Structural Approach To Identify a Lead Scaffold That Targets the Translesion Synthesis Polymerase Rev1

J Chem Inf Model. 2018 Nov 26;58(11):2266-2277. doi: 10.1021/acs.jcim.8b00535. Epub 2018 Oct 19.

Abstract

Translesion synthesis (TLS) is a mechanism of replication past damaged DNA through which multiple forms of human cancer survive and acquire resistance to first-line genotoxic chemotherapies. As such, TLS is emerging as a promising target for the development of a new class of anticancer agents. The C-terminal domain of the DNA polymerase Rev1 (Rev1-CT) mediates assembly of the functional TLS complex through protein-protein interactions (PPIs) with Rev1 interacting regions (RIRs) of several other TLS DNA polymerases. Utilizing structural knowledge of the Rev1-CT/RIR interface, we have identified the phenazopyridine scaffold as an inhibitor of this essential TLS PPI. We demonstrate direct binding of this scaffold to Rev1-CT, and the synthesis and evaluation of a small series of analogues have provided important structure-activity relationships for further development of this scaffold. Furthermore, we utilized the umbrella sampling method to predict the free energy of binding to Rev1-CT for each of our analogues. Binding energies calculated through umbrella sampling correlated well with experimentally determined IC50 values, validating this computational tool as a viable approach to predict the biological activity for inhibitors of the Rev1-CT/RIR PPI.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents / chemistry*
  • Antineoplastic Agents / pharmacology*
  • DNA Damage / drug effects
  • DNA Repair / drug effects
  • Drug Discovery*
  • Humans
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Neoplasms / drug therapy
  • Neoplasms / genetics
  • Neoplasms / metabolism
  • Nuclear Proteins / antagonists & inhibitors
  • Nuclear Proteins / chemistry
  • Nuclear Proteins / metabolism*
  • Nucleotidyltransferases / antagonists & inhibitors
  • Nucleotidyltransferases / chemistry
  • Nucleotidyltransferases / metabolism*
  • Phenazopyridine / analogs & derivatives*
  • Phenazopyridine / pharmacology*
  • Protein Interaction Maps / drug effects
  • Small Molecule Libraries / chemistry
  • Small Molecule Libraries / pharmacology
  • Thermodynamics

Substances

  • Antineoplastic Agents
  • Nuclear Proteins
  • Small Molecule Libraries
  • Nucleotidyltransferases
  • REV1 protein, human
  • Phenazopyridine