Mechanism of Inhibition of the Reproduction of SARS-CoV‑2 and Ebola Viruses by Remdesivir

• Published in: Biochemistry (Easton) Vol. 60; no. 24; pp. 1869 - 1875
• Main Authors: Wang, Jimin, Reiss, Krystle, Shi, Yuanjun, Lolis, Elias, Lisi, George P, Batista, Victor S
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 22.06.2021
• Subjects: Adenosine Monophosphate - analogs & derivatives; Adenosine Monophosphate - genetics; Adenosine Monophosphate - metabolism; Alanine - analogs & derivatives; Alanine - genetics; Alanine - metabolism; antiviral agents; Antiviral Agents - metabolism; Base Pairing; cell lines; chemistry; Coronavirus RNA-Dependent RNA Polymerase - antagonists & inhibitors; Coronavirus RNA-Dependent RNA Polymerase - genetics; Coronavirus RNA-Dependent RNA Polymerase - metabolism; Ebolavirus; Ebolavirus - drug effects; Enzyme Inhibitors - metabolism; exoribonucleases; Models, Molecular; nucleosides; Protein Biosynthesis - drug effects; protein synthesis; reproduction; RNA - genetics; RNA - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; RNA, Viral - genetics; RNA, Viral - metabolism; SARS-CoV-2 - drug effects; Severe acute respiratory syndrome coronavirus 2; Virus Replication - drug effects
• ISSN: 0006-2960; 1520-4995; 1943-295X; 1520-4995
• DOI: 10.1021/acs.biochem.1c00292

Remdesivir is an antiviral drug initially designed against the Ebola virus. The results obtained with it both in biochemical studies in vitro and in cell line assays in vivo were very promising, but it proved to be ineffective in clinical trials. Remdesivir exhibited far better efficacy when repurposed against SARS-CoV-2. The chemistry that accounts for this difference is the subject of this study. Here, we examine the hypothesis that remdesivir monophosphate (RMP)-containing RNA functions as a template at the polymerase site for the second run of RNA synthesis, and as mRNA at the decoding center for protein synthesis. Our hypothesis is supported by the observation that RMP can be incorporated into RNA by the RNA-dependent RNA polymerases (RdRps) of both viruses, although some of the incorporated RMPs are subsequently removed by exoribonucleases. Furthermore, our hypothesis is consistent with the fact that RdRp of SARS-CoV-2 selects RMP for incorporation over AMP by 3-fold in vitro, and that RMP-added RNA can be rapidly extended, even though primer extension is often paused when the added RMP is translocated at the i + 3 position (with i the nascent base pair at an initial insertion site of RMP) or when the concentrations of the subsequent nucleoside triphosphates (NTPs) are below their physiological concentrations. These observations have led to the hypothesis that remdesivir might be a delayed chain terminator. However, that hypothesis is challenged under physiological concentrations of NTPs by the observation that approximately three-quarters of RNA products efficiently overrun the pause.