Project 3: Pandemic Virus Protease Inhibitors

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Project 3 – Pandemic Virus Protease Inhibitors ABSTRACT Viral proteases are high-priority drug targets due to their essential functions in virus replication and also unambiguous evidence for druggability, with HIV and HCV drugs as major success stories. This project is organized with the goal of developing novel chemical inhibitors of coronavirus and flavivirus proteases. Specifically, SARS-CoV-2 has two proteases, Papain-Like Protease (PLPro) and Main Protease (MPro), that catalyze 3 and 11 viral polyprotein cleavage events, respectively. SARS-CoV-2 MPro is an attractive drug target due to the large number of essential cleavages at the earliest stages of viral infection and the fact that it has multiple druggable surfaces, including an active site cysteine amenable to covalent adduction. It also shares mechanistic and structural features with related coronavirus MPro proteins, which suggests that it may be possible to develop a pan-coronavirus MPro inhibitor for use against the current pandemic virus and for future use against future coronavirus zoonotic events. Similarly, flaviviruses such as Zika virus require protease function for the earliest viral life cycle stages. The Zika virus NS2B-NS3 protease also has multiple druggable surfaces, and amino acid and structural similarities with related flavivirus proteases suggest potential for broader spectrum inhibition. As preliminary studies, we have designed and optimized multiple assays for these viral proteases, contributed to the wealth of structural, biophysical, and computational knowledge of these drug targets, and already obtained multiple series of candidate small molecule inhibitors. We propose two specific aims in order to expedite the achievement of our central goal. In Aim 1, we will leverage our assays and work closely with our screening (Core B) and structural/computational/virology cores (Cores D-E) to identify additional small molecule inhibitors of these two enzymes in order to maximize chances of obtaining hit series for further development. In Aim 2, candidate hits will be prioritized for further development by testing in orthologous secondary and tertiary assays and, in close collaboration with our chemistry/DMPK and structural/computational cores (Cores C-D), elaborated by systematically designing and testing related commercial and novel synthesized molecules. At all stages of development, representative hits from each series will be evaluated quantitatively using cellular assays and, in close collaboration with our virology core (Core E), also tested rigorously using the best available systems for virus replication and pathogenesis in vivo. The major deliverable from this highly integrated and collaborative effort will be multiple novel lead inhibitors for pre-clinical and clinical testing with industry partners with the hope of soon-fortifying the arsenal of drugs that will be required to end the COVID-19 pandemic and help neutralize future outbreaks.