Sofosbuvir terminated RNA is more resistant to SARS-CoV-2 proofreader than RNA terminated by Remdesivir

Steffen Jockusch; Chuanjuan Tao; Xiaoxu Li; Minchen Chien; Shiv Kumar; Irina Morozova; Sergey Kalachikov; James J Russo; Jingyue Ju

doi:10.1038/s41598-020-73641-9

Sofosbuvir terminated RNA is more resistant to SARS-CoV-2 proofreader than RNA terminated by Remdesivir

Sci Rep. 2020 Oct 6;10(1):16577. doi: 10.1038/s41598-020-73641-9.

Authors

Steffen Jockusch^#^{1

2}, Chuanjuan Tao^#^{1

3}, Xiaoxu Li^{1

3}, Minchen Chien^{1

3}, Shiv Kumar^{1

3}, Irina Morozova^{1

3}, Sergey Kalachikov^{1

3}, James J Russo^{1

3}, Jingyue Ju^{4

5

6}

Affiliations

¹ Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA.
² Department of Chemistry, Columbia University, New York, NY, 10027, USA.
³ Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA.
⁴ Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY, 10027, USA. [email protected].
⁵ Department of Chemical Engineering, Columbia University, New York, NY, 10027, USA. [email protected].
⁶ Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, 10032, USA. [email protected].

^# Contributed equally.

Abstract

SARS-CoV-2 is responsible for COVID-19, resulting in the largest pandemic in over a hundred years. After examining the molecular structures and activities of hepatitis C viral inhibitors and comparing hepatitis C virus and coronavirus replication, we previously postulated that the FDA-approved hepatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) might inhibit SARS-CoV-2. We subsequently demonstrated that Sofosbuvir triphosphate is incorporated by the relatively low fidelity SARS-CoV and SARS-CoV-2 RNA-dependent RNA polymerases (RdRps), serving as an immediate polymerase reaction terminator, but not by a host-like high fidelity DNA polymerase. Other investigators have since demonstrated the ability of Sofosbuvir to inhibit SARS-CoV-2 replication in lung and brain cells; additionally, COVID-19 clinical trials with EPCLUSA and with Sofosbuvir plus Daclatasvir have been initiated in several countries. SARS-CoV-2 has an exonuclease-based proofreader to maintain the viral genome integrity. Any effective antiviral targeting the SARS-CoV-2 RdRp must display a certain level of resistance to this proofreading activity. We report here that Sofosbuvir terminated RNA resists removal by the exonuclease to a substantially higher extent than RNA terminated by Remdesivir, another drug being used as a COVID-19 therapeutic. These results offer a molecular basis supporting the current use of Sofosbuvir in combination with other drugs in COVID-19 clinical trials.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adenosine Monophosphate / analogs & derivatives*
Adenosine Monophosphate / chemistry
Adenosine Monophosphate / pharmacology
Adenosine Monophosphate / therapeutic use
Alanine / analogs & derivatives*
Alanine / chemistry
Alanine / pharmacology
Alanine / therapeutic use
Antiviral Agents / chemistry
Antiviral Agents / pharmacology*
Antiviral Agents / therapeutic use
Betacoronavirus / drug effects*
Betacoronavirus / enzymology
COVID-19
Coronavirus Infections / drug therapy*
Coronavirus Infections / virology
Coronavirus RNA-Dependent RNA Polymerase
Drug Discovery / methods
Drug Repositioning / methods
Exonucleases / metabolism*
Hepacivirus / drug effects
Hepacivirus / enzymology
Hepatitis C / drug therapy
Hepatitis C / virology
Humans
Pandemics
Pneumonia, Viral / drug therapy*
Pneumonia, Viral / virology
Prodrugs / pharmacology*
Prodrugs / therapeutic use
RNA, Viral / chemistry
RNA, Viral / drug effects*
RNA, Viral / metabolism
RNA-Dependent RNA Polymerase / antagonists & inhibitors
RNA-Dependent RNA Polymerase / metabolism
SARS-CoV-2
Sofosbuvir / chemistry
Sofosbuvir / pharmacology*
Sofosbuvir / therapeutic use
Viral Nonstructural Proteins / antagonists & inhibitors
Viral Nonstructural Proteins / metabolism
Virus Replication / drug effects

Substances

Antiviral Agents
Prodrugs
RNA, Viral
Viral Nonstructural Proteins
remdesivir
Adenosine Monophosphate
Coronavirus RNA-Dependent RNA Polymerase
NSP12 protein, SARS-CoV-2
RNA-Dependent RNA Polymerase
Exonucleases
Alanine
Sofosbuvir