Kshatresh Dubey | Department of Chemistry


Ramalingaswami Fellow
Department of Chemistry
Center for Informatics
School of Natural Sciences (SoNS)
Block-A, Shiv Nadar University
Gautam Buddha Nagar Uttar Pradesh
Profile Summary 

I am a Chemistry convert. I did my masters in Physics where I studied the core Physics. I got interested in Biochemistry during my Ph.D. where I studied the conformational and structural properties of Class II fusion virus using MD simulations, Free energy calculations, and Molecular Docking. After submitting my PhD thesis I joined Prof. R. Sanakaramakrishanan of Department of Biological Sciences and Bioengineering, IIT-Kanpur as an Institutional Postdoc where I studied the membrane simulations for water and ion transports through membrane proteins. 

In early 2014, I received highly prestigious PBC fellowship for Outstanding postdocs by Govt of Israel to pursue my research with Prof. Sason Shaik of The Hebrew University of Jerusalem, Israel. Prof. Sason's group is world's leading research group for the mechanistic study of Cytochrome P450 enzymes. At this point, I got my interest in the enzyme mechanism. I worked on the mechanistic studies Cytochrome P450BM3, P450CAM, and other CYP family enzyme, I explained the paradigm of long-range biological electron transfer mechanism using Marcus theory and focused on the mechanism of substrate oxidation by CYP450. Working with Prof Sason I got expertise QM/MM calculations, Density Functional Theory, reaction mechanism, and enzyme catalysis. 

After finishing my tenure at The Hebrew University of Jerusalem, I got the prestigious Sven Lilly Foundation fellowship Sweden, to work with Prof Lynn Kamerlin at Department of Cell and Molecular Biology, Uppsala University, Sweden. Prof Lynn group is well known for its seminal work on the enzyme evolution, and I studied the mechanism of enzyme evolution using my QM/MM and MD simulation skills. Later on, I moved to the University of Barcelona with Prof Carme Rovira who is well known for Car-Parrinello Molecular Dynamics (CPMD) and Ab-initio Molecular Dynamics where I learned CPMD and CP2K for Quantum Mechanical Molecular Dynamics. 

For a detailed list of Publications see:


Educational Qualifications 
Deen Dayal Upadhyay Gorakhpur University Gorakhpur
Deen Dayal Upadhyay Gorakhpur University Gorakhpur
Work Experience 
Indian Institute of Technology Kanpur,
Kanpur India
The Hebrew University of Israel,
Jerusalem, Israel
Senior Researcher,
Uppsala University Sweden,
Uppsala Sweden
University of Barcelona,
Barcelona, Spain
Ramalingamswami Fellow,
Shiv Nadar University,
I currently work here

Senior Research Fellowship (CSIR)


PBC Fellowship for outstanding postdocs


Sven and Lilly Fellowship, Sweden


Ramalingamswami re-entry fellowship

Scholarly Activity

Journal Publications (accepted or published)

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. DOI: https://doi.org/10.1021/jacs.9b13029

Simone Savino, Annika JE Borg, Alexander Dennig, Martin Pfeiffer, Francesca De Giorgi, Hansjörg Weber, Kshatresh Dutta Dubey, Carme Rovira, Andrea Mattevi, Bernd Nidetzky, Nature Catalysis, 2, 1115-1123, 2019. 

Kshatresh Dutta Dubey* and Sason Shaik. Cytochrome P450—The Wonderful Nanomachine Revealed through Dynamic Simulations of the Catalytic Cycle . Acc. Chem. Res., 2019, 52 (2), pp 389–399

Kshatresh Dutta Dubey* and Sason Shaik. Choreography of the Reductase and P450BM3 Domains Toward Electron Transfer Is Instigated by the Substrate. J. Am. Chem. Soc., 2018, 140 (2), pp 683–690. 

Binju Wang, Jiarui Lu, Kshatresh Dutta Dubey, Geng Gong, Wenzen Lai and Sason Shaik, How do Enzymes Utilize Reactive OH Radicals? Lessons from Nonheme HppE and Fenton Systems. J. Am. Chem. Soc., 2016, 138 (27), pp 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. 

Aitao Li, Binju Wang, Adriana Ilie, Kshatresh Dutta Dubey, Gert Bange, Ivan V Korendovych, Sason Shaik and Manfred Reetz. A redox-mediated Kemp eliminase. Nature Communications, 2017, 8, 14876.

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.