Covalent inhibitors of host cell entry by SARS-CoV-2 for treatment of COVID-19

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Project Summary Current strategies to overcome virus outbreaks are focused on development of effective vaccines as well as novel treatments that can either block infection or prevent mortality from the resulting disease. One of the strategies that has shown promise is the use of serum from patients who have recovered from infection. This strategy relies on the presence of high titers of neutralizing antibodies that bind to antigens on the virus and block uptake into host cells. For the SARS-CoV-2 virus this requires antibodies that bind to regions on the receptor binding domain (RBD) of the viral ‘spike’ (S) protein and block its interaction with the host receptor, angiotensin converting enzyme 2 (ACE2). Significant efforts over the past 15 years of studies on related coronaviruses has produced a detailed picture of the interactions between these two protein domains. These studies have facilitated strategies to select optimal neutralizing antibodies likely to have the greatest therapeutic value. While antibodies are effective biological therapies, they suffer from limitations that make their widespread use for a global pandemic limited. This includes the high cost of production, poor uptake by oral or localized administration and general incompatibility with long-term storage and stockpiling. Furthermore, interactions with the target viral proteins are reversible and can be rendered ineffective for antibody neutralization through single point mutations in virus variants. In this proposal, we outline plans to develop a phage display screening approach to identify synthetic cyclic peptides that carry a covalent ‘warhead’ to induce specific and permanent binding to the SARS-CoV-2 S protein at highly conserved and functionally important residues. This approach will lead to the identification of fully synthetic molecules that irreversibly block key interactions between the S protein RBD and the host cell receptor, ACE2. Such molecules will possess the selectivity of antibodies but can be synthesized and handled like small molecule drugs. Furthermore, their covalent binding mode will lead to prolonged therapeutic effects and reduced ability to induce resistance causing mutations in the S protein.