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Liashuk OS, Andriashvili VA, Tolmachev AO, Grygorenko OO. Chemoselective Reactions of Functionalized Sulfonyl Halides. CHEM REC 2024; 24:e202300256. [PMID: 37823680 DOI: 10.1002/tcr.202300256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Chemoselective transformations of functionalized sulfonyl fluorides and chlorides are surveyed comprehensively. It is shown that sulfonyl fluorides provide an excellent selectivity control in their reactions. Thus, numerous conditions are tolerated by the SO2 F group - from amide and ester formation to directed ortho-lithiation and transition-metal-catalyzed cross-couplings. Meanwhile, sulfur (VI) fluoride exchange (SuFEx) is also compatible with numerous functional groups, thus confirming its title of "another click reaction". On the contrary, with a few exceptions, most transformations of functionalized sulfonyl chlorides typically occur at the SO2 Cl moiety.
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Affiliation(s)
- Oleksandr S Liashuk
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Vladyslav A Andriashvili
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Andriy O Tolmachev
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd. (www.enamine.net), Winston Churchill Street 78, Kyїv, 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, Kyїv, 01601, Ukraine
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Padilla A, Manganaro JF, Huesgen L, Roess DA, Brown MA, Crans DC. Targeting Epigenetic Changes Mediated by Members of the SMYD Family of Lysine Methyltransferases. Molecules 2023; 28:molecules28042000. [PMID: 36838987 PMCID: PMC9967872 DOI: 10.3390/molecules28042000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
A comprehensive understanding of the mechanisms involved in epigenetic changes in gene expression is essential to the clinical management of diseases linked to the SMYD family of lysine methyltransferases. The five known SMYD enzymes catalyze the transfer of donor methyl groups from S-adenosylmethionine (SAM) to specific lysines on histones and non-histone substrates. SMYDs family members have distinct tissue distributions and tissue-specific functions, including regulation of development, cell differentiation, and embryogenesis. Diseases associated with SMYDs include the repressed transcription of SMYD1 genes needed for the formation of ion channels in the heart leading to heart failure, SMYD2 overexpression in esophageal squamous cell carcinoma (ESCC) or p53-related cancers, and poor prognosis associated with SMYD3 overexpression in more than 14 types of cancer including breast cancer, colon cancer, prostate cancer, lung cancer, and pancreatic cancer. Given the importance of epigenetics in various pathologies, the development of epigenetic inhibitors has attracted considerable attention from the pharmaceutical industry. The pharmacologic development of the inhibitors involves the identification of molecules regulating both functional SMYD SET (Suppressor of variegation, Enhancer of Zeste, Trithorax) and MYND (Myeloid-Nervy-DEAF1) domains, a process facilitated by available X-ray structures for SMYD1, SMYD2, and SMYD3. Important leads for potential pharmaceutical agents have been reported for SMYD2 and SMYD3 enzymes, and six epigenetic inhibitors have been developed for drugs used to treat myelodysplastic syndrome (Vidaza, Dacogen), cutaneous T-cell lymphoma (Zoinza, Isrodax), and peripheral T-cell lymphoma (Beleodag, Epidaza). The recently demonstrated reversal of SMYD histone methylation suggests that reversing the epigenetic effects of SMYDs in cancerous tissues may be a desirable target for pharmacological development.
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Affiliation(s)
- Alyssa Padilla
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA
| | - John F. Manganaro
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
| | - Lydia Huesgen
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA
| | - Deborah A. Roess
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA
| | - Mark A. Brown
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523-1678, USA
- Graduate Degree Program in Ecology, Department of Ethnic Studies, Global Health and Health Disparities, Colorado School of Public Health, Colorado State University, Fort Collins, CO 80523-1612, USA
- Correspondence: (M.A.B.); (D.C.C.)
| | - Debbie C. Crans
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA
- Correspondence: (M.A.B.); (D.C.C.)
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3
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Discovery of the 4-aminopiperidine-based compound EM127 for the site-specific covalent inhibition of SMYD3. Eur J Med Chem 2022; 243:114683. [PMID: 36116234 DOI: 10.1016/j.ejmech.2022.114683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 08/01/2022] [Accepted: 08/11/2022] [Indexed: 11/22/2022]
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.
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Wan S, Bhati AP, Wright DW, Wall ID, Graves AP, Green D, Coveney PV. Ensemble Simulations and Experimental Free Energy Distributions: Evaluation and Characterization of Isoxazole Amides as SMYD3 Inhibitors. J Chem Inf Model 2022; 62:2561-2570. [PMID: 35508076 PMCID: PMC9131449 DOI: 10.1021/acs.jcim.2c00255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Optimization of binding affinities for ligands to their target protein is a primary objective in rational drug discovery. Herein, we report on a collaborative study that evaluates various compounds designed to bind to the SET and MYND domain-containing protein 3 (SMYD3). SMYD3 is a histone methyltransferase and plays an important role in transcriptional regulation in cell proliferation, cell cycle, and human carcinogenesis. Experimental measurements using the scintillation proximity assay show that the distributions of binding free energies from a large number of independent measurements exhibit non-normal properties. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to predict the binding free energies and to provide a detailed chemical insight into the nature of ligand-protein binding. Our results show that the 1-trajectory ESMACS protocol works well for the set of ligands studied here. Although one unexplained outlier exists, we obtain excellent statistical ranking across the set of compounds from the ESMACS protocol and good agreement between calculations and experiments for the relative binding free energies from the TIES protocol. ESMACS and TIES are again found to be powerful protocols for the accurate comparison of the binding free energies.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Agastya P Bhati
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - David W Wright
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Ian D Wall
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Alan P Graves
- GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Darren Green
- GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, U.K.,Advanced Research Computing Centre, University College London, London WC1H 0AJ U.K.,Institute for Informatics, Faculty of Science, University of Amsterdam, 1098XH Amsterdam, The Netherlands
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5
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Feoli A, Viviano M, Cipriano A, Milite C, Castellano S, Sbardella G. Lysine methyltransferase inhibitors: where we are now. RSC Chem Biol 2022; 3:359-406. [PMID: 35441141 PMCID: PMC8985178 DOI: 10.1039/d1cb00196e] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/10/2021] [Indexed: 12/14/2022] Open
Abstract
Protein lysine methyltransferases constitute a large family of epigenetic writers that catalyse the transfer of a methyl group from the cofactor S-adenosyl-l-methionine to histone- and non-histone-specific substrates. Alterations in the expression and activity of these proteins have been linked to the genesis and progress of several diseases, including cancer, neurological disorders, and growing defects, hence they represent interesting targets for new therapeutic approaches. Over the past two decades, the identification of modulators of lysine methyltransferases has increased tremendously, clarifying the role of these proteins in different physio-pathological states. The aim of this review is to furnish an updated outlook about the protein lysine methyltransferases disclosed modulators, reporting their potency, their mechanism of action and their eventual use in clinical and preclinical studies.
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Affiliation(s)
- Alessandra Feoli
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Monica Viviano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Alessandra Cipriano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Ciro Milite
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Sabrina Castellano
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
| | - Gianluca Sbardella
- Department of Pharmacy, Epigenetic Med Chem Lab, University of Salerno via Giovanni Paolo II 132 I-84084 Fisciano SA Italy +39-089-96-9602 +39-089-96-9770
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Saeedi M, Eslami A, Mirfazli SS, Zardkanlou M, Faramarzi MA, Mahdavi M, Akbarzadeh T. Design and Synthesis of Novel 5-Arylisoxazole-1,3,4-thiadiazole Hybrids as α-Glucosidase Inhibitors. LETT DRUG DES DISCOV 2021. [DOI: 10.2174/1570180817999201104125018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
α-Glucosidase inhibitors have occupied a significant position in the treatment
of type 2 diabetes. In this respect, the development of novel and efficient non-sugar-based
inhibitors is in high demand.
Objective:
Design and synthesis of new 5-arylisoxazole-1,3,4-thiadiazole hybrids possessing α-
glucosidase inhibitory activity were developed.
Methods:
Different derivatives were synthesized by the reaction of various 5-arylisoxazole-3-
carboxylic acids and ethyl 2-((5-amino-1,3,4-thiadiazol-2-yl)thio)acetate. Finally, they were evaluated
for their α-glucosidase inhibitory activity.
Results:
It was found that ethyl 2-((5-(5-(2-chlorophenyl)isoxazole-3-carboxamido)-1,3,4-thiadiazol-
2-yl)thio)acetate (5j) was the most potent compound (IC50 = 180.1 μM) compared with acarbose as
the reference drug (IC50 = 750.0 μM). Also, the kinetic study of 5j revealed a competitive inhibition
and docking study results indicated desired interactions of that compound with amino acid residues
located close to the active site of α-glucosidase.
Conclusion:
Good α-glucosidase inhibitory activity obtained by the title compounds introduced
them as an efficient scaffold, which merits to be considered in anti-diabetic drug discovery
developments.
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Affiliation(s)
- Mina Saeedi
- Medicinal Plants Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Azadeh Eslami
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyedeh Sara Mirfazli
- Department of Medicinal Chemistry, School of Pharmacy-International Campus, Iran University of Medical Sciences, Tehran, Iran
| | - Mahsa Zardkanlou
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. Box 14155-6451, Tehran 1417614411, Iran
| | - Mohammad Ali Faramarzi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, P.O. Box 14155-6451, Tehran 1417614411, Iran
| | - Mohammad Mahdavi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Tahmineh Akbarzadeh
- Persian Medicine and Pharmacy Research Center, Tehran University of Medical Sciences, Tehran, Iran
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7
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Talibov VO, Fabini E, FitzGerald EA, Tedesco D, Cederfeldt D, Talu MJ, Rachman MM, Mihalic F, Manoni E, Naldi M, Sanese P, Forte G, Lepore Signorile M, Barril X, Simone C, Bartolini M, Dobritzsch D, Del Rio A, Danielson UH. Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase. Chembiochem 2021; 22:1597-1608. [PMID: 33400854 PMCID: PMC8248052 DOI: 10.1002/cbic.202000736] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/30/2020] [Indexed: 12/15/2022]
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.
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Affiliation(s)
- Vladimir O. Talibov
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Edoardo Fabini
- Department of Pharmacy and BiotechnologyAlma Mater Studiorum University of BolognaVia Belmeloro 640126BolognaItaly
- Institute for Organic Synthesis and PhotoreactivityNational Research CouncilVia P. Gobetti 10140129BolognaItaly
| | - Edward A. FitzGerald
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
- Beactica Therapeutics ABVirdings allé 2754 50UppsalaSweden
| | - Daniele Tedesco
- Department of Pharmacy and BiotechnologyAlma Mater Studiorum University of BolognaVia Belmeloro 640126BolognaItaly
- Institute for Organic Synthesis and PhotoreactivityNational Research CouncilVia P. Gobetti 10140129BolognaItaly
| | - Daniela Cederfeldt
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Martin J. Talu
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Moira M. Rachman
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de FarmaciaUniversitat de BarcelonaAv. Joan XXIII 27–3108028BarcelonaSpain
| | - Filip Mihalic
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Elisabetta Manoni
- Institute for Organic Synthesis and PhotoreactivityNational Research CouncilVia P. Gobetti 10140129BolognaItaly
| | - Marina Naldi
- Department of Pharmacy and BiotechnologyAlma Mater Studiorum University of BolognaVia Belmeloro 640126BolognaItaly
- Centre for Applied Biomedical ResearchAlma Mater Studiorum University of BolognaVia Zamboni, 33Bologna40126Italy
| | - Paola Sanese
- Medical Genetics, National Institute for GastroenterologyIRCCS ‘S. de Bellis' Research Hospital70013BariItaly
| | - Giovanna Forte
- Medical Genetics, National Institute for GastroenterologyIRCCS ‘S. de Bellis' Research Hospital70013BariItaly
| | - Martina Lepore Signorile
- Medical Genetics, National Institute for GastroenterologyIRCCS ‘S. de Bellis' Research Hospital70013BariItaly
| | - Xavier Barril
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) and Facultat de FarmaciaUniversitat de BarcelonaAv. Joan XXIII 27–3108028BarcelonaSpain
- Catalan Institution for Research and Advanced Studies (ICREA)Passeig Lluis Companys 2308010BarcelonaSpain
| | - Cristiano Simone
- Medical Genetics, National Institute for GastroenterologyIRCCS ‘S. de Bellis' Research Hospital70013BariItaly
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO)University of Bari Aldo Moro70124BariItaly
| | - Manuela Bartolini
- Department of Pharmacy and BiotechnologyAlma Mater Studiorum University of BolognaVia Belmeloro 640126BolognaItaly
| | - Doreen Dobritzsch
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
| | - Alberto Del Rio
- Institute for Organic Synthesis and PhotoreactivityNational Research CouncilVia P. Gobetti 10140129BolognaItaly
- Innovamol Consulting SrlVia Giardini 470/H41124ModenaItaly
| | - U. Helena Danielson
- Department of Chemistry–BMCUppsala UniversityHusargatan 3754 24UppsalaSweden
- Science for Life LaboratoryUppsala UniversityUppsala752 37Sweden
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