Enhancing the Antiviral Efficacy of RNA-Dependent RNA Polymerase Inhibition by Combination with Modulators of Pyrimidine Metabolism

Qi Liu; Amita Gupta; Ayse Okesli-Armlovich; Wenjie Qiao; Curt R Fischer; Mark Smith; Jan E Carette; Michael C Bassik; Chaitan Khosla

doi:10.1016/j.chembiol.2020.05.002

Enhancing the Antiviral Efficacy of RNA-Dependent RNA Polymerase Inhibition by Combination with Modulators of Pyrimidine Metabolism

Cell Chem Biol. 2020 Jun 18;27(6):668-677.e9. doi: 10.1016/j.chembiol.2020.05.002. Epub 2020 May 21.

Authors

Qi Liu¹, Amita Gupta², Ayse Okesli-Armlovich¹, Wenjie Qiao³, Curt R Fischer⁴, Mark Smith⁴, Jan E Carette⁵, Michael C Bassik⁶, Chaitan Khosla⁷

Affiliations

¹ Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Stanford Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA.
² Stanford Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.
³ Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
⁴ Stanford Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA.
⁵ Stanford Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
⁶ Stanford Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
⁷ Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Stanford Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA. Electronic address: khosla@stanford.edu.

Abstract

Genome-wide analysis of the mode of action of GSK983, a potent antiviral agent, led to the identification of dihydroorotate dehydrogenase as its target along with the discovery that genetic knockdown of pyrimidine salvage sensitized cells to GSK983. Because GSK983 is an ineffective antiviral in the presence of physiological uridine concentrations, we explored combining GSK983 with pyrimidine salvage inhibitors. We synthesized and evaluated analogs of cyclopentenyl uracil (CPU), an inhibitor of uridine salvage. We found that CPU was converted into its triphosphate in cells. When combined with GSK983, CPU resulted in large drops in cellular UTP and CTP pools. Consequently, CPU-GSK983 suppressed dengue virus replication in the presence of physiological concentrations of uridine. In addition, the CPU-GSK983 combination markedly enhanced the effect of RNA-dependent RNA polymerase (RdRp) inhibition on viral infection. Our findings highlight a new host-targeting strategy for potentiating the antiviral activity of RdRp inhibitors.

Keywords: RNA-dependent RNA polymerase; antiviral therapy; combination; cytidine monophosphate kinase; dengue; dihydroorotate dehydrogenase; pyrimidine metabolism; uridine-cytidine kinase.

Publication types

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

MeSH terms

Animals
Antiviral Agents / chemistry
Antiviral Agents / metabolism
Antiviral Agents / pharmacology*
Carbazoles / chemistry
Carbazoles / metabolism
Carbazoles / pharmacology
Cells, Cultured
Chlorocebus aethiops
Dengue Virus / drug effects*
Enzyme Inhibitors / chemistry
Enzyme Inhibitors / metabolism
Enzyme Inhibitors / pharmacology*
Female
Humans
Male
Microbial Sensitivity Tests
Molecular Structure
Pyrimidines / antagonists & inhibitors*
Pyrimidines / metabolism
RNA-Dependent RNA Polymerase / antagonists & inhibitors*
RNA-Dependent RNA Polymerase / metabolism
Uridine / analogs & derivatives
Uridine / metabolism
Uridine / pharmacology*
Virus Replication / drug effects

Substances

Antiviral Agents
Carbazoles
Enzyme Inhibitors
N-((1R)-6-chloro-2,3,4,9-tetrahydro-1H-carbazol-1-yl)-2-pyridinecarboxamide
Pyrimidines
RNA-Dependent RNA Polymerase
Uridine

Abstract

Publication types

MeSH terms

Substances

Grants and funding