I design small molecules in silico, combining quantum mechanics, molecular dynamics, structure-based design and machine learning to find new medicines for infectious diseases and neurological disorders.
My research brings together computational chemistry, structural biology and structural bioinformatics for rational drug design, and uses them to understand the molecular mechanisms behind disease. I build and apply computational frameworks to design inhibitors of proteins involved in infectious diseases and neurological disorders.
During my doctoral and postdoctoral training I developed expertise in quantum-mechanical calculations, molecular dynamics, pharmacophore design and machine learning. I have studied noncovalent interactions (hydrogen, halogen and chalcogen bonds) with high-level ab initio methods, protein–protein and protein–membrane interactions with MD simulations, and designed novel ligands through pharmacophore modeling, virtual screening and docking.
I have designed small-molecule inhibitors and characterized protein–ligand interactions for targets including PfATP4 and the Pf cytochrome bc1 complex (malaria), the influenza ribonucleoprotein complex, the dopamine D3 receptor and the dopamine transporter. I also developed an implicit curved-membrane model for curvature-sensing and curvature-generating proteins, now implemented in CHARMM.
“Integrating physics-based modeling with data-driven AI to accelerate the discovery of bioactive compounds, and to optimize their selectivity and pharmacokinetics.”
I was computational lead on small-molecule programs against Plasmodium falciparum ATP4 and the cytochrome bc1 complex. The work covered homology models, docking campaigns, MD-based binding free energies, and SAR hypotheses that guided potency and resistance optimization.
Conformational dynamics of the dopamine D3 receptor and dopamine transporter: phosphorylation-dependent states, biased agonism and receptor–transporter interactions, studied with long-timescale MD and enhanced sampling.
Implicit-membrane models for curved geometries, implemented in CHARMM, and used to explain how ESCRT-III, I-BAR domains and amphipathic helices sense and generate curvature, and how peptides and toxins form pores.
High-level quantum chemistry of hydrogen, halogen, chalcogen and pnicogen bonds, from CH···X⁻ anion binding to halide receptor design. This foundation informs how I read protein–ligand interaction networks today.
Schrödinger (Glide, FEP+), MOE, AutoDock/Vina, GOLD
GROMACS, AMBER, NAMD, CHARMM · enhanced sampling · alchemical free energy
Gaussian, GAMESS · high-level ab initio analysis
PyTorch, TensorFlow, scikit-learn · CNN & GNN for activity / ADMET
RDKit, pandas, NumPy · SAR, clustering, library curation
RNA-seq, differential expression, WGCNA, GO / KEGG enrichment
Full, up-to-date list on Google Scholar and ORCID.
A multi-institution collaboration identifying a potent inhibitor of MyoA, the class XIV myosin that powers motility of malaria and Toxoplasma parasites. Now on bioRxiv.
Read the preprint →A collaborative medicinal chemistry study revisiting 2-substituted-4(1H)-quinolones as antimalarials that target the parasite's bc1 complex.
Read the paper →A collaborative study revealing how the influenza virus assembles its ribonucleoprotein complex and carries out processive RNA synthesis, a protein–protein interaction target for antivirals.
Read the paper →Mapping how mutations in PfATP4, a leading antimalarial target, affect its function and its response to inhibitors.
Read the paper →First Place (Postdoctoral) at the Mid-Atlantic Pharmacology Society meeting, and Outstanding Postdoctoral Fellow Poster at Drexel Discovery Day.
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).
Read the C&EN article →Away from the computer, I like to keep moving. I play racket sports, I train every day, and on vacation I head for open country and the mountains.
My favorite way to unwind. A good rally needs the same focus and patience as a long simulation.
Fast reflexes, spin and quick decisions. It's a great reset between long working sessions.
At least an hour every day, running or lifting. It's where I do some of my clearest thinking.
On vacation I go where it's quiet: rolling countryside, mountain trails and fresh air, a natural pull for someone who grew up in Nepal.
I'm always glad to talk about new positions, especially in computational drug discovery, structure-based design, and infectious-disease or CNS targets.