Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3

Marco Daniele Parenti, Marina Naldi, Elisabetta Manoni, Edoardo Fabini, Daniela Cederfelt, Vladimir O. Talibov, Valeria Gressani, Ummu Guven, Valentina Grossi, Candida Fasano, Paola Sanese, Katia De Marco, Alexander A. Shtil, Alexander V. Kurkin, Andrea Altieri, U. Helena Danielson, Giuseppina Caretti, Cristiano Simone, Greta Varchi, Manuela BartoliniAlberto Del Rio

Research output: Contribution to journalArticlepeer-review

Abstract

Recent findings support the hypothesis that inhibition of SMYD3 methyltransferase may be a therapeutic avenue for some of the deadliest cancer types. Herein, active site-selective covalent SMYD3 inhibitors were designed by introducing an appropriate reactive cysteine trap into reversible first-generation SMYD3 inhibitors. The 4-aminopiperidine derivative EM127 (11C) bearing a 2-chloroethanoyl group as reactive warhead showed selectivity for Cys186, located in the substrate/histone binding pocket. Selectivity towards Cys186 was retained even at high inhibitor/enzyme ratio, as shown by mass spectrometry. The mode of interaction with the SMYD3 substrate/histone binding pocket was revealed by crystallographic studies. In enzymatic assays, 11C showed a stronger SMYD3 inhibitory effect compared to the reference inhibitor EPZ031686. Remarkably, 11C attenuated the proliferation of MDA-MB-231 breast cancer cell line at the same low micromolar range of concentrations that reduced SMYD3 mediated ERK signaling in HCT116 colorectal cancer and MDA-MB-231 breast cancer cells. Furthermore, 11C (5 μM) strongly decreased the steady-state mRNA levels of genes important for tumor biology such as cyclin dependent kinase 2, c-MET, N-cadherin and fibronectin 1, all known to be regulated, at least in part, by SMYD3. Thus, 11C is as a first example of second generation SMYD3 inhibitors; this agent represents a covalent and a site specific SMYD3 binder capable of potent and prolonged attenuation of methyltransferase activity.

Original languageEnglish (US)
Article number114683
JournalEuropean Journal of Medicinal Chemistry
Volume243
DOIs
StatePublished - Dec 5 2022

Keywords

  • Cancer target therapy
  • Covalent inhibitor
  • Epigenetic inhibitors
  • Lysine methyltransferase
  • SMYD3

ASJC Scopus subject areas

  • Pharmacology
  • Drug Discovery
  • Organic Chemistry

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