[go: up one dir, main page]

 
 
Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (22,662)

Search Parameters:
Keywords = drug target

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
15 pages, 1684 KiB  
Article
Bis(2-butoxyethyl) Ether-Promoted O2-Mediated Oxidation of Alkyl Aromatics to Ketones under Clean Conditions
by Yangyang Xie, Zeping Li, Xudong Xu, Han Jiang, Keyi Chen, Jinhua Ou, Kaijian Liu, Yihui Zhou and Kejun Luo
Molecules 2024, 29(20), 4909; https://doi.org/10.3390/molecules29204909 (registering DOI) - 17 Oct 2024
Viewed by 79
Abstract
Conventional oxidation processes for alkyl aromatics to ketones employ oxidants that tend to generate harmful byproducts and cause severe equipment corrosion, ultimately creating critical environmental problems. Thus, in this study, a practical, efficient, and green method was developed for the synthesis of aromatic [...] Read more.
Conventional oxidation processes for alkyl aromatics to ketones employ oxidants that tend to generate harmful byproducts and cause severe equipment corrosion, ultimately creating critical environmental problems. Thus, in this study, a practical, efficient, and green method was developed for the synthesis of aromatic ketones by applying a bis(2-butoxyethyl) ether/O2 system under external catalyst-, additive-, and base-free conditions. This O2-mediated oxidation system can tolerate various functional groups and is suitable for large-scale synthesis. Diverse target ketones were prepared under clean conditions in moderate-to-high yields. The late-stage functionalization of drug derivatives with the corresponding ketones and one-pot sequential chemical conversions to ketone downstream products further broaden the application prospects of this approach. Full article
Show Figures

Figure 1

Figure 1
<p>(<b>a</b>) Scaled-up oxidation reaction; (<b>b</b>) several one-pot sequential conversions; (<b>c</b>) time course of oxygenation.</p>
Full article ">Figure 2
<p>Control experiments.</p>
Full article ">Figure 3
<p>Plausible bis(2-butoxyethyl) ether promoted oxidation mechanism.</p>
Full article ">Scheme 1
<p>Oxidation of alkyl aromatics to ketones.</p>
Full article ">
11 pages, 978 KiB  
Article
Estimating Progression-Free Survival in Patients with Primary High-Grade Glioma Using Machine Learning
by Agnieszka Kwiatkowska-Miernik, Piotr Gustaw Wasilewski, Bartosz Mruk, Katarzyna Sklinda, Maciej Bujko and Jerzy Walecki
J. Clin. Med. 2024, 13(20), 6172; https://doi.org/10.3390/jcm13206172 (registering DOI) - 16 Oct 2024
Viewed by 314
Abstract
Background/Objectives: High-grade gliomas are the most common primary malignant brain tumors in adults. These neoplasms remain predominantly incurable due to the genetic diversity within each tumor, leading to varied responses to specific drug therapies. With the advent of new targeted and immune [...] Read more.
Background/Objectives: High-grade gliomas are the most common primary malignant brain tumors in adults. These neoplasms remain predominantly incurable due to the genetic diversity within each tumor, leading to varied responses to specific drug therapies. With the advent of new targeted and immune therapies, which have demonstrated promising outcomes in clinical trials, there is a growing need for image-based techniques to enable early prediction of treatment response. This study aimed to evaluate the potential of radiomics and artificial intelligence implementation in predicting progression-free survival (PFS) in patients with highest-grade glioma (CNS WHO 4) undergoing a standard treatment plan. Methods: In this retrospective study, prediction models were developed in a cohort of 51 patients with pathologically confirmed highest-grade glioma (CNS WHO 4) from the authors’ institution and the repository of the Cancer Imaging Archive (TCIA). Only patients with confirmed recurrence after complete tumor resection with adjuvant radiotherapy and chemotherapy with temozolomide were included. For each patient, 109 radiomic features of the tumor were obtained from a preoperative magnetic resonance imaging (MRI) examination. Four clinical features were added manually—sex, weight, age at the time of diagnosis, and the lobe of the brain where the tumor was located. The data label was the time to recurrence, which was determined based on follow-up MRI scans. Artificial intelligence algorithms were built to predict PFS in the training set (n = 75%) and then validate it in the test set (n = 25%). The performance of each model in both the training and test datasets was assessed using mean absolute percentage error (MAPE). Results: In the test set, the random forest model showed the highest predictive performance with 1-MAPE = 92.27% and a C-index of 0.9544. The decision tree, gradient booster, and artificial neural network models showed slightly lower effectiveness with 1-MAPE of 88.31%, 80.21%, and 91.29%, respectively. Conclusions: Four of the six models built gave satisfactory results. These results show that artificial intelligence models combined with radiomic features could be useful for predicting the progression-free survival of high-grade glioma patients. This could be beneficial for risk stratification of patients, enhancing the potential for personalized treatment plans and improving overall survival. Further investigation is necessary with an expanded sample size and external multicenter validation. Full article
Show Figures

Figure 1

Figure 1
<p>Assuming that each small square represents a pixel, the morphological and first-order features of images (<b>A</b>,<b>B</b>) would be the same, but the images differ in texture.</p>
Full article ">Figure 2
<p>Study flowchart. (<b>a</b>) Magnetic resonance (MR) imaging; the study is based on contrast-enhanced T1—w images. (<b>b</b>) Identification of a region of interest (ROI) and semi-automatic image segmentation. (<b>c</b>) Normalization and radiomic feature extraction from the defined ROI; 109 radiomic features were obtained in the study. (<b>d</b>) Data preprocessing and analysis; five different machine learning (ML) models were trained on the received data (AI—artificial intelligence, DL—deep learning). (<b>e</b>) Results.</p>
Full article ">Figure 3
<p>Flowchart of the patient selection process.</p>
Full article ">Figure 4
<p>Glioma CNS WHO 4 in the left parietal lobe. T1-weighted image after administration of contrast agent; the blue color was used to mark the tumor segmented by the semi-automated method.</p>
Full article ">Figure 5
<p>Kaplan–Meier curve of PFS for patients in the study group.</p>
Full article ">Figure 6
<p>Performance of the five models for predicting the PFS presented using 1-MAPE.</p>
Full article ">Figure 7
<p>Kaplan–Meier curve of predicted PFS for the test set by the random forest model marked in blue and Kaplan–Meier curve of PFS for patients in the study group marked in orange.</p>
Full article ">
26 pages, 8774 KiB  
Review
RNA Binding Proteins as Potential Therapeutic Targets in Colorectal Cancer
by Vikash Singh, Amandeep Singh, Alvin John Liu, Serge Y. Fuchs, Arun K. Sharma and Vladimir S. Spiegelman
Cancers 2024, 16(20), 3502; https://doi.org/10.3390/cancers16203502 - 16 Oct 2024
Viewed by 436
Abstract
RNA-binding proteins (RBPs) play critical roles in regulating post-transcriptional gene expression, managing processes such as mRNA splicing, stability, and translation. In normal intestine, RBPs maintain the tissue homeostasis, but when dysregulated, they can drive colorectal cancer (CRC) development and progression. Understanding the molecular [...] Read more.
RNA-binding proteins (RBPs) play critical roles in regulating post-transcriptional gene expression, managing processes such as mRNA splicing, stability, and translation. In normal intestine, RBPs maintain the tissue homeostasis, but when dysregulated, they can drive colorectal cancer (CRC) development and progression. Understanding the molecular mechanisms behind CRC is vital for developing novel therapeutic strategies, and RBPs are emerging as key players in this area. This review highlights the roles of several RBPs, including LIN28, IGF2BP1–3, Musashi, HuR, and CELF1, in CRC. These RBPs regulate key oncogenes and tumor suppressor genes by influencing mRNA stability and translation. While targeting RBPs poses challenges due to their complex interactions with mRNAs, recent advances in drug discovery have identified small molecule inhibitors that disrupt these interactions. These inhibitors, which target LIN28, IGF2BPs, Musashi, CELF1, and HuR, have shown promising results in preclinical studies. Their ability to modulate RBP activity presents a new therapeutic avenue for treating CRC. In conclusion, RBPs offer significant potential as therapeutic targets in CRC. Although technical challenges remain, ongoing research into the molecular mechanisms of RBPs and the development of selective, potent, and bioavailable inhibitors should lead to more effective treatments and improved outcomes in CRC. Full article
Show Figures

Figure 1

Figure 1
<p>(<b>A</b>,<b>B</b>) show 3D representations of the binding and surface view of inhibitor Ln7 with RNA binding protein Ln28 (PDBID: 5UDZ). (<b>C</b>) shows 2D representations of binding interactions of Ln7. (<b>D</b>) The binding energy of inhibitors with RNA binding protein Ln28 along with interacting residues. Color code: green = carbon, white = hydrogen, blue = nitrogen, and red = oxygen.</p>
Full article ">Figure 2
<p>(<b>A</b>,<b>B</b>) show 3D representations of the binding and surface view of inhibitor R12–8–44–3 with RNA binding protein Musash1 (PDBID: 2RS2). (<b>C</b>) shows 2D representations of binding interactions of Musashi1. (<b>D</b>) The binding energy of inhibitors with RNA binding protein Musashi 1 along with interacting residues. Color code: green = carbon, white = hydrogen, blue = nitrogen, and red = oxygen.</p>
Full article ">Figure 2 Cont.
<p>(<b>A</b>,<b>B</b>) show 3D representations of the binding and surface view of inhibitor R12–8–44–3 with RNA binding protein Musash1 (PDBID: 2RS2). (<b>C</b>) shows 2D representations of binding interactions of Musashi1. (<b>D</b>) The binding energy of inhibitors with RNA binding protein Musashi 1 along with interacting residues. Color code: green = carbon, white = hydrogen, blue = nitrogen, and red = oxygen.</p>
Full article ">Figure 3
<p>(<b>A</b>,<b>B</b>) show 3D representations of the binding and surface view of inhibitor palmatine with RNA binding protein Musash2 (PDBID: 6DBP). (<b>C</b>) shows 2D representations of binding interactions of Musashi2. (<b>D</b>) The binding energy of inhibitors with RNA binding protein Musashi 2 along with interacting residues. Color code: green = carbon, white = hydrogen, blue = nitrogen, and red = oxygen.</p>
Full article ">Figure 4
<p>(<b>A</b>,<b>B</b>) show 3D representations of the binding and surface view of inhibitor C11 with RNA binding protein HUR (PDBID: 4ED5). (<b>C</b>) shows 2D representations of binding interactions of HUR. (<b>D</b>) The binding energy of inhibitors with RNA binding protein HUR along with interacting residues. Color code: green = carbon, white = hydrogen, blue = nitrogen, and red = oxygen.</p>
Full article ">Figure 4 Cont.
<p>(<b>A</b>,<b>B</b>) show 3D representations of the binding and surface view of inhibitor C11 with RNA binding protein HUR (PDBID: 4ED5). (<b>C</b>) shows 2D representations of binding interactions of HUR. (<b>D</b>) The binding energy of inhibitors with RNA binding protein HUR along with interacting residues. Color code: green = carbon, white = hydrogen, blue = nitrogen, and red = oxygen.</p>
Full article ">Figure 5
<p>(<b>A</b>,<b>B</b>) show 3D representations of the binding and surface view of inhibitor compound27 with RNA binding protein CELFI (PDBID: 3NMR). (<b>C</b>) shows 2D representations of binding interactions of CELFI. (<b>D</b>) The binding energy of inhibitors with RNA binding protein CELFI along with interacting residues. Color code: green = carbon, white = hydrogen, blue = nitrogen, and red = oxygen.</p>
Full article ">
32 pages, 3166 KiB  
Review
Review of Gold Nanoparticles: Synthesis, Properties, Shapes, Cellular Uptake, Targeting, Release Mechanisms and Applications in Drug Delivery and Therapy
by Joel Georgeous, Nour AlSawaftah, Waad H. Abuwatfa and Ghaleb A. Husseini
Pharmaceutics 2024, 16(10), 1332; https://doi.org/10.3390/pharmaceutics16101332 - 16 Oct 2024
Viewed by 454
Abstract
The remarkable versatility of gold nanoparticles (AuNPs) makes them innovative agents across various fields, including drug delivery, biosensing, catalysis, bioimaging, and vaccine development. This paper provides a detailed review of the important role of AuNPs in drug delivery and therapeutics. We begin by [...] Read more.
The remarkable versatility of gold nanoparticles (AuNPs) makes them innovative agents across various fields, including drug delivery, biosensing, catalysis, bioimaging, and vaccine development. This paper provides a detailed review of the important role of AuNPs in drug delivery and therapeutics. We begin by exploring traditional drug delivery systems (DDS), highlighting the role of nanoparticles in revolutionizing drug delivery techniques. We then describe the unique and intriguing properties of AuNPs that make them exceptional for drug delivery. Their shapes, functionalization, drug-loading bonds, targeting mechanisms, release mechanisms, therapeutic effects, and cellular uptake methods are discussed, along with relevant examples from the literature. Lastly, we present the drug delivery applications of AuNPs across various medical domains, including cancer, cardiovascular diseases, ocular diseases, and diabetes, with a focus on in vitro and in vivo cancer research. Full article
Show Figures

Figure 1

Figure 1
<p>History of the development of AuNPs [<a href="#B16-pharmaceutics-16-01332" class="html-bibr">16</a>].</p>
Full article ">Figure 2
<p>Different shapes of AuNPs.</p>
Full article ">Figure 3
<p>Top-down vs. bottom-up approach in the synthesis of AuNPs, adapted with changes from [<a href="#B44-pharmaceutics-16-01332" class="html-bibr">44</a>].</p>
Full article ">Figure 4
<p>Summary of the chemical and biological AuNPs synthesis methods.</p>
Full article ">Figure 5
<p>AuNPs’ surface modification.</p>
Full article ">Figure 6
<p>Benefits of AuNPs’ surface functionalization.</p>
Full article ">Figure 7
<p>How AuNPs with ligands attach to receptors on target cells in the body.</p>
Full article ">Figure 8
<p>Different routes taken by AuNPs to penetrate the skin.</p>
Full article ">
19 pages, 3781 KiB  
Article
Endophytic Penicillium oxalicum AUMC 14898 from Opuntia ficus-indica: A Novel Source of Tannic Acid Inhibiting Virulence and Quorum Sensing of Extensively Drug-Resistant Pseudomonas aeruginosa
by Hoda S. Nouh, Nessma A. El-Zawawy, Mohamed Halawa, Ebrahim M. Shalamesh, Sameh Samir Ali, Grażyna Korbecka-Glinka, Awad Y. Shala and Shimaa El-Sapagh
Int. J. Mol. Sci. 2024, 25(20), 11115; https://doi.org/10.3390/ijms252011115 - 16 Oct 2024
Viewed by 407
Abstract
Pseudomonas aeruginosa is a harmful pathogen that causes a variety of acute and chronic infections through quorum sensing (QS) mechanisms. The increasing resistance of this bacterium to numerous antibiotics has created a demand for new medications that specifically target QS. Endophytes can be [...] Read more.
Pseudomonas aeruginosa is a harmful pathogen that causes a variety of acute and chronic infections through quorum sensing (QS) mechanisms. The increasing resistance of this bacterium to numerous antibiotics has created a demand for new medications that specifically target QS. Endophytes can be the source of compounds with antibacterial properties. This research is the first to examine tannic acid (TA) produced by endophytic fungus as a potential biotherapeutic agent. A novel endophytic fungal isolate identified as Penicillium oxalicum was derived from the cladodes of Opuntia ficus-indica (L.). The species identification for this isolate was confirmed through sequencing of the internal transcribed spacer region. The metabolites from the culture of this isolate were extracted using ethyl acetate, then separated and characterized using chromatographic methods. This led to the acquisition of TA, a compound that shows strong anti-QS and excellent antibacterial effects against extensively drug-resistant P. aeruginosa strains. Furthermore, it was shown that treating P. aeruginosa with the obtained TA reduced the secretion of virulence factors controlled by QS in a dose-dependent manner, indicating that TA inhibited the QS characteristics of P. aeruginosa. Simultaneously, TA significantly inhibited the expression of genes associated with QS, including rhlR/I, lasR/I, and pqsR. In addition, in silico virtual molecular docking showed that TA could efficiently bind to QS receptor proteins. Our results showed that P. oxalicum could be a new source of TA for the treatment of infections caused by extensively drug-resistant P. aeruginosa. Full article
Show Figures

Figure 1

Figure 1
<p>Experimental design used in this study.</p>
Full article ">Figure 2
<p>Morphological and molecular identification of <span class="html-italic">Penicillium oxalicum</span> AUMC 14898: (<b>A</b>) Colonies grown on potato dextrose agar at 30 °C for 7days. (<b>B</b>) Conidiophores and conidia at 40× magnification. (<b>C</b>) Phylogenetic tree based on ITS sequences of 18S rDNA, including the fungal strain isolated in this study (<span class="html-italic">Penicillium oxalicum</span> AUMC14898, arrowed).</p>
Full article ">Figure 3
<p>HPLC chromatogram of purified compound (<b>A</b>) and standard compound (<b>B</b>).</p>
Full article ">Figure 4
<p>TEM images of <span class="html-italic">P. aeruginosa</span> PA-05 strain at 5000× magnification. (<b>A</b>) Untreated cells with intact cell membranes. (<b>B</b>) Treated cells with TA resulted in great morphological changes of the bacteria and lysis of cells (black arrows) in addition to development of vacuoles (red arrows).</p>
Full article ">Figure 5
<p>(<b>A</b>) Reduction of several virulence characteristics of <span class="html-italic">P. aeruginosa</span> PA-05 isolate by baicalein (BCL) and tannic acid (TA). (<b>B</b>) RT-qPCR analysis of various genes involved in quorum sensing (QS) of PA-05 isolate. The results are represented as ratios corresponding to the fold change of genes treated with tannic acid (TA) at sub-MIC value (75 µg/mL), as well as control (without treatment). For comparison of the experimental groups, two-way ANOVA was performed followed by Šídák’s multiple comparisons test. **** <span class="html-italic">p</span> &lt; 0.0001.</p>
Full article ">Figure 6
<p>Effect of tannic acid (TA) and baicalein (BCL) at sub-MIC concentrations on motility of <span class="html-italic">P. aeruginosa</span> strain PA-05. Swimming (<b>A</b>) and swarming (<b>B</b>). Bar graphs show the average percentages of triplicate results. Values are mean ± standard error. For comparison of the experimental groups, one-way ANOVA was performed followed by Tukey’s multiple comparison test. ** <span class="html-italic">p</span>-value &lt; 0.01 and **** <span class="html-italic">p</span> &lt; 0.0001.</p>
Full article ">Figure 7
<p>Molecular docking of tannic acid with LasR, RhlR and PqsR proteins represented in 3D and 2D conformations.</p>
Full article ">Figure 8
<p>A proposed mechanism of antibacterial and anti-QS actions of tannic acid against <span class="html-italic">P. aeruginosa</span>.</p>
Full article ">
13 pages, 5131 KiB  
Article
Mirror-Image RNA: A Right-Handed Z-Form RNA and Its Ligand Complex
by Yi Song, Shiyu Wang and Yan Xu
Molecules 2024, 29(20), 4900; https://doi.org/10.3390/molecules29204900 - 16 Oct 2024
Viewed by 246
Abstract
Until now, Z-form RNAs were believed to only adopt a left-handed double-helix structure. In this study, we describe the first observation of a right-handed Z-form RNA in NMR solution formed by L-nucleic acid RNA and present the first resolution of structure of the [...] Read more.
Until now, Z-form RNAs were believed to only adopt a left-handed double-helix structure. In this study, we describe the first observation of a right-handed Z-form RNA in NMR solution formed by L-nucleic acid RNA and present the first resolution of structure of the complex between a right-handed Z-form RNA and a curaxin ligand. These results provide a platform for the design of topology specific to Z-form-targeting compounds and are valuable for the development of new potent anticancer drugs. Full article
(This article belongs to the Section Chemical Biology)
Show Figures

Figure 1

Figure 1
<p>Synthetic scheme of <sup>F</sup>G and relative phosphoramidite compound.</p>
Full article ">Figure 2
<p>Enantiomers of A-form and Z-form RNA duplex structures. (<b>a</b>) CD spectra of the A–Z transition of L-RNA r(CGC<sup>F</sup>GCG)<sub>2</sub> at various NaClO<sub>4</sub> concentrations at 10 °C. A negative Cotton effect appears around 285 nm with increasing NaClO<sub>4</sub> concentration. (<b>b</b>) CD spectra of L-RNA r(CGCGCG)<sub>2</sub> at various NaClO<sub>4</sub> concentrations at 10 °C. (<b>c</b>) <sup>19</sup>F NMR spectra of L-RNA r(CGC<sup>F</sup>GCG)<sub>2</sub> in 5 mM Na-PO<sub>4</sub> buffer (pH 7.0) and various NaClO<sub>4</sub> concentrations. Red and black spots indicated Z-form and A-form RNA, respectively. (<b>d</b>) CD spectra of A-form RNA mirror enantiomers: left-handed L-RNA r(CGCGCG)<sub>2</sub> and right-handed D-RNA r(CGCGCG)<sub>2</sub> in presence of 5 mM Na-PO<sub>4</sub> buffer (pH 7.0) and 1.5 M NaClO<sub>4</sub> at 10 °C. (<b>e</b>) CD spectra of Z-form RNA mirror enantiomers: left-handed D-RNA r(CGC<sup>F</sup>GCG)<sub>2</sub> and right-handed L-RNA r(CGC<sup>F</sup>GCG)<sub>2</sub> (The words in red color label highlights the typical structure which is major studying target in this study) in presence of 5 mM Na-PO<sub>4</sub> buffer (pH 7.0) and 1.5 M NaClO<sub>4</sub> at 10 °C.</p>
Full article ">Figure 3
<p>Structural determination of right-handed Z-form RNA r(C<sub>1</sub>G<sub>2</sub>C<sub>3</sub><sup>F</sup>G<sub>4</sub>C<sub>5</sub>G<sub>6</sub>)<sub>2</sub>. (<b>a</b>,<b>c</b>,<b>d</b>) show wide-ranging connectivity paths (red lines) [C<sub>1</sub>(H6/H5′′)-G<sub>2</sub>(H8/H1′)-C<sub>3</sub>(H6/H5′′), C<sub>5</sub>(H6/H5′′)-G<sub>6</sub>(H8/H1′)] in the RNA strand of right-handed Z helices in a contour plot of the 2D-NOESY spectrum. (<b>a</b>) C<sub>1</sub>(H6/H5′′), C<sub>3</sub>(H6/H5′′), and C<sub>5</sub>(H6/H5′′) were found to upshift 2.85, 2.70, and 2.66 ppm (green arrows). Strong intra-residue cross-peaks of C<sub>1</sub>(H6/H5′′), C<sub>3</sub>(H6/H5′′), and C<sub>5</sub>(H6/H5′′) were observed. Additional anomeric–aromatic proton interactions were assigned as C<sub>1</sub>(H6/H5′), C<sub>5</sub>(H6/H5′), and G<sub>6</sub>H8/C<sub>5</sub>H5′, as marked by black arrows. (<b>b</b>) The cross-peaks of the imino proton of G<sub>2</sub> and amino proton of C<sub>5</sub>, as well as the imino proton of <sup>F</sup>G<sub>4</sub> and the amino proton of C<sub>3</sub> associated with G<sub>6</sub>H1/C<sub>1</sub>H1′, <sup>F</sup>G<sub>4</sub>H1/C<sub>3</sub>H5, and G<sub>2</sub>H1/<sup>F</sup>G<sub>4</sub>H1′ were observed (green lines). Intraresidue NOE cross-peaks of the imino and amino protons of G<sub>2</sub> and <sup>F</sup>G<sub>4</sub> are shown. (<b>c</b>) Strong H8–H1′ cross-peaks were observed (green arrows). C<sub>1</sub>(H6/H5), C<sub>3</sub>(H6/H5), C<sub>5</sub>(H6/H5), G<sub>6</sub>(H8/H3′), and C<sub>5</sub>H6/<sup>F</sup>G<sub>4</sub>H1′ are labeled by black arrows. (<b>d</b>) The Z-RNA structure-specific cross-peaks were observed between the C<sub>5</sub> amino proton and C<sub>1</sub>H5, as well as between the C<sub>1</sub> amino proton and C<sub>5</sub>H5 from inter-stranded interactions. These signals are linked to C<sub>1</sub>(H6/H5) and C<sub>5</sub>(H6/H5) in (<b>c</b>) by red lines.</p>
Full article ">Figure 4
<p>The structural model of right-handed Z-form RNA r(C<sub>1</sub>G<sub>2</sub>C<sub>3</sub><sup>F</sup>G<sub>4</sub>C<sub>5</sub>G<sub>6</sub>)<sub>2</sub>. (<b>a</b>) Structural right-handed Z-form RNA r(CGC<sup>F</sup>GCG)<sub>2</sub> viewed from the major groove. (<b>b</b>) rG with <span class="html-italic">syn</span>conformation and rC with <span class="html-italic">anti</span>-conformation form Watson–Crick base pairs through three hydrogen bonds in Z-form RNA. (<b>c</b>) The stacking pattern within the GpC step in Z-RNA as viewed along the helix z-axis, showing only intra- but not inter-strand stacking. (<b>d</b>) An extended model of the right-handed Z-form RNA helix from Z-form RNA r(CGC<sup>F</sup>GCG)<sub>2</sub> visualized in side (up) and top (bottom) views to show their base pair locations and groove architecture, in which white represent base pairs and orange indicates phosphate–ribose backbones. The duplex diameter is shown, and the major or minor groove is indicated.</p>
Full article ">Figure 5
<p>Study of the CBL0137 ligand binding to Z-form RNA. (<b>a</b>) The structure of CBL0137, comprising a carbazole moiety with a positive charged N-side chain. (<b>b</b>) The CD titration of Z-form RNA r(CGC<sup>F</sup>GCG)<sub>2</sub> with increasing concentrations of CBL0137 at 10 °C in 5 mM Na-PO<sub>4</sub> buffer (pH 7.0). The ratio of CBL0137 to RNA is indicated at the top. (c-f) The overlay of NOE spectra. The signals in red and blue from the complex of CBL0137 and RNA. The signals in black from Z-form RNA as a control. (<b>c</b>–<b>e</b>) display strong intermolecular NOEs between RNA and CBL0137. C<sub>5</sub>H6/CH<sub>2</sub>(9), C<sub>3</sub>H6/CH<sub>2</sub>(9), G<sub>2</sub>H1′/CH<sub>2</sub>(9), <sup>F</sup>G<sub>4</sub>H1′/CH<sub>2</sub>(9), C<sub>5</sub>H5/CH<sub>2</sub>(9), and C<sub>3</sub>H6/2,7H are marked by black arrows. The signals derived from CH<sub>2</sub>(9) or C<sub>3</sub>H6 are connected by green lines. (<b>f</b>) The black arrows indicate the NOEs between amino protons C<sub>5</sub>NH2<sub>1</sub> and the aromatic protons (1H, 8H) of CBL0137, and the NOEs between amino protons <sup>F</sup>G<sub>4</sub>NH2<sub>2</sub> and the aromatic protons (4H, 5H) of CBL0137.</p>
Full article ">Figure 6
<p>The molecular dynamic model of CBL0137 ligand binding to Z-form right-hand RNA. (<b>a</b>) Solution structure of the CBL0137-RNA complex with cartoon representation. CBL0137 (in green CPK representation) symmetrically binding with Z-form RNA (orange) in a 2:1 molecular ratio. (<b>b</b>) An expanded view of CBL0137 (in green stick representation) and base pairs indicates the π-π stacking formation between the carbazole moiety and base pairs of G<sub>2</sub>:C<sub>5</sub> and C<sub>3</sub>:<sup>F</sup>G<sub>4</sub> as pink dashed lines connected by each aromatic ring’s center. (<b>c</b>) A side view showing the close proximity between the cationic N-side chain (shown as a blue sphere) of CBL0137 and the anionic phosphate group (shown as a red sphere) of C<sub>3</sub> (~2.862 Å in distance). (<b>d</b>) The solvent hydrophobicity representation of the surface of RNA (white) shows CBL0137 (in green stick representation) positioned in the cleft pocket.</p>
Full article ">Scheme 1
<p>Illustration of mirror-image RNA. The left column displays a right-handed helix A-form D-RNA and its mirror-image, a left-handed A-form L-RNA consisting of L-nucleic acids. The right column shows the left-handed helix Z-form D-RNA and its mirror-image with a right-handed Z-form L-RNA consisting of L-nucleic acids (The words in red highlight the typical structure, which is the main focus of this study).</p>
Full article ">
17 pages, 5286 KiB  
Article
Synthesis, Urease Inhibition, Molecular Docking, and Optical Analysis of a Symmetrical Schiff Base and Its Selected Metal Complexes
by Samuel Bonne, Muhammad Saleem, Muhammad Hanif, Joseph Najjar, Salahuddin Khan, Muhammad Zeeshan, Tehreem Tahir, Anser Ali, Changrui Lu and Ting Chen
Molecules 2024, 29(20), 4899; https://doi.org/10.3390/molecules29204899 - 16 Oct 2024
Viewed by 240
Abstract
Designing and developing small organic molecules for use as urease inhibitors is challenging due to the need for ecosystem sustainability and the requirement to prevent health risks related to the human stomach and urinary tract. Moreover, imaging analysis is widely utilized for tracking [...] Read more.
Designing and developing small organic molecules for use as urease inhibitors is challenging due to the need for ecosystem sustainability and the requirement to prevent health risks related to the human stomach and urinary tract. Moreover, imaging analysis is widely utilized for tracking infections in intracellular and in vivo systems, which requires drug molecules with emissive potential, specifically in the low-energy region. This study comprises the synthesis of a Schiff base ligand and its selected transition metals to evaluate their UV/fluorescence properties, inhibitory activity against urease, and molecular docking. Screening of the symmetrical cage-like ligand and its metal complexes with various eco-friendly transition metals revealed significant urease inhibition potential. The IC50 value of the ligand for urease inhibition was 21.80 ± 1.88 µM, comparable to that of thiourea. Notably, upon coordination with transition metals, the ligand–nickel and ligand–copper complexes exhibited even greater potency than the reference compound, with IC50 values of 11.8 ± 1.14 and 9.31 ± 1.31 µM, respectively. The ligand–cobalt complex exhibited an enzyme inhibitory potential comparable with thiourea, while the zinc and iron complexes demonstrated the least activity, which might be due to weaker interactions with the investigated protein. Meanwhile, all the metal complexes demonstrated a pronounced optical response, which could be utilized for fluorescence-guided targeted drug delivery applications in the future. Molecular docking analysis and IC50 values from in vitro urease inhibition screening showed a trend of increasing activity from compounds 7d to 7c to 7b. Enzyme kinetics studies using the Lineweaver–Burk plot indicated mixed-type inhibition against 7c and non-competitive inhibition against 7d. Full article
Show Figures

Figure 1

Figure 1
<p>The absorption spectra of the ligand and its corresponding metal complexes.</p>
Full article ">Figure 2
<p>Chemical structure of the ligand’s complex tautomeric forms and their Huckel structures; (<b>a</b>,<b>d</b>) are chemical structures of two tautomers; (<b>b</b>,<b>e</b>) are HOMO; and (<b>c</b>,<b>f</b>) are the LUMO Huckel representations.</p>
Full article ">Figure 3
<p>Fluorescence spectra related to the ligand and its respective complexes.</p>
Full article ">Figure 4
<p>(<b>a</b>) Lineweaver–Burk plots showing urease inhibition using urea as substrate with concentrations of 3.12, 6.25, 12.5, 25, 50, and 100 mM and inhibitor as compound <b>7c</b> with concentrations of 0, 6.25, 12.5, 25, and 50 µM. Insets represent graphical representations of slope and intercept vs. inhibitor concentration (inset (<b>b</b>,<b>c</b>)).</p>
Full article ">Figure 5
<p>(<b>a</b>) Lineweaver–Burk plots showing urease inhibition when compound (<b>7d</b>) is present with concentrations of 0, 6.25, 12.5, 25, and 50 µM with the urea as the substrate with concentrations of 3.12, 6.25, 12.5, 25, 50, and 100 mM. (<b>b</b>) Representation of the graph of intercept verses <b>7d</b> concentrations.</p>
Full article ">Figure 6
<p>(<b>a</b>) Docked complex of the objective Jack Bean urease protein (PDB: 3LA4) with compounds <b>6</b> and <b>7a</b>–<b>e</b>; (<b>b</b>) 3D representation showing the key interacting groups between Jack Bean urease (PDB: 3LA4) and compound <b>6</b>; (<b>c</b>) <b>7a</b>; (<b>d</b>) <b>7b</b>; (<b>e</b>) <b>7c</b>; (<b>f</b>) <b>7d</b>; (<b>g</b>) <b>7e</b>.</p>
Full article ">Figure 6 Cont.
<p>(<b>a</b>) Docked complex of the objective Jack Bean urease protein (PDB: 3LA4) with compounds <b>6</b> and <b>7a</b>–<b>e</b>; (<b>b</b>) 3D representation showing the key interacting groups between Jack Bean urease (PDB: 3LA4) and compound <b>6</b>; (<b>c</b>) <b>7a</b>; (<b>d</b>) <b>7b</b>; (<b>e</b>) <b>7c</b>; (<b>f</b>) <b>7d</b>; (<b>g</b>) <b>7e</b>.</p>
Full article ">Figure 6 Cont.
<p>(<b>a</b>) Docked complex of the objective Jack Bean urease protein (PDB: 3LA4) with compounds <b>6</b> and <b>7a</b>–<b>e</b>; (<b>b</b>) 3D representation showing the key interacting groups between Jack Bean urease (PDB: 3LA4) and compound <b>6</b>; (<b>c</b>) <b>7a</b>; (<b>d</b>) <b>7b</b>; (<b>e</b>) <b>7c</b>; (<b>f</b>) <b>7d</b>; (<b>g</b>) <b>7e</b>.</p>
Full article ">Scheme 1
<p>Mechanism of urea hydrolysis by urease.</p>
Full article ">Scheme 2
<p>Synthetic pathway adopted for the accomplishment of target molecules: (I) C<sub>2</sub>H<sub>5</sub>OH; H<sub>2</sub>SO<sub>4</sub>; reflux; overnight. (II) N<sub>2</sub>H<sub>4</sub>.H<sub>2</sub>O; C<sub>2</sub>H<sub>5</sub>OH; reflux; overnight. (III) Aminoisocyanate; C<sub>2</sub>H<sub>5</sub>OH; reflux; 4–5 h. (IV) Pyridine-2,6-dicarbaldehyde; THF; reflux; overnight. (V) In situ; reflux; 12–14 h. (IV) Metal salt solution; C<sub>2</sub>H<sub>5</sub>OH; reflux; 3–4 h; <b>7a</b> [ligand–Fe(II)]; <b>7b</b> [ligand–Co(II)]; <b>7c</b> [ligand–Ni(II)]; <b>7d</b> [ligand–Cu(II)]; <b>7e</b> [ligand–Zn(II)].</p>
Full article ">
14 pages, 2832 KiB  
Article
Multi-Omics Analysis Identified Drug Repurposing Targets for Chronic Obstructive Pulmonary Disease
by Fang Wang and Carlos A. Barrero
Int. J. Mol. Sci. 2024, 25(20), 11106; https://doi.org/10.3390/ijms252011106 - 16 Oct 2024
Viewed by 206
Abstract
Despite recent advances in chronic obstructive pulmonary disease (COPD) research, few studies have identified the potential therapeutic targets systematically by integrating multiple-omics datasets. This project aimed to develop a systems biology pipeline to identify biologically relevant genes and potential therapeutic targets that could [...] Read more.
Despite recent advances in chronic obstructive pulmonary disease (COPD) research, few studies have identified the potential therapeutic targets systematically by integrating multiple-omics datasets. This project aimed to develop a systems biology pipeline to identify biologically relevant genes and potential therapeutic targets that could be exploited to discover novel COPD treatments via drug repurposing or de novo drug discovery. A computational method was implemented by integrating multi-omics COPD data from unpaired human samples of more than half a million subjects. The outcomes from genome, transcriptome, proteome, and metabolome COPD studies were included, followed by an in silico interactome and drug-target information analysis. The potential candidate genes were ranked by a distance-based network computational model. Ninety-two genes were identified as COPD signature genes based on their overall proximity to signature genes on all omics levels. They are genes encoding proteins involved in extracellular matrix structural constituent, collagen binding, protease binding, actin-binding proteins, and other functions. Among them, 70 signature genes were determined to be druggable targets. The in silico validation identified that the knockout or over-expression of SPP1, APOA1, CTSD, TIMP1, RXFP1, and SMAD3 genes may drive the cell transcriptomics to a status similar to or contrasting with COPD. While some genes identified in our pipeline have been previously associated with COPD pathology, others represent possible new targets for COPD therapy development. In conclusion, we have identified promising therapeutic targets for COPD. This hypothesis-generating pipeline was supported by unbiased information from available omics datasets and took into consideration disease relevance and development feasibility. Full article
Show Figures

Figure 1

Figure 1
<p>(<b>A</b>) Genes consistently up-regulated (gene name in red) or down-regulated (gene name in blue) across COPD stages. Each circle represents the number of DEGs identified in individual GOLD levels. (<b>B</b>) The numbers of DEGs identified across different stages of COPD. The flows between each GOLD column represent the status change of genes in the down-regulated (blue), up-regulated (red), and not differentially expressed (grey) categories. DEG: Differentially expressed genes.</p>
Full article ">Figure 2
<p>(<b>A</b>) DEGs between healthy subjects and GOLD 4 COPD patients. Dotted lines represent the DEG cutoffs of adjusted <span class="html-italic">p</span> &lt; 0.05 and |log2 fold change| ≥ 1. Significantly up-regulated and down-regulated genes are shown as red and blue dots. (<b>B</b>) Top 20 over-represented biological process pathways in GOLD 4 patients. Color indicates the adjusted <span class="html-italic">p</span> from the GO enrichment analysis, and <span class="html-italic">x</span>-axis represents the count of the measured genes in the pathway.</p>
Full article ">Figure 3
<p>Venn diagram of the number of signature genes at each omics level, with overlapping signature genes and their corresponding <span class="html-italic">p</span> and fold change. The names of the overlapping up-regulated and down-regulated genes are shown in red and blue, respectively. <span class="html-italic">p</span>_min: The <span class="html-italic">p</span> of the most significant variant implicating the gene is reported in the table based on its association with the lung function. In the proteomics data, nominal <span class="html-italic">p</span> are provided due to the lack of raw data.</p>
Full article ">Figure 4
<p>(<b>A</b>) Illustration of distances between genes in the network. The grey circle is the candidate gene, and the white circles are the additional genes in the network. Black lines represent physical or functional interactions between the genes. Blue lines were added to denote candidate genes’ distances d from the network’s genes. (<b>B</b>) Shortest distances of a candidate gene from all omics signature genes in the protein-protein interaction network. Interacting proteins are linked with black lines. The shortest distances of a candidate gene (gray circle) to signature genes from the transcriptomics (red circles), genomics (green circles), and proteomics signature genes (blue circles) and proteins linked to COPD-associated metabolomics (yellow circles) are 1, 1, and 2 respectively. (<b>C</b>) Ninety-two prioritized candidate genes with close proximity to all omics levels. Numbers represent the shortest distance of the candidate gene from the omics level on each row. (<b>D</b>) Top 20 significantly enriched pathways for the 92 COPD signature genes. Color indicates the adjusted <span class="html-italic">p</span> from the GO enrichment analysis, and <span class="html-italic">x</span>-axis represents the count of the measured genes in the pathway.</p>
Full article ">Figure 5
<p>(<b>A</b>) Druggable gene targets (blue section of the pie chart) among the 92 COPD signature genes and their druggable gene tiers. The grey section of the pie chart represents genes that are not classified as druggable or have unknown druggability. (<b>B</b>) COPD signature genes with high connectivity scores through <span class="html-italic">in silico</span> perturbation evaluation based on gene knock-down (red bar) or gene over-expression (green bar) treatment in cell line experiments. Dashed lines represent high connectivity score of 90% or −90%. A549 is a cell line of human adenocarcinoma alveolar basal epithelial cells. HCC515 is a cell line of human non-small-cell lung adenocarcinoma.</p>
Full article ">
17 pages, 13801 KiB  
Review
Innovative Use of Nanomaterials in Treating Retinopathy of Prematurity
by Kevin Y. Wu, Xingao C. Wang, Maude Anderson and Simon D. Tran
Pharmaceuticals 2024, 17(10), 1377; https://doi.org/10.3390/ph17101377 - 16 Oct 2024
Viewed by 254
Abstract
Background/Objectives: Retinopathy of prematurity (ROP) is a severe condition primarily affecting premature infants with a gestational age (GA) of 30 weeks or less and a birth weight (BW) of 1500 g or less. The objective of this review is to examine the risk [...] Read more.
Background/Objectives: Retinopathy of prematurity (ROP) is a severe condition primarily affecting premature infants with a gestational age (GA) of 30 weeks or less and a birth weight (BW) of 1500 g or less. The objective of this review is to examine the risk factors, pathogenesis, and current treatments for ROP, such as cryotherapy, laser photocoagulation, and anti-VEGF therapy, while exploring the limitations of these approaches. Additionally, this review evaluates emerging nanotherapeutic strategies to address these challenges, aiming to improve ROP management. Methods: A comprehensive literature review was conducted to gather data on the pathogenesis, traditional treatment methods, and novel nanotherapeutic approaches for ROP. This included assessing the efficacy and safety profiles of cryotherapy, laser treatment, anti-VEGF therapy, and nanotherapies currently under investigation. Results: Traditional treatments, while effective in reducing disease progression, exhibit limitations, including long-term complications, tissue damage, and systemic side effects. Nanotherapeutic approaches, on the other hand, have shown potential in offering targeted drug delivery with reduced systemic toxicity, improved ocular drug penetration, and sustained release, which could decrease the frequency of treatments and enhance therapeutic outcomes. Conclusions: Nanotherapies represent a promising advancement in ROP treatment, offering safer and more effective management strategies. These innovations could address the limitations of traditional therapies, reducing complications and improving outcomes for premature infants affected by ROP. Further research is needed to confirm their efficacy and safety in clinical practice. Full article
Show Figures

Figure 1

Figure 1
<p>This fundus photograph illustrates Stage 1 disease, where the boundary between the central, vascularized retina, and the peripheral, avascular retina is clearly visible. Gilbert C et al. (1998, updated 2007). Prevention of childhood blindness teaching set. London: International Centre for Eye Health <a href="http://www.iceh.org.uk" target="_blank">www.iceh.org.uk</a>, (accessed on 5 May 2024) licensed under Creative Commons CC BY-NC 2.0.</p>
Full article ">Figure 2
<p>Stage 3 ‘plus’ disease is depicted with extensive fibrovascular proliferation and prominently dilated, tortuous retinal blood vessels. Gilbert C et al. (1998, updated 2007). Prevention of childhood blindness teaching set. London: International Centre for Eye Health <a href="http://www.iceh.org.uk" target="_blank">www.iceh.org.uk</a>, (accessed on 5 May 2024) licensed under Creative Commons CC BY-NC 2.0.</p>
Full article ">Figure 3
<p>A summary of the characteristics and properties of important nano-based drug delivery systems used in ocular drug delivery.</p>
Full article ">Figure 4
<p>Lipid nanoparticles in delivery of therapeutics. (<b>A</b>) Plain lipid NP, where the core can be of liquid, solid crystalline, or lyotropic liquid form. (<b>B</b>) Lipid NP with surface modifications for enhanced delivery of therapeutics through receptor-mediated targeting. (<b>C</b>) Lipid NPs containing siRNA with targeting properties for efficient delivery of therapeutics. Disclaimer: Reprinted with permission from ScienceDirect, Copyright 2024, under a Creative Common License, CC BY 4.0, <a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a> (accessed on 5 May 2024), Advanced Drug Delivery Reviews, Vol 203, Yaghmur et al., “Lipid nanoparticles for targeted delivery of anticancer therapeutics: Recent advances in development of siRNA and lipoprotein-mimicking nanocarriers”, no changes made [<a href="#B37-pharmaceuticals-17-01377" class="html-bibr">37</a>].</p>
Full article ">Figure 5
<p>The structural layers of the retina and their respective contents.</p>
Full article ">Figure 6
<p>(<b>A</b>,<b>B</b>) Microglia-derived exosomes benefit visual function, whilst reducing retinal photoreceptor apoptosis in OIR mice. (<b>A</b>) Measurements of scotopic electroretinography (ERG), maximal response, OP, and photopic ERG in injected group, control group, and normal group. The b-wave amplitude of scotopic and photopic ERG, a-, and b-wave of maximal response, and OP P3 amplitude were compared amongst the 3 groups. (<b>B</b>) Images of retinal cryosections with TUNEL (Red) staining of microglia-derived exosomes and control groups. The number of TUNEL-positive nuclei are shown in red and the arrows indicate the apoptosis nucleus. Scale bars, 50 mm. All data are expressed as the mean ± S.D., n = 3. * <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. Disclamer: Reprinted with permission from ScienceDirect, Copyright 2024, under a Creative Common License, CC BY-NC-ND 4.0, <a href="https://creativecommons.org/licenses/by-nc-nd/4.0/" target="_blank">https://creativecommons.org/licenses/by-nc-nd/4.0/</a> (accessed on 5 May 2024), Molecular Therapy Nucleic Acids, Vol 16, Xu et al., “Exosomes from Microglia Attenuate Photoreceptor Injury and Neovascularization in an Animal Model of Retinopathy of Prematurity”, <a href="https://www.sciencedirect.com/science/article/pii/S2162253119301246" target="_blank">https://www.sciencedirect.com/science/article/pii/S2162253119301246</a> (accessed on 5 May 2024), no changes made [<a href="#B58-pharmaceuticals-17-01377" class="html-bibr">58</a>].</p>
Full article ">
20 pages, 2552 KiB  
Review
Advances and Functional Integration of Hydrogel Composites as Drug Delivery Systems in Contemporary Dentistry
by Dragos Nicolae Fratila, Dragos Ioan Virvescu, Ionut Luchian, Monica Hancianu, Elena Raluca Baciu, Oana Butnaru and Dana Gabriela Budala
Gels 2024, 10(10), 661; https://doi.org/10.3390/gels10100661 - 16 Oct 2024
Viewed by 463
Abstract
This study explores the recent advances of and functional insights into hydrogel composites, materials that have gained significant attention for their versatile applications across various fields, including contemporary dentistry. Hydrogels, known for their high water content and biocompatibility, are inherently soft but often [...] Read more.
This study explores the recent advances of and functional insights into hydrogel composites, materials that have gained significant attention for their versatile applications across various fields, including contemporary dentistry. Hydrogels, known for their high water content and biocompatibility, are inherently soft but often limited by mechanical fragility. Key areas of focus include the customization of hydrogel composites for biomedical applications, such as drug delivery systems, wound dressings, and tissue engineering scaffolds, where improved mechanical properties and bioactivity are critical. In dentistry, hydrogels are utilized for drug delivery systems targeting oral diseases, dental adhesives, and periodontal therapies due to their ability to adhere to the mucosa, provide localized treatment, and support tissue regeneration. Their unique properties, such as mucoadhesion, controlled drug release, and stimuli responsiveness, make them ideal candidates for treating oral conditions. This review highlights both experimental breakthroughs and theoretical insights into the structure–property relationships within hydrogel composites, aiming to guide future developments in the design and application of these multifunctional materials in dentistry. Ultimately, hydrogel composites represent a promising frontier for advancing materials science with far-reaching implications in healthcare, environmental technology, and beyond. Full article
Show Figures

Figure 1

Figure 1
<p>Potential uses of hydrogels in the dental field.</p>
Full article ">Figure 2
<p>Hydrogel characteristics and classification (with IPN—interpenetrating polymer network).</p>
Full article ">Figure 3
<p>The action mechanisms of a smart hydrogel.</p>
Full article ">Figure 4
<p>Structures of hydrogels and nanogels.</p>
Full article ">Figure 5
<p>The pathway of a drug delivery system to treat periodontal disease.</p>
Full article ">
18 pages, 5253 KiB  
Article
Targeted PHA Microsphere-Loaded Triple-Drug System with Sustained Drug Release for Synergistic Chemotherapy and Gene Therapy
by Shuo Wang, Chao Zhang, Huandi Liu, Xueyu Fan, Shuangqing Fu, Wei Li and Honglei Zhang
Nanomaterials 2024, 14(20), 1657; https://doi.org/10.3390/nano14201657 (registering DOI) - 16 Oct 2024
Viewed by 282
Abstract
The combination of paclitaxel (PTX) with other chemotherapy drugs (e.g., gemcitabine, GEM) or genetic drugs (e.g., siRNA) has been shown to enhance therapeutic efficacy against tumors, reduce individual drug dosages, and prevent drug resistance associated with single-drug treatments. However, the varying solubility of [...] Read more.
The combination of paclitaxel (PTX) with other chemotherapy drugs (e.g., gemcitabine, GEM) or genetic drugs (e.g., siRNA) has been shown to enhance therapeutic efficacy against tumors, reduce individual drug dosages, and prevent drug resistance associated with single-drug treatments. However, the varying solubility of chemotherapy drugs and genetic drugs presents a challenge in co-delivering these agents. In this study, nanoparticles loaded with PTX were prepared using the biodegradable polymer material poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx). These nanoparticles were surface-modified with target proteins (Affibody molecules) and RALA cationic peptides to create core-shell structured microspheres with targeted and cationic functionalization. A three-drug co-delivery system (PTX@PHBHHx-ARP/siRNAGEM) were developed by electrostatically adsorbing siRNA chains containing GEM onto the microsphere surface. The encapsulation efficiency of PTX in the nanodrug was found to be 81.02%, with a drug loading of 5.09%. The chemogene adsorption capacity of siRNAGEM was determined to be 97.3%. Morphological and size characterization of the nanodrug revealed that PTX@PHBHHx-ARP/siRNAGEM is a rough-surfaced microsphere with a particle size of approximately 150 nm. This nanodrug exhibited targeting capabilities toward BT474 cells with HER2 overexpression while showing limited targeting ability toward MCF-7 cells with low HER2 expression. Results from the MTT assay demonstrated that PTX@PHBHHx-ARP/siRNAGEM exhibits high cytotoxicity and excellent combination therapy efficacy compared to physically mixed PTX/GEM/siRNA. Additionally, Western blot analysis confirmed that siRNA-mediated reduction of Bcl-2 expression significantly enhanced cell apoptosis mediated by PTX or GEM in tumor cells, thereby increasing cell sensitivity to PTX and GEM. This study presents a novel targeted nanosystem for the co-delivery of chemotherapy drugs and genetic drugs. Full article
Show Figures

Figure 1

Figure 1
<p>SEM (<b>a</b>), TEM (<b>b</b>), and FTIR (<b>c</b>) analysis.</p>
Full article ">Figure 2
<p>Release curves of PTX and siRNA<sub>GEM</sub> in PTX@PHBHHx-ARP/siRNA<sub>GEM</sub>. (<b>a</b>) The PTX drug release curve. (<b>b</b>) The release curve of siRNA<sub>GEM</sub>.</p>
Full article ">Figure 3
<p>Drug uptake by BT474 and MCF-7 cells. (<b>a</b>) CLSM analysis of BT474 cells treated with PTX@PHBHHx-ARP/siRNA<sub>GEM</sub> for different times. Panel (<b>b</b>) CLSM analysis of MCF-7 cells treated with PTX@PHBHHx-ARP/siRNA<sub>GEM</sub> for different times. Scale bar: 20 μm.</p>
Full article ">Figure 4
<p>Survival of BT474 and MCF-7 cells treated with PTX, GEM, physical mixture of PTX/GEM/siRNA and PTX@PHBHHx-ARP/siRNA<sub>GEM</sub>. (<b>a</b>) The survival rates of the two cell types after 48 h incubation with PTX monotherapy. (<b>b</b>) The survival rates of the two cell types after 48 h incubation with GEM monotherapy. (<b>c</b>) The survival rates of the two cell types after 48 h of incubation with the physical mixture of PTX/GEM/siRNA. (<b>d</b>) The survival rates of the two cell types after 48 h incubation with PTX@PHBHHx-ARP/siRNA<sub>GEM</sub>.</p>
Full article ">Figure 5
<p>Western blot of Bcl-2 in (<b>a</b>) BT474 cells and (<b>b</b>) MCF-7 cells treated with free PTX, GEM, PTX/GEM/siRNA, and PTX@PHBHHx-ARP/siRNA<sub>GEM</sub>, respectively. (<b>c</b>) Significance analysis of Bcl-2 in BT474 cells. (<b>d</b>) Significance analysis of Bcl-2 in MCF-7 cells. Statistical analysis: * <span class="html-italic">p</span> &lt; 0.05, **** <span class="html-italic">p</span> &lt; 0.0001 and ns (No significant difference).</p>
Full article ">Figure 6
<p>Scatter plots of apoptosis in (<b>a</b>) MCF-7 cells and (<b>b</b>) BT474 cells treated with free PTX, GEM, PTX/GEM/siRNA, and PTX@PHBHHx-ARP/siRNA<sub>GEM</sub>, respectively.</p>
Full article ">Scheme 1
<p>The assembly process of PTX@PHBHHx-ARP/siRNA<sub>GEM</sub> and their synergistic cancer therapy.</p>
Full article ">
30 pages, 5645 KiB  
Article
Exploring the Antidiabetic Potential of Salvia officinalis Using Network Pharmacology, Molecular Docking and ADME/Drug-Likeness Predictions
by Chimaobi J. Ononamadu and Veronique Seidel
Plants 2024, 13(20), 2892; https://doi.org/10.3390/plants13202892 (registering DOI) - 16 Oct 2024
Viewed by 323
Abstract
A combination of network pharmacology, molecular docking and ADME/drug-likeness predictions was employed to explore the potential of Salvia officinalis compounds to interact with key targets involved in the pathogenesis of T2DM. These were predicted using the SwissTargetPrediction, Similarity Ensemble Approach and BindingDB databases. [...] Read more.
A combination of network pharmacology, molecular docking and ADME/drug-likeness predictions was employed to explore the potential of Salvia officinalis compounds to interact with key targets involved in the pathogenesis of T2DM. These were predicted using the SwissTargetPrediction, Similarity Ensemble Approach and BindingDB databases. Networks were constructed using the STRING online tool and Cytoscape (v.3.9.1) software. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis and molecular docking were performed using DAVID, SHINEGO 0.77 and MOE suite, respectively. ADME/drug-likeness parameters were computed using SwissADME and Molsoft L.L.C. The top-ranking targets were CTNNB1, JUN, ESR1, RELA, NR3C1, CREB1, PPARG, PTGS2, CYP3A4, MMP9, UGT2B7, CYP2C19, SLCO1B1, AR, CYP19A1, PARP1, CYP1A2, CYP1B1, HSD17B1, and GSK3B. Apigenin, caffeic acid, oleanolic acid, rosmarinic acid, hispidulin, and salvianolic acid B showed the highest degree of connections in the compound-target network. Gene enrichment analysis identified pathways involved in insulin resistance, adherens junctions, metabolic processes, IL-17, TNF-α, cAMP, relaxin, and AGE-RAGE in diabetic complications. Rosmarinic acid, caffeic acid, and salvianolic acid B showed the most promising interactions with PTGS2, DPP4, AMY1A, PTB1B, PPARG, GSK3B and RELA. Overall, this study enhances understanding of the antidiabetic activity of S. officinalis and provides further insights for future drug discovery purposes. Full article
(This article belongs to the Section Phytochemistry)
Show Figures

Figure 1

Figure 1
<p>Venn diagram depiction of the biological targets common (intersection) to <span class="html-italic">S. officinalis</span> compounds and T2DM.</p>
Full article ">Figure 2
<p>(<b>A</b>) Protein–Protein Interaction (PPI) network and (<b>B</b>) top-ranked 20 (Hub Genes) T2DM targets of <span class="html-italic">S. officinalis</span> compounds. The sizes of the nodes in (<b>A</b>) are proportional to the magnitude of the degree.</p>
Full article ">Figure 3
<p>Compound-target network. The sizes of the nodes are proportional to the magnitude of the degree. Red circles = T2DM targets and blue circles = <span class="html-italic">S. officinalis</span> compounds.</p>
Full article ">Figure 4
<p>Top-ranked 10 (core) <span class="html-italic">S. officinalis</span> compounds predicted to interact with T2DM targets.</p>
Full article ">Figure 5
<p>Target-pathway (TP) network of enriched T2DM-related KEGG pathways for the identified targets. Orange = KEGG Pathways, Green = Targets.</p>
Full article ">Figure 6
<p>GO and KEGG pathway analysis showing the top-ranked enrichments of (<b>A</b>) molecular function and (<b>B</b>) biological process for the common targets/genes associated with <span class="html-italic">S. officinalis</span> compounds and T2DM.</p>
Full article ">Figure 7
<p>GO and KEGG pathway analysis showing the top-ranked enrichments of (<b>A</b>) cellular compartment (<b>B</b>) KEGG pathways for the common targets/genes associated with <span class="html-italic">S. officinalis</span> compounds and T2DM.</p>
Full article ">Figure 8
<p>Docked pose of rosmarinic acid with (<b>A</b>) PGTS2 (<b>B</b>) AMY1A and (<b>C</b>) DDP4.</p>
Full article ">Figure 9
<p>Docked pose of salvianolic acid B acid with (<b>A</b>) PPARG, (<b>B</b>) GSK3B and (<b>C</b>) RELA.</p>
Full article ">Figure 10
<p>Docked pose of caffeic acid with PTP1B.</p>
Full article ">
17 pages, 731 KiB  
Review
Targeted Drug Delivery in Periorbital Non-Melanocytic Skin Malignancies
by Benedetta Tirone, Anna Scarabosio, Pier Luigi Surico, Pier Camillo Parodi, Fabiana D’Esposito, Alessandro Avitabile, Caterina Foti, Caterina Gagliano and Marco Zeppieri
Bioengineering 2024, 11(10), 1029; https://doi.org/10.3390/bioengineering11101029 (registering DOI) - 15 Oct 2024
Viewed by 445
Abstract
Targeted drug delivery has emerged as a transformative approach in the treatment of periorbital skin malignancies, offering the potential for enhanced efficacy and reduced side effects compared to traditional therapies. This review provides a comprehensive overview of targeted therapies in the context of [...] Read more.
Targeted drug delivery has emerged as a transformative approach in the treatment of periorbital skin malignancies, offering the potential for enhanced efficacy and reduced side effects compared to traditional therapies. This review provides a comprehensive overview of targeted therapies in the context of periorbital malignancies, including basal cell carcinoma, squamous cell carcinoma, sebaceous gland carcinoma, and Merkel cell carcinoma. It explores the mechanisms of action for various targeted therapies, such as monoclonal antibodies, small molecule inhibitors, and immunotherapies, and their applications in treating these malignancies. Additionally, this review addresses the management of ocular and periocular side effects associated with these therapies, emphasizing the importance of a multidisciplinary approach to minimize impact and ensure patient adherence. By integrating current findings and discussing emerging trends, this review aims to highlight the advancements in targeted drug delivery and its potential to improve treatment outcomes and quality of life for patients with periorbital skin malignancies. Full article
(This article belongs to the Special Issue Recent Advances and Trends in Ophthalmic Diseases Treatment)
Show Figures

Figure 1

Figure 1
<p>Prevalence of non-melanocytic skin cancers.</p>
Full article ">Figure 2
<p>Checkpoint inhibitors’ mechanisms of action.</p>
Full article ">Figure 3
<p>Erlotinib is a small-molecule inhibitor that targets the epidermal growth factor receptor (EGFR), a transmembrane tyrosine kinase receptor involved in cell proliferation and survival. It works by competitively inhibiting the ATP-binding site of EGFR’s tyrosine kinase domain. By blocking EGFR activation, erlotinib prevents the downstream signaling pathways (such as the RAS-RAF-MEK-ERK and PI3K-AKT pathways) that promote tumor cell growth, survival, and proliferation.</p>
Full article ">Figure 4
<p>Simplified diagram summarizing the main molecules used for the various non-melanocytic periocular tumors.</p>
Full article ">
22 pages, 19388 KiB  
Article
Network Pharmacology Approaches Used to Identify Therapeutic Molecules for Chronic Venous Disease Based on Potential miRNA Biomarkers
by Oscar Salvador Barrera-Vázquez, Juan Luis Escobar-Ramírez and Gil Alfonso Magos-Guerrero
J. Xenobiot. 2024, 14(4), 1519-1540; https://doi.org/10.3390/jox14040083 (registering DOI) - 15 Oct 2024
Viewed by 349
Abstract
Chronic venous disease (CVD) is a prevalent condition in adults, significantly affecting the global elderly population, with a higher incidence in women than in men. The modulation of gene expression through microRNA (miRNA) partly regulated the development of cardiovascular disease (CVD). Previous research [...] Read more.
Chronic venous disease (CVD) is a prevalent condition in adults, significantly affecting the global elderly population, with a higher incidence in women than in men. The modulation of gene expression through microRNA (miRNA) partly regulated the development of cardiovascular disease (CVD). Previous research identified a functional analysis of seven genes (CDS2, HDAC5, PPP6R2, PRRC2B, TBC1D22A, WNK1, and PABPC3) as targets of miRNAs related to CVD. In this context, miRNAs emerge as essential candidates for CVD diagnosis, representing novel molecular and biological knowledge. This work aims to identify, by network analysis, the miRNAs involved in CVD as potential biomarkers, either by interacting with small molecules such as toxins and pollutants or by searching for new drugs. Our study shows an updated landscape of the signaling pathways involving miRNAs in CVD pathology. This latest research includes data found through experimental tests and uses predictions to propose both miRNAs and genes as potential biomarkers to develop diagnostic and therapeutic methods for the early detection of CVD in the clinical setting. In addition, our pharmacological network analysis has, for the first time, shown how to use these potential biomarkers to find small molecules that may regulate them. Between the small molecules in this research, toxins, pollutants, and drugs showed outstanding interactions with these miRNAs. One of them, hesperidin, a widely prescribed drug for treating CVD and modulating the gene expression associated with CVD, was used as a reference for searching for new molecules that may interact with miRNAs involved in CVD. Among the drugs that exhibit the same miRNA expression profile as hesperidin, potential candidates include desoximetasone, curcumin, flurandrenolide, trifluridine, fludrocortisone, diflorasone, gemcitabine, floxuridine, and reversine. Further investigation of these drugs is essential to improve the treatment of cardiovascular disease. Additionally, supporting the clinical use of miRNAs as biomarkers for diagnosing and predicting CVD is crucial. Full article
Show Figures

Figure 1

Figure 1
<p>Network analysis of CVD-associated miRNAs with their expression, sources, countries of origin, and detection methods. The network depicts the interconnected structure of miRNAs derived from CVD patients, organized by their expression, sources, countries of origin, and detection methods. In the network, miRNAs are denoted as blue (upregulated) or red (downregulated) nodes, green nodes represent countries, yellow nodes represent sources, and gray nodes represent detection methods. The connections between the nodes signify the frequency of independent study reports. The three most outstanding sources were the proximal part of the significant saphenous vein tissue, vein tissues, and peripheral blood mononuclear cells. China was the country with the most available finds from miRNAs. Microarrays and RT-PCR are the most effective methods for diagnosing CVD. At least two tissues are expected to contain five specific miRNAs: miR-34a, miR-34c, miR-202-3, miR-1202, and miR-130a. The network, constructed using Cytoscape software (v.3.10.2), comprises 78 nodes and 193 edges, with a diameter and a network density of 6 and 0.106, respectively. Please refer to the <a href="#app1-jox-14-00083" class="html-app">Supplementary Materials (Figure S1)</a> for a better image resolution.</p>
Full article ">Figure 2
<p>Network analysis of miRNAs associated with CVD and their predicted targets. (<b>A</b>) The bar plot visually presents the number of targetable genes in the miRNA curated dataset. In the plot, gray bars represent upregulated genes, blue bars denote downregulated genes, and orange bars indicate genes with undetermined expression (ND). (<b>B</b>) We constructed a structural network using reported and predicted interactions between miRNAs and their targeted genes. This network consists of 1882 nodes and 5267 edges, with a diameter and a network density of 12 and 0.001. The network was created using Cytoscape software (v.3.10.2). Please refer to the <a href="#app1-jox-14-00083" class="html-app">Supplementary Materials (Figure S2)</a> for a better image resolution.</p>
Full article ">Figure 3
<p>The structural network represents the ten most connected nodes, including miRNAs and targets. Nodes are color-coded from orange to yellow based on their degree of connection, representing the most connected genes and miRNAs in the network. The most relevant nodes in this network are WNK-1, hsa-miR-106b-3p, IL1NR, hsa-miR-92a-3p, PPP6R2, hsa-miR-454-3p, PRRC2B, hsa-miR-548ac, hsa-miR-128-3p, and ADIPOQ. The network consists of 921 nodes and 1256 edges, with a diameter and a network density of 7 and 0.003, respectively. This network was created using Cytoscape software (v.3.10.2). Please refer to the <a href="#app1-jox-14-00083" class="html-app">Supplementary Materials (Figure S3)</a> for a better image resolution.</p>
Full article ">Figure 4
<p>The structural network of small molecules, phlebotonic, and miRNAs. The structural network depicts the targeted miRNAs (green nodes) between small molecules (yellow nodes) and the phlebotonic hesperidin (pink node). It was observed that curcumin exhibited the highest connection of miRNAs with the reported phlebotonic hesperidin. The network involves 246 nodes and 1153 edges, with a diameter and a network density of 6 and 0.038, respectively. The network construction utilized Cytoscape software (v.3.10.2). Please refer to the <a href="#app1-jox-14-00083" class="html-app">Supplementary Materials (Figure S4)</a> for a better image resolution.</p>
Full article ">Figure 5
<p>Structural network of hesperidin-specific miRNAs that are also altered by small molecules. This structural network depicts the miRNA profiles shared by both miRNAs that are specifically upregulated or downregulated by the reference compound hesperidin and the small molecules studied in this work. These shared miRNA profiles between hesperidin and small molecules allow the selection of potential candidates for CVD treatment. Downregulated miRNAs are shown in red, upregulated in blue, and those shared with small molecules in orange. The network involves 93 nodes and 320 edges, with a diameter and a density of 4 and 0.075, respectively. This network was created using Cytoscape software (v.3.10.2). Please refer to the <a href="#app1-jox-14-00083" class="html-app">Supplementary Materials (Figure S5)</a> for a better image resolution.</p>
Full article ">Scheme 1
<p>Flow diagram of the bibliographical screening performed for this research.</p>
Full article ">
19 pages, 5159 KiB  
Article
Peptide Activator Stabilizes DJ-1 Structure and Enhances Its Activity
by Jing-Yuan Shih and Yuan-Hao Howard Hsu
Int. J. Mol. Sci. 2024, 25(20), 11075; https://doi.org/10.3390/ijms252011075 (registering DOI) - 15 Oct 2024
Viewed by 231
Abstract
DJ-1 is a vital enzyme involved in the maintenance of mitochondrial health, and its mutation has been associated with an increased risk of Parkinson’s disease (PD). Effective regulation of DJ-1 activity is essential for the well-being of mitochondria, and DJ-1 is thus a [...] Read more.
DJ-1 is a vital enzyme involved in the maintenance of mitochondrial health, and its mutation has been associated with an increased risk of Parkinson’s disease (PD). Effective regulation of DJ-1 activity is essential for the well-being of mitochondria, and DJ-1 is thus a potential target for PD drug development. In this study, two peptides (15EEMETIIPVDVMRRA29 and 47SRDVVICPDA56) were utilized with the aim of enhancing the activity of DJ-1. The mechanisms underlying the activity enhancement by these two peptides were investigated using hydrogen/deuterium exchange mass spectrometry (HDXMS). The HDXMS results revealed distinct mechanisms. Peptide 1 obstructs the access of solvent to the dimer interface and stabilizes the α/β hydrolase structure, facilitating substrate binding to a stabilized active site. Conversely, peptide 2 induces a destabilization of the α/β hydrolase core, enhancing substrate accessibility and subsequently increasing DJ-1 activity. The binding of these two peptides optimizes the activity site within the dimeric structure. These findings offer valuable insights into the mechanisms underlying the activity enhancement of DJ-1 by the two peptides, potentially aiding the development of new drugs that can enhance the activity of DJ-1 and, consequently, advance PD treatment. Full article
(This article belongs to the Special Issue Biomolecular Structure, Function and Interactions)
Show Figures

Figure 1

Figure 1
<p>The dimerization configuration of DJ-1. The crystal structure of DJ-1 (PDB: 2OR3) showing the three cysteine residues in yellow and two critical residues in red related to the dimerization of DJ-1.</p>
Full article ">Figure 2
<p>Purification and verification of DJ-1. (<b>A</b>) SDS-PAGE analysis of DJ-1, stained with Coomassie blue, revealing distinct bands at approximately 21 kDa. From left to right, the samples are DJ-1, the oxidized form of DJ-1 with two bands, and DTT-reduced DJ-1. (<b>B</b>) Western blot analysis by using anti-DJ-1 as the primary antibody revealed clearly defined bands at approximately 21 kDa. The samples are DJ-1, the oxidized form of DJ-1, and reduced DJ-1. (<b>C</b>) DJ-1 was treated with the DSS cross-linker for SDS-PAGE. Following DSS cross-linking, prominent dimer bands were observed at 42 kDa. The samples, from left to right, are DJ-1, DSS-crosslinked DJ-1, and DSS-crosslinked DJ-1 following the addition of P1 and P2.</p>
Full article ">Figure 3
<p>DJ-1 activity measurement. (<b>A</b>) The deglycation assay of DJ-1 involved the breakdown of hemithioacetal and resulted in a significant decrease in absorbance. The control corresponds to no DJ-1 protein. (<b>B</b>) The activity of DJ-1 was measured using a deglycation assay. The samples included were degassed assay DJ-1, DJ-1 without degassed assay, oxidized DJ-1, and reduced DJ-1; variation was discovered in deglycation activity under different conditions. (<b>C</b>) DJ-1 with or without P1 and P2 was added to the prepared substrate, and the resultant mixture was incubated at 37 °C for 30 min. (<b>D</b>) Calculated activities from (<b>C</b>).</p>
Full article ">Figure 4
<p>Peptide map of DJ-1 protein. DJ-1 protein was digested using a self-packed pepsin column on ice, and the resulting peptic fragments were retained on a peptide trap. Subsequently, the peptides were eluted through a C18 column by using a gradient for mass spectrometry analysis. The MS/MS data were exported to X! Tandem for sequence identification. The solid and the dashed lines are the identified peptides and the solid lines are selected for further structural presentation.</p>
Full article ">Figure 5
<p>Deuteration levels of DJ-1. DJ-1 was incubated with or without P1 and P2 at 37 °C for 10 min, followed by deuteration in an H/D exchange reaction from 10 to 10,000 s. The reactions were quenched using ice-cold quench solution containing formic acid and guanidine hydrochloride. The deuterated protein was then subjected to mass spectrometry analysis. The number of deuterons incorporated in each peptide was measured, and the deuteration levels were subsequently calculated.</p>
Full article ">Figure 6
<p><b>H</b>/D exchange mass spectrum in the region 104–112 upon P1 and P2 binding. DJ-1 underwent deuteration from 0 to 10,000 s, and the results at 0, 10, 300, and 10,000 s are presented. (<b>A</b>) Mass spectrum of the sequence 104–112 after HDXMS. (<b>B</b>) HDXMS results of DJ-1 interacting with P1. (<b>C</b>) HDXMS results of DJ-1 interacting with P2.</p>
Full article ">Figure 7
<p>Effects of P1 and P2 peptide binding on DJ-1, as analyzed using HDXMS. DJ-1 protein was incubated with P1 and P2 peptides for 10 min. The changes in HDXMS levels at 10 s and 10,000 s were mapped onto the DJ-1 crystal structure (2OR3.PDB). The representations of P1 treatment at 10 s (<b>A</b>), P1 treatment at 10,000 s (<b>B</b>), P2 treatment at 10 s (<b>C</b>), and P2 treatment at 10,000 s (<b>D</b>) are shown to illustrate the changes in HDXMS levels.</p>
Full article ">Figure 8
<p>Changes in H/D exchange observed in HDXMS after binding of DJ-1 with peptide 1. DJ-1 bound to P1 was deuterated for 10, 30, 100, 300, 1000, 3000, and 10,000 s. The HDXMS results of the selected peptides are presented in the linear graph. The structural graph depicts the changes in each fragment at 10,000 s. The assorted colors in the heat map represent the various levels of changes. All experiments were conducted in triplicate, and the errors represent the standard deviation.</p>
Full article ">Figure 9
<p>Changes in H/D exchange observed in HDXMS after binding of DJ-1 with peptide 2. DJ-1 bound to P2 was deuterated for 10, 30, 100, 300, 1000, 3000, and 10,000 s. The HDXMS results of the selected peptides are presented in the linear graph. The structural graph depicts the changes in each fragment at 10,000 s. The assorted colors in the heat map depict various levels of changes. All experiments were conducted in triplicate, and the errors represent the standard deviation.</p>
Full article ">Figure 10
<p>Peptide binding effects of the reduced DJ-1, as observed through HDXMS. (<b>A</b>) Differences in HDXMS results between the originally reduced DJ-1 and the DTT-reduced DJ-1. Peptides P1 (<b>B</b>) and P2 (<b>C</b>) were bound to the original DJ-1 without further reduction at 37 °C. The differences in deuteration levels at 10,000 s after H/D exchange of DJ-1 with or without peptide binding are shown. The deuteration differences are mapped onto the DJ-1 structure.</p>
Full article ">
Back to TopTop