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Kshatresh Dutta Dubey, Ph. D - Publications

Affiliations: 
Institute of Chemistry Hebrew University, Jerusalem, Jerusalem, Israel 
Area:
Computational Biophysics
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41/58 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Siddiqui SA, Stuyver T, Shaik S, Dubey KD. Designed Local Electric Fields-Promising Tools for Enzyme Engineering. Jacs Au. 3: 3259-3269. PMID 38155642 DOI: 10.1021/jacsau.3c00536  0.642
2023 Taher M, Dubey KD, Mazumdar S. Computationally guided bioengineering of the active site, substrate access pathway, and water channels of thermostable cytochrome P450, CYP175A1, for catalyzing the alkane hydroxylation reaction. Chemical Science. 14: 14316-14326. PMID 38098704 DOI: 10.1039/d3sc02857g  0.332
2023 Kardam V, Dubey KD. Tyr 118-Mediated Electron Transfer is Key to the Chlorite Decomposition in Heme-Dependent Chlorite Dismutase. Inorganic Chemistry. 62: 18322-18330. PMID 37885054 DOI: 10.1021/acs.inorgchem.3c03334  0.767
2023 Siddiqui SA, Shaik S, Kalita S, Dubey KD. A porphyrin-based molecular cage guided by designed local-electric field is highly selective and efficient. Chemical Science. 14: 10329-10339. PMID 37772104 DOI: 10.1039/d3sc01720f  0.752
2023 Fuhrman Javitt L, Kalita S, Dubey KD, Ehre D, Shaik S, Lahav M, Lubomirsky I. Electro-Freezing of Supercooled Water Is Induced by Hydrated Al and Mg Ions: Experimental and Theoretical Studies. Journal of the American Chemical Society. PMID 37602827 DOI: 10.1021/jacs.3c05004  0.743
2023 Ahmad A, Siddiqui SA, Mittal G, Sukumar N, Dubey KD, Kapat A. Design and Synthesis of Co-Initiators via Base Catalysed Sequential Conjugate Addition: Application in Photoinduced Radical Polymerisation Reaction. Chemistry (Weinheim An Der Bergstrasse, Germany). e202301844. PMID 37503865 DOI: 10.1002/chem.202301844  0.562
2023 Tripathi A, Dubey KD. A single site mutation can induce functional promiscuity in homoserine kinase. Organic & Biomolecular Chemistry. PMID 37212194 DOI: 10.1039/d3ob00459g  0.755
2023 Singh W, Santos SFG, Yadav S, Black GW, Dubey KD. Substrate Conformation Regulates Aromatic C-H Vs C-F Bond Activation in Heme-Dependent Tyrosine Hydroxylase. Biochemistry. PMID 37092990 DOI: 10.1021/acs.biochem.3c00087  0.637
2023 Yadav R, Munan S, Kardam V, Dubey KD, Samanta A. Esterase specific Fluorescent Probe: Mechanistic Understanding Using QM/MM Calculation and Cell States Discrimination. Chemistry (Weinheim An Der Bergstrasse, Germany). e202300244. PMID 37014630 DOI: 10.1002/chem.202300244  0.775
2023 Yadav S, Shaik S, Dubey KD. Decarboxylation and Protonation Enigma in the H85Q Mutant of Cytochrome P450. The Journal of Physical Chemistry. B. PMID 36959730 DOI: 10.1021/acs.jpcb.3c00143  0.694
2023 Kalita S, Bergman H, Dubey KD, Shaik S. How Can Static and Oscillating Electric Fields Serve in Decomposing Alzheimer's and Other Senile Plaques? Journal of the American Chemical Society. PMID 36735972 DOI: 10.1021/jacs.2c12305  0.732
2022 Dubey KD, Stuyver T, Shaik S. Local Electric Fields: From Enzyme Catalysis to Synthetic Catalyst Design. The Journal of Physical Chemistry. B. PMID 36469939 DOI: 10.1021/acs.jpcb.2c06422  0.736
2022 T G S, Siddiqui SA, Dubey KD. Unraveling key interactions and the mechanism of demethylation during hAGT-mediated DNA repair simulations. Frontiers in Molecular Biosciences. 9: 975046. PMID 36188219 DOI: 10.3389/fmolb.2022.975046  0.601
2022 Kardam V, Kalita S, Dubey KD. Computations reveal a crucial role of an aromatic dyad in the catalytic function of plant cytochrome P450 mint superfamily. Journal of Inorganic Biochemistry. 237: 111990. PMID 36115330 DOI: 10.1016/j.jinorgbio.2022.111990  0.75
2022 Yadav S, Kardam V, Tripathi A, T G S, Dubey KD. The Performance of Different Water Models on the Structure and Function of Cytochrome P450 Enzymes. Journal of Chemical Information and Modeling. PMID 36073971 DOI: 10.1021/acs.jcim.2c00505  0.724
2022 Guha S, El-Deeb IY, Yadav S, Das R, Dubey KD, Baruah M, Ludovic G, Sen S. Capturing a Pentacyclic Fragment-Based Library Derived from Perophoramidine: Their Design, Synthesis and Evaluation as Anticancer Compounds via DNA Double-Strand Breaks (DSB) and PARP-1 Inhibition. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 35952312 DOI: 10.1002/chem.202202405  0.605
2022 Singh W, Santos SFG, James P, Black GW, Huang M, Dubey KD. Single-Site Mutation Induces Water-Mediated Promiscuity in Lignin Breaking Cytochrome P450. Acs Omega. 7: 21109-21118. PMID 35755387 DOI: 10.1021/acsomega.2c00524  0.332
2022 Dwivedi M, Mukhopadhyay S, Yadav S, Dubey KD. A multidrug efflux protein in Mycobacterium tuberculosis; tap as a potential drug target for drug repurposing. Computers in Biology and Medicine. 146: 105607. PMID 35617724 DOI: 10.1016/j.compbiomed.2022.105607  0.593
2022 Devi SS, Kardam V, Dubey KD, Dwivedi M. Deciphering the immunogenic T-cell epitopes from spike protein of SARS-CoV-2 concerning the diverse population of India. Journal of Biomolecular Structure & Dynamics. 1-20. PMID 35132938 DOI: 10.1080/07391102.2022.2037462  0.734
2022 Yadav S, Shaik S, Siddiqui SA, Kalita S, Dubey KD. Local Electric Fields Dictate Function: The Different Product Selectivities Observed for Fatty Acid Oxidation by Two Deceptively Very Similar P450-Peroxygenases OleT and BSβ. Journal of Chemical Information and Modeling. PMID 35129977 DOI: 10.1021/acs.jcim.1c01453  0.751
2021 Dubey KD, Wang B, Si Y, Tarique Moin S. Editorial: Molecular Dynamics Simulations of Metalloproteins and Metalloenzymes. Frontiers in Chemistry. 9: 789299. PMID 34912786 DOI: 10.3389/fchem.2021.789299  0.385
2021 Kalita S, Shaik S, Dubey KD. MD simulations and QM/MM calculations reveal the key mechanistic elements which are responsible for the efficient C-H amination reaction performed by a bioengineered P450 enzyme. Chemical Science. 12: 14507-14518. PMID 34881002 DOI: 10.1039/d1sc03489h  0.787
2021 Dubey KD, Singh W. Simulations reveal the key role of Arg15 in the promiscuous activity in the HisA enzyme. Organic & Biomolecular Chemistry. 19: 10652-10661. PMID 34854451 DOI: 10.1039/d1ob02029c  0.324
2021 Siddiqui SA, Dubey KD. Can the local electric field be a descriptor of catalytic activity? A case study on chorismate mutase. Physical Chemistry Chemical Physics : Pccp. PMID 34757367 DOI: 10.1039/d1cp03978d  0.631
2021 Banerjee S, Yadav S, Banerjee S, Fakayode SO, Parvathareddy J, Reichard W, Surendranathan S, Mahmud F, Whatcott R, Thammathong J, Meibohm B, Miller DD, Jonsson CB, Dubey KD. Drug Repurposing to Identify Nilotinib as a Potential SARS-CoV-2 Main Protease Inhibitor: Insights from a Computational and Study. Journal of Chemical Information and Modeling. PMID 34666487 DOI: 10.1021/acs.jcim.1c00524  0.6
2021 Yadav S, Pandey V, Kumar Tiwari R, Ojha RP, Dubey KD. Does Antibody Stabilize the Ligand Binding in GP120 of HIV-1 Envelope Protein? Evidence from MD Simulation. Molecules (Basel, Switzerland). 26. PMID 33466381 DOI: 10.3390/molecules26010239  0.62
2020 Kalita S, Shaik S, Kisan HK, Dubey KD. 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. 10: 11481-11492. DOI: 10.1021/Acscatal.0C02775  0.535
2019 Dubey KD, Shaik S. Cytochrome P450-The Wonderful Nanomachine Revealed through Dynamic Simulations of the Catalytic Cycle. Accounts of Chemical Research. PMID 30633519 DOI: 10.1021/Acs.Accounts.8B00467  0.585
2018 Dubey KD, Shaik S. Choreography of the Reductase and P450BM3 Domains Toward Electron Transfer Is Instigated by the Substrate. Journal of the American Chemical Society. PMID 29277994 DOI: 10.1021/Jacs.7B10072  0.532
2017 Dubey KD, Wang B, Vajpai M, Shaik S. MD simulations and QM/MM calculations show that single-site mutations of cytochrome P450alter the active site's complexity and the chemoselectivity of oxidation without changing the active species. Chemical Science. 8: 5335-5344. PMID 29568477 DOI: 10.1039/C7Sc01932G  0.629
2017 Li A, Wang B, Ilie A, Dubey KD, Bange G, Korendovych IV, Shaik S, Reetz MT. A redox-mediated Kemp eliminase. Nature Communications. 8: 14876. PMID 28348375 DOI: 10.1038/Ncomms14876  0.642
2016 Wang B, Lu J, Dubey KD, Dong G, Lai W, Shaik S. How do Enzymes Utilize Reactive OH radicals? Lessons from Non-Heme HppE and Fenton Systems. Journal of the American Chemical Society. PMID 27309496 DOI: 10.1021/Jacs.6B03555  0.696
2016 Ramanan R, Dubey KD, Wang B, Mandal D, Shaik S. Emergence of Function in P450-Proteins: A Combined QM/MM and MD Study of the Reactive Species in the H2O2-Dependent Cytochrome P450SPα and Its Regio- and Enantioselective Hydroxylation of Fatty Acids. Journal of the American Chemical Society. PMID 27059179 DOI: 10.1021/Jacs.6B01716  0.722
2015 Dubey KD, Wang B, Shaik S. Molecular Dynamics and QM/MM Calculations predict the Substrate-Induced Gating of Cytochrome P450 BM3 and the Regio and Stereo-selctivity of Fatty Acid Hydroxylation. Journal of the American Chemical Society. PMID 26716578 DOI: 10.1021/Jacs.5B08737  0.633
2015 Wang B, Li C, Dubey KD, Shaik S. Quantum mechanical/molecular mechanical calculated reactivity networks reveal how cytochrome P450cam and Its T252A mutant select their oxidation pathways. Journal of the American Chemical Society. 137: 7379-90. PMID 26011529 DOI: 10.1021/Jacs.5B02800  0.674
2015 Wang B, Li C, Dubey KD, Shaik S. Quantum Mechanical/Molecular Mechanical Calculated Reactivity Networks Reveal How Cytochrome P450cam and Its T252A Mutant Select Their Oxidation Pathways Journal of the American Chemical Society. 137: 7379-7390. DOI: 10.1021/jacs.5b02800  0.608
2014 Chaubey AK, Dubey KD, Ojha RP. MD simulation of LNA-modified human telomeric G-quadruplexes: a free energy calculation Medicinal Chemistry Research. DOI: 10.1007/S00044-014-1182-Y  0.349
2013 Dubey KD, Tiwari RK, Ojha RP. Recent advances in protein-ligand interactions: molecular dynamics simulations and binding free energy. Current Computer-Aided Drug Design. 9: 518-31. PMID 24138393 DOI: 10.2174/15734099113096660036  0.321
2012 Chaubey AK, Dubey KD, Ojha RP. Stability and free energy calculation of LNA modified quadruplex: A molecular dynamics study Journal of Computer-Aided Molecular Design. 26: 289-299. PMID 22456858 DOI: 10.1007/S10822-012-9548-Z  0.33
2012 Dubey KD, Ojha RP. Conformational flexibility, binding energy, role of salt bridge and alanine-mutagenesis for c-Abl kinase complex Journal of Molecular Modeling. 18: 1679-1689. PMID 21811775 DOI: 10.1007/S00894-011-1199-9  0.314
2011 Dubey KD, Ojha RP. Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor. Journal of Biological Physics. 37: 69-78. PMID 22210962 DOI: 10.1007/S10867-010-9199-Z  0.329
Low-probability matches (unlikely to be authored by this person)
2011 Dubey KD, Ojha RP. Conformational flexibility and binding energy profile of c-Abl tyrosine kinase complexed with Imatinib: An insight from MD study Molecular Simulation. 37: 1151-1163. DOI: 10.1080/08927022.2011.586346  0.298
2017 Dubey KD, Tiwari G, Ojha RP. Targeting domain-III hinging of dengue envelope (DENV-2) protein by MD simulations, docking and free energy calculations. Journal of Molecular Modeling. 23: 102. PMID 28255859 DOI: 10.1007/S00894-017-3259-2  0.293
2020 Sar S, Tripathy A, Dubey KD, Sen S. Iodine catalyzed aerobic diazenylation-amination of indole derivatives. The Journal of Organic Chemistry. PMID 32019297 DOI: 10.1021/Acs.Joc.9B03392  0.292
2012 Dubey KD, Chaubey AK, Ojha RP. Role of polarization in ligand docking and binding affinity prediction for inhibitors of dengue virus Medicinal Chemistry Research. 21: 1030-1038. DOI: 10.1007/S00044-011-9617-1  0.278
2011 Dubey KD, Chaubey AK, Ojha RP. Role of pH on dimeric interactions for DENV envelope protein: An insight from molecular dynamics study Biochimica Et Biophysica Acta - Proteins and Proteomics. 1814: 1796-1801. PMID 22005292 DOI: 10.1016/J.Bbapap.2011.09.012  0.268
2021 Chauhan J, Maddi SR, Dubey KD, Sen S. Developing C2-Aroyl Indoles as Novel Inhibitors of IDO1 and Understanding Their Mechanism of Inhibition Mass Spectroscopy, QM/MM Calculations and Molecular Dynamics Simulation. Frontiers in Chemistry. 9: 691319. PMID 34336787 DOI: 10.3389/fchem.2021.691319  0.268
2022 Rai RK, Karri R, Dubey KD, Roy G. Regulation of Tyrosinase Enzyme Activity by Glutathione Peroxidase Mimics. Journal of Agricultural and Food Chemistry. PMID 35861245 DOI: 10.1021/acs.jafc.2c02359  0.261
2019 Savino S, Borg AJE, Dennig A, Pfeiffer M, de Giorgi F, Weber H, Dubey KD, Rovira C, Mattevi A, Nidetzky B. Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis. Nature Catalysis. 2: 1115-1123. PMID 31844840 DOI: 10.1038/s41929-019-0382-8  0.252
2013 Dubey KD, Chaubey AK, Ojha RP. Stability of trimeric DENV envelope protein at low and neutral pH: An insight from MD study Biochimica Et Biophysica Acta - Proteins and Proteomics. 1834: 53-64. PMID 22940270 DOI: 10.1016/J.Bbapap.2012.08.014  0.242
2023 Maurya V, Singh R, Singh RK, Pandey S, Yadav P, Parashar P, Gaind R, Dubey KD, Naresh Patwari G, Tandon V. Unraveling topoisomerase IA gate dynamics in presence of PPEF and its preclinical evaluation against multidrug-resistant pathogens. Communications Biology. 6: 195. PMID 36807602 DOI: 10.1038/s42003-023-04412-1  0.165
2023 Chauhan J, Cecon E, Labani N, Gbahou F, Real F, Bomsel M, Dubey KD, Das R, Dam J, Jockers R, Sen S. Development of indolealkylamine derivatives as potential multi-target agents for COVID-19 treatment. European Journal of Medicinal Chemistry. 249: 115152. PMID 36724633 DOI: 10.1016/j.ejmech.2023.115152  0.163
2024 Patel M, Jaiswal A, Naseer A, Tripathi A, Joshi A, Minocha T, Kautu A, Gupta S, Joshi KB, Pandey MK, Kumar R, Dubey KD, Nazir A, Verma S, Gour N. Amyloidogenic Propensity of Metabolites in the Uric Acid Pathway and Urea Cycle Critically Impacts the Etiology of Metabolic Disorders. Acs Chemical Neuroscience. PMID 38369717 DOI: 10.1021/acschemneuro.3c00563  0.158
2017 Sur S, Tiwari V, Sinha D, Kamran MZ, Dubey KD, Suresh Kumar G, Tandon V. Naphthalenediimide-Linked Bisbenzimidazole Derivatives as Telomeric G-Quadruplex-Stabilizing Ligands with Improved Anticancer Activity. Acs Omega. 2: 966-980. PMID 30023623 DOI: 10.1021/acsomega.6b00523  0.141
2022 Kumar A, Chauhan J, Dubey KD, Sen S, Munshi P. Tuning Potency of Bioactive Molecules via Polymorphic Modifications: A Case Study. Molecular Pharmaceutics. PMID 35099977 DOI: 10.1021/acs.molpharmaceut.1c01018  0.128
2021 Maiti P, Manna J, Thammathong J, Evans B, Dubey KD, Banerjee S, Dunbar GL. Tetrahydrocurcumin Has Similar Anti-Amyloid Properties as Curcumin:  In Vitro Comparative Structure-Activity Studies. Antioxidants (Basel, Switzerland). 10. PMID 34679727 DOI: 10.3390/antiox10101592  0.124
2011 Dubey KD, Ojha RP. Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor Journal of Biological Physics. 37: 69-78. DOI: 10.1007/s10867-010-9199-z  0.108
2011 Dubey KD, Ojha RP. Computational techniques in binding affinity prediction of drugs Advanced Methods and Applications in Chemoinformatics: Research Progress and New Applications. 333-347. DOI: 10.4018/978-1-60960-860-6.ch015  0.07
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