Developing Broad-Spectrum Antivirals Targeting Coronavirus Replicase and Helicase

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ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of COVID-19 has caused over 700,000 deaths in the U.S. and over 4.8 million deaths worldwide. The pandemic’s true public health, economic and social cost continues to expand. Inadequate vaccination rates coupled with the perpetual evolution of SARS-CoV-2 variants of concern (VOCs) have fueled waves COVID-19 in unvaccinated and vaccinated groups. We led IND-enabling preclinical studies for two COVID-19 antiviral therapies: the FDA approved intravenous drug remdesivir and the oral antiviral, molnupiravir, which is now in Phase 3 clinical trial. For COVID- 19 and future emerging CoV epidemics, we need multiple oral broadly-active antivirals with disparate mechanisms of action to robustly inhibit virus replication and minimize the potential for resistance in outpatients. Here, in Project 2 of the READDI-AC program, we leverage decades of drug discovery, medicinal chemistry, biochemistry, enzymology and coronavirology expertise for the identification, validation, optimization and preclinical evaluation of novel small molecule antivirals targeting the conserved CoV RNA-dependent RNA polymerase (RdRp, nsp12) and helicase (Hel, nsp13). Together with the READDI-AC Core Labs and pharmaceutical leaders Takeda and Chimerix we articulate a platform for drug discovery and development in the following Specific Aims: 1) Identify and validate small molecules targeting SARS-CoV-2 RdRp and Helicase active and allosteric sites using multiple complementary approaches for discovery (e.g. fragment based, DNA- encoded library, small molecule enzymatic assay, and cell-based antiviral screens). As RdRp is a validated drug target, early discovery efforts prioritize Hel. Validated biochemical assays and cell-based antiviral assays drive hit discovery and iterative structure activity relationship (SAR) studies to improve upon and understand activity. We use “Fleximer” medicinal chemistry to generate new chemical matter from existing nucleoside analogs (e.g. Molnupiravir) and/or optimize hits from screening efforts. Top candidates will be evaluated and down selected based on antiviral performance in primary culture systems. 2) Medicinal chemistry transforms hits into leads in iterative SAR studies. For each lead, the breadth of antiviral activity, mechanism of action and resistance are determined in both biochemical and virologic assays. 3) We collaborate with industry partners to optimize leads into drug candidates for pharmacokinetic, safety and preclinical efficacy studies in robust models of acute and chronic COVID-19 disease. We have five leads currently in hand from Takeda, Chimerix, Pardes and academic collaborators for in vivo testing. Project 2 will provide a comprehensive IND-enabling preclinical data package for successful RdRp and Hel molecules positioning them for human trials.