Introduction
Our research group is working on various biological problems related to diseases with the application of Next generation sequencing, SNP analysis, and mutational analysis of genomes. We have sufficient academic and commercial softwares for the analysis of biological data. We also investigate the drug targets along with novel compounds by methodologies like homology modelling, docking, dynamics. We guide the students of UG/PG for their project dissertations also offer Doctoral Degree.
Ongoing projects:
1. Protein–protein interactions (PPIs) are the physical contacts of high specificity established between two or more protein molecules as a result of biochemical events. Study of protein-protein interactions along with their inhibitors is important in drug design and understanding molecular mechanisms of human diseases. A database is being created to store the exponentially growing information about protein-protein interactions provided by high-throughput screening experiments.
2. PPIs are essential interactions that help to understand the biochemistry of a cell, cell development, and responses to stimuli. Many biological processes involve the formation of protein-protein complexes hence are important within the cellular network. This project aims to apply molecular dynamics simulations to study functional and conformational properties of interface regions based on protein complexes.
3. SARS-CoV2 pandemic is currently the most threatening issue and has led to worldwide deaths. An effective vaccine against it has not been developed, thus requiring concerned efforts at various scales. In this project we are performing molecular modelling studies on SARS-CoV2 target proteins.
Figure: MAPK-RAF-ERK Signalling Pathway
Schematic depicting the methodology involved in computing the distance energy matrix of a hypothetical case of two interacting proteins that possess a single chain each at the atomic level in a native bound PPI complex
Structure of c-Src kinase protein (PDBID: 1Y57) composed of SH2 domain, SH3 domain, N-lobe and C-lobe. B) Native ligand imatinib derivative (green) bound to the active site residues (blue)
Degree sorted PPI network of diabetes related proteins. Red= high degree distribution, orange= least degree distribution, green= intermediate
Publications:
1. Lokhande KB, Doiphode S, Vyas R, Swamy KV. Molecular docking and simulation studies on SARS-CoV-2 Mpro reveals Mitoxantrone, Leucovorin, Birinapant, and Dynasore as potent drugs against COVID-19 J BiomolStructDyn. 2020;1-12. https://doi.org/10.1080/07391102.2020.1805019PMCID: PMC7484567
2. Bapat, S. “Modeling of protein complexes involved in signaling pathway for Non-Small Cell Lung Cancer” (2019) In. Vyas, R. (Eds.) Advances in Bioengineering, Springer, ISBN: 978-981-15-2062-4
3. Bapat, S., Vyas, R., Karthikeyan, M., “Exploring energy profiles of protein-protein interactions (PPIs) using DFT method.” (2019) Letters in Drug Design & Discovery 16 (6), 670-677. DOI : 10.2174/1570180815666180815151141
4. Bapat, S., Vyas, R., Karthikeyan, M. , Muthukrishnan, M., “Synthesis, Biological Evaluation and Molecular Modeling Studies of Novel Chromone/Aza-Chromone Fused α- Aminophosphonates as Src Kinase Inhibitors” (2019) Journal of Scientific and Industrial Research- NISCAIR 78 (02), 111-117
5. Bapat, S., et al. "2018 Index IEEE/ACM Transactions on Computational Biology and Bioinformatics Vol. 15." IEEE/ACM Transactions on Computational Biology and Bioinformatics 16.1 (2019): 1.
6. Nalla, V., Shaikh, A., Bapat, S., Vyas, R., Karthikeyan, M., Yogeeswari, P., Sriram, D. &Muthukrishnan, M., (2018). Identification of potent chromone embedded [1, 2, 3]-triazoles as novel anti-tubercular agents. Royal Society Open Science, 5(4),p.171750.https://doi.org/10.1098/rsos.171750
Computational Tools:
BioinformaticsTools Schrödinger Maestro, MOE, AutoDock Vina, GLIDE, GROMACS, NAMD, CytoScape, VMD.
ChemoinformaticsTools ChemAxon Marvin Suite, ChemDraw, ScreeningAssistant.
Awards:
International Conference on Recent Trends in Bioengineering.
Topic: PPI2 Server: A webserver on protein-protein interaction inhibitors.
1 February 2020
Secured Best Paper Award
International Conference on Recent Trends in Bioengineering.
Topic: Computational studies of novel chromone inhibitors on Src kinase family
17 February 2019
Secured Best Poster Award
International Conference on Recent Trends in Bioengineering.
Topic: Synthesis, biological evaluation and molecular modeling studies of novel chromone/aza- chromone fused α-aminophosphonates as Src kinase inhibitors.
16 February 2018
Secured Best Paper Award