Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents

  • J Med Chem. 2023 Mar 23;66(6):4059-4085. doi: 10.1021/acs.jmedchem.2c02059.
Yosuke Nishigaya  1 ,  Shohei Takase  2 ,  Tatsunobu Sumiya  1 ,  Ko Kikuzato ,  Tomohiro Sato ,  Hideaki Niwa ,  Shin Sato ,  Akiko Nakata ,  Takeshi Sonoda ,  Noriaki Hashimoto  1 ,  Ryosuke Namie  1 ,  Teruki Honma ,  Takashi Umehara ,  Mikako Shirouzu ,  Hiroo Koyama ,  Minoru Yoshida  3 ,  Akihiro Ito  2 ,  Fumiyuki Shirai
Affiliations
  • 1. Watarase Research Center, Discovery Research Headquarters, Kyorin Pharmaceutical Co. Ltd., 1848 Nogi, Shimotsuga-gun, Tochigi 329-0114, Japan.
  • 2. School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
  • 3. Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
PMID: 36882960 DOI: 10.1021/acs.jmedchem.2c02059
Abstract

Identification of structurally novel inhibitors of lysine methyltransferase G9a has been a subject of intense research in cancer Epigenetics. Starting with the high-throughput screening (HTS) hit rac-10a obtained from the chemical library of the University of Tokyo Drug Discovery Initiative, the structure-activity relationship of the unique substrate-competitive inhibitors was established with the help of X-ray crystallography and fragment molecular orbital (FMO) calculations for the ligand-protein interaction. Further optimization of the in vitro characteristics and drug metabolism and pharmacokinetics (DMPK) properties led to the identification of 26j (RK-701), which is a structurally distinct potent inhibitor of G9a/GLP (IC50 = 27/53 nM). Compound 26j exhibited remarkable selectivity against Other related methyltransferases, dose-dependent attenuation of cellular H3K9me2 levels, and tumor growth inhibition in MOLT-4 cells in vitro. Moreover, compound 26j showed inhibition of tumor initiation and growth in a carcinogen-induced hepatocellular carcinoma (HCC) in vivo mouse model without overt acute toxicity.