Computationally Driven Discovery of a BCR-ABL1 Kinase Inhibitor with Activity in Multidrug-Resistant Chronic Myeloid Leukemia

J Med Chem. 2024 Oct 10;67(19):17820-17832. doi: 10.1021/acs.jmedchem.4c01852. Epub 2024 Sep 23.

Abstract

The permeability glycoprotein, encoded by the ABCB1 gene, is widely implicated in multidrug resistance (MDR), as it has been shown to reduce the intracellular concentration of most small molecule therapeutics, including the majority of the breakpoint cluster region Abelson proto-oncogene 1 (BCR-ABL1) kinase inhibitors used in the treatment of Philadelphia chromosome positive (Ph+) leukemias. With this in mind, we describe an integrated theoretical and experimental approach to shed light on substituent effects in the pendant anilino moiety of 4-anilinoquinazolines and 4-anilinoquinoline-3-carbonitrile-based kinase inhibitors and their influence on P-gp-mediated efflux. This analysis culminated in the identification of a hydroxylamine-bearing, dual cSRC/BCR-ABL1 kinase inhibitor 16a that exhibits a marked reduction in P-gp-mediated efflux ratio and potent activity in a Ph+ patient-derived cell line (K562) and an MDR-Ph+ patient-derived cell line (K562/Dox) overexpressing P-gp. Overall, we demonstrate that the P-gp-mediated efflux ratio can be minimized by computationally driven optimization of the molecular dipole and/or cpKa without recourse to intramolecular hydrogen bonds.

MeSH terms

  • Antineoplastic Agents / chemical synthesis
  • Antineoplastic Agents / chemistry
  • Antineoplastic Agents / pharmacology
  • Drug Discovery
  • Drug Resistance, Multiple / drug effects
  • Drug Resistance, Neoplasm* / drug effects
  • Fusion Proteins, bcr-abl* / antagonists & inhibitors
  • Fusion Proteins, bcr-abl* / metabolism
  • Humans
  • Leukemia, Myelogenous, Chronic, BCR-ABL Positive* / drug therapy
  • Leukemia, Myelogenous, Chronic, BCR-ABL Positive* / pathology
  • Molecular Docking Simulation
  • Protein Kinase Inhibitors* / chemical synthesis
  • Protein Kinase Inhibitors* / chemistry
  • Protein Kinase Inhibitors* / pharmacology
  • Proto-Oncogene Mas*
  • Structure-Activity Relationship

Substances

  • Protein Kinase Inhibitors
  • Fusion Proteins, bcr-abl
  • Proto-Oncogene Mas
  • MAS1 protein, human
  • Antineoplastic Agents
  • BCR-ABL1 fusion protein, human