Identification of Pyrimidine-Based Lead Compounds for Understudied Kinases Implicated in Driving Neurodegeneration

J Med Chem. 2022 Jan 27;65(2):1313-1328. doi: 10.1021/acs.jmedchem.1c00440. Epub 2021 Aug 1.

Abstract

The pyrimidine core has been utilized extensively to construct kinase inhibitors, including eight FDA-approved drugs. Because the pyrimidine hinge-binding motif is accommodated by many human kinases, kinome-wide selectivity of resultant molecules can be poor. This liability was seen as an advantage since it is well tolerated by many understudied kinases. We hypothesized that nonexemplified aminopyrimidines bearing side chains from well-annotated pyrimidine-based inhibitors with off-target activity on understudied kinases would provide us with useful inhibitors of these lesser studied kinases. Our strategy paired mixing and matching the side chains from the 2- and 4-positions of the parent compounds with modifications at the 5-position of the pyrimidine core, which is situated near the gatekeeper residue of the binding pocket. Utilizing this approach, we imparted improved kinome-wide selectivity to most members of the resultant library. Importantly, we also identified potent biochemical and cell-active lead compounds for understudied kinases like DRAK1, BMP2K, and MARK3/4.

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

  • Apoptosis Regulatory Proteins / antagonists & inhibitors*
  • Binding Sites
  • Humans
  • Neurodegenerative Diseases / drug therapy
  • Neurodegenerative Diseases / enzymology
  • Protein Kinase Inhibitors / chemistry*
  • Protein Kinase Inhibitors / pharmacology*
  • Protein Serine-Threonine Kinases / antagonists & inhibitors*
  • Pyrimidines / chemistry*
  • Structure-Activity Relationship

Substances

  • Apoptosis Regulatory Proteins
  • Protein Kinase Inhibitors
  • Pyrimidines
  • MARK3 protein, human
  • MARK4 protein, human
  • BMP2K protein, human
  • Protein Serine-Threonine Kinases
  • STK17A protein, human