About Me
My research focuses on integrating computational chemistry, structural biology and structural bioinformatics to utilize in rational and tailored drug design and to understand the molecular mechanism of the underlying diseases mechanism and the biological processes. More specifically, I aim to develop and apply computational frameworks for rational drug design targeting proteins involved in various infectious diseases and neurological disorders.
Background & Current Research
During my doctoral and postdoctoral training, I have developed expertise in quantum mechanical calculations, molecular dynamics simulations, pharmacophore design, and machine learning approaches for understanding molecular biology and small molecule drug discovery. My work has included studying various noncovalent interactions like hydrogen bonds, halogen bonds and chalcogen bonds using quantum mechanical calculations, studying protein-protein and protein-membrane interactions using molecular dynamics simulation and designing novel drugs utilizing pharmacophore modeling, virtual screening and molecular docking.
I have successfully designed several small molecule inhibitors and/or studied protein-inhibitor interactions targeting PfATP4 (malaria), ribonucleoprotein complex assembly (influenza), PfCyt bc1 complex (malaria), Dopamine D3 receptor (neural and other neurodegenerative diseases), and Dopamine Transporter (addiction, and neuropsychiatric diseases). I studied the membrane pore-forming activities of various antimicrobial peptides and bacterial toxins. I have developed an implicit curve membrane model to study the curvature sensitive and curvature generating peptides which is implemented in CHARMM MD simulation package. Additionally, I had been involved in analyzing RNAseq data of various biological samples utilizing differential gene expression analysis, WGCNA, GO enrichment analysis and KEGG pathways analysis.
These experiences have shaped my central research philosophy: integrating bioinformatics and physics-based modeling with data-driven AI approaches to accelerate the identification of bioactive compounds, optimizing their selectivity and pharmacokinetic profiles.
Research Interests
Publications
Journal Articles — newest first
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2025Molecular basis of influenza ribonucleoprotein complex assembly and processive RNA synthesisScience, 2025; 388(6748): eadq7597
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2024Biased Signaling Agonists Promote Distinct Phosphorylation and Conformational States of the Dopamine D3 ReceptorInternational Journal of Molecular Sciences, 2024; 25(19): 10470
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20243-Position Biaryl Endochin-like Quinolones with Enhanced Antimalarial PerformanceACS Infectious Diseases, 2024; 10(7): 2419–2442
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2024Acute Administration of HIV-1 Tat Protein Drives Glutamatergic Alterations in a Rodent Model of HIV-Associated Neurocognitive DisordersMolecular Neurobiology, 2024; 61(10): 8467–8480
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2024Mutational Analysis of an Antimalarial Drug Target PfATP4PNAS, 2024; 121(20): e2321066121
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2024EAAT2 activation regulates glutamate excitotoxicity and reduces impulsivity in a rodent model of Parkinson's diseaseMolecular Neurobiology, 2024
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2023Overview of the structure and function of the dopamine transporter and its protein interactionsFrontiers in Physiology, 2023; 14: 1150234
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2023Monoterpenoid aryl hydrocarbon receptor allosteric antagonists protect against ultraviolet skin damage in female miceNature Communications, 2023; 14(1): 2728
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2021Distinct Modes of Action of IAPP Oligomers on MembranesJournal of Chemical Information and Modeling, 2021; 61(9): 4645–4655
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2021Mechanism of negative membrane curvature generation by I-BAR domainsStructure, 2021; 29(12): 1440–1452.e4
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2021Lipid interactions of an actinoporin pore-forming oligomerBiophysical Journal, 2021; 120(8): 1357–1366
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2020Experimental and Computational Characterization of Oxidized and Reduced Protegrin Pores in Lipid BilayersThe Journal of Membrane Biology, 2020; 253(3): 287–298
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2020Mechanisms of negative membrane curvature sensing and generation by ESCRT III subunit Snf7Protein Science, 2020; 29(6): 1473–1485
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2018Membrane Curvature Sensing by Amphipathic Helices: Insights from Implicit Membrane ModelingBiophysical Journal, 2018; 114(9): 2128–2141
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2016Sulfur-Oxygen Chalcogen Bonding Mediates AdoMet Recognition in the Lysine Methyltransferase SET7/9ACS Chemical Biology, 2016; 11(3): 748–754
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2016Enhancing the Reduction Potential of Quinones via Complex FormationThe Journal of Organic Chemistry, 2016; 81(10): 4316–4324
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2016NX...Y halogen bonds: Comparison with NH...Y H-bonds and CX...Y halogen bondsPhysical Chemistry Chemical Physics, 2016; 18(27): 18015–18023
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2015Angular dependence of hydrogen bond energy in neutral and charged systems containing CH and NH proton donorsChemical Physics Letters, 2015; 630: 6–11
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2015Anionic CH...X⁻ Hydrogen Bonds: Origin of Their Strength, Geometry, and Other PropertiesChemistry – A European Journal, 2015; 21(4): 1474–1481
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2016Building a Better Halide Receptor: Optimum Choice of Spacer, Binding Unit, and Halo substitutionChemPhysChem, 2016; 17(6): 836–844
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2015Competitive Halide Binding by Halogen Versus Hydrogen Bonding: Bis-triazole PyridiniumChemistry – A European Journal, 2015; 21(38): 13330–13335
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2015Long-range behavior of non-covalent bonds: Neutral and charged H-bonds, pnicogen, chalcogen, and halogen bondsChemical Physics, 2015; 456: 34–40
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2015Microsolvation of anions by molecules forming CH...X⁻ hydrogen bondsChemical Physics, 2015; 463: 137–144
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2015Substituent Effects on the Binding of Halides by Neutral and Dicationic Bis(triazolium) ReceptorsThe Journal of Physical Chemistry A, 2015; 119(52): 13064–13073
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2014Effect of Ionic Charge on the CH...π Hydrogen BondThe Journal of Physical Chemistry A, 2014; 118(40): 9575–9587
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2013Sustained Water Oxidation by a Catalyst Cage-Isolated in a Metal-Organic FrameworkAngewandte Chemie International Edition, 2013; 52(28): 7224–7227
Conference Presentations — newest first
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Conformational analysis of phosphorylated Dopamine transporter and its interactions with Dopamine D3 receptorMid-Atlantic Pharmacology Society Annual Meeting, Philadelphia, PA, 2025
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Structure-activity relationship and computational modeling of pyrazole amide core-based PfATP4 inhibitorsGordon Research Conference, East Greenwich, RI, 2024
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Molecular Characterization of the Interactions between Dopamine Transporter and Dopamine D3 ReceptorMid-Atlantic Pharmacology Society Annual Meeting, Philadelphia, PA, 2024
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Molecular Characterization of the Interactions between Dopamine Transporter and Dopamine D3 ReceptorDiscovery Day, Philadelphia, PA, 2024
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Molecular Mechanisms of Agonist Dependent Biased Signaling of Dopamine D3 ReceptorsMid-Atlantic Pharmacology Society Annual Meeting, Philadelphia, PA, 2023
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Molecular Mechanisms of Agonist Dependent Biased Signaling of Dopamine D3 ReceptorsDiscovery Day, Philadelphia, PA, 2023
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Molecular mechanisms of Agonist dependent biased signaling of Dopamine D3 ReceptorsNeuroscience Meeting, Washington, D.C., 2023
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Conformational Analysis of Agonist Dependent Phosphorylation Signatures of Dopamine D3 ReceptorMid-Atlantic Pharmacology Society Annual Meeting, Philadelphia, PA, 2022
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Structural Analysis of the Interaction of Pyrazole and Benzimidazole Core Compounds with PfATP4Annual ASPET Meeting, Philadelphia, PA, 2022
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Mechanisms of Negative Membrane Curvature Sensing and Generation64th Annual Meeting of Biophysical Society, San Diego, CA, 2020
News & Highlights
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JUN 2013Press CoverageResearch highlighted in Chemical & Engineering News
Our paper on sustained water oxidation by a catalyst cage-isolated in a metal-organic framework was featured in ACS's flagship news magazine C&EN (Vol. 91, Issue 26) as a research highlight.
Read the C&EN article →
// More updates coming soon
Contact & Collaboration
I'm always interested in discussing new research collaborations, particularly in the areas of computational drug discovery, structural bioinformatics, and infectious disease research.