TY - JOUR
T1 - Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3
AU - Parenti, Marco Daniele
AU - Naldi, Marina
AU - Manoni, Elisabetta
AU - Fabini, Edoardo
AU - Cederfelt, Daniela
AU - Talibov, Vladimir O.
AU - Gressani, Valeria
AU - Guven, Ummu
AU - Grossi, Valentina
AU - Fasano, Candida
AU - Sanese, Paola
AU - De Marco, Katia
AU - Shtil, Alexander A.
AU - Kurkin, Alexander V.
AU - Altieri, Andrea
AU - Danielson, U. Helena
AU - Caretti, Giuseppina
AU - Simone, Cristiano
AU - Varchi, Greta
AU - Bartolini, Manuela
AU - Del Rio, Alberto
N1 - Funding Information:
This work was supported by the Italian Association for Cancer Research (AIRC) IG 19172 to A.D.R, IG 23794 to C.S. and IG 21353 to G.C, the Emilia Romagna region POR FSE 2014/2020 project ONCOPENTA to A.D.R. and M.B, RFBR N# grant 20–53-7808 to A.S., Bilateral CNR / RFBR grant to A.D.R., the Italian Ministry of Health ‘‘Ricerca Corrente; 2019–2021″ to C.S. and ‘‘Starting Grant’’ SG-2019-12371540 to P.S., by the Italian Ministry of Education, University and Research (MIUR) ‘‘PRIN - Research Projects of National Relevance‘‘(PRIN 2017, n.2017WNKSLRLS4) to C.S. and Cariplo 2017-0604 to G.C.. Authors are thankful to the BioMAX beamline staff (MAX IV laboratory, Lund, Sweden) for the assistance with diffraction data collection and Doreen Dobritzsch for support in the structural analysis.
Publisher Copyright:
© 2022 Elsevier Masson SAS
PY - 2022/12/5
Y1 - 2022/12/5
N2 - 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.
AB - 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.
KW - Cancer target therapy
KW - Covalent inhibitor
KW - Epigenetic inhibitors
KW - Lysine methyltransferase
KW - SMYD3
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U2 - 10.1016/j.ejmech.2022.114683
DO - 10.1016/j.ejmech.2022.114683
M3 - Article
C2 - 36116234
AN - SCOPUS:85138099182
SN - 0223-5234
VL - 243
JO - European Journal of Medicinal Chemistry
JF - European Journal of Medicinal Chemistry
M1 - 114683
ER -