Rationalization of activity cliffs of a sulfonamide inhibitor of DNA methyltransferases with induced-fit docking

Int J Mol Sci. 2014 Feb 21;15(2):3253-61. doi: 10.3390/ijms15023253.

Abstract

Inhibitors of human DNA methyltransferases (DNMT) are of increasing interest to develop novel epi-drugs for the treatment of cancer and other diseases. As the number of compounds with reported DNMT inhibition is increasing, molecular docking is shedding light to elucidate their mechanism of action and further interpret structure-activity relationships. Herein, we present a structure-based rationalization of the activity of SW155246, a distinct sulfonamide compound recently reported as an inhibitor of human DNMT1 obtained from high-throughput screening. We used flexible and induce-fit docking to develop a binding model of SW155246 with a crystallographic structure of human DNMT1. Results were in excellent agreement with experimental information providing a three-dimensional structural interpretation of 'activity cliffs', e.g., analogues of SW155246 with a high structural similarity to the sulfonamide compound, but with no activity in the enzymatic assay.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • DNA (Cytosine-5-)-Methyltransferases / antagonists & inhibitors*
  • DNA (Cytosine-5-)-Methyltransferases / metabolism
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / metabolism*
  • Humans
  • Molecular Docking Simulation
  • Naphthols / chemistry
  • Naphthols / metabolism*
  • Protein Binding
  • Protein Structure, Tertiary
  • Structure-Activity Relationship
  • Sulfonamides / chemistry
  • Sulfonamides / metabolism*

Substances

  • Enzyme Inhibitors
  • Naphthols
  • SW155246
  • Sulfonamides
  • DNA (Cytosine-5-)-Methyltransferases