Small molecule inhibitors and degraders of picornavirus 2A proteases as direct-acting antivirals

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ABSTRACT – Project 2: Small molecule inhibitors and degraders of picornavirus 2A proteases Traditional direct-acting antivirals (DAAs) target a viral protein by occupying an enzymatic pocket; dissociation of the drug leads to immediate regain of function. Consequently, most antivirals must have high-affinity, stoichiometric binding to be effective, and point mutations that reduce affinity can rapidly give rise to antiviral resistance. The established method to prevent resistance is the use of combinations of direct-acting antivirals that act via independent targets and mechanisms. In this project, we will pursue two innovative approaches to develop DAAs targeting the enterovirus (EV) 2A protease, a viral protein with at least two essential functions: (1) it catalyzes a required cleavage of the viral polyprotein and (2) it mediates a protein-protein interaction that is essential for replication. First, we will pursue targeted protein degradation (TPD) against 2A as an antiviral strategy. TPD is a new paradigm in drug development in which a small molecule that binds the target of interest is conjugated to an E3 ligase ligand resulting in protein degradation. This approach allows a wider range of protein targets because its event-driven pharmacology does not require stoichiometric inhibition of the viral protein and because the affinity required for effective protein degradation is generally lower. We previously developed the first small molecule antiviral degrader by coupling telaprevir, an FDA-approved inhibitor of the hepatitis C virus NS3-4A protease, to a ligand of the CRBNCRL E3 ubiquitin ligase. The resulting NS3 degraders inhibit HCV in vitro, including point mutants that are known to be telaprevir-resistant. Since telaprevir was recently shown to have broad-spectrum activity against enterovirus 2A proteins, we will build upon our prior work to develop telaprevir-based degraders of 2A that remove the protein from the cell and ablate all of 2A’s functions. Second, we will perform high-throughput screens for DAAs that bind to 2A and inhibit its function as a mediator of essential protein-protein interactions. Compounds discovered in these screens will be validated as 2A ligands and tested for antiviral activity, with validated ligands advanced as leads for degrader development and compounds with antiviral activity advanced as lead compounds for development of DAAs. We will also undertake screening of DNA-encoded libraries to more broadly sample chemical space and to discover additional chemical matter suitable for inhibitor and degrader development. We will also determine if DAAs targeting the active site (Aim 1) and the 2A interacting site (Aim 2) can be combined for superior efficacy and resistance profile. This work leverages the innovative discoveries made by our labs in the areas of TPD and 2A biology along with the collective expertise of our groups and the AViDD in virology, medicinal chemistry, chemical biology biochemistry, structural biology, and drug discovery. Our work developing DAAs targeting the multifunctional EV 2A protease will have wide-reaching impact by validating two new antiviral mechanisms for targeting 2A and by demonstrating the utility of TPD as an antiviral strategy.