Dr. Parth Sarthi Sen Gupta is an Associate professor in School of Biosciences and Bioengineering, D Y Patil International University. He has published more than 50 research articles and book chapter in reputed peer reviewed Journals. He is a Computational Biologist working in designing and development of therapeutics against various diseases. His research work on COVID19 has been highlighted by various national and international news agencies and recognized by World health organizations.
EDUCATION
Experience
2022 - Present
Assistant Professor (Senior Grade)
School of Bioengineering and Biological Sciences
D Y PATIL INTERNATIONAL UNIVERSITY,Pune
2018 - 2022
Post-Doctoral Research Scientist
Department of Chemical Sciences
Indian Institute of Science Education and Research, Berhampur,Ganjam
RESEARCH, TEACHING, or OTHER INTERESTS
Multidisciplinary, Biotechnology, Biochemistry, Genetics and Molecular Biology, Immunology and Microbiology
Mechanistic insights into ESBL activity of subclass A2 in Class A beta-lactamase revealing a distinct strategy towards conferring drug resistance Riya Karan, Anish Pyne, Saroj K. Panda, Parth S. Sen Gupta, Saugata Hazra Journal of Biomolecular Structure and Dynamics, 2026 actamases) which spread across the bacterial population through horizontal gene transfer causes serious nosocomial infections. Since ESBLs have developed to increase their substrate specificity and hydrolyse most cephalosporins, penicillins, and monobactams, research into them is urgently needed. However, despite attempts functional classification, based on sequence identity, fold similarity, the presence or absence of insertions, particularly in loop regions and mode of action, a universally accepted framework remains elusive. Previous studies have broadly categorized Class A beta-lactamases into subclasses A1 and A2, yet the mechanistic intricacies of subclass A2 only as ESBL demand a more nuanced, multilevel analysis, underlying their role in antibiotic resistance. To bridge this knowledge gap, we employed on a comprehensive investigation encompassing sequence, structure, molecular docking, and dynamic analyses to elucidate the mechanistic approach of antibiotic resistance profiles for these two subclasses. Our sequence and structural studies revealed differences, particularly in insertions, structural alignments, and loop regions, including the omega loop and loops near the active site. Molecular docking study demonstrated better binding of the bigger substrate in the active site cavity of A2 subclass representatives. Dynamic analyses further confirmed our findings, employing root mean square deviation (RMSD), root mean square fluctuation (RMSF), flexibility of the extended and omega loops, radius of gyration (Rg), solvent-accessible surface area (SASA), clustering, hydrogen bonding patterns, principal component analysis (PCA), and free energy landscape (FEL). This study provides insights into the molecular distinctions and resistance mechanisms of these subclasses, paving the way for advanced research in antibiotic resistance and strengthening novel therapeutic strategies.
Comparative binding efficacy of Ivermectin and Remdesivir against the spike protein of Omicron variants: An in silico perspective Ritwik Patra, Parth Sarthi Sen Gupta, Saroj Kumar Panda, Malay Kumar Rana, Suprabhat Mukherjee Indian Journal of Biochemistry and Biophysics, 2025 The recent emergence of SARS-CoV-2 Omicron variants (B.1.1.529) has come out as an added complication in combating COVID-19. Different repurposed drugs like ivermectin, hydroxychloroquine, remdesivir, molnupiravir are being investigated to treat these variants. Herein, we investigate the comparative binding efficacy of ivermectin, remdesivir, hydroxychloroquine, favipiravir, paxlovid, and molnupiravir against the mutant spike protein of omicron variants. Molecular docking data revealed that ivermectin (∆G=-430.56) and remdesivir (∆G=-352.78) exhibit the higher binding efficacy to the spike protein mutants (N501Y, Q493R, Q498R, S373P, S375F, T478K, S371L, H655Y, N679K, P681H) of the Omicron variants, wild type SARS-CoV-2 and a hypothetical spike protein bearing all the mutations. Normal mode analysis and molecular dynamic simulation hinted at the stability of binding of ivermectin and remdesivir to spike protein mutant (T478K) compared to the less active drugs.This study highlights the significance of computational methods in enhancing drug discovery and repurposing through expedited analyses of molecular interactions, stability, and binding efficacy. It serves as an essential preliminary phase in pinpointing the potential therapeutic candidates for subsequent validation via in-vitro and in-vivo investigations. Collectively, this in silico study proposed that ivermectin and remdesivir could serve as promising therapeutics in intervening with the omicron variants.
Dual Inhibition of IDO1 and TDO: A Unified Therapeutic Strategy to Combat Alzheimer’s Disease and Cancer Arpita Robel Khamle, Saroj Kumar Panda, Varshini Dayanand Kore, Suprabhat Mukherjee, Parth Sarthi Sen Gupta ACS Chemical Neuroscience, 2025 The kynurenine pathway, regulated by the enzymes indoleamine 2,3-dioxygenase 1 (IDO1) and tryptophan 2,3-dioxygenase (TDO), plays a pivotal role in immune regulation and neuroinflammation in human. Dysregulation of this pathway has been strongly associated with the pathogenesis of Alzheimer's disease and various cancers. In this study, we present a comprehensive computational investigation to identify potential dual inhibitors of IDO1 and TDO, aiming to simultaneously target the molecular mechanisms underlying these two devastating conditions. A natural compound library was subjected to an integrated screening approach involving virtual screening, ADMET profiling, and molecular dynamics simulations. Our analysis identifies hydroxy sanguinarine, chelirubine, 17-decarboxy-neobitanin, and epicatechin-5-O-glucuronide as the potent leads that exhibited strong binding affinity, favorable pharmacokinetic properties, and stable protein-ligand interactions with both the enzymes. Dual inhibition of IDO1 and TDO is proposed to restore immune surveillance in cancer while mitigating neurodegenerative processes in Alzheimer's disease via modulation of the kynurenine pathway. To the best of our knowledge, this is the first attempt exploring the dual targeting of IDO1 and TDO as a unified therapeutic strategy for combating both Alzheimer's disease and cancer. These findings would provide information for future experimental validation and the development of innovative multitarget therapeutics.
Spike Protein-Fibrinogen Interaction: A Novel Immune Evasion Strategy of SARS-CoV-2? Saroj Kumar Panda, Shashi Singh, Parth Sarthi Sen Gupta ACS Pharmacology and Translational Science, 2025 The host protein fibrinogen has been found to interact with the N-terminal domain (NTD) of the spike protein in SARS-CoV-2. However, the evolutionary benefit of this binding to the virus still remains unclear. Herein, we put forward with rationale and supporting evidence that the binding of fibrinogen to its more conserved NTD is an immune evasion strategy adopted by the virus to outsmart the NTD targeted neutralizing antibodies.
Computational Assessment of Clinical Drugs against SARS-CoV-2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors Saroj Kumar Panda, Pratyush Pani, Parth Sarthi Sen Gupta, Nimai Mahanandia, Malay Kumar Rana Chemphyschem, 2025 The emergence of new SARS‐CoV‐2 variants of concern (VOC) is a propulsion for accelerated potential therapeutic discovery. SARS‐CoV‐2’s main protease (Mpro), essential for host cell viral replication, is a pre‐eminent druggable protein target. Here, we perform extensive drug re‐profiling of the comprehensive Excelra database, which compiles various under‐trial drug candidates for COVID‐19 treatment. For mechanistic understanding, the most promising screened‐out molecules with targets are subjected to molecular dynamics (MD) simulations. Post‐MD analyses demonstrate Darunavir, Ponatinib, and Tomivosertib forming a stable complex with Mpro, characterized by less fluctuation of Cα atoms, smooth and stable root‐mean‐square deviation (RMSD), and robust contact with the active site residues. Likewise, they all have lower binding free energy with Mpro, demonstrating strong affinity. In free energy landscape profiles, the distances from His41 and Cys145 exhibit a single energy minima basin, implying their preponderance in proximity to Mpro's catalytic dyad. Overall, the computational assessment earmarks promising candidates from the Excelra database, emphasizing on carrying out exhaustive biochemical experiments along with clinical trials. The work lays the foundation for potential therapeutic interventions in treating COVID‐19.
Neuroprotective Effect of Potential Phytochemicals in the Prevention of Neurodegenerative Diseases Unnati Darak, Priyatosh Ranjan, Parth Sarthi Sen Gupta Natural Scaffolds for Prevention and Treatment of Neurodegenerative Disorders, 2025 Neurodegenerative disorders (NDs) are highly intricate conditions, typically identified by the progressive build-up of misfolded and aggregated proteins, resulting in the loss of neurons and their synaptic connections. These disorders, including Alzheimer’s disease (AD), prion disease (PrD), Parkinson’s disease (PD), Huntington’s disease (HD), multiple sclerosis (MS), and others, are among the most prevalent diseases worldwide, affecting millions of individuals. Unfortunately, there is currently no specific treatment available for these disorders. While various drugs are available that offer symptomatic relief and improve daily function, the overall outcomes are unsatisfactory. Presently, researchers are focusing on phytopharmaceuticals due to their numerous advantages over synthetic drugs, such as broad-spectrum activity and fewer side effects. The multifactorial efficacy of phytochemicals, with their diverse beneficial properties, including antioxidant, anti-inflammatory, anti-apoptotic, anti-amyloidogenic, mitochondrial repair, and multi-target effects, is drawing attention to bioactive compounds for the management of neurodegenerative disorders. Additionally, phytochemicals have the ability to restore neuronal cell death as agonists of neurotrophic factors, which induce neuroprotection. This chapter discusses the neuroprotective role of various phytochemicals and their derivatives against the most frequent neurodegenerative disorders, such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and prion disease.
In silico evidence of monkeypox F14 as a ligand for the human TLR1/2 dimer Ankita Chakraborty, Nabarun Chandra Das, Parth Sarthi Sen Gupta, Saroj Kumar Panda, Malay Kumar Rana, Srinivasa Reddy Bonam, Jagadeesh Bayry, Suprabhat Mukherjee Frontiers in Immunology, 2025 Recent emergence of zoonotic monkeypox virus (Mpox) in human has triggered the virologists to develop plausible preventive measures. Hitherto, our understanding on the mechanism of immunopathogenesis of Mpox infection is elusive. However, available experimental evidences suggest induction of inflammation as the main cause of pathogenesis. Toll-like receptors (TLRs) are critical in initiating and modulating the host immune response to pathogens. Inflammatory responses observed in various poxvirus infections have, in fact, been shown to be mediated through TLR activation. Therefore, by in silico approaches, this study seeks to identify the Mpox antigen(s) (MAg) that are most likely to interact with human cell-surface TLRs. The Mpox proteomics data available in UniProt database contain 174 protein sequences, among which 105 immunoreactive proteins were modeled for 3D structure and examined for comparative protein-protein interactions with the TLRs through molecular docking and molecular dynamics simulation. F14, an 8.28 kDa infective protein of Mpox, was found to exhibit strong binding affinity (ΔG=-12.5 Kcal mol-1) to TLR1/2 dimer to form a compact thermodynamically stable protein complex. Interestingly, a significant level of conformational change was also observed in both F14 and TLR6 while forming F14-TLR1/2 complex. Based on these data we propose F14 as a putative ligand of human TLR1/2 to initiate proinflammatory signaling in the Mpox-infected host.
Integrated experimental and computational evaluation of novel benzopyran-2-one congeners as reactive oxygen species scavengers in inflammation M Bhalla, S Shukla, VR Gujrati, AK Saxena, K Shanker, VD Kore, ... Computers in Biology and Medicine 209, 111701 , 2026 2026
Mechanistic insights into ESBL activity of subclass A2 in Class A beta-lactamase revealing a distinct strategy towards conferring drug resistance R Karan, A Pyne, SK Panda, PS Sen Gupta, S Hazra Journal of Biomolecular Structure and Dynamics 44 (8), 3964-3985 , 2026 2026
In silico evidence of monkeypox F14 as a ligand for the human A Chakraborty¹, NC Das¹, PSS Gupta, SK Panda, MK Rana, SR Bonam Innovative Insights into Pattern Recognition and Signaling in Innate Immunity , 2026 2026
A simple and sensitive colorimetric biosensor based on three different hydrothermally synthesized AuNP-CQD nanocolloids functionalized with aptamer for the biosensing of … A Dey, PSS Gupta, A Lakhera, R Bhatla, DK Yadav, D Hazra, H Pandya, ... Surfaces and Interfaces, 109483 , 2026 2026
Decoding Ceftazidime-Avibactam Resistance in Newly Identified Klebsiella pneumoniae Carbapenemase (KPC) 107 Variant by Modulating the Active Site … R Karan, K Dhankhar, A Singh, SK Panda, T Sen, PS Sen Gupta, S Hazra ACS Infectious Diseases , 2025 2025 Citations: 1
Comparative binding efficacy of Ivermectin and Remdesivir against the spike protein of Omicron variants: An in silico perspective R Patra, PSS Gupta, SK Panda, MK Rana, S Mukherjee Indian Journal of Biochemistry and Biophysics (IJBB) 62 (12), 1369-1381 , 2025 2025
Corrigendum to" Targeting mitochondrial ribosomal protein expression by andrographolide and melatonin for colon cancer treatment"[Cancer Lett. 619 (2025) 1-11 217647] A Midde, N Arri, T Kristian, S Mukherjee, PSS Gupta, Y Zhang, ... Cancer letters 630, 217784 , 2025 2025
Dual Inhibition of IDO1 and TDO: A Unified Therapeutic Strategy to Combat Alzheimer’s Disease and Cancer AR Khamle, SK Panda, VD Kore, S Mukherjee, PS Sen Gupta ACS Chemical Neuroscience 16 (17), 3312-3322 , 2025 2025 Citations: 2
Targeting mitochondrial ribosomal protein expression by andrographolide and melatonin for colon cancer treatment A Midde, N Arri, T Kristian, S Mukherjee, PSS Gupta, Y Zhang, ... Cancer letters 619, 217647 , 2025 2025 Citations: 9
In silico evaluation of S -adenosyl-L-homocysteine analogs as inhibitors of nsp14-viral cap N7 methyltranferase and PLpro of SARS-CoV-2: synthesis, molecular … R Srivastava, SK Panda, PS Sen Gupta, A Chaudhary, F Naaz, AK Yadav, ... Journal of Biomolecular Structure and Dynamics 43 (7), 3258-3275 , 2025 2025 Citations: 2
Neuroprotective Effect of Potential Phytochemicals in the Prevention of Neurodegenerative Diseases U Darak, P Ranjan, PSS Gupta Natural Scaffolds for Prevention and Treatment of Neurodegenerative … , 2025 2025
Spike Protein–Fibrinogen Interaction: A Novel Immune Evasion Strategy of SARS-CoV-2? SK Panda, S Singh, PS Sen Gupta ACS Pharmacology & Translational Science 8 (4), 1182-1184 , 2025 2025 Citations: 4
In Silico Evidence of Monkeypox F14 as a Ligand for the Human TLR1/2 Dimer A Chakraborty, DN Chandra Das, PSS Gupta, SK Panda, MK Rana, ... Frontiers in Immunology 16, 1544443 , 2025 2025 Citations: 5
Natural Scaffolds for Prevention and Treatment of Neurodegenerative Disorders NK Sethiya, DN Chauhan, K Shah, NS Chauhan CRC Press , 2025 2025 Citations: 1
Front Cover: Computational Assessment of Clinical Drugs against SARS‐CoV‐2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors (ChemPhysChem 2/2025) SK Panda, P Pani, PS Sen Gupta, N Mahanandia, M Kumar Rana ChemPhysChem 26 (2), e202580201 , 2025 2025
Neuroprotective Effect of Potential Phytochemicals in the Prevention of Neurodegenerative Diseases PSSG Unnati Darak, Priyatosh Ranjan CRC Press, 17 , 2025 2025
Computational Assessment of Clinical Drugs against SARS-CoV-2: Foreseeing Molecular Mechanisms and Potent Mpro Inhibitors SK Panda, P Pani, PSS Gupta, NC Mahanandia, MK Rana Chemphyschem, e202400814 , 2025 2025 Citations: 3
Revisiting Luteolin Against the Mediators of Human Metastatic Colorectal Carcinoma: A Biomolecular Approach A Chakraborty, A Midde, P Chakraborty, S Adhikary, S Kumar, N Arri, ... Journal of cellular biochemistry, e30654 , 2025 2025 Citations: 8
Genotyping, in silico screening and molecular dynamics simulation of SNPs of MGMT and ERCC1 gene in lung cancer patients treated with platinum-based doublet chemotherapy S Singh, A Gupta, N Singh, PS Sengupta, SK Panda, S Sharma Journal of Biomolecular Structure and Dynamics 42 (20), 11231-11250 , 2024 2024 Citations: 9
OPEN ACCESS EDITED BY PSS Gupta, M Letek, VP Dwivedi, M Arumugam Design and development of new therapeutics against infectious diseases using … , 2024 2024
MOST CITED SCHOLAR PUBLICATIONS
Binding Mechanism and Structural Insights into the Identified Protein Target of Covid-19 with In-Vitro Effective Drug Ivermectin PSS Gupta, S Biswal, SK Panda, AK Ray, MK Rana Journal of Biomolecular Structure and Dynamics 38 (1) , 2020 2020 Citations: 79
Computer-aided discovery of bis-indole derivatives as multi-target drugs against cancer and bacterial infections: DFT, docking, virtual screening, and molecular dynamics studies PSS Gupta, HR Bhat, S Biswal, MK Rana Journal of Molecular Liquids 320, 114375 , 2020 2020 Citations: 67
Salt-bridge energetics in halophilic proteins A Nayek, PS Sen Gupta, S Banerjee, B Mondal, AK Bandyopadhyay Plos one 9 (4), e93862 , 2014 2014 Citations: 63
ACE-2-derived biomimetic peptides for the inhibition of spike protein of SARS-CoV-2 SK Panda, PS Sen Gupta, S Biswal, AK Ray, MK Rana Journal of proteome research 20 (2), 1296-1303 , 2021 2021 Citations: 58
Designing AbhiSCoVac-A single potential vaccine for all ‘corona culprits’: Immunoinformatics and immune simulation approaches A Choudhury, PSS Gupta, SK Panda, MK Rana, S Mukherjee Journal of molecular liquids 351, 118633 , 2022 2022 Citations: 55
Designing efficient multi-epitope peptide-based vaccine by targeting the antioxidant thioredoxin of bancroftian filarial parasite S Gorai, NC Das, PSS Gupta, SK Panda, MK Rana, S Mukherjee Infection, Genetics and Evolution 98, 105237 , 2022 2022 Citations: 51
Repurposing of FDA-approved drugs as potential inhibitors of the SARS-CoV-2 main protease: Molecular insights into improved therapeutic discovery AK Ray, PSS Gupta, SK Panda, S Biswal, U Bhattacharya, MK Rana Computers in biology and medicine 142, 105183 , 2022 2022 Citations: 50
Alkylated benzimidazoles: Design, synthesis, docking, DFT analysis, ADMET property, molecular dynamics and activity against HIV and YFV R Srivastava, SK Gupta, F Naaz, PSS Gupta, M Yadav, VK Singh, A Singh, ... Computational biology and chemistry 89, 107400 , 2020 2020 Citations: 50
Cell Surface Fibroblast Activation Protein-2 (Fap2) of Fusobacterium nucleatum as a Vaccine Candidate for Therapeutic Intervention of Human Colorectal Cancer … S Padma, R Patra, PS Sen Gupta, SK Panda, MK Rana, S Mukherjee Vaccines 11 (3), 525 , 2023 2023 Citations: 49
Binding insight of clinically oriented drug famotidine with the identified potential target of SARS-CoV-2 PS Sen Gupta, S Biswal, D Singha, MK Rana Journal of Biomolecular Structure and Dynamics 39 (14), 5327-5333 , 2021 2021 Citations: 47
Anti-HIV potential of diarylpyrimidine derivatives as non-nucleoside reverse transcriptase inhibitors: Design, synthesis, docking, TOPKAT analysis and molecular dynamics … VK Singh, R Srivastava, PSS Gupta, F Naaz, H Chaurasia, R Mishra, ... Journal of Biomolecular Structure and Dynamics 39 (7), 2430-2446 , 2021 2021 Citations: 47
Designing of a novel multi-epitope peptide based vaccine against Brugia malayi: An in silico approach NC Das, R Patra, PSS Gupta, P Ghosh, M Bhattacharya, MK Rana, ... Infection, Genetics and Evolution 87, 104633 , 2021 2021 Citations: 41
Big data analytics for healthcare: datasets, techniques, life cycles, management, and applications P Keikhosrokiani Academic Press , 2022 2022 Citations: 36
In-silico evidences on filarial cystatin as a putative ligand of human TLR4 NC Das, PS Sen Gupta, S Biswal, R Patra, MK Rana, S Mukherjee Journal of Biomolecular Structure and Dynamics 40 (19), 8808-8824 , 2022 2022 Citations: 35
Identification and investigation of a cryptic binding pocket of the P37 envelope protein of monkeypox virus by molecular dynamics simulations PS Sen Gupta, SK Panda, AK Nayak, MK Rana The Journal of Physical Chemistry Letters 14 (13), 3230-3235 , 2023 2023 Citations: 31
Ivermectin, famotidine, and doxycycline: a suggested combinatorial therapeutic for the treatment of COVID-19 PS Sen Gupta, MK Rana ACS Pharmacology & Translational Science 3 (5), 1037-1038 , 2020 2020 Citations: 29
SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files PSS Gupta, S Mondal, B Mondal, RNU Islam, S Banerjee, ... Bioinformation 10 (3), 164-166 , 2014 2014 Citations: 27
Reverse vaccinology assisted design of a novel multi-epitope vaccine to target Wuchereria bancrofti cystatin: An immunoinformatics approach NC Das, PSS Gupta, SK Panda, MK Rana, S Mukherjee International Immunopharmacology 115, 109639 , 2023 2023 Citations: 25
SBION2: Analyses of salt bridges from multiple structure files, version 2 PSS Gupta, A Nayek, S Banerjee, P Seth, S Das, VP Sur, C Roy, ... Bioinformation 11 (1), 39 , 2015 2015 Citations: 23
