Date of Award

Spring 5-15-2023

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Biochemistry)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



Drug discovery targeting protein nucleic acid (PNI) and protein-protein interactions (PPI) remains a difficult task. How to identify druggable conformations and discover compounds binding to these conformations is an unsolved problem. Here, I describe how we apply computational and experimental approaches to probe the conformational landscape of a key immune antagonist protein from the Zaire ebolavirus. Viral Protein 35 (VP35) binds to the viral pathogen associated molecular pattern, double stranded RNA (dsRNA), and blocks activation of the interferon (IFN) response. Long time scale molecular dynamics simulations reveal that VP35 adopts an alternative conformation which opens a pocket absent in experimental structures, a cryptic pocket. Simulations predict and we experimentally validate that this pocket exists and is allosterically coupled to the dsRNA binding site. High throughput screening identified new chemical matter that inhibits dsRNA binding. Subsequent structural and biochemical studies show that the inhibitors target the dsRNA binding site. One inhibitor also binds to the VP35 cryptic pocket. Our data shows the usefulness of considering protein conformational heterogeneity for drug discovery targeting PNIs and PPIs.


English (en)

Chair and Committee

Gaya K. Amarasinghe Gregory Bowman

Committee Members

Janice L. Robertson, Eric A. Galburt, Carolina B. Lopez,

Available for download on Wednesday, June 19, 2024