design and rapid production of a drug-screening target from the highly conserved HR1 region of the viral spike protein (S2)

SARS-CoV-2, a novel coronavirus, is the causative agent of the current worldwide pandemic that has already led to over 2 million infections, 125,000 deaths, and severe economic impact. Currently no preventatives, treatments, or vaccines are available, and care is solely supportive. Additionally, the 21st century has seen the emergence of multiple lethal human coronaviruses (SARS-CoV, MERS-CoV, and now SARS- CoV-2). There is an urgent need for new options to combat this and inevitable future pandemics. Coronaviruses infect cells using a conserved entry mechanism shared by enveloped viruses across multiple families in which two regions of the trimeric viral spike protein (HR1 and HR2) form a highly stable 6- helix bundle structure, juxtaposing the viral and cellular membranes to induce membrane fusion. Inhibiting formation of this 6-helix bundle stops viral entry and prevents infection. Our lab specializes in an innovative enantiomeric screening technology (mirror-image phage display) in concert with structure-guided design, to produce novel, synthetic, D-peptide viral entry inhibitors, including CPT31, our highly potent, broadly active HIV-1 D-peptide inhibitor that has been cleared by the FDA for clinical studies. Research by us and others on SARS, a highly related coronavirus that shares 86% identity (and 95% similarity) to SARS-CoV-2 in the spike HR1, indicate that these inhibition strategies should successfully block the current coronavirus. D-peptides (peptides composed of mirror-image D-amino acids) cannot be digested by proteases in the body and, therefore, possess significant therapeutic advantages including extended half-life, lower dosing, reduced immunogenicity (not digested for MHC presentation), and durability in protease-rich environments such as the respiratory tract. In this one-year grant application, we will first design and synthesize SARS-CoV-2 trimeric HR1-based peptides. These peptides accurately mimic HR1 as it appears on the virus during entry and are therefore invaluable drug screening targets. We will then use these mimics as targets in mirror-image phage display to identify D-peptide inhibitors of SARS-CoV-2 that block it and future SARS-related coronaviruses.