Bi-substrate Inhibitors of SARS-CoV-2 Nsp14 Methyltransferase

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ABSTRACT Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of the current pandemic of coronavirus disease 2019 (COVID-19), has posed an unprecedented global health threat in modern history. While the approvals of vaccines, antibodies, and antiviral drug remdesivir have offered hope to end this devastating pandemic, recent emergence and rapid spread of more infectious variants calls for renewed efforts to develop effective therapies to combat SARS-CoV-2 infection. In SARS-CoV-2, the RNA 5′-cap structure is methylated to ensure viral translation/replication and to evade host immune surveillance. We propose to discover selective inhibitors of guanine N7-methyltransferase (N7-MTase, Nsp14) because the active site of Nsp14 MTase is uniquely constricted while human RNA capping MTases are overly open. Furthermore, the constricted nature of the Nsp14 MTase active site has allowed us to design bi-substrate inhibitors. Our preliminary effort has led to a nanomolar inhibitor that shows excellent anti-SARS-CoV-2 activity and no significant cytotoxicity. In this application, we will perform lead optimization to improve the potency, selectivity and drug-like properties of our Nsp14 MTase inhibitors, aiming to identify MTase inhibitors for use in future proof-of-concept studies in animal models of SARS-CoV-2 infection. To accomplish the goal, we propose the following specific aims: Specific Aim 1. Design and synthesize SARS-CoV-2 Nsp14 MTase inhibitors and evaluate them in biochemical and antiviral assays; Specific Aim 2. Assess selected SARS-CoV-2 Nsp14 MTase inhibitors for their physiochemical and in vitro absorption, distribution, metabolism, excretion and toxicity (ADMET) properties; and Specific Aim 3. Determine in vivo pharmacokinetics (PK) parameters of advanced SARS-CoV-2 Nsp14 MTase inhibitors. We expect that the proposed research will significantly contribute to efforts in developing SARS-CoV-2 Nsp14 MTase inhibitors as COVID-19 therapeutics.