* PROTEIN DYNAMICS
We focus on understanding the relationship between protein structure, function, and dynamics. Research is focused into two major sub-groups: 1) molecular modeling of enzyme-substrate / enzyme-inhibitor interactions and 2) structure-based drug discovery. Studies are performed using computer simulation methods ranging from molecular dynamics simulations, Monte Carlo simulations, Brownian dynamics simulations, and protein-ligand docking. General properties that we address include change in protein structure and dynamics upon binding inhibitors and with mutations, ligand binding strength and specificity, and bound water structure.
* GREEN CHEMISTRY
Ionic liquids and super critical CO2 have been identified as promising green solvents for biotransformation, enzyme catalysis and long-term preservation of biomolecules. Our objective is to elucidate molecular level interactions between biomolecules and ionic liquids, modulated kinetics of protein folding and increased solubilization & enhanced extraction of proteins and other hydrophilic substances in water-in-CO2 reverse micelles, etc.
* NANO CLUSTERS
We, perform first-principle quantum mechanical calculations of gold, silver and gold-silver binary clusters to understand their electronic structures, magic number, vibrational spectra, adsorption behavior, response to electric field, catalysis, etc.
* In-vitro STUDIES
While rationalizing experimental behavior of biomolecules using molecular dynamics simulation remain our forte, we have moved on to use MD as a central engine of experimental research by validating our findings from computational studies using various spectroscopic & calorimetric techniques. With leads from our computational data we perform inhibitor synthesis, enzymatic assays and drug design in our laboratory.
- S. Gupta, S. Balasubramanian and S. Senapati, “Understanding the mechanism of HIV-1 protease inhibition by monoclonal antibodies” Journal of Molecular Graphics and Modeling (in press).
- S. Bardhan, M. H. Rahman, S. Banerjee, A. P. Singh and S. Senapati, “Extended H-Bonding through Protic Ionic Liquids Facilitates the Growth and Stability of Water Domains in Hydrophobic Environment” Langmuir (in press).
- S. Balasubramanian and S. Senapati, “Dynamics and Barrier of Movements of Sodium and Potassium Ions Across the Oxytricha nova G-Quadruplex Core” J. Phys. Chem. B, 124, 11055-11066 (2020).
- M. Ahsan, C. Pindi and S. Senapati, “Electrostatics Plays a Crucial Role in HIV-1 Protease Substrate Binding, Drugs Fail to Take the Advantage” Biochemistry, doi:10.1021/acs.biochem.0c00341 (2020).
- D. Sasmal, S. Banerjee, S. Senapati and T. Tripathy, “Effective removal of Th4+, Pb2+, Cd2+, malachite green, methyl violet and methylene blue from their aqueous solution by amylopectin dialdehyde-Schiff base” Journal of Environmental Chemical Engineering, 8, 103741 (2020).
- C. Pindi, V. R. Chirasani, M. H. Rahman, M. Ahsan, P. D. Revanasiddappa and S. Senapati, “Molecular Basis of Differential Stability and Temperature Sensitivity of ZIKA versus Dengue Virus Protein Shells” Scientific Reports, 10, 1-10 (2020).
- B. Mondal, S. Banerjee, J. Ray, S. Jana, S. Senapati and T. Tripathy, “Novel Dextrin‐Cysteine Schiff Base: A Highly Efficient Sensor for Mercury Ions in Aqueous Environment” ChemistrySelect, 5, 2082-2093 (2020).
- M. Naushad, S. K. Durairajan, A. K. Bera, S. Senapati and M. Li, “Natural Compounds with Anti-BACE1 Activity as Promising Therapeutic Drugs for Treating Alzheimerʼs Disease” Planta medica, 85, 1316-1325 (2019).
- S. M. Dixit, M. Ahsan and S. Senapati, “Steering the lipid transfer to unravel the mechanism of CETP inhibition” Biochemistry, 58, 3789-3801 (2019).
- M. Ahsan and S. Senapati, “Water Plays a Co-catalytic Role in Epoxide Ring Opening Reaction in Aspartate Proteases: A QM/MM Study” J. Phys. Chem. B, 123, 7955-7964 (2019).
- M. H. Rahman and S. Senapati, “Water Clathrates in Nanostructural Organization of Hydrated Ionic Liquids Manifest in Peculiar Density Trend” J. Phys. Chem. B., 123, 1592-1601 (2019).
- S. Gupta, S. Senapati, “Mechanism of inhibition of drug-resistant HIV-1 protease clinical isolates by TMC310911: A molecular dynamics study” J. Mol. Struc., 1198, 126893 (2019).
- R. Kannan, P. Prabakaran, R. Basu, C. Pindi, S. Senapati, V. Muthuvijayan and E. Prasad, “Mechanistic study on the antibacterial activity of self-assembled poly (aryl ether)-based amphiphilic dendrimers” ACS Appl. Bio Mater., 2, 3212-3224 (2019).
- A. Bose, P. Sengupta, U. Pal, S. Senapati, M. Ahsan, S. Roy, U. Das, K. Sen, “Encapsulation of Thymol in cyclodextrin nano-cavities: A multi spectroscopic and theoretical study” Spectrochim Acta A., 208, 339-348 (2019).
- D. Ghoshdastidar and S. Senapati, “Dehydrated DNA in B-form: Ionic Liquids in Rescue” Nucleic Acids Res., 46, 4344-4353 (2018).
- P. D. Revanasiddappa, R. Shankar, and S. Senapati, “Role of bound phospholipids in structural stability of cholesteryl ester transfer protein” J. Phys. Chem. B., 122, 4239–4248 (2018).
- K. Kundu, A.P. Singh, S. Panda, V. Singh, R.L. Gardas, S. Senapati, “Study on the Conformation of Entrapped Protein inside the Reverse Micellar Confinement Based on the Amino-Acid-Derived Ionic Liquid” Chem. Select., 3, 4768-4776 (2018).
- A. Garai, D. Ghoshdastidar, S. Senapati, P Maiti, “Ionic liquids make DNA rigid” J. Chem. Phys., 149, 045104 (2018).
- S. Panda, K. Kundu, A. Basaiahgari, A. P. Singh, S. Senapati, R. L. Gardas, “Aggregation behaviour of biocompatible choline carboxylate ionic liquids and their interactions with biomolecules through experimental and theoretical investigations” New J. Chem., 42, 7105-7118 (2018).
- A. Mukherjee, S. Sarkar, S. Gupta, S. Banerjee, S. Senapati, R. Gachhui, “DMSO strengthens chitin deacetylase-chitin interaction: physicochemical, kinetic, structural and catalytic insights” Carbohydr. Polym., 223, 115032 (2018).
- V.Chirasani and S. Senapati,, “How cholesteryl ester transfer protein can also be a potential triglyceride transporter” Scientific Reports. 7, Article number: 6159 (2017)
- Rajeswari Appadurai and S. Senapati, “How Mutations Can Resist Drug Binding Yet Keep HIV-1 Protease Functional” Biochemistry., 56 , 2907-2920 (2017).
- A. P. Singh, R. Gardas, and S. Senapati, “How water manifests the structural regimes in ionic liquids” Soft Matter., 13, 2348-2361 (2017).
- A. P. Singh, K. Kundu, V. Singh, R. Gardas, and S. Senapati, “Enhanced stability and water solubilizing capacity of water-in-oil microemulsions based on protic ionic liquids” Phys. Chem. Chem. Phys., 19, 26132-26144 (2017).
- A. P. Singh, D. Sithambaram, R. Sanghavi, P. K. Gupta, R. S. Verma, M. Doble, R. Gardas, and S. Senapati, “Environmentally benign tetramethylguanidium cation based ionic liquids” , New J. Chem., 41, 12268-12277 (2017).
- S. Panda, K. Kundu, A. P. Singh, S. Senapati*, R. L. Gardas*, “Understanding Differential Interaction of Protic and Aprotic Ionic Liquids inside Molecular Confinement”,J. Phys. Chem. B, 121, 9676-9687 (2017).
- SSK Durairajan, V. R. Chirasani, SG Shetty, A Iyaswamy, S Malampati, J Song, L Liu, J Huang, S Senapati, M Li, “Salvianolic acid B decreases the generation of amyloid-β by modulating BACE1 activity”,Curr. Alzheimer’s Res., 14, 1229–1237 (2017)
- S. Sarkar, S. Gupta, W. Chakraborty, S. Senapati, and R. Gachhui, “Homology modeling, molecular docking and molecular dynamics studies of the catalytic domain of chitin deacetylase from Cryptococcus laurentii strain RY1” Int. J. Biol. Macromol. 2017, 104, 1682-1691 , (2017).
- V.Chirasani, P.D. Revanasiddappa, and S. Senapati, “Structural plasticity of cholesteryl ester transfer protein assists its lipid transfer activity”,J. Biol. Chem.vol. 291 (37) p. 19462-73 (2016).
- M. Kiranmayi, V. Chirasani, P. Allu, L. Subramaniam, E. Martelli, B. Sahu, D. Vishnuprabhu, R. Kumaragurubaran, S. Sharma, D. Bodhini, M.Dixit, A. Munirajan, M. Khullar, V. Radha, V. Mohan, A. Mullasari, S. Naga Prasad S. Senapati, N. Mahapatra, “Catestatin Gly364Ser Variant Alters Systemic Blood Pressure and the Risk for Hypertension in Human Population via Endothelial Nitric Oxide Pathway”,Hypertens., 68:334-347 (2016)
- V. Chirasani, R. Sankar, S. Senapati, “Mechanism of Inhibition of Cholesteryl Ester Transfer Protein by Small Molecule Inhibitors”,J.Phys.Chem.B 2016, 120, 8254-8263 (2016).
- S.L.Rath, S. Senapati, “Mechanism of p27 Unfolding for CDK2 reactivation”,Scientific Reports, 6 Article number: 26450 (2016).
- R. Appadurai, S. Senapati, “Dynamical Network of HIV-1 Protease Mutants Reveals the Mechanism of Drug Resistance and Unhindered Activity”,Biochemistry, 55 (10), pp 1529-1540 (2016).
- D. Ghoshdastidar, S. Senapati, “Ion-Water Wires in Imidazolium-Based Ionic Liquid/Water Solutions Induce Unique Trends in Density”,Soft Matter, 12,3032-3045 (2016).
- D. Ghoshdastidar, D. Ghosh, S. Senapati, “High Nucleobase-Solubilizing Ability of Low-Viscous Ionic Liquid/Water Mixtures: Measurements and Mechanism”,J. Phys. Chem. B., 120, 492-503 (2016).
- N. Singh, S. Senapati, K. Bose, “Insights into the mechanism of human papillomavirus E2-induced procaspase-8 activation and cell death”,Sci. Rep.6:21408, (2016).
- J. Dominguez Rieg, V. Chirasani, H. Koepsell, S. Senapati, S. Mahata, T. Rieg, “Regulation of intestinal SGLT1 by catestatin in hyperleptinemic type 2 diabetic mice.”,Lab Invest, 96, 98-111 (2016).
- S. Bardhan, K. Kundu, B. Kar, G. Chakraborty, D. Ghosh, D. Sarkar, S. Das, S. Senapati, S.K. Saha, B.K. Pal “Synergistic interactions of surfactant blends in aqueous medium are reciprocated in non-polar medium with improved efficacy as a nanoreactor”,RSC Adv.6,55104 (2016).
- K. Kundu, A. Das, S. Bardhan, G. Chakraborty, D. Ghosh, B. Kar, S.K. Saha, S. Senapati, R.K. Mitra,B.K. Paul, “The mixing behaviour of anionic and non-ionic surfactant blends in aqueous environment correlates in fatty acid ester medium”,Colloids and Surfaces A: Physiochem. Eng. Aspects504, 331-342 (2016).
- A.P. Singh, R. Gardas, S. Senapati, “Divergent trend in density versus viscosity of ionic liquid/water mixtures: A molecular view from guanidium ionic liquids.”,Phys. Chem. Chem. Phys., 17, 25037-25048 (2015).
- D. Ghoshdastidar, S. Senapati, “Nanostructural Reorganization Manifests in Sui-GenerisDensity Trend of Imidazolium Acetate/Water Binary Mixtures.”, J. Phys. Chem.B, 119(34), 10911-10920(2015).
- D. Tewari, T. Ahmed, V. R. Chirasani , P. K. Singh, S. K. Maji, S. Senapati, A. K. Bera, “Modulation of the mitochondrial voltage dependent anion channel (VDAC) by curcumin”, Biochim Biophys Acta.1848(1 Pt A):151-8 (2015).
- S.S.K. Durairajan, Y. Huang, P. Yuen, L. Chen, K. Kwok, L. Liu, J. Song, Q. Han, L. Xue, S. K. Chung, J. Huang, L. Baum, S. Senapati, M. Li, “Effects of Huanglian-Jie-Du-Tang and its modified formula on the modulation of amyloid-β precursor protein processing in Alzheimer’s disease models”, PLoS ONE9, e102923 (2014)
- S. L. Rath, S. Senapati,”Why Are the Truncated Cyclin Es More Effective CDK2 Activators than the Full-Length Isoforms?”, Biochemistry53(28):4612-24 (2014)
- P. Allu, V. Chirasani, D. Ghosh, A. Mani, A. Bera, S. Maji, S. Senapati, A. Mullasari, N. Mahapatra,”Naturally occurring variants of the dysglycemic peptide pancreastatin: differential potencies for multiple cellular functions and structure-function correlation.”, J Biol Chem289(7), 4455-69, (2014).
- S. L. Rath, S. Senapati, “Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: Insights for rational drug design”, PLoS ONE :8(9), e73836, (2013).
- N. Kathiresan, S Senapati, “Probing the Conformational Flexibility of Monomeric FtsZ in GTP-Bound, GDP-Bound, and Nucleotide-Free States”, Biochemistry, 52, 3543 – 3551 (2013).
- A. Chandran, D. Ghoshdastidar, S. Senapati, Groove binding mechanism of Ionic liquids: A key factor in long-term stability of DNA in hydrated Ionic liquids? J. Am. Chem. Soc., 134, 20330-39, (2012).
- Sahu, P. Allu, L. Subramanian, P.J. Sonawane, P. Singh, B. Sasi, S. Senapati, S. Maji, A. Bera, B.S. Gomathi, A.S. Mullasari, N. Mahapatra, “Functional Genetic Variants of the Catecholamine-Release-Inhibitory Peptide Catestatin in an Indian Population: Allele-Specific Effects on Metabolic Traits” J Biol Chem, 287/52, 43840-52 (2012).
- N. Kathiresan, J. Mohan and S. Senapati. “Relating nucleotide dependent conformational changes in free tubulin dimer to tubulin assembly”. Biopolymers, 99/5, 282-291 (2012).
- N. Kathiresan and S. Senapati “Understanding the basis of drug resistance of the mutants of αβ-tubulin dimer via molecular dynamics simulations.” PLoS ONE7(8): e42351, (2012).
34. B. Sahu, J. Mohan, G. Sahu, P. Singh, B. Sasi, P. Allu, S. Maji, A. Bera, S. Senapati, N. Mahapatra, “Molecular mechanism of interactions of the physiological anti-hypertensive peptide catestatin with the neuronal nicotinic acetylcholine receptor”, J. Cell Sci. 125, 2323, (2012).
33. S. Karthik and S. Senapati, “Dynamic Flaps in HIV-1 Protease Adopt Unique Ordering at Different Stages in the Catalytic Cycle”, Proteins79, 1830, (2011).
32. A. Chandran, K. Prakash and S. Senapati, “Self-assembled Inverted Micelles Stabilize Ionic Liquid Domains in Supercritical CO2“, J. Am. Chem. Soc. 132, 12511, (2010).
31. A. Chandran, K. Prakash and S. Senapati, “Structure and Dynamics of Acetate Anion-based Ionic Liquids from Molecular Dynamics Study”, Chem. Phys. 374, 46, (2010).
30. A. Harishchander, D. A. Anand and S. Senapati, “Analysis of Resistance to Human Immunodeficiency Virus Protease Inhibitors Using Molecular Mechanics and Machine Learning Strategies”, American Medical Journal 1(2): 126-132, (2010).
29. B. R. Prasad and S. Senapati, “Explaining the differential solubility of flue gas components in ionic liquids from first-principle calculations”, J. Phys. Chem. B. 113,4739, (2009).
28. V. Torbeev, H. Raghuraman, K. Mandal, S. Senapati, S. Kent, “Dynamics of flap structures in three HIV-1 protease/inhibitor complexes”, J. Am. Chem. Soc. 131, 884, (2009).
27. G. Singh and S. Senapati, “Molecular Dynamics Simulations of Ligand-induced Flap Closing in HIV-1 Protease Approach X-ray Resolution: Establishment of the Role of Bound Water in the Flap Closing Mechanism “, Biochemistry. 47, 10657 (2008).
26. V. S. V. Chaitanya and S. Senapati, “Self-assembled Reverse Micelles in Supercritical CO2 Entrap Protein in Native State “, J. Am. Chem. Soc. 130, 1866 (2008).
25. S. Senapati, “How strongly can calcium ion influence the hydrogen-bond dynamics at complex aqueous interfaces?”, J. Chem. Phys. 126, 204710 (2007).
24. S. Senapati, Y. Cheng, and J. A. McCammon, “In-situ synthesis of a tacrine-triazole-based inhibitor of acetylcholinesterase: Configurational selection imposed by steric interactions”, J. Med. Chem. 49, 6222, (2006).
23. S. Senapati, J. M. Bui, and J. A. McCammon, “Induced Fit in Mouse Acetylcholinesterase upon Binding a Femtomolar Inhibitor: A Molecular Dynamics Study ”, J. Med. Chem. 48, 8155 (2005).
22. S. Senapati, C. F. Wong and J. A. McCammon, “Finite concentration effects on diffusion-controlled reactions”, J. Chem. Phys. 121, 7896 (2004).
21. S. Senapati and M. L. Berkowitz, “Computer simulation studies of water states in perfluoropolyether reverse micelles: Effects of changing the counterion”, J. Phys. Chem. A 108, 9768 (2004).
20. S. Senapati and M. L. Berkowitz, “Molecular dynamics simulation studies of ployether and perfluoropolyether surfactant based reverse micelles in supercritical carbon dioxide”, J. Phys. Chem. B 107, 12906 (2003).
19. S. Senapati and M. L. Berkowitz, “Water structure and dynamics in phosphate fluorosurfactant based reverse micelle: A computer simulation study”, J. Chem. Phys. 118, 1937 (2003).
18. S. Senapati, “A molecular dynamics simulation study of the dimethyl sulfoxide liquid-vapor interface”, J. Chem. Phys. 117, 1812 (2002).
17. C. D. Bruce, S. Senapati, M. L. Berkowitz, L. Perera, and M.D.E. Forbes, “Molecular dynamics simulations of sodium dodecyl sulfate micelle in water: The behavior of water”, J. Phys. Chem. B 106, 10902 (2002).
16. S. Senapati, J. S. Keiper, J. M. DeSimone, G. D. Wignall, Y. B. Melnichenko, H. Frienlinghaus, and M. L. Berkowitz, “Structure of phosphate fluorosurfactant based reverse micelles in supercritical carbon dioxide”, Langmuir 18, 7371 (2002).
15. S. Senapati and M. L. Berkowitz, “Computer simulation study of the interface width of the liquid/liquid interface”, Phys. Rev. Lett. 87, 176101 (2001).
14. S. Senapati and A. Chandra, “Effects of confinement on structure, dielectric and dynamics of water in small hydrophobic cavity”, J. Phys. Chem. B 105, 5106 (2001).
13. S. Senapati and A. Chandra, “Surface charge induced modifications of the structure and dynamics of mixed dipolar liquids at solid-liquid interfaces: A molecular dynamics simulation study”, J. Chem. Phys. 113, 8817 (2000).
12. S. Senapati and A. Chandra,”Structure of a mixed dipolar liquid near a metal surface: A combined approach of weighted density and perturbative approximations”, Phys. Rev. E 62, 1017 (2000).
11. S. Senapati and A. Chandra, “Dynamics of polarization relaxation in a dipolar mixture at solid-liquid interface”, J. Chem. Phys. 113, 377 (2000).
10. S. Senapati and A. Chandra, “Interfacial structure of a mixed dipolar liquid in contact with a charged solid surface”, J. Chem. Phys. 112, 10467 (2000).
9. S. Senapati and A. Chandra, “Interfacial structure of a solute-solvent mixture in contact with a semipermeable membrane”, Ind. J. Chem. A 39, 219 (2000).
8. S. Senapati and A. Chandra, “Molecular dynamics simulations of simple dipolar liquids in spherical cavity: Effects of confinement on structural, dielectric and dynamical properties”, J. Chem. Phys. 111, 1223 (1999).
7. D. Das, S. Senapati and A. Chandra, “Structure of dipolar liquids near charged solid surfaces: A nonlinear theory based on a density functional approach and Monte Carlo simulations”, J. Chem. Phys. 110, 8129 (1999).
6. S. Senapati and A. Chandra, “Nonlinear theory of metal-solvent interface using density functional approach”, Phys. Rev. E, 59, 3140 (1999).
5. S. Senapati and A. Chandra, “Structure and dynamics of mixed dipolar liquids near solid surfaces: A molecular dynamics simulation study”, Chem. Phys. 242, 353 (1999).
4. A. Chandra, S. Senapati and D. Sudha, “Dynamics of polarization relaxation at soild-liquid interface”, J. Chem. Phys. 109, 10439 (1998).
3. S. Senapati and A. Chandra, “Computer simulation of dipolar liquids near charged solid surfaces: Electric field induced modifications of structure and dynamics of interfacial solvent”, J. Mol. Struc(Theochem), 455, 1 (1998).
2. A. Chandra and S. Senapati, “Rotational dielectric friction and molecular relaxation at metal-solvent interfaces”, J. Mol. Liq. 77, 77 (1998).
1. S. Senapati and A. Chandra, “Molecular relaxation in simple dipolar liquids confined between two solid surfaces”, Chem. Phys. 231, 65 (1998).