About the Seminar
The viral matrix protein (VP40) is crucial to multiple steps of the Ebola Virus (EBOV) lifecycle, including the regulation of transcription and viral egress. In the cytosol, VP40 monomers spontaneously dimerize and migrate to the inner-cell membrane where a reorientation causes partial penetration of the membrane and hexamer formation. Further oligomerization of VP40 includes the formation of octamers vital to replication, and the filamentous self-aggregation responsible for enveloping the nucleocapsid and its egress. Much recent work has focused on VP40 oligomerization mechanisms and detailing associated protein residues. Despite this, drug discovery studies for VP40 have focused on targeting regions that many recent studies seem to suggest would not inhibit function, and no further or more rigorous evidence to verify the proposed small molecules as inhibitors has been published. We therefore propose a holistic approach for high-throughput drug discovery based on small molecule inhibition of membrane attracting, stabilizing, and/or penetrating residues of VP40, of which all are currently hypothesized to be essential for VP40 oligomerization. A combined computational-experimental workflow is detailed, beginning with high-throughput virtual screening of these critical protein-lipid interactions. Enhanced sampling molecular dynamics methods are devised in a site-specific manner, allowing us to then probe the differences in free energies between membrane interaction of the top ligand-bound VP40 structures and apo-VP40. Importantly, assays for measuring virus-like particle formation and VP40 lipid-binding, which have been previously developed, are adapted for additional rigor in detailing the highest affinity inhibitors of VP40.