Repurposing Therapeutics to Identify Novel Inhibitors Targeting 2'-O-Ribose Methyltransferase Nsp16 of SARS-CoV-2

Abstract

<p>Three coronaviruses (CoVs): severe acute respiratory syndrome coronavirus (SARS-CoV-1), Middle East respiratory syndrome coronavirus (MERS-CoV), and the recently identified SARS-CoV-2 in December 2019, have caused deadly pneumonia in humans since the beginning of the 21st century. The SARS-CoV-2 causes coronavirus disease-19 (COVID-19) with influenza-like symptoms ranging from mild discomfort to severe lung injury and multi-organ failure, eventually leading to death. As of April 30, 2020, more than three million (3,175,207) COVID-19 cases were reported worldwide, and more than 220,000 (224,172) patients have died (https://www.who.int/emergencies/diseases/novel-coronavirus-2019). Effective treatments and vaccines for SARS-CoV-2 infection do not currently exist. Thus, it will be of great benefit to identify and repurpose already well-characterized compounds and approved drugs for use in combating COVID-19.</p> <p> </p> <p>CoVs are positive-sense RNA viruses that replicate in the cytoplasm of infected cells. Replication and transcription of the CoV RNA genome are achieved by a complex RNA replication/transcription machinery, consisting of at least 16 viral nonstructural proteins (nsp). Previous studies demonstrated that nsp16 proteins of SARS-CoV-1 and MERS-CoV have methyltransferase (MTase) activities that catalyze methylation of the first transcribed nucleotide at the ribose 2’-O position (2’-O-Me). The 2’-O-Me of virus cap RNAs protects itself from degradation by 5′-3′ exoribonucleases, ensures efficient translation, and helps to prevent recognition by the host innate immune system. The importance of nsp16 2'-O-MTase activity for CoV infection and pathogenesis was previously documented by in vitro and in vivo studies. For SARS-CoV-1, the absence of nsp16 2′-O-MTase activity results in significant attenuation characterized by decreased viral replication, reduced weight loss, and limited breathing dysfunction in mice. In addition, nsp16 down-regulates the activities of innate immune sensing factors: retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 protein (MDA5). Thus, inhibition of nsp16 2’-O-MTase activities should restrain viral replication and enable recognition by the host innate immune system, making the nsp16-MTase a promising target for the identification of new anti-SARS-CoV-2 drugs. </p> <p> </p> <p>In the present study, we employed structural analysis, virtual screening, and systematic drug repurposing approaches to identify “approved” drugs which can act as promising inhibitors against nsp16 2′-O-MTase of SARS-CoV-2. We first performed comparative analysis of primary amino acid sequences and crystal structures of seven human CoVs and defined the key residues for nsp16 2-O’-MTase functions. From the virtual screening against nsp16 2′-O-MTase of SARS-CoV-2, we provide a ranking of the predicted binding affinities of 1,380 top hit compounds corresponding to 967 “approved” drugs. Furthermore, we have calculated various structural parameters of our top-ranking drugs. Our studies provided the foundation to further test and repurpose these candidate drugs experimentally and clinically for COVID-19 treatment. </p><br>

Drug Repurposing Screen for Compounds Inhibiting the Cytopathic Effect of SARS-CoV-2

“…We also confirmed the anti-SARS-CoV-2 activity of five compounds that were reported as virtual screening hits but had yet to be confirmed experimentally, including methdilazine by an AI prediction algorithm ( Grzybowski et al, 2020 ), GMC 2-113 by a virtual screen of RNA dependent RNA polymerase (RdRP) ( Dwivedy et al, 2020 ), maprotiline by a main protease docking ( Chauhan, 2020 ), deserpidine by a NPS-16 docking ( Jiang et al, 2020 ), and flunarizine by a spike protein docking screen ( Chernyshev, 2020 ). Our data supports the utility of these emerging technologies and the field of AI for advancing drug development.…”

<p>Role of IFN and Complements System: Innate Immunity in SARS-CoV-2</p>

“…As a result of this, the viral genome mimics the host mRNA and escapes from innate immune sensing factors, such as RIG-I and MDA-5, and type I IFN antiviral activities. 61,88,89 A known HIV inhibitor drug, dolutegravir (DG) showed an estimated binding free energy of 9.4 kcal/mol, and inhibits 2ʹ-O-MTase, while bictegravir conferred an estimated binding free energy (DG) of 8.4 kcal/mol against 2ʹ-O-MTase.…”

“…Moreover, natural ligand (SAM) analogues, namely trabodenoson, binodenoson, and regadenoson, may be potent inhibitors of the substrate-binding pockets of Nsp16. 86,89 Nsp1 inhibits host gene expression via targeting the 40s ribosomal subunit, which induces host mRNA degradation and IFN-dependent signaling. Therefore, Nsp1 is a promising drug target, and its inhibition would make SARS-CoV more susceptible to the host's antiviral defenses.…”