Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs

J Med Chem. 2015 Jun 11;58(11):4693-702. doi: 10.1021/acs.jmedchem.5b00232. Epub 2015 May 28.

Abstract

The bacterial DNA replication machinery presents new targets for the development of antibiotics acting via novel mechanisms. One such target is the protein-protein interaction between the DNA sliding clamp and the conserved peptide linear motifs in DNA polymerases. We previously established that binding of linear motifs to the Escherichia coli sliding clamp occurs via a sequential mechanism that involves two subsites (I and II). Here, we report the development of small-molecule inhibitors that mimic this mechanism. The compounds contain tetrahydrocarbazole moieties as "anchors" to occupy subsite I. Functional groups appended at the tetrahydrocarbazole nitrogen bind to a channel gated by the side chain of M362 and lie at the edge of subsite II. One derivative induced the formation of a new binding pocket, termed subsite III, by rearrangement of a loop adjacent to subsite I. Discovery of the extended binding area will guide further inhibitor development.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Binding Sites
  • Carbazoles / chemistry
  • Carbazoles / pharmacology*
  • Crystallography, X-Ray
  • DNA Replication*
  • DNA, Bacterial / metabolism
  • DNA-Directed DNA Polymerase / chemistry
  • Escherichia coli / growth & development
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism*
  • Fluorescence Polarization
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Mimicry*
  • Molecular Structure
  • Protein Binding
  • Structure-Activity Relationship
  • Surface Properties
  • Thermodynamics

Substances

  • Carbazoles
  • DNA, Bacterial
  • Escherichia coli Proteins
  • DNA-Directed DNA Polymerase

Associated data

  • PDB/4OVF
  • PDB/4OVG
  • PDB/4OVH
  • PDB/4PNU
  • PDB/4PNV
  • PDB/4PNW