2. Academic Validation
  3. Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3

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

  • Eur J Med Chem. 2022 Sep 8;243:114683. doi: 10.1016/j.ejmech.2022.114683.
Marco Daniele Parenti 1,  Marina Naldi 2,  Elisabetta Manoni 1,  Edoardo Fabini 3,  Daniela Cederfelt 4,  Vladimir O Talibov 5,  Valeria Gressani 6,  Ummu Guven 6,  Valentina Grossi 7,  Candida Fasano 7,  Paola Sanese 7,  Katia De Marco 7,  Alexander A Shtil 8,  Alexander V Kurkin 9,  Andrea Altieri 10,  U Helena Danielson 11,  Giuseppina Caretti 6,  Cristiano Simone 12,  Greta Varchi 1,  Manuela Bartolini 13,  Alberto Del Rio 14
Affiliations

Affiliations

  • 1 Institute of Organic Synthesis and Photoreactivity - National Research Council, 40129, Bologna, Italy.
  • 2 Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy; Centre for Applied Biomedical Research, Alma Mater Studiorum University of Bologna, Bologna, Italy.
  • 3 Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy.
  • 4 Department of Chemistry - BMC, Uppsala University, 751 23, Uppsala, Sweden.
  • 5 Department of Chemistry - BMC, Uppsala University, 751 23, Uppsala, Sweden; BioMAX beam line, MAX IV Laboratory, 22484, Lund, Sweden.
  • 6 Department of Biosciences, University of Milan, 20133, Milan, Italy.
  • 7 Medical Genetics National Institute for Gastroenterology, IRCCS 'S. de Bellis' Research Hospital, Castellana Grotte, Italy.
  • 8 Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia; Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russia.
  • 9 Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
  • 10 Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia; EDASA Scientific Srls, 66050, San Salvo (CH), Italy.
  • 11 Department of Chemistry - BMC, Uppsala University, 751 23, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
  • 12 Medical Genetics National Institute for Gastroenterology, IRCCS 'S. de Bellis' Research Hospital, Castellana Grotte, Italy; Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari Aldo Moro, Bari, 70124, Italy.
  • 13 Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy. Electronic address: [email protected].
  • 14 Institute of Organic Synthesis and Photoreactivity - National Research Council, 40129, Bologna, Italy; Innovamol Consulting Srl, Via San Faustino 167, 41126, Modena, Italy. Electronic address: [email protected].
PMID: 36116234 DOI: 10.1016/j.ejmech.2022.114683
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.

Keywords

Cancer target therapy; Covalent inhibitor; Epigenetic inhibitors; Lysine methyltransferase; SMYD3.

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