Vetrivel Umashankar

Comparative Genomic Analysis of Multidrug-Resistant Pseudomonas aeruginosa Clinical Isolates VRFPA06 and VRFPA08 with VRFPA07

ABSTRACT Pseudomonas aeruginosa isolates harboring acquired drug-resistant genes lead to increased mortality. Here, we have sequenced and annotated the genomes of two multidrug-resistant (MDR) P. aeruginosa isolates and a susceptible P. aeruginosa clinical isolate evidencing divergent antibiotic susceptibilities. Genomic analysis showed insight on the different genomic strategies adapted by P. aeruginosa to combat antimicrobial effects.

ICAM-1 K469E polymorphism is a genetic determinant for the clinical risk factors of T2D subjects with retinopathy in Indians: a population-based case–control study

Objective Elevated levels of intercellular adhesion molecule-1 (ICAM-1) are demonstrated in diabetes complications. The current study aims to understand association of K469E (rs5498) in ICAM-1 gene, in type 2 diabetic (T2D) subjects with retinopathy. Design Case–control study. Setting Sankara Nethralaya Diabetic Retinopathy Epidemiology and Molecular Genetic Study, an epidemiology study (on prevalence of diabetic retinopathy in T2D subjects (T2DR) from south India) and outpatient department of Sankara Nethralaya, a tertiary care hospital, in Chennai, India. Participants A total of 356 T2D subjects of >15 years of diabetes duration, with (n=199) and without (n=157) retinopathy. Methods The rs5498 polymorphism was genotyped by direct sequencing. Multivariate analysis for various clinical covariates was done using SPSS V.14. Comparative assessment of structure stability, folding rate of the variants were assessed using bioinformatics tools like STRIDE, MuPro, ModellerV97, fold rate server, etc. Results The AA genotype of rs5498 was seen at a higher frequency in the retinopathy group (p=0.012). The risk for diabetic retinopathy (DR) increased in the presence of AA genotype (OR=1.89–4.82) after the sequential addition of various clinical covariates. Multivariate logistic regression analysis showed 8.26 times high risk for developing DR in the AG genotype (p=0.003). Structural superimposition of ICAM-1 wild type (K469) and variant (E469) showed 0.943 Å of backbone root mean square deviation as calculated by PYMOL software. A difference in the fold rate time was also observed between the wild type (5.4/s) and variant (3.3/s). Conclusions This study shows that allele A of rs5498 in ICAM-1 is a putative risk predisposing allele for T2D retinopathy and its clinical covariates in Indian population. The folding rate of the protein decreases for the A allele implicating a potential effect on the structure and function of ICAM-1.

Chemical inhibition of fatty acid synthase: molecular docking analysis and biochemical validation in ocular cancer cells

Fatty acid biosynthesis is an attractive target for anti-cancer therapeutics. The ocular cancer, retinoblastoma cells were treated with fatty acid synthase (FASN) enzyme inhibitors: cerulenin, triclosan and orlistat. The IC50 and dose-dependent sensitivity of cancer cells to FASN inhibitors decrease in biologic enzyme activity, and cell morphology alterations were analysed. Molecular interactions of enzyme-inhibitor complexes were studied by molecular modelling and docking simulations. The crystal structures of ketoacyl synthase (PDB ID:3HHD) (cerulenin) and thioesterase (PDB ID:2PX6) (orlistat) domains of human FASN were utilized for docking, while for the non-crystallised human FASN enoyl reductase domain (triclosan), homology model was built and used for docking. All three inhibitors showed significant binding energy indicating stable complex formation with their respective FASN subunits. The predicted Ki value of the FASN inhibitors corroborated well with their corresponding anti-cancer effects.

Unraveling genomic and phenotypic nature of multidrug-resistant (MDR) Pseudomonas aeruginosa VRFPA04 isolated from keratitis patient

Multidrug-resistant (MDR) Pseudomonas aeruginosa VRFPA04, obtained from a keratitis patient was found to exhibit resistance to betalactam (Penicillins, cephalosporins, including carbapenems, except aztreonam), aminoglycosides, quinolone group of drugs and susceptible to colistin. The complete genome sequencing of the ocular isolate to measure and ascertain the degree of multidrug resistance in VRFPA04 strain resulted in 6,818,030bp (6.8Mb) genome sizes, which happen to be the third largest genome available in the Genbank to date. Two chromosomally integrated class I integrons carrying blaVIM-2 carbapenemase gene, multiple secretory systems consisting of types I-VI and VIII proteins and ocular virulence factors exo-T, Y, U and exotoxin A, a gene that inhibits protein synthesis which could have caused corneal cell death and Phytohormone auxin biosynthetic protein were detected in the genome of VRFPA04 Genome. In addition, 58 Regions of Genomic Plasticity (RGPs) regions, multiple phage genomes, genomic islands, CRISPR genes and RND family efflux pumps, such as MexCD-OprJ and MexEF-OprN and its regulators, MexT and MexR, were unraveled in VRFPA04. Thus, the current study reveals the virulence factors and resistome nature of an ocular isolate P aeruginosa VRFPA04 genome.

Resistome and pathogenomics of multidrug resistant (MDR) Pseudomonas aeruginosa VRFPA03, VRFPA05 recovered from alkaline chemical keratitis and post-operative endophthalmitis patient

Eye infections due to Pseudomonas aeruginosa is an important cause of ocular morbidity. We presents the whole genomic comparative analysis of two P. aeruginosa VRFPA03 and VRFPA05 isolated from alkaline chemical injury mediated keratitis and post-cataract surgery endophthalmitis patients, respectively. The blaDIM-1 gene in VRFPA03 and the blaGes-9 gene in VRFPA05 were identified and reported for the first time from an ocular isolate. The current study revealed novel integrons In1107 and In1108, comprised of multidrug-resistant genes. Ocular virulence factors mainly mediated by exoenzymes T, Y, and U and exotoxin A, elastase B, and phenazine-specific methyltransferase. Genomic analysis uncovered multiple known and unknown factors involved in P. aeruginosa mediated ocular infection, which may lead to drug discovery and diagnostic markers to improve human vision care.

Draft Genome Sequence of Multidrug-Resistant Pseudomonas aeruginosa Strain VRFPA02, Isolated from a Septicemic Patient in India

ABSTRACT Multidrug-resistant Pseudomonas aeruginosa strains, which are notable nosocomial pathogens, have greatly increased the mortality rate of septicemic patients due to treatment failure. Here, we report the draft genome sequence of P. aeruginosa strain VRFPA02, a human bloodstream isolate that has phenotypically proven to be resistant to a broad spectrum of antibiotics.

Virtual screening, molecular dynamics, and binding free energy calculations on human carbonic anhydrase IX catalytic domain for deciphering potential leads

Carbonic anhydrase IX is a tumor-associated membrane-bound metallo-enzyme which catalyzes the reversible hydration of carbon dioxide (CO2) to bicarbonate (HCO3−) and proton (H+) ions. It is a hypoxia-inducible enzyme and plays a critical role in tumor pH homeostasis favoring tumor cell invasiveness and drug resistance. Over expression of CAIX is documented in cancers of breast, lung, kidney, colon/rectum, etc. Chemical inhibition of CAIX activity has proven to be an effective therapeutic modality towards targeting cancer. Hence, in this study, we intend to identify potential molecules from NCI (National Cancer Institute) and Maybridge databases implementing high-throughput virtual screening. CAIX co-crystallized with acetazolamide (a known inhibitor of CAIX) (PDB ID: 3IAI) was used for reference-guided docking protocol. The potential inhibitors among the coupled data sets were finalized based on Glide docking score, Prime/MMGBSA scoring, significant intermolecular interactions, ADMET (absorption, distribution, metabolism and excretion, toxicity) prediction and stability of complex formation, molecular dynamics simulation, and comparative analysis. By this study, we propose NSC_93618, NSC_170253, NSC_93618, JFD03677, SEW06488, and BTB09372 to be highly significant, as all these compounds were found to qualify as potential leads surpassing all the stringent filtering process. However, NSC_93618 was found to be the most potential, as it featured with higher complex stability with strong bonded interactions, binding affinity synonymous to acetazolamide. Hence, these proposed compounds shall prove to be effective in targeting CAIX towards modulating carcinogenesis.

Comparative modeling of PON2 and analysis of its substrate binding interactions using computational methods

Paraoxonase (PON) constitutes a family of calcium-dependent mammalian enzymes comprising of PON1, PON2, and PON3. PON family shares ~60% sequence homology. These enzymes exhibit multiple activities like paraoxonase, arylesterase, and lactonase in a substrate dependent manner. Decreased PON activity has been reported in diseases like cardiovascular disease, atherosclerosis, and diabetes. Even though, PON2 is the oldest member of the family, PON1 is the only member studied in silico. In this study, the structure of PON2 was modeled using MODELLER 9v7 and its interactions with relevant ligands and its physiological substrate homocysteine thiolactone was performed using AutoDock 4.0. The results reveal that PON1 and PON2 share common ligand binding patterns for arylesterase and lactonase activity, whereas in case of paraoxon binding, the residues involved in the interactions were different. Interestingly, the substrate HCTL was found to have the lowest free energy of binding (ΔG) and highest affinity for PON2 than PON1.

Ornithine and its role in metabolic diseases: An appraisal

Ornithine is a non-essential amino acid produced as an intermediate molecule in urea cycle. It is a key substrate for the synthesis of proline, polyamines and citrulline. Ornithine also plays an important role in the regulation of several metabolic processes leading to diseases like hyperorithinemia, hyperammonemia, gyrate atrophy and cancer in humans. However, the mechanism of action behind the multi-faceted roles of ornithine is yet to be unraveled completely. Several types of cancers are also characterized by excessive polyamine synthesis from ornithine by different rate limiting enzymes. Hence, in this review we aim to provide extensive insights on potential roles of ornithine in many of the disease related cellular processes and also on the structural features of ornithine interacting proteins, enabling development of therapeutic modalities.

Studies on New Delhi Metallo-Beta-Lactamse-1 producing Acinetobacter baumannii isolated from donor swab in a tertiary eye care centre, India and structural analysis of its antibiotic binding interactions

Gram-negative bacilli, Enterobacteriaceae and Non-fermentors with resistance to carbapenems and metallo beta-lactams are the major cause of concern in clinical problems in current human healthcare. The most highly emerging dreadful Metallo Beta-lactamses is New Delhi metallo-beta-lactamase (blaNDM-1) which confers resistance to carbapenems; susceptible only to colistin and, less consistently to tigecycline, leading to no therapeutic options. In the present study, we demonstrate the effects of cephalosporins and carbepenems on biofilm producing A. baumanii clinical isolate and also to infer the probable inhibitory binding mode through molecular docking studies. The result of MIC on Biofilm producing A. baumanii and the docking analysis results were found to be concordant. Moreover, we also found cephalosporins and carbepenem groups to interact with 162-166 region of blaNDM-1, which is unique for NDM-1 and also documented to be a potential drug targeting region.