Federal Project Grant Award Summary

The University of Oregon received a $401,285 Project Grant award from the National Institute of General Medical Sciences (NIGMS) under the Biomedical Research and Research Training program (CFDA 93.859), effective February 24, 2026, through December 31, 2030. This R35 Maximizing Investigators' Research Award (MIRA) supports two distinct research projects investigating the molecular mechanisms of antimicrobial resistance through advanced computational methodologies. The first project focuses on ligand binding to riboswitches—regulatory RNA segments targeted as potential next-generation antibiotics—utilizing machine learning (ML) and enhanced sampling molecular dynamics (MD) simulations to characterize conformational dynamics and the effects of nucleotide mutations on small molecule inhibitor binding. The second project examines how resistant mutations in viral antigens, specifically severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein, affect neutralizing antibody binding mechanisms, with particular attention to long-range allosteric effects often overlooked in previous research.

Both projects employ neural network (NN) and explainable artificial intelligence (XAI) techniques to develop collective variables and conduct enhanced sampling simulations that will generate free energy landscapes and mechanistic insights into antimicrobial resistance. The research outcomes are intended to facilitate the rational design of more effective therapeutics and resilient antibiotics by elucidating previously unexplored molecular interaction mechanisms. This award represents NIGMS's commitment to supporting established investigators pursuing fundamental biomedical research that advances understanding of biological processes underlying disease treatment and prevention.