Biology subjects

Banik, A.

Publications and source records attributed to Banik, A..

4 recordsLinked to original sources

bioRxiv2020

Homology modeling and functional characterization of multidrug effluxor Mta protein from Bacillus Atrophaeus: An explanatory insilico approach

Phenotypically similar to B. subtilis, Bacillus atrophaeus is a Gram-positive, aerobic, spore-forming bacteria. It is a black-pigmented bacterial genus. Therefore, it is of interest to study the uncharacterized proteins in the genome. For a detailed computational sequence-structure-function analysis using available data and resources, an uncharacterized protein Mta (AKL87074.1) in the genome was selected. In this study, attempts were made to study the physicochemical properties, predict secondary structure, modeling the 3-D protein, pocket identification, protein-protein interaction and phylogenetic analysis of Mta protein. The predicted active site using CASTp is analyzed for understanding their multidrug resistance function. Because Mta is a MerR family member, these investigations on these functional aspects could lead us for better understanding of antibiotic resistance phenomenon.

bioinformatics↗

bioRxiv2020

Plant derived bioactive compounds as potential inhibitors of ZIKA virus: an in silico investigation

The ZIKA virus has caused a heavy concern everywhere the globe because of its high infectivity and mortality rate. Still, theres no specific drug or preventive medication to treat ZIKA infection despite comprehensive analysis by the researchers. This study was designed to demonstrate the efficacy of some plant derived bioactive compounds against ZIKV by using both structure and ligand based virtual screening methods. A number of 35 plant metabolites were screened against ZIKA NS2B-NS3 protease (5LC0), Envelop protein (5JHM), Capsid protein (5YGH) and NS5 RNA-dependent RNA polymerase protein (5U04) employing molecular docking approach. Results showed that there have been four metabolites, i.e. Chicoric acid, Luteone, Reserpine and Rosmarinic acid provide highest binding affinity to targeted ZIKV proteins. Crucial binding sites and drug surface hotspots are unraveled for every targeted viral protein. The ADME study showed that neither of the candidate compounds had side effects that would reduce their drug-like properties. As compared, the toxicity pattern analysis has unmasked the non-toxic essence of top drug candidates. The RMSD values of ligand-macromolecule complexes were 2 [A] apart from Envelop protein- Chicoric Acid, although the RMSF values showed normal atomic fluctuations within the molecular dynamics analysis, with the exception of Envelop protein- Chicoric Acid. The expected majority of the target class the highest drug candidates is enzyme classes (e.g. protease, hydrolase, phosphatase). In addition, the drug similarity prediction revealed several structural analogs from drugbank such as Isoformononetin (DB04202), Deserpidine (DB01089) and Rescinnamine (DB01180) etc. and these analogs could even be an option for the treatment of ZIKV infections. The study can pave the way for the creation of effective ZIKV medications and preventive measures. We highly recommend further in vivo trials for the experimental validation of our findings.

bioinformatics↗

bioRxiv2020

Screening and potent applicability analysis of commonly used pesticides against desert locust: an integrative entomo-informatics approach

The locust problem is a global threat for food security. Locusts can fly and migrate overseas within a zip and creating a large-scale devastation to the diversified agro-ecosystem. GIS based analysis showed the recent movement of locusts, among them Schistocerca gregaria and Locusta migratoria are predominant in Indian subcontinent and are found more notorious and devastating one. This devastation needs to be stopped to save human race from food deprivation. In our study, we screened some commonly used agricultural pesticides and strongly recommended three of them viz. biphenthrin, diafenthiuron and silafluofen which might be potential to control the desert locusts based on their binding affinity towards the locusts survival proteins. Our phylogenetic analysis reveals that these three recommended pesticides might also show potency to the other locust species as well as they are also way safer than the other commercially available pesticides. These proposed pesticides bioactive analogs from fungus and bacteria may also show efficacy as next generation controlling measures of locust as well as different kind of pests. These recommended pesticides are expected to be highly effective against locusts and needs to bring forward by the entomologists by performing experimental field trials. HighlightsO_LIGIS map unmasked the 2020 migratory pattern of locusts which now predominant towards Indian subcontinent. C_LIO_LIBiphenthrin, diafenthiuron and silafluofen showed maximum binding affinity. C_LIO_LIBiphenthrin and diafenthiuron were relatively safer than silafluofen. C_LIO_LIBioactive analogs from fungus and bacteria could be an alternative to control locusts. C_LIO_LIPesticides inhibition hotspots for desert locusts were unrevealed. C_LI

bioinformatics↗

bioRxiv2020

Identification of potential inhibitory analogs of metastasis tumor antigens (MTAs) using bioactive compounds: revealing therapeutic option to prevent malignancy

The deeper understanding of metastasis phenomenon and detection of drug targets could be a potential approach to minimize cancer mortality. In this study, attempts were taken to unmask novel therapeutics to prevent metastasis and cancer progression. Initially, we explored the physiochemical, structural and functional insights of three metastasis tumor antigens (MTAs) and evaluated some plant based bioactive compounds as potent MTA inhibitors. From 50 plant metabolites screened, isoflavone, gingerol, citronellal and asiatic acid showed maximum binding affinity with all three MTA proteins. The ADME analysis detected no undesirable toxicity that could reduce the drug likeness properties of top plant metabolites. Moreover, molecular dynamics studies revealed that the complexes were stable and showed minimum fluctuation at molecular level. We further performed ligand based virtual screening to identify similar drug molecules using a large collection of 3,76,342 compounds from DrugBank. The results suggested that several structural analogs (e.g. Tramadol, Nabumetone, DGLA, Hydrocortisone) may act as agonist to block the MTA proteins and inhibit cancer progression at early stage. The study could be useful to develop effective medications against cancer metastasis in future. Due to encouraging results, we highly recommend further in vitro and in vivo trials for the experimental validation of the findings.

bioinformatics↗