Antiviral drug screen identifies DNA-damage response inhibitor as potent blocker of SARS-CoV-2 replication

Gustavo Garcia Jr; Arun Sharma; Arunachalam Ramaiah; Chandani Sen; Arunima Purkayastha; Donald B Kohn; Mark S Parcells; Sebastian Beck; Heeyoung Kim; Malina A Bakowski; Melanie G Kirkpatrick; Laura Riva; Karen C Wolff; Brandon Han; Constance Yuen; David Ulmert; Prabhat K Purbey; Philip Scumpia; Nathan Beutler; Thomas F Rogers; Arnab K Chatterjee; Gülsah Gabriel; Ralf Bartenschlager; Brigitte Gomperts; Clive N Svendsen; Ulrich A K Betz; Robert D Damoiseaux; Vaithilingaraja Arumugaswami

doi:10.1016/j.celrep.2021.108940

Antiviral drug screen identifies DNA-damage response inhibitor as potent blocker of SARS-CoV-2 replication

Cell Rep. 2021 Apr 6;35(1):108940. doi: 10.1016/j.celrep.2021.108940. Epub 2021 Mar 18.

Authors

Gustavo Garcia Jr¹, Arun Sharma², Arunachalam Ramaiah³, Chandani Sen⁴, Arunima Purkayastha⁴, Donald B Kohn⁵, Mark S Parcells⁶, Sebastian Beck⁷, Heeyoung Kim⁸, Malina A Bakowski⁹, Melanie G Kirkpatrick⁹, Laura Riva⁹, Karen C Wolff⁹, Brandon Han¹⁰, Constance Yuen¹⁰, David Ulmert¹¹, Prabhat K Purbey¹², Philip Scumpia¹², Nathan Beutler¹³, Thomas F Rogers¹⁴, Arnab K Chatterjee⁹, Gülsah Gabriel⁷, Ralf Bartenschlager¹⁵, Brigitte Gomperts⁵, Clive N Svendsen¹⁶, Ulrich A K Betz¹⁷, Robert D Damoiseaux¹⁸, Vaithilingaraja Arumugaswami¹⁹

Affiliations

¹ Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
² Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
³ Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA; Section of Cell and Developmental Biology, University of California, San Diego, San Diego, CA 92093, USA.
⁴ UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
⁵ UCLA Children's Discovery and Innovation Institute, Mattel Children's Hospital UCLA, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA.
⁶ Department of Animal and Food Sciences, Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA.
⁷ Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
⁸ Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany.
⁹ Calibr, a division of Scripps Research Institute, 11119 North Torrey Pines Road, La Jolla, CA 92037, USA.
¹⁰ California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
¹¹ Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA.
¹² Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
¹³ Department of Immunology and Microbiology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
¹⁴ Department of Immunology and Microbiology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; UC San Diego Division of Infectious Diseases and Global Public Health, UC San Diego School of Medicine, La Jolla, CA 92093, USA.
¹⁵ Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany; German Center for Infection Research, Heidelberg partner site, Heidelberg, Germany; Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany.
¹⁶ Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
¹⁷ Merck KGaA, Darmstadt, Germany. Electronic address: ulrich.betz@merckgroup.com.
¹⁸ Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: rdamoiseaux@mednet.ucla.edu.
¹⁹ Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Los Angeles, CA 90095, USA; California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: varumugaswami@mednet.ucla.edu.

Abstract

SARS-CoV-2 has currently precipitated the COVID-19 global health crisis. We developed a medium-throughput drug-screening system and identified a small-molecule library of 34 of 430 protein kinase inhibitors that were capable of inhibiting the SARS-CoV-2 cytopathic effect in human epithelial cells. These drug inhibitors are in various stages of clinical trials. We detected key proteins involved in cellular signaling pathways mTOR-PI3K-AKT, ABL-BCR/MAPK, and DNA-damage response that are critical for SARS-CoV-2 infection. A drug-protein interaction-based secondary screen confirmed compounds, such as the ATR kinase inhibitor berzosertib and torin2 with anti-SARS-CoV-2 activity. Berzosertib exhibited potent antiviral activity against SARS-CoV-2 in multiple cell types and blocked replication at the post-entry step. Berzosertib inhibited replication of SARS-CoV-1 and the Middle East respiratory syndrome coronavirus (MERS-CoV) as well. Our study highlights key promising kinase inhibitors to constrain coronavirus replication as a host-directed therapy in the treatment of COVID-19 and beyond as well as provides an important mechanism of host-pathogen interactions.

Keywords: ATR kinase; COVID-19; DNA-damage response pathway; SARS-CoV-2; berzosertib; high-throughput screen; mTOR-PI3K-AKT pathway; nucleoside analogs; protein kinase inhibitors.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

A549 Cells
Animals
Antiviral Agents / pharmacology*
COVID-19 / metabolism
COVID-19 / pathology
COVID-19 Drug Treatment*
Chlorocebus aethiops
DNA Damage*
Drug Evaluation, Preclinical
HEK293 Cells
HeLa Cells
Humans
Isoxazoles / pharmacology*
MAP Kinase Signaling System / drug effects
Middle East Respiratory Syndrome Coronavirus / metabolism
Pyrazines / pharmacology*
SARS-CoV-2 / physiology*
Vero Cells
Virus Replication / drug effects*

Substances

Antiviral Agents
Isoxazoles
Pyrazines
berzosertib

Abstract

Publication types

MeSH terms

Substances

Grants and funding