Structural understanding of non-nucleoside inhibition in an elongating herpesvirus polymerase

Nat Commun. 2021 May 24;12(1):3040. doi: 10.1038/s41467-021-23312-8.

Abstract

All herpesviruses encode a conserved DNA polymerase that is required for viral genome replication and serves as an important therapeutic target. Currently available herpesvirus therapies include nucleoside and non-nucleoside inhibitors (NNI) that target the DNA-bound state of herpesvirus polymerase and block replication. Here we report the ternary complex crystal structure of Herpes Simplex Virus 1 DNA polymerase bound to DNA and a 4-oxo-dihydroquinoline NNI, PNU-183792 (PNU), at 3.5 Å resolution. PNU bound at the polymerase active site, displacing the template strand and inducing a conformational shift of the fingers domain into an open state. These results demonstrate that PNU inhibits replication by blocking association of dNTP and stalling the enzyme in a catalytically incompetent conformation, ultimately acting as a nucleotide competing inhibitor (NCI). Sequence conservation of the NCI binding pocket further explains broad-spectrum activity while a direct interaction between PNU and residue V823 rationalizes why mutations at this position result in loss of inhibition.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Antiviral Agents / pharmacology
  • Binding Sites
  • DNA-Directed DNA Polymerase / chemistry*
  • DNA-Directed DNA Polymerase / drug effects*
  • DNA-Directed DNA Polymerase / genetics*
  • DNA-Directed DNA Polymerase / metabolism
  • Drug Resistance, Viral / drug effects
  • Exodeoxyribonucleases
  • Herpesviridae / drug effects*
  • Herpesviridae / enzymology*
  • Nucleotides
  • Quinolines / pharmacology
  • Viral Proteins
  • Virus Replication

Substances

  • Antiviral Agents
  • Nucleotides
  • PNU183792
  • Quinolines
  • Viral Proteins
  • DNA-Directed DNA Polymerase
  • Exodeoxyribonucleases
  • DNA polymerase, Simplexvirus