Discovery of Novel Inhibitors Targeting the Menin-Mixed Lineage Leukemia Interface Using Pharmacophore- and Docking-Based Virtual Screening

J Chem Inf Model. 2016 Sep 26;56(9):1847-55. doi: 10.1021/acs.jcim.6b00185. Epub 2016 Aug 24.


Disrupting the interaction between mixed lineage leukemia (MLL) fusion protein and menin provides a therapeutic approach for MLL-mediated leukemia. Here, we aim to discover novel inhibitors targeting the menin-MLL interface with virtual screening. Both structure-based molecular docking and ligand-based pharmacophore models were established, and the models used for compound screening show a remarkable ability to retrieve known active ligands from decoy molecules. Verified by a fluorescence polarization assay, five hits with novel scaffolds were identified. Among them, DCZ_M123 exhibited potent inhibitory activity with an IC50 of 4.71 ± 0.12 μM and a KD of 14.70 ± 2.13 μM, and it can effectively inhibit the human MLL-rearranged leukemia cells MV4;11 and KOPN8 with GI50 values of 0.84 μM and 0.54 μM, respectively.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents / chemistry
  • Antineoplastic Agents / metabolism*
  • Antineoplastic Agents / pharmacology*
  • Drug Design
  • Drug Screening Assays, Antitumor
  • Humans
  • Molecular Docking Simulation
  • Myeloid-Lymphoid Leukemia Protein / antagonists & inhibitors*
  • Myeloid-Lymphoid Leukemia Protein / chemistry
  • Myeloid-Lymphoid Leukemia Protein / metabolism*
  • Protein Conformation
  • Proto-Oncogene Proteins / metabolism
  • Quantitative Structure-Activity Relationship
  • User-Computer Interface


  • Antineoplastic Agents
  • MEN1 protein, human
  • Proto-Oncogene Proteins
  • Myeloid-Lymphoid Leukemia Protein