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Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase |
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| Authors: | Dr Vladimir O Talibov Dr Edoardo Fabini Edward A FitzGerald Dr Daniele Tedesco Daniela Cederfeldt Martin J Talu Moira M Rachman Filip Mihalic Dr Elisabetta Manoni Dr Marina Naldi Dr Paola Sanese Dr Giovanna Forte Dr Martina Lepore Signorile Prof Xavier Barril Dr Cristiano Simone Prof Manuela Bartolini Dr Doreen Dobritzsch Dr Alberto Del Rio Prof U Helena Danielson |
| Affiliation: | 1. Department of Chemistry–BMC, Uppsala University, Husargatan 3, 754 24 Uppsala, Sweden;2. Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy;3. Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Spain;4. Institute for Organic Synthesis and Photoreactivity, National Research Council, Via P. Gobetti 101, 40129 Bologna, Italy;5. Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis' Research Hospital, 70013 Bari, Italy;6. Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de Farmacia, Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Spain
Catalan Institution for Research and Advanced Studies (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain;7. Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis' Research Hospital, 70013 Bari, Italy Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari Aldo Moro, 70124 Bari, Italy |
| Abstract: | SMYD3 is a multifunctional epigenetic enzyme with lysine methyltransferase activity and various interaction partners. It is implicated in the pathophysiology of cancers but with an unclear mechanism. To discover tool compounds for clarifying its biochemistry and potential as a therapeutic target, a set of drug-like compounds was screened in a biosensor-based competition assay. Diperodon was identified as an allosteric ligand; its R and S enantiomers were isolated, and their affinities to SMYD3 were determined (KD=42 and 84 μM, respectively). Co-crystallization revealed that both enantiomers bind to a previously unidentified allosteric site in the C-terminal protein binding domain, consistent with its weak inhibitory effect. No competition between diperodon and HSP90 (a known SMYD3 interaction partner) was observed although SMYD3–HSP90 binding was confirmed (KD=13 μM). Diperodon clearly represents a novel starting point for the design of tool compounds interacting with a druggable allosteric site, suitable for the exploration of noncatalytic SMYD3 functions and therapeutics with new mechanisms of action. |
| Keywords: | biophysical methods epigenetic enzymes ligand discovery SMYD3 biology |
