Dr. Kshatresh Dubey | Department of Chemistry

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Dr. Kshatresh
Dutta
Dubey
Assistant Professor
Department of Chemistry
School of Natural Sciences (SNS)
kshatresh.dubey@snu.edu.in
A227B
Block-A, Shiv Nadar University
Gautam Buddha Nagar Uttar Pradesh
India
91-0120-7170100
Extn: 
727
Profile Summary 

Research Interest:

I am an interdisciplinary researcher who works on the interface of Physics, Chemistry, and Biology. We apply Physics based principles like Molecular Dynamics Simulations and Free energy calculations to study the conformational changes in biomolecules and binding affinity of drugs/ligands for a targeted protein/nucleic acid. The mechanism and functions of enzymes are also a core research area of my group, where we study the catalytic parameters e.g., Km using Molecular Mechanics and Kcat using hybrid QM/MM Calculations. Core research areas are:

1) De novo Enzyme Designing and Protein engineering

2) Molecular Modelling and Computational drug designing

3) Protein-protein Interactions and Protein-ligand Interactions using a computational approach

4) Molecular Docking, MD Simulations, and Free Energy Calculations

5) Density Functional Theory (DFT) calculations, QM/MM Calculations and Ab-initio MD simulations using Cp2K

For a detailed list of Publications see:

https://scholar.google.co.il/citations?hl=en&user=K7T8ggkAAAAJ&view_op=list_works&sortby=pubdate

Educational Qualifications 
2013
Ph.D.
Deen Dayal Upadhyay Gorakhpur University Gorakhpur
2003
M.Sc.
Deen Dayal Upadhyay Gorakhpur University Gorakhpur
Work Experience 
12/12
12/13
Postdoc,
Indian Institute of Technology Kanpur,
Kanpur India
01/14
09/17
Postdoc,
The Hebrew University of Israel,
Jerusalem, Israel
10/17
09/18
Senior Researcher,
Uppsala University Sweden,
Uppsala Sweden
10/18
02/19
Postdoc,
University of Barcelona,
Barcelona, Spain
03/19
01/22
Ramalingaswami Fellow,
Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Delhi-NCR
02/22 – Present
Assistant Professor,
Department of Chemistry, School of Natural Sciences, Shiv Nadar University Delhi-NCR,
A227B
I currently work here
Research Areas 
Chemical Biology & Protein Chemistry
Chemical Reaction Engineering and Catalysis
BIOINFORMATICS
Courses Taught(Selected) 
Evolution of life (CCC423)
Molecular modelling (CHY114)
Informatics and Drug Discovery (CHY522)
Research Methodology (CHY600)
Chemical Equilibrium (CHY211)
Informatics & Molecular Modelling (CHY332)
Awards(Selected): 
2011

Senior Research Fellowship (CSIR)

2014

PBC Fellowship for outstanding postdocs

2017

Sven and Lilly Fellowship, Sweden

2018

Ramalingaswami re-entry fellowship

2023

Academic Editor of PLOS ONE

2022

Associate Editor of Frontiers in Chemistry

Scholarly Activity

Journal Publications (accepted or published)

  • Surajit Kalita, Hagai Bergman, Kshatresh Dutta Dubey* and Sason Shaik*. How Can Static and Oscillating Electric Fields Serve in Decomposing Alzheimer’s and Other Senile Plaques? J. Am. Chem. Soc. 2023, 145, 6, 3543–3553
  • Surajit Kalita, Sason Shaik*, and Kshatresh Dutta Dubey*. MD Simulations and QM/MM Calculations Reveals the Key Mechanistic Elements which are Responsible for the Efficient C-H Amination Reactions Performed by a Bioengineered P450 Enzyme. Chemical Science, 12, 14507-14518, 2021, 2021.
  • Surajit Kalita, Sason Shaik*, Hemata Kisan and Kshatresh Dutta Dubey*. A Paradigm Shift in the Catalytic Cycle of P450 – The Preparatory Choreography During O2 Binding, and Origins of the Necessity for Two Protonation Pathways, ACS Catalysis, 2020,10,11481-11492
  • Kshatresh Dutta Dubey*, Thijs Stuyver, Surajit Kalita, Sason Shaik*, Solvent-Organization And Rate-Regulation Of A Menshutkin Reaction By Oriented-External Electric Fields Are Revealed By Combined MD And QM/MM Calculations.  J. Am. Chem. Soc, 2020, 142,22,9955-9965
  • Simone Savino, Annika JE Borg, Alexander Dennig, Martin Pfeiffer, Francesca De Giorgi, Hansjörg Weber, Kshatresh Dutta Dubey, Carme Rovira, Andrea Mattevi, Bernd Nidetzky. Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis. Nature Catalysis, 2, 1115-1123, 2019. 
  • Kshatresh Dutta Dubey, Binju Wang, Manu Vajpai and Sason Shaik, MD simulations and QM/MM calculations show that single-site mutations of cytochrome P450BM3 alter the active site’s complexity and the chemoselectivity of oxidation without changing the active species. Chemical Science., 2017, 8, 5335-5344.
  • Binju Wang, Jiarui Lu, Kshatresh Dutta Dubey, Geng Dong, Wenzhen Lai; Sason Shaik, How do Enzymes Utilize Reactive OH radicals? Lessons from Non-Heme HppE and Fenton Systems. J. Am. Chem. Soc, 2016, 138, 8489–8496.
  • Rajeev Ramanan, Kshatresh Dutta Dubey, Binju Wang, Debasish Mandal and Sason Shaik, Emergence of Function in P450-Proteins: A Combined Quantum Mechanical/Molecular Mechanical and Molecular Dynamics Study of the Reactive Species in the H2O2-Dependent Cytochrome P450SPα and Its Regio- and Enantioselective Hydroxylation of Fatty Acids. J. Am. Chem. Soc., 2016, 138 (21), pp 6786–6797. 
  • Kshatresh Dutta Dubey, Binju Wang and Sason Shaik. Molecular dynamics and QM/MM calculations predict the substrate-induced gating of cytochrome P450 BM3 and the regio-and stereoselectivity of fatty acid hydroxylation. J. Am. Chem. Soc., 2016, 138 (3), pp 837–845
  • Binju Wang, Chunsen Li, Kshatresh Dutta Dubey and Sason Shaik, Quantum mechanical/molecular mechanical calculated reactivity networks reveal how cytochrome P450cam and Its T252A mutant select their oxidation pathways. J. Am. Chem. Soc., 2015, 137 (23), pp 7379–7390.