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Ascomycetous fungi are found associated with a wide variety of substrates which range from fresh water to marine ecosystems, tropical to temperate forest soils and deserts, throughout the world over. These demystifying fungi exist as... more
Ascomycetous fungi are found associated with a wide variety of substrates which range from fresh water to marine ecosystems, tropical to temperate forest soils and deserts, throughout the world over. These demystifying fungi exist as endophytes, pathogens and saprobes. They have been studied due to their ability to contaminate foods and feedstuffs, causing an elaboration of mycotoxins. The objectives of the study included extensive analyses of the morphological features of fungi, especially Aspergilli, which have been presented while studying them on specific mycological media. It is also an elaborate compilation of substantive macro- and micro-morphological characterization of different Aspergilli isolated from the spice Foeniculum vulgare used in India and other countries in the world. Further, a first of its kind attempt has been made to study their relative abundance and frequency of occurrence, molecular phylogeny and genetic relatedness to characterize the Aspergilli into spec...
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Dengue virus is a mosquito-borne human pathogen, causing disease that ranges from mild febrile illness to life-threatening hemorrhage fever/ shock syndrome. The altered antigenicity and virulence in the dengue virus, resulting from the... more
Dengue virus is a mosquito-borne human pathogen, causing disease that ranges from mild febrile illness to life-threatening hemorrhage fever/ shock syndrome. The altered antigenicity and virulence in the dengue virus, resulting from the accumulation and fixation of the favorable mutations in the genome, is the cause of concern nowadays. The present study focuses on the comparative study of polyproteins of viral strains within each dengue serotype to understand the trend of intra-serotype polyprotein variation and its effect on the antigenicity. Polyprotein sequences of viral strains in each serotype were investigated using multivariate statistical analysis, phylogenetic analysis and multiple sequence alignment methods. Epitope prediction was done by Bepipred-1.0 server and experimental epitope data were extracted from Immune Epitope Database with BLAST search. The study reveals that the polyproteins of viral strains of a serotype have variable amino acid composition that corresponds ...
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Research Interests: Biochemistry, Genetics, Algorithms, Data Mining, Computational Biology, and 15 moreBiology, Drug Discovery, Infectious Diseases, Medicine, Multidisciplinary, Biological Sciences, Humans, Computer Simulation, Approach, Characterization, CHEMICAL SCIENCES, Candidates, In Silico, Druggability, and Hierarchical
Abstract Proteins are complex macromolecules involved in essential biological processes in a living organism. Determining the three-dimensional structure of the protein is central to understand its functional role at the molecular level.... more
Abstract Proteins are complex macromolecules involved in essential biological processes in a living organism. Determining the three-dimensional structure of the protein is central to understand its functional role at the molecular level. Experimental approaches such as X-ray crystallography, nuclear magnetic resonance, and cryogenic electron microscopy have been developed by researchers to solve the protein structures. However, the high-cost and effort-intensive nature associated with these methods is limiting their usage for deciphering protein structures. Thus, as an alternative, the development of computational methods to model protein structure has gained importance to the scientific community. The existing computational methods can be broadly classified into two major categories, namely, the template-based (homology modeling and threading) and the template-free modeling (ab initio). This chapter provides an overview of the available computational approaches for modeling protein structures along with various relevant resources and case study of the widely used methods.
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Leishmaniasis is a serious world health problem and its current therapies have several limitations demanding to develop novel therapeutics for this disease. The present study aims to prioritize novel broad-spectrum targets using... more
Leishmaniasis is a serious world health problem and its current therapies have several limitations demanding to develop novel therapeutics for this disease. The present study aims to prioritize novel broad-spectrum targets using proteomics and protein-protein interaction network (PPIN) data for 11 Leishmania species. Proteome comparison and host non-homology analysis resulted in 3605 pathogen-specific conserved core proteins. Gene ontology analysis indicated their involvement in major molecular functions like DNA binding, transportation, dioxygenase, and catalytic activity. PPIN analysis of these core proteins identified eight hub proteins (viz., vesicle-trafficking protein (LBRM2903_190011800), ribosomal proteins S17 (LBRM2903_34004790) and L2 (LBRM2903_080008100), eukaryotic translation initiation factor 3 (LBRM2903_350086700), replication factor A (LBRM2903_150008000), U3 small nucleolar RNA-associated protein (LBRM2903_340025600), exonuclease (LBRM2903_200021800), and mitochondrial RNA ligase (LBRM2903_200074100)). Among the hub proteins, six were classified as drug targets and two as vaccine candidates. Further, druggability analysis indicated three hub proteins, namely eukaryotic translation initiation factor 3, ribosomal proteins S17 and L2 as druggable. Their three-dimensional structures were modelled and docked with the identified ligands (2-methylthio-N6-isopentenyl-adenosine-5'-monophosphate, artenimol and omacetaxine mepesuccinate). These ligands could be experimentally validated (in vitro and in vivo) and repurposed for the development of novel antileishmanial agents.
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The highly contagious disease COVID-19, caused by SARS-CoV-2, has emerged as a global pandemic. The high rate of contact transmission of this virus is the major cause of concern nowadays. Owing to the absence of any effective... more
The highly contagious disease COVID-19, caused by SARS-CoV-2, has emerged as a global pandemic. The high rate of contact transmission of this virus is the major cause of concern nowadays. Owing to the absence of any effective drugs/vaccines against COVID-19, many countries adopted ‘lockdown’ to minimize transmission of virus. The other means that was applied during lockdown, to mitigate the growth of infection is the ‘test, trace, track and isolate’. However, different countries responded differently to these control measures with different outcome in the growth of infection. For now, several countries have started ‘unlock’, to handle the severe economic stress, created in response to lockdown. Again, lifting lockdown is another global threat, having the chance of second wave of infection. In such situation, the major challenge is to prevent the spread of infection, amid resumption of work. The present review is aimed to outline the prospect and future direction of disease managemen...
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Research Interests: Bioinformatics, Genetics, Computer Science, Database Systems, Molecular Biology, and 14 moreGenomics, Computational Biology, Biology, Clostridium difficile, PHP, Medicine, Computer User Interface Design, Intestines, Anti-Bacterial Agents, Pharmaceutical Formulation Technology, Drug Targeting, Internet, Psychology and Cognitive Sciences, and Medical and Health Sciences
Research Interests: Genetics, Molecular Evolution, Biology, Evolution, Medicine, and 15 moreGene expression, Correspondence Analysis, Multivariate Analysis, Biological Sciences, Phylogeny, Cluster Analysis, Genome, Codon Usage, Codon, Base Sequence, Nucleotides, Poxviridae, Molecular Sequence Data, Medical and Health Sciences, and Codon usage bias
Intra-species variations in gene and protein composition of Bdellovibrio bacteriovorous HD100, the predatory microorganism that preys on other Gramnegative bacteria, have been analyzed. Major sources of variations at the gene level are... more
Intra-species variations in gene and protein composition of Bdellovibrio bacteriovorous HD100, the predatory microorganism that preys on other Gramnegative bacteria, have been analyzed. Major sources of variations at the gene level are gene expression, local GC-bias and horizontal gene transfer and those at the protein level are alcoholicity, hydropathicity, aromaticity and frequencies of charged residues. Some cell-wall surface anchor family proteins and transporter proteins with distinct composition, secondary structures and potential disordered structures contribute significantly to intra-proteome compositional variation. The study, in contradiction to earlier reports, identifies some genes with atypical codon usage, presumably acquired by Bdellovibrio in recent past. The majority of the closest homologs of these putative HGTs belong to different classes of Gram-negative bacteria and it is hypothesized that these genes might have been incorporated into Bdellovibrio genome as a result of its interaction with prey cells.
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Cancer is an outcome of uncontrolled cell division eventually associated with dysregulated epigenetic mechanisms, including DNA methylation. DNA methyltransferase 1 is ubiquitously expressed in the proliferating cells and is essential for... more
Cancer is an outcome of uncontrolled cell division eventually associated with dysregulated epigenetic mechanisms, including DNA methylation. DNA methyltransferase 1 is ubiquitously expressed in the proliferating cells and is essential for the maintenance of DNA methylation. It causes the abnormal silencing of tumor suppressor genes in human cancer which is necessary for proliferation, cell cycle progression, and survival. DNMT1 is involved in tumorigenesis of several cancers, its upregulation potentially upscale the promoter level inactivation of transcription of a tumor inhibitory gene by introducing repressive methylation marks on the CpG islands. This epigenetic perturbation caused by DNMT is targeted for cancer therapeutics. To demonstrate the proliferative inhibitory potential of brazilin in human breast cancer cell line (MCF-7) with concurrent mitigation of DNMT1 functional expression and to understand its effect on downstream targets like cell cycle inhibitor p21. The impact of brazilin on the growth and proliferation of the MCF-7 cells was determined using the XTT assay. The global DNA 5-methyl cytosine methylation pattern was analyzed upon brazilin treatment. The gene and protein expression of DNMTs were determined with quantitative RTPCR and western blots respectively. The potential binding sites of transcription factors in the human DNMT1 promoter were predicted using the MatInspector tool on the Genomatix software. The chromatin immunoprecipitation (ChIP) assay was performed to demonstrate the transcription factors occupancy at the promoter. Methylation of promoter CpG islands was determined by the methylation-specific PCR (MSP) upon brazilin treatment. The molecular docking of the human DNMT1 with brazilin (ligand) was performed using the Schrödinger suite. The heterotetracyclic compound brazilin, present in the wood of Caesalpinia sappan, inhibited the proliferation of the human breast cancer cell line (MCF-7) and reduced the DNMT1 expression with a decrease in global DNA methylation. Brazilin, by activating p38 MAPK and elevating p53 levels within the exposed cells. The elevated level of p53 enriched the occupancy at binding sites within 200 bp upstream to the transcription start site in the DNMT1 promoter, resulting in reduced DNMT1 gene expression. Furthermore, the brazilin restored the p21 levels in the exposed cells as the CpGs in the p21 promoter (-128 bp/+17 bp) were significantly demethylated as observed in the methylation-specific PCR (MSP). Highly potential anti-proliferative molecule brazilin can modulate the DNMT1 functional expression and restore the cell cycle inhibitor p21expression. We propose that brazilin can be used in therapeutic interventions to restore the deregulated epigenetic mechanisms in cancer.
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Background: MicroRNAs (miRNAs) are a class of small non-coding, endogenous RNAs that regulate gene expression at post-transcriptional level. In plants, miRNAs are usually of 18-24 nucleotide in length and play humongous role by aiding in... more
Background: MicroRNAs (miRNAs) are a class of small non-coding, endogenous RNAs that regulate gene expression at post-transcriptional level. In plants, miRNAs are usually of 18-24 nucleotide in length and play humongous role by aiding in development, growth, defense, biotic and abiotic stress responses, etc. Objective: Arachis hypogaea is an economically important oil seed crop and human dietary source cultivated mostly in tropical and subtropical regions. In the present study, an initiative was taken to uncover miRNAs, their targets and functions in this important plant species. Method: Comparative genomics strategy coupled with bioinformatics approaches was deployed for the identification of miRNAs, their corresponding targets and functions by exploiting biological databases and tools. Results: The study was able to identify 34 conserved miRNA candidates, belonging to 17 miRNA families, contributed by 23 and 3 precursor miRNAs from A. hypogaea Expressed Sequence Tags (EST) and Gen...
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Staphylococcus aureus, the causative agent of nosocomial infections worldwide, has acquired resistance to almost all antibiotics stressing the need to develop novel drugs against this pathogen. In S. aureus N315, 302 genes have been... more
Staphylococcus aureus, the causative agent of nosocomial infections worldwide, has acquired resistance to almost all antibiotics stressing the need to develop novel drugs against this pathogen. In S. aureus N315, 302 genes have been identified as essential genes, indispensable for growth and survival of the pathogen. The functions of 40 proteins encoded by S. aureus essential genes were found to be hypothetical and thus referred as essential hypothetical proteins (EHPs). The present study aims to carry out functional characterization of EHPs using bioinformatics tools/databases, whose performance was assessed by Receiver operating characteristic curve analysis. Evaluation of physicochemical parameters, homology search against known proteins, domain analysis, subcellular localization analysis and virulence prediction assisted us to characterize EHPs. Functional assignment for 35 EHPs was made with high confidence. They belong to different functional classes like enzymes, binding prot...
Research Interests: Bioinformatics, Computational Biology, Mitochondria, Humans, Bacteria, and 12 moreStaphylococcus aureus, ROC Curve, Gram Positive Bacteria, Drug targets, Molecular weight, In Silico, Hypothetical Proteins, Virulence Factors, Biological Macromolecules, Protein Transport, Biochemistry and cell biology, and Functional Annotation
MicroRNAs (miRNAs) are a family of non-coding RNAs that play a central role in fine-tuning gene expression regulation. Over the past decade, identification and annotation of miRNAs have become a major focus in epigenomics research.... more
MicroRNAs (miRNAs) are a family of non-coding RNAs that play a central role in fine-tuning gene expression regulation. Over the past decade, identification and annotation of miRNAs have become a major focus in epigenomics research. However, detection and characterization of miRNA are challenging due to its small size (~22 nucleotide-long) and susceptibility to degradation. The difficulties involved in experimental prediction and characterization of miRNA coding genes have led to the development of in silico-based approaches. Although several algorithms have been developed in recent years, a comprehensive assessment of the principles, methodological insights, and estimate of the strengths and weaknesses of computational methods are limited. The present review is dealt with the detailed methodological insights of different tools used for identifying miRNA coding genes falling under four computational approaches. The parameters considered in these tools along with their specificity are also delineated. Furthermore, the strengths and weaknesses of these four computational approaches, and the bioinformatics resources pertaining to target identification, expression analysis, regulatory network analysis, and SNP identification are stated in this review. The methodological details of miRNA prediction methods and bioinformatics resources related to miRNA research in one platform would facilitate the miRNA research community to develop efficient tools for uncovering novel miRNAs and understanding their role in regulatory networks.
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Horizontal gene transfer is a phenomenon by which one organism transfers its genetic material to other organism but not to its offspring. Transformation, Transduction and bacterial conjugation is the common method by which gene gets... more
Horizontal gene transfer is a phenomenon by which one organism transfers its genetic material to other organism but not to its offspring. Transformation, Transduction and bacterial conjugation is the common method by which gene gets laterally transferred. Horizontal gene transfer is a frequent event between microbes especially bacteria and the transferred genes provides selective benefit to the recipient organism. Horizontal gene transfer also plays a key role in determining the evolutionary history of the organism where the extent of lateral transfer is high. Single bioinformatics or molecular biology tool is incapable of systematically identifying all laterally transferred genes in a single organism. The integration of different available methods can bring out the best possible results.In this article we aimed to review the phenomenon of Horizontal gene transfer as a whole. We also set sights on the methods of analyzing the event insillico and overcome the problems associated with...
Mycobacterium abscessus, a non-tuberculous rapidly growing mycobacterium, is recognized as an emerging human pathogen causing a variety of infections ranging from skin and soft tissue infections to severe pulmonary infections. Lack of an... more
Mycobacterium abscessus, a non-tuberculous rapidly growing mycobacterium, is recognized as an emerging human pathogen causing a variety of infections ranging from skin and soft tissue infections to severe pulmonary infections. Lack of an optimal treatment regimen and emergence of multi-drug resistance in clinical isolates necessitate the development of better/new drugs against this pathogen. The present study aims at identification and qualitative characterization of promising drug targets in M. abscessus using a novel hierarchical in silico approach, encompassing three phases of analyses. In phase I, five sets of proteins were mined through chokepoint, plasmid, pathway, virulence factors, and resistance genes and protein network analysis. These were filtered in phase II, in order to find out promising drug target candidates through subtractive channel of analysis. The analysis resulted in 40 therapeutic candidates which are likely to be essential for the survival of the pathogen an...
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Human thyroid stimulating hormone (TSH) is a glycoprotein secreted by the anterior part of the pituitary gland. TSH plays an important physiological role in the regulation of hypothalamic-pituitary-thyroid axis by modulating the release... more
Human thyroid stimulating hormone (TSH) is a glycoprotein secreted by the anterior part of the pituitary gland. TSH plays an important physiological role in the regulation of hypothalamic-pituitary-thyroid axis by modulating the release of the thyroid hormones from the thyroid gland. It induces iodine uptake by the thyroid, promotes thyroid epithelial differentiation and growth, and protects thyroid cells from apoptosis. Impairment of TSH signal transduction pathway leads to thyroid disorders such as goitre, hypothyroidism and hyperthyroidism, which can have complex clinical manifestations. TSH signaling is largely effected through two separate pathways, the adenylate cyclase and the phospholipase C pathways. In spite of its biomedical importance, a concise signaling map of TSH pathway is not available in the public domain. Therefore, we have generated a detailed signaling map of TSH pathway by systematically cataloging the molecular reactions induced by TSH including protein-protei...
TNF-related weak inducer of apoptosis (TWEAK) is a new member of the TNF superfamily. It signals through TNFRSF12A, commonly known as Fn14. The TWEAK-Fn14 interaction regulates cellular activities including proliferation, migration,... more
TNF-related weak inducer of apoptosis (TWEAK) is a new member of the TNF superfamily. It signals through TNFRSF12A, commonly known as Fn14. The TWEAK-Fn14 interaction regulates cellular activities including proliferation, migration, differentiation, apoptosis, angiogenesis, tissue remodeling and inflammation. Although TWEAK has been reported to be associated with autoimmune diseases, cancers, stroke, and kidney-related disorders, the downstream molecular events of TWEAK-Fn14 signaling are yet not available in any signaling pathway repository. In this paper, we manually compiled from the literature, in particular those reported in human systems, the downstream reactions stimulated by TWEAK-Fn14 interactions. Our manual amassment of the TWEAK-Fn14 pathway has resulted in cataloging of 46 proteins involved in various biochemical reactions and TWEAK-Fn14 induced expression of 28 genes. We have enabled the availability of data in various standard exchange formats from NetPath, a reposito...
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Food and waterborne diseases are a growing concern in terms of human morbidity and mortality worldwide, even in the 21st century, emphasizing the need for new therapeutic interventions for these diseases. The current study aims at... more
Food and waterborne diseases are a growing concern in terms of human morbidity and mortality worldwide, even in the 21st century, emphasizing the need for new therapeutic interventions for these diseases. The current study aims at prioritizing broad-spectrum antibacterial targets, present in multiple food and waterborne bacterial pathogens, through a comparative genomics strategy coupled with a protein interaction network analysis. The pathways unique and common to all the pathogens under study (viz., methane metabolism, d-alanine metabolism, peptidoglycan biosynthesis, bacterial secretion system, two-component system, C5-branched dibasic acid metabolism), identified by comparative metabolic pathway analysis, were considered for the analysis. The proteins/enzymes involved in these pathways were prioritized following host non-homology analysis, essentiality analysis, gut flora non-homology analysis and protein interaction network analysis. The analyses revealed a set of promising broad-spectrum antibacterial targets, present in multiple food and waterborne pathogens, which are essential for bacterial survival, non-homologous to host and gut flora, and functionally important in the metabolic network. The identified broad-spectrum candidates, namely, integral membrane protein/virulence factor (MviN), preprotein translocase subunits SecB and SecG, carbon storage regulator (CsrA), and nitrogen regulatory protein P-II 1 (GlnB), contributed by the peptidoglycan pathway, bacterial secretion systems and two-component systems, were also found to be present in a wide range of other disease-causing bacteria. Cytoplasmic proteins SecG, CsrA and GlnB were considered as drug targets, while membrane proteins MviN and SecB were classified as vaccine targets. The identified broad-spectrum targets can aid in the design and development of antibacterial agents not only against food and waterborne pathogens but also against other pathogens.
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Research Interests: Bioinformatics, Medicinal Chemistry, Molecular Dynamics Simulation, Molecular modeling, Homology Modeling, and 10 moreLymphatic Filariasis, Molecular docking, Van Der Waals, Drug-Protein Interaction, Three Dimensional, Drug Targeting, MD Simulation, Molecular Dynamic Simulation, Wuchereria bancrofti , and Pharmacology and pharmaceutical sciences
The present report proposes a new method for the chaos game representation (CGR) of different families of proteins. Using concatenated amino acid sequences of proteins belonging to a particular family and a 12-sided regular polygon, each... more
The present report proposes a new method for the chaos game representation (CGR) of different families of proteins. Using concatenated amino acid sequences of proteins belonging to a particular family and a 12-sided regular polygon, each vertex of which represents a group of amino acid residues leading to conservative substitutions, the method can generate the CGR of the family and allows pictorial representation of the pattern characterizing the family. An estimation of the percentages of points plotted in different segments of the CGR (grid points) allows quantification of the nonrandomness of the CGR patterns generated. The CGRs of different protein families exhibited distinct visually identifiable patterns. This implies that different functional classes of proteins follow specific statistical biases in the distribution of different mono-, di-, tri-, or higher order peptides along their primary sequences. The potential of grid counts as the discriminative and diagnostic signature of a family of proteins is discussed.
Research Interests: Algorithms, Nonlinear dynamics, Fractals, Higher Order Thinking, Computer Software, and 11 moreHumans, Animals, Proteins, Molecular Graphics, Amino Acid Profile, THEORETICAL AND COMPUTATIONAL CHEMISTRY, S100 protein family, Amino Acid Sequence, Pattern Generation, Biochemistry and cell biology, and Higher order
Research Interests: Evolutionary Biology, Genetics, Multivariate Statistics, Molecular Evolution, Gene expression, and 15 moreCorrespondence Analysis, Mutation, Animals, Amino Acids, Plasmodium falciparum, Genetic variation, Molecular weight, Codon, Genome sequence, Protozoan Proteins, Proteome, Biochemistry and cell biology, Nucleotide substitution, Amino acid composition, and conserved sequence
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Research Interests: Information Systems, Genetics, Genomics, Horizontal Gene Transfer, Multivariate Analysis, and 13 morePhylogeny, Gram-negative bacteria, Secondary Structure, Protein Secondary Structure Prediction, Leg, Codon, Cell Wall, Proteome, Outer Membrane Protein, Low molecular weight, Protein Biosynthesis, Bdellovibrio, and Amino acid composition
Usage of guanine and cytosine at three codon sites in eubacterial genes vary distinctly with potential expressivity, as predicted by Codon Adaptation Index (CAI). In bacteria with moderate/high GC-content, G(3) follows a biphasic... more
Usage of guanine and cytosine at three codon sites in eubacterial genes vary distinctly with potential expressivity, as predicted by Codon Adaptation Index (CAI). In bacteria with moderate/high GC-content, G(3) follows a biphasic relationship, while C(3) increases with CAI. In AT-rich bacteria, correlation of CAI is negative with G(3), but non-specific with C(3). Correlations of CAI with residues encoded by G-starting codons are positive, while with those by C-starting codons are usually negative/random. Average Size/Complexity Score and aromaticity of gene-products decrease with CAI, confirming general validity of cost-minimization principle in free-living eubacteria. Alcoholicity of bacterial gene-products usually decreases with expressivity.
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Research Interests: Gene expression, Correspondence Analysis, Animals, Parasites, Amino Acids, and 15 moreTrypanosoma Cruzi, Trypanosoma brucei, Trypanosoma brucei brucei, Genetic variation, Codon, Protozoan Proteins, Amino Acid Sequence, Base Sequence, Amino Acid Substitution Rates, Leishmania Major, Biochemistry and cell biology, Gene Expression Regulation, Molecular Sequence Data, Amino acid composition, and conserved sequence
Sporadic outbreaks of plague, lack of a vaccine, emergence of multidrug-resistant strains of Yersinia pestis, and its potential use in bioterrorism, call for an urgent need to develop new drugs for plague. We have used comparative... more
Sporadic outbreaks of plague, lack of a vaccine, emergence of multidrug-resistant strains of Yersinia pestis, and its potential use in bioterrorism, call for an urgent need to develop new drugs for plague. We have used comparative metabolic pathway analysis to identify 245 drug-target candidate enzymes in Y. pestis CO92 which are non-homologous to host Homo sapiens and likely to be essential for the pathogen's survival. Further analysis revealed that 25 of these are potential choke point enzymes. As a case study, structure of a choke point enzyme, MurE ligase, was modeled and docking studies performed against a library of compounds leading to identification of a potential inhibitor. This approach enables rapid potential drug-target identification, thereby facilitating search for new antimicrobials.
Research Interests: Thermodynamics, Organic Chemistry, Metabolomics, Humans, Sequence alignment, and 11 moreDrug Design, Plague, Docking, Anti-Bacterial Agents, Species Specificity, Amino Acid Sequence, Yersinia Pestis, Structure activity Relationship, Metabolic Pathways, Molecular Sequence Data, and Pharmacology and pharmaceutical sciences
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Biases in the codon usage and base compositions at three codon sites in different genes of A+T-rich Gram-negative bacterium Haemophillus influenzae and G+C-rich Gram-positive bacterium Mycobacterium tuberculosis have been examined to... more
Biases in the codon usage and base compositions at three codon sites in different genes of A+T-rich Gram-negative bacterium Haemophillus influenzae and G+C-rich Gram-positive bacterium Mycobacterium tuberculosis have been examined to address the following questions: (1) ...
Research Interests: Genetics, Gene expression, Tuberculosis, Mycobacterium tuberculosis, Mutation, and 14 moreEscherichia coli, Gram Positive, Animals, Dictyostelium, Gene, Codon Usage, Codon Adaptation Index, Gram-negative bacteria, Codon, Protein Biosynthesis, Nucleic Acid, Haemophilus influenzae, Codon bias, and Dictyostelium discoideum
Clostridium difficileis considered to be one of the most important causes of health care-associated infections currently. The prevalence and severity of C. difficileinfection have increased significantly worldwide in the past decade... more
Clostridium difficileis considered to be one of the most important causes of health care-associated
infections currently. The prevalence and severity of C. difficileinfection have increased significantly
worldwide in the past decade which has led to the increased research interest. Here, using comparative
genomics strategy coupled with bioinformatics tools we have identified potential drug targets in
C. difficileand determined their three-dimensional structures in order to develop a database, named
Clostridium-DT
DB
. Currently, the database comprises the potential drug targets with their structural
information from three strains of C. difficile,namely hypervirulent PCR-ribotype 027 strain R20291,
PCR-ribotype 012 strain 630, and PCR-ribotype 027 strain CD196
infections currently. The prevalence and severity of C. difficileinfection have increased significantly
worldwide in the past decade which has led to the increased research interest. Here, using comparative
genomics strategy coupled with bioinformatics tools we have identified potential drug targets in
C. difficileand determined their three-dimensional structures in order to develop a database, named
Clostridium-DT
DB
. Currently, the database comprises the potential drug targets with their structural
information from three strains of C. difficile,namely hypervirulent PCR-ribotype 027 strain R20291,
PCR-ribotype 012 strain 630, and PCR-ribotype 027 strain CD196