05; ** <span class="html-italic">p</span> &lt; 0.01; *** <span class="html-italic">p</span> &lt; 0.001 (compared with the untreated group).</p>
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<p>Western blot of the dorsal skin of rats after two-time (<b>A</b>) and four-time (<b>B</b>) treatment with 0.4 mM farnesol, 0.8 mM farnesol, HPMC, and commercial clindamycin gels. (<b>C</b>) Semiquantitative analyses of Western blot of proinflammatory cytokines, using the ImageJ software. * <span class="html-italic">p</span> &lt; 0.05; ** <span class="html-italic">p</span> &lt; 0.01; *** <span class="html-italic">p</span> &lt; 0.001 (compared with the untreated group).</p>
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20 pages, 4077 KiB  
Review
Nano-Drug Design Based on the Physiological Properties of Glutathione
by Wenhua Li, Minghui Li and Jing Qi
Molecules 2021, 26(18), 5567; https://doi.org/10.3390/molecules26185567 - 13 Sep 2021
Cited by 14 | Viewed by 4083
Abstract
Glutathione (GSH) is involved in and regulates important physiological functions of the body as an essential antioxidant. GSH plays an important role in anti-oxidation, detoxification, anti-aging, enhancing immunity and anti-tumor activity. Herein, based on the physiological properties of GSH in different diseases, mainly [...] Read more.
Glutathione (GSH) is involved in and regulates important physiological functions of the body as an essential antioxidant. GSH plays an important role in anti-oxidation, detoxification, anti-aging, enhancing immunity and anti-tumor activity. Herein, based on the physiological properties of GSH in different diseases, mainly including the strong reducibility of GSH, high GSH content in tumor cells, and the NADPH depletion when GSSH is reduced to GSH, we extensively report the design principles, effect, and potential problems of various nano-drugs in diabetes, cancer, nervous system diseases, fluorescent probes, imaging, and food. These studies make full use of the physiological and pathological value of GSH and develop excellent design methods of nano-drugs related to GSH, which shows important scientific significance and prominent application value for the related diseases research that GSH participates in or responds to. Full article
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Figure 1

Figure 1
<p>Structure and synthesis procedure of GSH and GSSH.</p>
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<p>Nano-drugs for diabetes designment based on GSH. (<b>A</b>) GSH was encapsulated into Enteric eudragit L100-cysteine to prepare reduced glutathione nanoparticles (Eul-cys/GSH NPs) [<a href="#B30-molecules-26-05567" class="html-bibr">30</a>]; (<b>B</b>) GSH-bound magnetic nanoparticles (SPION@silica-NH<sub>2</sub>). GSH was reacted with maleic anhydride to form SPION@silica-GSH nanoparticles [<a href="#B31-molecules-26-05567" class="html-bibr">31</a>]; (<b>C</b>) transmission electron microscope images of CuO nanoparticles and Au nanoparticles enzyme [<a href="#B32-molecules-26-05567" class="html-bibr">32</a>,<a href="#B33-molecules-26-05567" class="html-bibr">33</a>].</p>
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<p>Pathogenesis of GSH involved in: (<b>A</b>) mechanism of polyol pathway [<a href="#B21-molecules-26-05567" class="html-bibr">21</a>]; (<b>B</b>) mechanism of ferroptosis [<a href="#B58-molecules-26-05567" class="html-bibr">58</a>].</p>
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<p>Schematic design of different GSH responsive anticancer drugs with disulfide bond. (<b>A</b>) Camptothecin and chlorambucil conjugated with disulfide bond (SS) supramolecular anticancer drugs. Nanoparticles cleavage to CPT with GSH [<a href="#B67-molecules-26-05567" class="html-bibr">67</a>]; (<b>B</b>) GSH-responsive degradable PEO-b-PHMssEt micelles. PEO-b-PHMssEt cleavage to PEO-b-PHMSH with GSH [<a href="#B68-molecules-26-05567" class="html-bibr">68</a>]; (<b>C</b>) the disulfide bond-bridged prodrugs PTX-SS-CIT cleavage to different compounds with GSH [<a href="#B60-molecules-26-05567" class="html-bibr">60</a>]; (<b>D</b>) redox-responsive conjugates by bridging PTX and OA with disulfide bond (PTX-S-S-OA). PTX-S-S-OA cleavage to PTX with GSH [<a href="#B70-molecules-26-05567" class="html-bibr">70</a>].</p>
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<p>Schematic design of different GSH-responsive anticancer drugs with -S-. (<b>A</b>) Schematic representation of the preparation of PEGylated prodrug NPs of PTX-S-OA and cleavage by GSH or ROS [<a href="#B73-molecules-26-05567" class="html-bibr">73</a>]; (<b>B</b>) schematic representation of DTX-S-LA self-assemble in water and cleavage with GSH in tumor cells [<a href="#B61-molecules-26-05567" class="html-bibr">61</a>]; (<b>C</b>) schematic representation of CUR-S-CUR prodrug self-assemble and its uptake by tumor cells [<a href="#B75-molecules-26-05567" class="html-bibr">75</a>].</p>
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<p>Self-assembled Pt (IV) nanoparticles for specific delivery of Pt drugs. (<b>A</b>) Pt (IV) was reduced with GSH to Pt (II) [<a href="#B76-molecules-26-05567" class="html-bibr">76</a>]. (<b>B</b>) Pt(IV)NP-cRGD was reduced with GSH to Pt (II) [<a href="#B77-molecules-26-05567" class="html-bibr">77</a>].</p>
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<p>Dual reaction of probe (Cy-O-Eb) with GSH/H<sub>2</sub>O<sub>2</sub> [<a href="#B81-molecules-26-05567" class="html-bibr">81</a>]. The Se-N bond (strong fluorescence) in Cy-O-Eb was reduced with GSH to form Se-H bond (weak fluorescence). Se-N was regenerated and the fluorescence was restored under the effect of H<sub>2</sub>O<sub>2</sub>.</p>
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