1
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Ahmed-Belkacem R, Sutto-Ortiz P, Delpal A, Troussier J, Canard B, Vasseur JJ, Decroly E, Debart F. 5'-cap RNA/SAM mimetic conjugates as bisubstrate inhibitors of viral RNA cap 2'-O-methyltransferases. Bioorg Chem 2024; 143:107035. [PMID: 38199140 DOI: 10.1016/j.bioorg.2023.107035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/24/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
Viral RNA cap 2'-O-methyltransferases are considered promising therapeutic targets for antiviral treatments, as they play a key role in the formation of viral RNA cap-1 structures to escape the host immune system. A better understanding of how they interact with their natural substrates (RNA and the methyl donor SAM) would enable the rational development of potent inhibitors. However, as few structures of 2'-O-MTases in complex with RNA have been described, little is known about substrate recognition by these MTases. For this, chemical tools mimicking the state in which the cap RNA substrate and SAM cofactor are bound in the enzyme's catalytic pocket may prove useful. In this work, we designed and synthesized over 30 RNA conjugates that contain a short oligoribonucleotide (ORN with 4 or 6 nucleotides) with the first nucleotide 2'-O-attached to an adenosine by linkers of different lengths and containing S or N-heteroatoms, or a 1,2,3-triazole ring. These ORN conjugates bearing or not a cap structure at 5'-extremity mimic the methylation transition state with RNA substrate/SAM complex as bisubstrates of 2'-O-MTases. The ORN conjugates were synthesized either by the incorporation of a dinucleoside phosphoramidite during RNA elongation or by click chemistry performed on solid-phase post-RNA elongation. Their ability to inhibit the activity of the nsp16/nsp10 complex of SARS-CoV-2 and the NS5 protein of dengue and Zika viruses was assessed. Significant submicromolar IC50 values and Kd values in the µM range were found, suggesting a possible interaction of some ORN conjugates with these viral 2'-O-MTases.
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Affiliation(s)
| | | | - Adrien Delpal
- AFMB, University of Aix-Marseille, CNRS, Marseille, France
| | - Joris Troussier
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Bruno Canard
- AFMB, University of Aix-Marseille, CNRS, Marseille, France
| | | | | | - Françoise Debart
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France.
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2
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Schnee P, Pleiss J, Jeltsch A. Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. Crit Rev Biochem Mol Biol 2024; 59:20-68. [PMID: 38449437 DOI: 10.1080/10409238.2024.2318547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/10/2024] [Indexed: 03/08/2024]
Abstract
Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.
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Affiliation(s)
- Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
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3
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Wang S, Klein SO, Urban S, Staudt M, Barthes NPF, Willmann D, Bacher J, Sum M, Bauer H, Peng L, Rennar GA, Gratzke C, Schüle KM, Zhang L, Einsle O, Greschik H, MacLeod C, Thomson CG, Jung M, Metzger E, Schüle R. Structure-guided design of a selective inhibitor of the methyltransferase KMT9 with cellular activity. Nat Commun 2024; 15:43. [PMID: 38167811 PMCID: PMC10762027 DOI: 10.1038/s41467-023-44243-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Inhibition of epigenetic regulators by small molecules is an attractive strategy for cancer treatment. Recently, we characterised the role of lysine methyltransferase 9 (KMT9) in prostate, lung, and colon cancer. Our observation that the enzymatic activity was required for tumour cell proliferation identified KMT9 as a potential therapeutic target. Here, we report the development of a potent and selective KMT9 inhibitor (compound 4, KMI169) with cellular activity through structure-based drug design. KMI169 functions as a bi-substrate inhibitor targeting the SAM and substrate binding pockets of KMT9 and exhibits high potency, selectivity, and cellular target engagement. KMT9 inhibition selectively downregulates target genes involved in cell cycle regulation and impairs proliferation of tumours cells including castration- and enzalutamide-resistant prostate cancer cells. KMI169 represents a valuable tool to probe cellular KMT9 functions and paves the way for the development of clinical candidate inhibitors as therapeutic options to treat malignancies such as therapy-resistant prostate cancer.
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Affiliation(s)
- Sheng Wang
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Sebastian O Klein
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Sylvia Urban
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Maximilian Staudt
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Nicolas P F Barthes
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dominica Willmann
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Johannes Bacher
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Manuela Sum
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Helena Bauer
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Ling Peng
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Georg A Rennar
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Christian Gratzke
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Katrin M Schüle
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Holger Greschik
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Calum MacLeod
- Drug Discovery, Pharmaron UK Ltd, Hoddesdon, United Kingdom
| | | | - Manfred Jung
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany
| | - Eric Metzger
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany.
| | - Roland Schüle
- Klinik für Urologie und Zentrale Klinische Forschung, Klinikum der Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
- CIBSS Centre of Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
- Deutsches Konsortium für Translationale Krebsforschung, Standort Freiburg, Freiburg, Germany.
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4
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Yu L, Wei Y, Lu T, Li Z, Lai S, Yan Y, Chen C, Wen W. The SMYD3-dependent H3K4me3 status of IGF2 intensifies local Th2 differentiation in CRSwNP via positive feedback. Cell Commun Signal 2023; 21:345. [PMID: 38037054 PMCID: PMC10688075 DOI: 10.1186/s12964-023-01375-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Chronic rhinosinusitis with nasal polyps (CRSwNP) is a heterogeneous and common upper airway disease divided into various inflammatory endotypes. Recent epidemiological findings showed a T helper 2 (Th2)-skewed dominance in CRSwNP patients. Histone modification alterations can regulate transcriptional and translational expression, resulting in abnormal pathogenic changes and the occurrence of diseases. Trimethylation of histone H3 lysine 4 (H3K4me3) is considered an activator of gene expression through modulation of accessibility for transcription, which is closely related to CRSwNP. H3K4me3 levels in the human nasal epithelium may change under Th2-biased inflammatory conditions, resulting in exaggerated local nasal Th2 responses via the regulation of naïve CD4+ T-cell differentiation. Here, we revealed that the level of SET and MYND domain-containing protein 3 (SMYD3)-mediated H3K4me3 was increased in NPs from Th2 CRSwNP patients compared with those from healthy controls. We demonstrated that SMYD3-mediated H3K4me3 is increased in human nasal epithelial cells under Th2-biased inflammatory conditions via S-adenosyl-L-methionine (SAM) production and further found that the H3K4me3high status of insulin-like growth factor 2 (IGF2) produced in primary human nasal epithelial cells could promote naïve CD4+ T-cell differentiation into Th2 cells. Moreover, we found that SAM production was dependent on the c-Myc/methionine adenosyltransferase 2A (MAT2A) axis in the nasal epithelium. Understanding histone modifications in the nasal epithelium has immense potential utility in the development of novel classes of therapeutics targeting Th2 polarization in Th2 CRSwNP. Video Abstract.
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Affiliation(s)
- Lei Yu
- Department of Otolaryngology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Yi Wei
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
- Otorhinolaryngology Institute of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
- Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, P.R. China
| | - Tong Lu
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Zhengqi Li
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Shimin Lai
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Yan Yan
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Changhui Chen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China
| | - Weiping Wen
- Department of Otolaryngology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China.
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China.
- Otorhinolaryngology Institute of Sun Yat-Sen University, Guangzhou, Guangdong, P.R. China.
- Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou, Guangdong, P.R. China.
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5
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Lin B, Xiang L, Yuan Z, Hou Q, Ruan Y, Zhang J. ReACT (redox-activated chemical tagging) chemistry enables direct derivatization and fluorescence detection of S-adenosyl-L-homocysteine (SAH). Org Biomol Chem 2023; 21:7085-7089. [PMID: 37602780 DOI: 10.1039/d3ob01073b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2023]
Abstract
S-Adenosyl-L-homocysteine (SAH) is a universal byproduct and product inhibitor of the methyltransferase-catalyzed methylation reaction. Here based on ReACT (redox-activated chemical tagging) chemistry, direct derivatization and fluorescence measurement of SAH were achieved with features such as mild reaction conditions and simple operation.
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Affiliation(s)
- Bohong Lin
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Lingling Xiang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Zhijun Yuan
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Qi Hou
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Yaoping Ruan
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Jing Zhang
- Artemisinin Research Center and The First Affiliated Hospital, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
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6
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Wang S, You X, Liu X, Fengwei Zhang, Zhou H, Shang X, Cai L. SMYD3 induces sorafenib resistance by activating SMAD2/3-mediated epithelial-mesenchymal transition in hepatocellular carcinoma. iScience 2023; 26:106994. [PMID: 37534166 PMCID: PMC10391607 DOI: 10.1016/j.isci.2023.106994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/19/2023] [Accepted: 05/25/2023] [Indexed: 08/04/2023] Open
Abstract
Drug resistance prominently hampers the effects of systemic therapy of sorafenib to hepatocellular carcinoma (HCC). Epigenetics have critical regulatory roles in drug resistance. However, the contributions of histone methylatransferase SET and MYND domain containing 3 (SMYD3) to sorafenib resistance in HCC remain largely unknown. Here, using our established sorafenib-resistant HCC cell and xenograft models, we found SMYD3 was markedly elevated in sorafenib-resistant tumors and cells. Functionally, loss- and gain-of-function studies showed that SMYD3 promoted the migration, invasion, metastasis and stemness of sorafenib-resistant HCC cells. Mechanistically, SMYD3 is required for SMAD2/3-mediated epithelial-mesenchymal transition (EMT) in sorafenib-resistant HCC cells by interacting with SMAD2/3 and epigenetically promoting the expression of SOX4, ZEB1, SNAIL1 and MMP9 genes. In summary, our data demonstrate that targeting SMYD3 is an effective approach to overcome sorafenib resistance in HCC.
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Affiliation(s)
- Shanshan Wang
- Central Laboratory, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, 208 Huancheng Dong Road, Hangzhou 310003, Zhejiang, China
| | - Xin You
- College of Life Science, Northeast Agricultural University, Harbin 150030, Heilong Jiang, China
| | - Xiaoshu Liu
- Central Laboratory, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, 208 Huancheng Dong Road, Hangzhou 310003, Zhejiang, China
| | - Fengwei Zhang
- Central Laboratory, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, 208 Huancheng Dong Road, Hangzhou 310003, Zhejiang, China
| | - Hongjuan Zhou
- Central Laboratory, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, 208 Huancheng Dong Road, Hangzhou 310003, Zhejiang, China
| | - Xuechai Shang
- Central Laboratory, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, 208 Huancheng Dong Road, Hangzhou 310003, Zhejiang, China
| | - Long Cai
- Central Laboratory, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, 208 Huancheng Dong Road, Hangzhou 310003, Zhejiang, China
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7
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Liu R, Wu J, Guo H, Yao W, Li S, Lu Y, Jia Y, Liang X, Tang J, Zhang H. Post-translational modifications of histones: Mechanisms, biological functions, and therapeutic targets. MedComm (Beijing) 2023; 4:e292. [PMID: 37220590 PMCID: PMC10200003 DOI: 10.1002/mco2.292] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/25/2023] Open
Abstract
Histones are DNA-binding basic proteins found in chromosomes. After the histone translation, its amino tail undergoes various modifications, such as methylation, acetylation, phosphorylation, ubiquitination, malonylation, propionylation, butyrylation, crotonylation, and lactylation, which together constitute the "histone code." The relationship between their combination and biological function can be used as an important epigenetic marker. Methylation and demethylation of the same histone residue, acetylation and deacetylation, phosphorylation and dephosphorylation, and even methylation and acetylation between different histone residues cooperate or antagonize with each other, forming a complex network. Histone-modifying enzymes, which cause numerous histone codes, have become a hot topic in the research on cancer therapeutic targets. Therefore, a thorough understanding of the role of histone post-translational modifications (PTMs) in cell life activities is very important for preventing and treating human diseases. In this review, several most thoroughly studied and newly discovered histone PTMs are introduced. Furthermore, we focus on the histone-modifying enzymes with carcinogenic potential, their abnormal modification sites in various tumors, and multiple essential molecular regulation mechanism. Finally, we summarize the missing areas of the current research and point out the direction of future research. We hope to provide a comprehensive understanding and promote further research in this field.
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Affiliation(s)
- Ruiqi Liu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jiajun Wu
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Haiwei Guo
- Otolaryngology & Head and Neck CenterCancer CenterDepartment of Head and Neck SurgeryZhejiang Provincial People's HospitalAffiliated People's Hospital, Hangzhou Medical CollegeHangzhouZhejiangChina
| | - Weiping Yao
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Shuang Li
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentJinzhou Medical UniversityJinzhouLiaoningChina
| | - Yanwei Lu
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Yongshi Jia
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
| | - Xiaodong Liang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
- Graduate DepartmentBengbu Medical College, BengbuAnhuiChina
| | - Jianming Tang
- Department of Radiation OncologyThe First Hospital of Lanzhou UniversityLanzhou UniversityLanzhouGansuChina
| | - Haibo Zhang
- Cancer CenterDepartment of Radiation OncologyZhejiang Provincial People's HospitalAffiliated People's HospitalHangzhou Medical CollegeHangzhouZhejiangChina
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8
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Zhu HP, Chai J, Qin R, Leng HJ, Wen X, Peng C, He G, Han B. Discovery of tetrahydrofuranyl spirooxindole-based SMYD3 inhibitors against gastric cancer via inducing lethal autophagy. Eur J Med Chem 2023; 246:115009. [PMID: 36527933 DOI: 10.1016/j.ejmech.2022.115009] [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: 11/02/2022] [Revised: 11/29/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
SMYD3 is a histone methyltransferase involved in transcriptional regulation, and its overexpression in various forms of cancer justifies that blocking SMYD3 functions can serve as a novel therapeutic strategy in cancer treatment. Herein, a series of novel tetrahydrofuranyl spirooxindoles were designed and synthesized based on a structure-based drug design strategy. Subsequent biochemical analysis suggested that these novel SMYD3 inhibitors showed good anticancer activity against stomach adenocarcinoma both in vitro and in vivo. Among them, compound 7r exhibited potent inhibitory capacities against SMYD3 and BGC823 cells with IC50 values of 0.81 and 0.75 μM, respectively. Mechanistic investigations showed that 7r could suppress Akt methylation and activation by SMYD3 and trigger lethal autophagic flux inhibition via the Akt-mTOR pathway. Collectively, our results may bridge the rational discovery of privileged structures, epigenetic targeting of SMYD3, and regulation of autophagic cell death.
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Affiliation(s)
- Hong-Ping Zhu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China; Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, 610106, China
| | - Jinlong Chai
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Rui Qin
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Hai-Jun Leng
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, 610106, China
| | - Xiang Wen
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Gu He
- Department of Dermatology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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9
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Short Linear Motifs in Colorectal Cancer Interactome and Tumorigenesis. Cells 2022; 11:cells11233739. [PMID: 36496998 PMCID: PMC9737320 DOI: 10.3390/cells11233739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Colorectal tumorigenesis is driven by alterations in genes and proteins responsible for cancer initiation, progression, and invasion. This multistage process is based on a dense network of protein-protein interactions (PPIs) that become dysregulated as a result of changes in various cell signaling effectors. PPIs in signaling and regulatory networks are known to be mediated by short linear motifs (SLiMs), which are conserved contiguous regions of 3-10 amino acids within interacting protein domains. SLiMs are the minimum sequences required for modulating cellular PPI networks. Thus, several in silico approaches have been developed to predict and analyze SLiM-mediated PPIs. In this review, we focus on emerging evidence supporting a crucial role for SLiMs in driver pathways that are disrupted in colorectal cancer (CRC) tumorigenesis and related PPI network alterations. As a result, SLiMs, along with short peptides, are attracting the interest of researchers to devise small molecules amenable to be used as novel anti-CRC targeted therapies. Overall, the characterization of SLiMs mediating crucial PPIs in CRC may foster the development of more specific combined pharmacological approaches.
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10
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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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11
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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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12
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Fasano C, Lepore Signorile M, De Marco K, Forte G, Sanese P, Grossi V, Simone C. Identifying novel SMYD3 interactors on the trail of cancer hallmarks. Comput Struct Biotechnol J 2022; 20:1860-1875. [PMID: 35495117 PMCID: PMC9039736 DOI: 10.1016/j.csbj.2022.03.037] [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] [Received: 10/08/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 12/30/2022] Open
Abstract
SMYD3 overexpression in several human cancers highlights its crucial role in carcinogenesis. Nonetheless, SMYD3 specific activity in cancer development and progression is currently under debate. Taking advantage of a library of rare tripeptides, which we first tested for their in vitro binding affinity to SMYD3 and then used as in silico probes, we recently identified BRCA2, ATM, and CHK2 as direct SMYD3 interactors. To gain insight into novel SMYD3 cancer-related roles, here we performed a comprehensive in silico analysis to cluster all potential SMYD3-interacting proteins identified by screening the human proteome for the previously tested tripeptides, based on their involvement in cancer hallmarks. Remarkably, we identified mTOR, BLM, MET, AMPK, and p130 as new SMYD3 interactors implicated in cancer processes. Further studies are needed to characterize the functional mechanisms underlying these interactions. Still, these findings could be useful to devise novel therapeutic strategies based on the combined inhibition of SMYD3 and its newly identified molecular partners. Of note, our in silico methodology may be useful to search for unidentified interactors of other proteins of interest.
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Affiliation(s)
- Candida Fasano
- Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis’ Research Hospital, Castellana Grotte (Ba), Italy
- Corresponding authors at: Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis’ Research Hospital, Castellana Grotte (Ba), Italy (C.Fasano, C. Simone).
| | - Martina Lepore Signorile
- Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis’ Research Hospital, Castellana Grotte (Ba), Italy
| | - Katia De Marco
- Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis’ Research Hospital, Castellana Grotte (Ba), Italy
| | - Giovanna Forte
- Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis’ Research Hospital, Castellana Grotte (Ba), Italy
| | - Paola Sanese
- Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis’ Research Hospital, Castellana Grotte (Ba), Italy
| | - Valentina Grossi
- Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis’ Research Hospital, Castellana Grotte (Ba), Italy
| | - Cristiano Simone
- Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis’ Research Hospital, Castellana Grotte (Ba), Italy
- Medical Genetics, Department of Biomedical Sciences and Human Oncology (DIMO), University of Bari Aldo Moro, Bari, Italy
- Corresponding authors at: Medical Genetics, National Institute for Gastroenterology, IRCCS ‘S. de Bellis’ Research Hospital, Castellana Grotte (Ba), Italy (C.Fasano, C. Simone).
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13
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Design, synthesis, and biological evaluation of SMYD3 inhibitors possessing N-thiazole benzenesulfonamide moiety as potential anti-cancer agents. JOURNAL OF SAUDI CHEMICAL SOCIETY 2022. [DOI: 10.1016/j.jscs.2022.101482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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Talukdar A, Mukherjee A, Bhattacharya D. Fascinating Transformation of SAM-Competitive Protein Methyltransferase Inhibitors from Nucleoside Analogues to Non-Nucleoside Analogues. J Med Chem 2022; 65:1662-1684. [PMID: 35014841 DOI: 10.1021/acs.jmedchem.1c01208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The abnormal expression of protein methyltransferase (PMT) has been linked with many diseases such as diabetes, neurological disorders, and cancer. S-Adenyl-l-methionine (SAM) is a universal methyl donor and gets converted to S-adenyl-l-homocysteine (SAH), an endogenous competitive inhibitor of SAM. Initially developed SAM/SAH mimetic nucleoside analogues were pan methyltransferase inhibitors. The gradual understanding achieved through ligand-receptor interaction paved the way for various rational approaches of drug design leading to potent and selective nucleoside inhibitors. The present perspective is based on the systematic evolution of selective SAM-competitive heterocyclic non-nucleoside inhibitors from nucleoside inhibitors. This fascinating transition has resolved several issues inherent to nucleoside analogues such as poor pharmacokinetics leading to poor in vivo efficacy. The perspective has brought together various concepts and strategies of drug design that contributed to this rational transition. We firmly believe that the strategies described herein will serve as a template for the future development of drugs in general.
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Affiliation(s)
- Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India.,Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Ayan Mukherjee
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India.,Academy of Scientific and Innovative Research, Ghaziabad 201002, India
| | - Debomita Bhattacharya
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, WB, India
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15
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Xiao S, Guo S, Han J, Sun Y, Wang M, Chen Y, Fang X, Yang F, Mu Y, Zhang L, Ding Y, Zhang N, Jiang H, Chen K, Zhao K, Luo C, Chen S. High-Throughput-Methyl-Reading (HTMR) assay: a solution based on nucleotide methyl-binding proteins enables large-scale screening for DNA/RNA methyltransferases and demethylases. Nucleic Acids Res 2021; 50:e9. [PMID: 34718755 PMCID: PMC8789064 DOI: 10.1093/nar/gkab989] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 08/26/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Epigenetic therapy has significant potential for cancer treatment. However, few small potent molecules have been identified against DNA or RNA modification regulatory proteins. Current approaches for activity detection of DNA/RNA methyltransferases and demethylases are time-consuming and labor-intensive, making it difficult to subject them to high-throughput screening. Here, we developed a fluorescence polarization-based ‘High-Throughput Methyl Reading’ (HTMR) assay to implement large-scale compound screening for DNA/RNA methyltransferases and demethylases-DNMTs, TETs, ALKBH5 and METTL3/METTL14. This assay is simple to perform in a mix-and-read manner by adding the methyl-binding proteins MBD1 or YTHDF1. The proteins can be used to distinguish FAM-labelled substrates or product oligonucleotides with different methylation statuses catalyzed by enzymes. Therefore, the extent of the enzymatic reactions can be coupled with the variation of FP binding signals. Furthermore, this assay can be effectively used to conduct a cofactor competition study. Based on the assay, we identified two natural products as candidate compounds for DNMT1 and ALKBH5. In summary, this study outlines a powerful homogeneous approach for high-throughput screening and evaluating enzymatic activity for DNA/RNA methyltransferases and demethylases that is cheap, easy, quick, and highly sensitive.
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Affiliation(s)
- Senhao Xiao
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Siqi Guo
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmacy, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Jie Han
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanli Sun
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Mingchen Wang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Yantao Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xueyu Fang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Feng Yang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yajuan Mu
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Liang Zhang
- Department of Pharmacology and Chemical Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yiluan Ding
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Naixia Zhang
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,Analytical Research Center for Organic and Biological Molecules, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Kaixian Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education; Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai 264005, China
| | - Cheng Luo
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Shijie Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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16
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Novel insights into SMYD2 and SMYD3 inhibitors: from potential anti-tumoural therapy to a variety of new applications. Mol Biol Rep 2021; 48:7499-7508. [PMID: 34510321 DOI: 10.1007/s11033-021-06701-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/07/2021] [Indexed: 01/02/2023]
Abstract
The revelance of the epigenetic regulation of cancer led to the design and testing of many drugs targeting epigenetic modifiers. The Su(Var)3-9, Enhancer-of-zeste and Trithorax (SET) and myeloid, Nervy, and DEAF-1 (MYND) domain-containing protein 2 (SMYD2) and 3 (SMYD3) are methyltransferases which act on histone and non-histone proteins to promote tumorigenesis in many cancer types. In addition to their oncogenic roles, SMYD2 and SMYD3 are involved in many other physiopathological conditions. In this review we will focus on the advances made in the last five years in the field of pharmacology regarding drugs targeting SMYD2 (such as LLY-507 or AZ505) and SMYD3 (such as BCI-121 or EPZ031686) and their potential cellular and molecular mechanisms of action and application in anti-tumoural therapy and/or against other diseases.
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17
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Playing on the Dark Side: SMYD3 Acts as a Cancer Genome Keeper in Gastrointestinal Malignancies. Cancers (Basel) 2021; 13:cancers13174427. [PMID: 34503239 PMCID: PMC8430692 DOI: 10.3390/cancers13174427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/29/2021] [Accepted: 08/30/2021] [Indexed: 01/17/2023] Open
Abstract
Simple Summary The activity of SMYD3 in promoting carcinogenesis is currently under debate. Growing evidence seems to confirm that SMYD3 overexpression correlates with poor prognosis, cancer growth and invasion, especially in gastrointestinal tumors. In this review, we dissect the emerging role played by SMYD3 in the regulation of cell cycle and DNA damage response by promoting homologous recombination (HR) repair and hence cancer cell genomic stability. Considering the crucial role of PARP1 in other DNA repair mechanisms, we also discuss a recently evaluated synthetic lethality approach based on the combined use of SMYD3 and PARP inhibitors. Interestingly, a significant proportion of HR-proficient gastrointestinal tumors expressing high levels of SMYD3 from the PanCanAtlas dataset seem to be eligible for this innovative strategy. This promising approach could be taken advantage of for therapeutic applications of SMYD3 inhibitors in cancer treatment. Abstract The SMYD3 methyltransferase has been found overexpressed in several types of cancers of the gastrointestinal (GI) tract. While high levels of SMYD3 have been positively correlated with cancer progression in cellular and advanced mice models, suggesting it as a potential risk and prognosis factor, its activity seems dispensable for autonomous in vitro cancer cell proliferation. Here, we present an in-depth analysis of SMYD3 functional role in the regulation of GI cancer progression. We first describe the oncogenic activity of SMYD3 as a transcriptional activator of genes involved in tumorigenesis, cancer development and transformation and as a co-regulator of key cancer-related pathways. Then, we dissect its role in orchestrating cell cycle regulation and DNA damage response (DDR) to genotoxic stress by promoting homologous recombination (HR) repair, thereby sustaining cancer cell genomic stability and tumor progression. Based on this evidence and on the involvement of PARP1 in other DDR mechanisms, we also outline a synthetic lethality approach consisting of the combined use of SMYD3 and PARP inhibitors, which recently showed promising therapeutic potential in HR-proficient GI tumors expressing high levels of SMYD3. Overall, these findings identify SMYD3 as a promising target for drug discovery.
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18
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Mechanism of the Conformational Change of the Protein Methyltransferase SMYD3: A Molecular Dynamics Simulation Study. Int J Mol Sci 2021; 22:ijms22137185. [PMID: 34281237 PMCID: PMC8267938 DOI: 10.3390/ijms22137185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
SMYD3 is a SET-domain-containing methyltransferase that catalyzes the transfer of methyl groups onto lysine residues of substrate proteins. Methylation of MAP3K2 by SMYD3 has been implicated in Ras-driven tumorigenesis, which makes SMYD3 a potential target for cancer therapy. Of all SMYD family proteins, SMYD3 adopt a closed conformation in a crystal structure. Several studies have suggested that the conformational changes between the open and closed forms may regulate the catalytic activity of SMYD3. In this work, we carried out extensive molecular dynamics simulations on a series of complexes with a total of 21 μs sampling to investigate the conformational changes of SMYD3 and unveil the molecular mechanisms. Based on the C-terminal domain movements, the simulated models could be depicted in three different conformational states: the closed, intermediate and open states. Only in the case that both the methyl donor binding pocket and the target lysine-binding channel had bound species did the simulations show SMYD3 maintaining its conformation in the closed state, indicative of a synergetic effect of the cofactors and target lysine on regulating the conformational change of SMYD3. In addition, we performed analyses in terms of structure and energy to shed light on how the two regions might regulate the C-terminal domain movement. This mechanistic study provided insights into the relationship between the conformational change and the methyltransferase activity of SMYD3. The more complete understanding of the conformational dynamics developed here together with further work may lay a foundation for the rational drug design of SMYD3 inhibitors.
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19
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Histone H3K4 Methyltransferases as Targets for Drug-Resistant Cancers. BIOLOGY 2021; 10:biology10070581. [PMID: 34201935 PMCID: PMC8301125 DOI: 10.3390/biology10070581] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022]
Abstract
The KMT2 (MLL) family of proteins, including the major histone H3K4 methyltransferase found in mammals, exists as large complexes with common subunit proteins and exhibits enzymatic activity. SMYD, another H3K4 methyltransferase, and SET7/9 proteins catalyze the methylation of several non-histone targets, in addition to histone H3K4 residues. Despite these structural and functional commonalities, H3K4 methyltransferase proteins have specificity for their target genes and play a role in the development of various cancers as well as in drug resistance. In this review, we examine the overall role of histone H3K4 methyltransferase in the development of various cancers and in the progression of drug resistance. Compounds that inhibit protein-protein interactions between KMT2 family proteins and their common subunits or the activity of SMYD and SET7/9 are continuously being developed for the treatment of acute leukemia, triple-negative breast cancer, and castration-resistant prostate cancer. These H3K4 methyltransferase inhibitors, either alone or in combination with other drugs, are expected to play a role in overcoming drug resistance in leukemia and various solid cancers.
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20
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Gradl S, Steuber H, Weiske J, Szewczyk MM, Schmees N, Siegel S, Stoeckigt D, Christ CD, Li F, Organ S, Abbey M, Kennedy S, Chau I, Trush V, Barsyte-Lovejoy D, Brown PJ, Vedadi M, Arrowsmith C, Husemann M, Badock V, Bauser M, Haegebarth A, Hartung IV, Stresemann C. Discovery of the SMYD3 Inhibitor BAY-6035 Using Thermal Shift Assay (TSA)-Based High-Throughput Screening. SLAS DISCOVERY 2021; 26:947-960. [PMID: 34154424 DOI: 10.1177/24725552211019409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
SMYD3 (SET and MYND domain-containing protein 3) is a protein lysine methyltransferase that was initially described as an H3K4 methyltransferase involved in transcriptional regulation. SMYD3 has been reported to methylate and regulate several nonhistone proteins relevant to cancer, including mitogen-activated protein kinase kinase kinase 2 (MAP3K2), vascular endothelial growth factor receptor 1 (VEGFR1), and the human epidermal growth factor receptor 2 (HER2). In addition, overexpression of SMYD3 has been linked to poor prognosis in certain cancers, suggesting SMYD3 as a potential oncogene and attractive cancer drug target. Here we report the discovery of a novel SMYD3 inhibitor. We performed a thermal shift assay (TSA)-based high-throughput screening (HTS) with 410,000 compounds and identified a novel benzodiazepine-based SMYD3 inhibitor series. Crystal structures revealed that this series binds to the substrate binding site and occupies the hydrophobic lysine binding pocket via an unprecedented hydrogen bonding pattern. Biochemical assays showed substrate competitive behavior. Following optimization and extensive biophysical validation with surface plasmon resonance (SPR) analysis and isothermal titration calorimetry (ITC), we identified BAY-6035, which shows nanomolar potency and selectivity against kinases and other PKMTs. Furthermore, BAY-6035 specifically inhibits methylation of MAP3K2 by SMYD3 in a cellular mechanistic assay with an IC50 <100 nM. Moreover, we describe a congeneric negative control to BAY-6035. In summary, BAY-6035 is a novel selective and potent SMYD3 inhibitor probe that will foster the exploration of the biological role of SMYD3 in diseased and nondiseased tissues.
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Affiliation(s)
- Stefan Gradl
- Bayer AG, Global Drug Discovery, Berlin, Germany
| | | | - Joerg Weiske
- Bayer AG, Global Drug Discovery, Berlin, Germany
| | - Magda M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | | | | | | | | | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Shawna Organ
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Megha Abbey
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Steven Kennedy
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Irene Chau
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Viacheslav Trush
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | | | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
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21
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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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22
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Bhat KP, Ümit Kaniskan H, Jin J, Gozani O. Epigenetics and beyond: targeting writers of protein lysine methylation to treat disease. Nat Rev Drug Discov 2021; 20:265-286. [PMID: 33469207 DOI: 10.1038/s41573-020-00108-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Protein lysine methylation is a crucial post-translational modification that regulates the functions of both histone and non-histone proteins. Deregulation of the enzymes or 'writers' of protein lysine methylation, lysine methyltransferases (KMTs), is implicated in the cause of many diseases, including cancer, mental health disorders and developmental disorders. Over the past decade, significant advances have been made in developing drugs to target KMTs that are involved in histone methylation and epigenetic regulation. The first of these inhibitors, tazemetostat, was recently approved for the treatment of epithelioid sarcoma and follicular lymphoma, and several more are in clinical and preclinical evaluation. Beyond chromatin, the many KMTs that regulate protein synthesis and other fundamental biological processes are emerging as promising new targets for drug development to treat diverse diseases.
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Affiliation(s)
- Kamakoti P Bhat
- Department of Biology, Stanford University, Stanford, CA, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA, USA.
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23
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Ishii M, Nakakido M, Caaveiro JMM, Kuroda D, Okumura CJ, Maruyama T, Entzminger K, Tsumoto K. Structural basis for antigen recognition by methylated lysine-specific antibodies. J Biol Chem 2020; 296:100176. [PMID: 33303630 PMCID: PMC7948472 DOI: 10.1074/jbc.ra120.015996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/05/2020] [Accepted: 12/10/2020] [Indexed: 12/05/2022] Open
Abstract
Proteins are modulated by a variety of posttranslational modifications including methylation. Despite its importance, the majority of protein methylation modifications discovered by mass spectrometric analyses are functionally uncharacterized, partly owing to the difficulty in obtaining reliable methylsite-specific antibodies. To elucidate how functional methylsite-specific antibodies recognize the antigens and lead to the development of a novel method to create such antibodies, we use an immunized library paired with phage display to create rabbit monoclonal antibodies recognizing trimethylated Lys260 of MAP3K2 as a representative substrate. We isolated several methylsite-specific antibodies that contained unique complementarity determining region sequence. We characterized the mode of antigen recognition by each of these antibodies using structural and biophysical analyses, revealing the molecular details, such as binding affinity toward methylated/nonmethylated antigens and structural motif that is responsible for recognition of the methylated lysine residue, by which each antibody recognized the target antigen. In addition, the comparison with the results of Western blotting analysis suggests a critical antigen recognition mode to generate cross-reactivity to protein and peptide antigen of the antibodies. Computational simulations effectively recapitulated our biophysical data, capturing the antibodies of differing affinity and specificity. Our exhaustive characterization provides molecular architectures of functional methylsite-specific antibodies and thus should contribute to the development of a general method to generate functional methylsite-specific antibodies by de novo design.
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Affiliation(s)
- Misaki Ishii
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Jose M M Caaveiro
- Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | | | | | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan; Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan; Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan; Laboratory of Medical Proteomics, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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24
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Rugo HS, Jacobs I, Sharma S, Scappaticci F, Paul TA, Jensen-Pergakes K, Malouf GG. The Promise for Histone Methyltransferase Inhibitors for Epigenetic Therapy in Clinical Oncology: A Narrative Review. Adv Ther 2020; 37:3059-3082. [PMID: 32445185 PMCID: PMC7467409 DOI: 10.1007/s12325-020-01379-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 12/21/2022]
Abstract
Epigenetic processes are essential for normal development and the maintenance of tissue-specific gene expression in mammals. Changes in gene expression and malignant cellular transformation can result from disruption of epigenetic mechanisms, and global disruption in the epigenetic landscape is a key feature of cancer. The study of epigenetics in cancer has revealed that human cancer cells harbor both genetic alterations and epigenetic abnormalities that interplay at all stages of cancer development. Unlike genetic mutations, epigenetic aberrations are potentially reversible through epigenetic therapy, providing a therapeutically relevant treatment option. Histone methyltransferase inhibitors are emerging as an epigenetic therapy approach with great promise in the field of clinical oncology. The recent accelerated approval of the enhancer of zeste homolog 2 (EZH2; also known as histone-lysine N-methyltransferase EZH2) inhibitor tazemetostat for metastatic or locally advanced epithelioid sarcoma marks the first approval of such a compound for the treatment of cancer. Many other histone methyltransferase inhibitors are currently in development, some of which are being tested in clinical studies. This review focuses on histone methyltransferase inhibitors, highlighting their potential in the treatment of cancer. We also discuss the role for such epigenetic drugs in overcoming epigenetically driven drug resistance mechanisms, and their value in combination with other therapeutic approaches such as immunotherapy.
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25
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Chern TR, Liu L, Petrunak E, Stuckey JA, Wang M, Bernard D, Zhou H, Lee S, Dou Y, Wang S. Discovery of Potent Small-Molecule Inhibitors of MLL Methyltransferase. ACS Med Chem Lett 2020; 11:1348-1352. [PMID: 32551023 DOI: 10.1021/acsmedchemlett.0c00229] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 02/06/2023] Open
Abstract
The mixed-lineage leukemia (MLL) protein, also known as MLL1, is a lysine methyltransferase specifically responsible for methylation of histone 3 lysine 4. MLL has been pursued as an attractive therapeutic target for the treatment of acute leukemia carrying the MLL fusion gene or MLL leukemia. Herein, we report the design, synthesis, and evaluation of an S-adenosylmethionine-based focused chemical library which led to the discovery of potent small-molecule inhibitors directly targeting the MLL SET domain. Determination of cocrystal structures for a number of these MLL inhibitors reveals that they adopt a unique binding mode that locks the MLL SET domain in an open, inactive conformation.
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26
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Zhang L, Jin Y, Yang H, Li Y, Wang C, Shi Y, Wang Y. SMYD3 promotes epithelial ovarian cancer metastasis by downregulating p53 protein stability and promoting p53 ubiquitination. Carcinogenesis 2020; 40:1492-1503. [PMID: 31002112 DOI: 10.1093/carcin/bgz078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/28/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022] Open
Abstract
Epithelial ovarian cancer (EOC) has a very poor prognosis because of tumor invasiveness. Here, we reported that SET and MYND domain containing protein 3 (SMYD3), a lysine methyltransferase, was frequently upregulated in EOC and associated with poor prognosis. A series of in vitro assays demonstrated that SMYD3 significantly upgraded the migration ability of EOC cells. The results of in vivo EOC metastasis models further confirmed that overexpression of SMYD3 promoted EOC progression. Mechanistic investigations indicated that SMYD3 cloud decrease p53 protein stability and induce epithelial-mesenchymal transition in EOC cells. SMYD3 interacts with p53 directly via the post-SET domain and destabilizes p53 by inducing p53 translocation from the nucleus to the cytoplasm and promoting p53 ubiquitination modification independent of MDM2. Furthermore, the mass spectrometry results showed that SMYD3 interacts with UBE2R2, an ubiquitin-conjugating enzyme (E2) of the ubiquitin-proteasome pathway. The combination of UBE2R2-SMYD3-p53 significantly promotes the ubiquitination and degradation of p53. These results pointed that SMYD3 might be a new E3 ligase of p53. Further analysis confirmed that lysines 381, 382 and 386 of p53 are the key sites for the ubiquitination modification of SMYD3 to p53. In summary, our results define the important role of SMYD3 in the metastasis process of EOC and present a new therapeutic target against EOC.
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Affiliation(s)
- Liwei Zhang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, China
| | - Yue Jin
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, China
| | - Hao Yang
- Shanghai Key Laboratory for Molecular Imaging, Shanghai University of Medicine and Health Sciences, Shanghai, China
| | - Yu Li
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, China
| | - Chao Wang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, China
| | - Yongheng Shi
- Department of Pathology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Wang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Key Laboratory of Gynecologic Oncology, Shanghai, China
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27
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Su DS, Qu J, Schulz M, Blackledge CW, Yu H, Zeng J, Burgess J, Reif A, Stern M, Nagarajan R, Pappalardi MB, Wong K, Graves AP, Bonnette W, Wang L, Elkins P, Knapp-Reed B, Carson JD, McHugh C, Mohammad H, Kruger R, Luengo J, Heerding DA, Creasy CL. Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors. ACS Med Chem Lett 2020; 11:133-140. [PMID: 32071679 DOI: 10.1021/acsmedchemlett.9b00493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/27/2019] [Indexed: 01/07/2023] Open
Abstract
We report herein the discovery of isoxazole amides as potent and selective SET and MYND Domain-Containing Protein 3 (SMYD3) inhibitors. Elucidation of the structure-activity relationship of the high-throughput screening (HTS) lead compound 1 provided potent and selective SMYD3 inhibitors. The SAR optimization, cocrystal structures of small molecules with SMYD3, and mode of inhibition (MOI) characterization of compounds are described. The synthesis and biological and pharmacokinetic profiles of compounds are also presented.
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28
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SMYD3: An Oncogenic Driver Targeting Epigenetic Regulation and Signaling Pathways. Cancers (Basel) 2020; 12:cancers12010142. [PMID: 31935919 PMCID: PMC7017119 DOI: 10.3390/cancers12010142] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/26/2019] [Accepted: 01/01/2020] [Indexed: 12/20/2022] Open
Abstract
SMYD3 is a member of the SMYD lysine methylase family and plays an important role in the methylation of various histone and non-histone targets. Aberrant SMYD3 expression contributes to carcinogenesis and SMYD3 upregulation was proposed as a prognostic marker in various solid cancers. Here we summarize SMYD3-mediated regulatory mechanisms, which are implicated in the pathophysiology of cancer, as drivers of distinct oncogenic pathways. We describe SMYD3-dependent mechanisms affecting cancer progression, highlighting SMYD3 interplay with proteins and RNAs involved in the regulation of cancer cell proliferation, migration and invasion. We also address the effectiveness and mechanisms of action for the currently available SMYD3 inhibitors. The findings analyzed herein demonstrate that a complex network of SMYD3-mediated cytoplasmic and nuclear interactions promote oncogenesis across different cancer types. These evidences depict SMYD3 as a modulator of the transcriptional response and of key signaling pathways, orchestrating multiple oncogenic inputs and ultimately, promoting transcriptional reprogramming and tumor transformation. Further insights into the oncogenic role of SMYD3 and its targeting of different synergistic oncogenic signals may be beneficial for effective cancer treatment.
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29
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Wang Y, Dix MM, Bianco G, Remsberg JR, Lee HY, Kalocsay M, Gygi SP, Forli S, Vite G, Lawrence RM, Parker CG, Cravatt BF. Expedited mapping of the ligandable proteome using fully functionalized enantiomeric probe pairs. Nat Chem 2019; 11:1113-1123. [PMID: 31659311 PMCID: PMC6874898 DOI: 10.1038/s41557-019-0351-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/10/2019] [Indexed: 11/29/2022]
Abstract
A fundamental challenge in chemical biology and medicine is to understand and expand the fraction of the human proteome that can be targeted by small molecules. We recently described a strategy that integrates fragment-based ligand discovery with chemical proteomics to furnish global portraits of reversible small-molecule/protein interactions in human cells. Excavating clear structure-activity relationships from these 'ligandability' maps, however, was confounded by the distinct physicochemical properties and corresponding overall protein-binding potential of individual fragments. Here, we describe a compelling solution to this problem by introducing a next-generation set of fully functionalized fragments differing only in absolute stereochemistry. Using these enantiomeric probe pairs, or 'enantioprobes', we identify numerous stereoselective protein-fragment interactions in cells and show that these interactions occur at functional sites on proteins from diverse classes. Our findings thus indicate that incorporating chirality into fully functionalized fragment libraries provides a robust and streamlined method to discover ligandable proteins in cells.
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Affiliation(s)
- Yujia Wang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Melissa M Dix
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Giulia Bianco
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jarrett R Remsberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Hsin-Yu Lee
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Marian Kalocsay
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gregory Vite
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - R Michael Lawrence
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Christopher G Parker
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
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30
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Fabini E, Talibov VO, Mihalic F, Naldi M, Bartolini M, Bertucci C, Del Rio A, Danielson UH. Unveiling the Biochemistry of the Epigenetic Regulator SMYD3. Biochemistry 2019; 58:3634-3645. [PMID: 31389685 DOI: 10.1021/acs.biochem.9b00420] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
SET and MYND domain-containing protein 3 (SMYD3) is a lysine methyltransferase that plays a central role in a variety of cancer diseases, exerting its pro-oncogenic activity by methylation of key proteins, of both nuclear and cytoplasmic nature. However, the role of SMYD3 in the initiation and progression of cancer is not yet fully understood and further biochemical characterization is required to support the discovery of therapeutics targeting this enzyme. We have therefore developed robust protocols for production, handling, and crystallization of SMYD3 and biophysical and biochemical assays for clarification of SMYD3 biochemistry and identification of useful lead compounds. Specifically, a time-resolved biosensor assay was developed for kinetic characterization of SMYD3 interactions. Functional differences in SMYD3 interactions with its natural small molecule ligands SAM and SAH were revealed, with SAM forming a very stable complex. A variety of peptides mimicking putative substrates of SMYD3 were explored in order to expose structural features important for recognition. The interaction between SMYD3 and some peptides was influenced by SAM. A nonradioactive SMYD3 activity assay using liquid chromatography-mass spectrometry (LC-MS) analysis explored substrate features of importance also for methylation. Methylation was notable only toward MAP kinase kinase kinase 2 (MAP3K2_K260)-mimicking peptides, although binary and tertiary complexes were detected also with other peptides. The analysis supported a random bi-bi mechanistic model for SMYD3 methyltransferase catalysis. Our work unveiled complexities in SMYD3 biochemistry and resulted in procedures suitable for further studies and identification of novel starting points for design of effective and specific leads for this potential oncology target.
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Affiliation(s)
- Edoardo Fabini
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy.,Institute of Organic Synthesis and Photoreactivity (ISOF) , National Research Council (CNR) , Bologna , Italy
| | | | - Filip Mihalic
- Department of Chemistry - BMC , Uppsala University , Uppsala , Sweden
| | - Marina Naldi
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy.,Center for Applied Biomedical Research (C.R.B.A.) , S. Orsola-Malpighi Hospital , Bologna , Italy
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy
| | - Carlo Bertucci
- Department of Pharmacy and Biotechnology , Alma Mater Studiorum University of Bologna , Bologna , Italy
| | - Alberto Del Rio
- Institute of Organic Synthesis and Photoreactivity (ISOF) , National Research Council (CNR) , Bologna , Italy.,Innovamol Consulting Srl , Modena , Italy
| | - U Helena Danielson
- Department of Chemistry - BMC , Uppsala University , Uppsala , Sweden.,Science for Life Laboratory , Uppsala University , Uppsala , Sweden
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31
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Dilworth D, Barsyte-Lovejoy D. Targeting protein methylation: from chemical tools to precision medicines. Cell Mol Life Sci 2019; 76:2967-2985. [PMID: 31104094 PMCID: PMC11105543 DOI: 10.1007/s00018-019-03147-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 12/15/2022]
Abstract
The methylation of proteins is integral to the execution of many important biological functions, including cell signalling and transcriptional regulation. Protein methyltransferases (PMTs) are a large class of enzymes that carry out the addition of methyl marks to a broad range of substrates. PMTs are critical for normal cellular physiology and their dysregulation is frequently observed in human disease. As such, PMTs have emerged as promising therapeutic targets with several inhibitors now in clinical trials for oncology indications. The discovery of chemical inhibitors and antagonists of protein methylation signalling has also profoundly impacted our general understanding of PMT biology and pharmacology. In this review, we present general principles for drugging protein methyltransferases or their downstream effectors containing methyl-binding modules, as well as best-in-class examples of the compounds discovered and their impact both at the bench and in the clinic.
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Affiliation(s)
- David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.
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32
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Huang C, Liew SS, Lin GR, Poulsen A, Ang MJY, Chia BCS, Chew SY, Kwek ZP, Wee JLK, Ong EH, Retna P, Baburajendran N, Li R, Yu W, Koh-Stenta X, Ngo A, Manesh S, Fulwood J, Ke Z, Chung HH, Sepramaniam S, Chew XH, Dinie N, Lee MA, Chew YS, Low CB, Pendharkar V, Manoharan V, Vuddagiri S, Sangthongpitag K, Joy J, Matter A, Hill J, Keller TH, Foo K. Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3. ACS Med Chem Lett 2019; 10:978-984. [PMID: 31223458 DOI: 10.1021/acsmedchemlett.9b00170] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 05/23/2019] [Indexed: 11/28/2022] Open
Abstract
SMYD3 is a histone methyltransferase that regulates gene transcription, and its overexpression is associated with multiple human cancers. A novel class of tetrahydroacridine compounds which inhibit SMYD3 through a covalent mechanism of action is identified. Optimization of these irreversible inhibitors resulted in the discovery of 4-chloroquinolines, a new class of covalent warheads. Tool compound 29 exhibits high potency by inhibiting SMYD3's enzymatic activity and showing antiproliferative activity against HepG2 in 3D cell culture. Our findings suggest that covalent inhibition of SMYD3 may have an impact on SMYD3 biology by affecting expression levels, and this warrants further exploration.
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Affiliation(s)
- Chuhui Huang
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Si Si Liew
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Grace R. Lin
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Anders Poulsen
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Melgious J. Y. Ang
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Brian C. S. Chia
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Sin Yin Chew
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Zekui P. Kwek
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - John L. K. Wee
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Esther H. Ong
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Priya Retna
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Nithya Baburajendran
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Rong Li
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Weixuan Yu
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Xiaoying Koh-Stenta
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Anna Ngo
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Sravanthy Manesh
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Justina Fulwood
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Zhiyuan Ke
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Hwa Hwa Chung
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | | | - Xin Hui Chew
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Nurul Dinie
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - May Ann Lee
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Yun Shan Chew
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Choon Bing Low
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Vishal Pendharkar
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Vithya Manoharan
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Susmitha Vuddagiri
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Kanda Sangthongpitag
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Joma Joy
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Alex Matter
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Jeffrey Hill
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Thomas H. Keller
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
| | - Klement Foo
- Experimental Drug Development Centre, 10 Biopolis Road #05-01 Chromos, Singapore 138670
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33
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Hit identification of SMYD3 enzyme inhibitors using structure-based pharmacophore modeling. Future Med Chem 2019; 11:1107-1117. [DOI: 10.4155/fmc-2018-0462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: SMYD3 enzyme is overexpressed in many types of cancer and its role in the methylation of cytoplasmic mitogen-activated protein kinase, kinase kinase 2 (MAP3K2), has been linked to promotion of Kras-driven cancer in pancreatic ductal and lung adenocarcinoma. Materials & methods: A hybrid 3D structure-based pharmacophore model was generated using crystal structures of SMYD3 complexed with sinefungin and was used to search for potential SMYD3 inhibitors through virtual screening of the Maybridge database. The retrieved hits from screening were further docked into the binding site of SMYD3 using CDOCKER docking algorithms. The top-ranked hits were selected and their inhibitory activity was evaluated. Results & conclusion: The results obtained helped us to find an SMYD3 small molecule hit inhibitor scaffold.
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34
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Small-molecule inhibitors of lysine methyltransferases SMYD2 and SMYD3: current trends. Future Med Chem 2019; 11:901-921. [DOI: 10.4155/fmc-2018-0380] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Lysine methyltransferases SMYD2 and SMYD3 are involved in the epigenetic regulation of cell differentiation and functioning. Overexpression and deregulation of these enzymes have been correlated to the insurgence and progression of different tumors, making them promising molecular targets in cancer therapy even if their role in tumors is not yet fully understood. In this light, selective small-molecule inhibitors are required to fully understand and validate these enzymes, as this is a prerequisite for the development of successful targeted therapeutic strategies. The present review gives a systematic overview of the chemical probes developed to selectively target SMYD2 and SMYD3, with particular focus on the structural features important for high inhibitory activity, on the mode of inhibition and on the efficacy in cell-based and in in vivo models.
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35
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Natesan R, Aras S, Effron SS, Asangani IA. Epigenetic Regulation of Chromatin in Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1210:379-407. [PMID: 31900918 DOI: 10.1007/978-3-030-32656-2_17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Epigenetics refers to mitotically/meiotically heritable mechanisms that regulate gene transcription without a need for changes in the DNA code. Covalent modifications of DNA, in the form of methylation, and histone post-translational modifications, in the form of acetylation and methylation, constitute the epigenetic code of a cell. Both DNA and histone modifications are highly dynamic and often work in unison to define the epigenetic state of a cell. Most epigenetic mechanisms regulate gene transcription by affecting localized/genome-wide transitions between heterochromatin and euchromatin states, thereby altering the accessibility of the transcriptional machinery and in turn, reduce/increase transcriptional output. Altered chromatin structure is associated with cancer progression, and epigenetic plasticity primarily governs the resistance of cancer cells to therapeutic agents. In this chapter, we specifically focus on regulators of histone methylation and acetylation, the two well-studied chromatin post-translational modifications, in the context of prostate cancer.
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Affiliation(s)
- Ramakrishnan Natesan
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shweta Aras
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Samuel Sander Effron
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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36
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Pivovarova Y, Liu J, Lesigang J, Koldyka O, Rauschmeier R, Hu K, Dong G. Structure of a Novel Dimeric SET Domain Methyltransferase that Regulates Cell Motility. J Mol Biol 2018; 430:4209-4229. [PMID: 30148980 PMCID: PMC7141177 DOI: 10.1016/j.jmb.2018.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/17/2018] [Accepted: 08/21/2018] [Indexed: 11/21/2022]
Abstract
Lysine methyltransferases (KMTs) were initially associated with transcriptional control through their methylation of histones and other nuclear proteins, but have since been found to regulate many other cellular activities. The apical complex lysine (K) methyltransferase (AKMT) of the human parasite Toxoplasma gondii was recently shown to play a critical role in regulating cellular motility. Here we report a 2.1-Å resolution crystal structure of the conserved and functional C-terminal portion (aa289-709) of T. gondii AKMT. AKMT dimerizes via a unique intermolecular interface mediated by the C-terminal tetratricopeptide repeat-like domain together with a specific zinc-binding motif that is absent from all other KMTs. Disruption of AKMT dimerization impaired both its enzyme activity and parasite egress from infected host cells in vivo. Structural comparisons reveal that AKMT is related to the KMTs in the SMYD family, with, however, a number of distinct structural features in addition to the unusual dimerization interface. These features are conserved among the apicomplexan parasites and their free-living relatives, but not found in any known KMTs in animals. AKMT therefore is the founding member of a new subclass of KMT that has important implications for the evolution of the apicomplexans.
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Affiliation(s)
- Yulia Pivovarova
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Jun Liu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Johannes Lesigang
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | | | - Rene Rauschmeier
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Ke Hu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Gang Dong
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
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37
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Hirano T, Mori S, Kagechika H. Recent Advances in Chemical Tools for the Regulation and Study of Protein Lysine Methyltransferases. CHEM REC 2018; 18:1745-1759. [DOI: 10.1002/tcr.201800034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Tomoya Hirano
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Shuichi Mori
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku Tokyo 101-0062 Japan
| | - Hiroyuki Kagechika
- Institute of Biomaterials and BioengineeringTokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku Tokyo 101-0062 Japan
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38
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Abstract
Protein lysine methylation is a distinct posttranslational modification that causes minimal changes in the size and electrostatic status of lysine residues. Lysine methylation plays essential roles in regulating fates and functions of target proteins in an epigenetic manner. As a result, substrates and degrees (free versus mono/di/tri) of protein lysine methylation are orchestrated within cells by balanced activities of protein lysine methyltransferases (PKMTs) and demethylases (KDMs). Their dysregulation is often associated with neurological disorders, developmental abnormalities, or cancer. Methyllysine-containing proteins can be recognized by downstream effector proteins, which contain methyllysine reader domains, to relay their biological functions. While numerous efforts have been made to annotate biological roles of protein lysine methylation, limited work has been done to uncover mechanisms associated with this modification at a molecular or atomic level. Given distinct biophysical and biochemical properties of methyllysine, this review will focus on chemical and biochemical aspects in addition, recognition, and removal of this posttranslational mark. Chemical and biophysical methods to profile PKMT substrates will be discussed along with classification of PKMT inhibitors for accurate perturbation of methyltransferase activities. Semisynthesis of methyllysine-containing proteins will also be covered given the critical need for these reagents to unambiguously define functional roles of protein lysine methylation.
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Affiliation(s)
- Minkui Luo
- Chemical Biology Program , Memorial Sloan Kettering Cancer Center , New York , New York 10065 , United States.,Program of Pharmacology, Weill Graduate School of Medical Science , Cornell University , New York , New York 10021 , United States
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39
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Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation. PLoS One 2018; 13:e0197372. [PMID: 29856759 PMCID: PMC5983452 DOI: 10.1371/journal.pone.0197372] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/01/2018] [Indexed: 12/13/2022] Open
Abstract
A key challenge in the development of precision medicine is defining the phenotypic consequences of pharmacological modulation of specific target macromolecules. To address this issue, a variety of genetic, molecular and chemical tools can be used. All of these approaches can produce misleading results if the specificity of the tools is not well understood and the proper controls are not performed. In this paper we illustrate these general themes by providing detailed studies of small molecule inhibitors of the enzymatic activity of two members of the SMYD branch of the protein lysine methyltransferases, SMYD2 and SMYD3. We show that tool compounds as well as CRISPR/Cas9 fail to reproduce many of the cell proliferation findings associated with SMYD2 and SMYD3 inhibition previously obtained with RNAi based approaches and with early stage chemical probes.
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Abstract
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Post-translational
modifications of histones by protein methyltransferases
(PMTs) and histone demethylases (KDMs) play an important role in the
regulation of gene expression and transcription and are implicated
in cancer and many other diseases. Many of these enzymes also target
various nonhistone proteins impacting numerous crucial biological
pathways. Given their key biological functions and implications in
human diseases, there has been a growing interest in assessing these
enzymes as potential therapeutic targets. Consequently, discovering
and developing inhibitors of these enzymes has become a very active
and fast-growing research area over the past decade. In this review,
we cover the discovery, characterization, and biological application
of inhibitors of PMTs and KDMs with emphasis on key advancements in
the field. We also discuss challenges, opportunities, and future directions
in this emerging, exciting research field.
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Affiliation(s)
- H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Michael L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai , New York, New York 10029, United States
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41
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CADD medicine: design is the potion that can cure my disease. J Comput Aided Mol Des 2017; 31:249-253. [PMID: 28070730 DOI: 10.1007/s10822-016-0004-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/19/2016] [Indexed: 01/24/2023]
Abstract
The acronym "CADD" is often used interchangeably to refer to "Computer Aided Drug Discovery" and "Computer Aided Drug Design". While the former definition implies the use of a computer to impact one or more aspects of discovering a drug, in this paper we contend that computational chemists are most effective when they enable teams to apply true design principles as they strive to create medicines to treat human disease. We argue that teams must bring to bear multiple sub-disciplines of computational chemistry in an integrated manner in order to utilize these principles to address the multi-objective nature of the drug discovery problem. Impact, resourcing principles, and future directions for the field are also discussed, including areas of future opportunity as well as a cautionary note about hype and hubris.
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42
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Rajajeyabalachandran G, Kumar S, Murugesan T, Ekambaram S, Padmavathy R, Jegatheesan SK, Mullangi R, Rajagopal S. Therapeutical potential of deregulated lysine methyltransferase SMYD3 as a safe target for novel anticancer agents. Expert Opin Ther Targets 2016; 21:145-157. [PMID: 28019723 DOI: 10.1080/14728222.2017.1272580] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
INTRODUCTION SET and MYND domain containing-3 (SMYD3) is a member of the lysine methyltransferase family of proteins, and plays an important role in the methylation of various histone and non-histone targets. Proper functioning of SMYD3 is very important for the target molecules to determine their different roles in chromatin remodeling, signal transduction and cell cycle control. Due to the abnormal expression of SMYD3 in tumors, it is projected as a prognostic marker in various solid cancers. Areas covered: Here we elaborate on the general information, structure and the pathological role of SMYD3 protein. We summarize the role of SMYD3-mediated protein interactions in oncology pathways, mutational effects and regulation of SMYD3 in specific types of cancer. The efficacy and mechanisms of action of currently available SMYD3 small molecule inhibitors are also addressed. Expert opinion: The findings analyzed herein demonstrate that aberrant levels of SMYD3 protein exert tumorigenic effects by altering the epigenetic regulation of target genes. The partial involvement of SMYD3 in some distinct pathways provides a vital opportunity in targeting cancer effectively with fewer side effects. Further, identification and co-targeting of synergistic oncogenic pathways is suggested, which could provide much more beneficial effects for the treatment of solid cancers.
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Affiliation(s)
| | - Swetha Kumar
- a Bioinformatics, Jubilant Biosys Ltd ., Bangalore , India
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43
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Spellmon N, Sun X, Xue W, Holcomb J, Chakravarthy S, Shang W, Edwards B, Sirinupong N, Li C, Yang Z. New open conformation of SMYD3 implicates conformational selection and allostery. AIMS BIOPHYSICS 2016; 4:1-18. [PMID: 28050603 PMCID: PMC5189988 DOI: 10.3934/biophy.2017.1.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly “closed” substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an “open” conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD). The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation.
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Affiliation(s)
- Nicholas Spellmon
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Xiaonan Sun
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Wen Xue
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Joshua Holcomb
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Srinivas Chakravarthy
- Center for Synchrotron Radiation Research and Instrumentation and Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Weifeng Shang
- Center for Synchrotron Radiation Research and Instrumentation and Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Brian Edwards
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Nualpun Sirinupong
- Nutraceuticals and Functional Food Research and Development Center, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
| | - Chunying Li
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA, USA
| | - Zhe Yang
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, Michigan, USA
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44
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Dysregulation of histone methyltransferases in breast cancer - Opportunities for new targeted therapies? Mol Oncol 2016; 10:1497-1515. [PMID: 27717710 DOI: 10.1016/j.molonc.2016.09.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/14/2016] [Accepted: 09/14/2016] [Indexed: 01/24/2023] Open
Abstract
Histone methyltransferases (HMTs) catalyze the methylation of lysine and arginine residues on histone tails and non-histone targets. These important post-translational modifications are exquisitely regulated and affect chromatin compaction and transcriptional programs leading to diverse biological outcomes. There is accumulating evidence that genetic alterations of several HMTs impinge on oncogenic or tumor-suppressor functions and influence both cancer initiation and progression. HMTs therefore represent an opportunity for therapeutic targeting in those patients with tumors in which HMTs are dysregulated, to reverse the histone marks and transcriptional programs associated with aggressive tumor behavior. In this review, we describe the known histone methyltransferases and their emerging roles in breast cancer tumorigenesis.
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45
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Mazur PK, Gozani O, Sage J, Reynoird N. Novel insights into the oncogenic function of the SMYD3 lysine methyltransferase. Transl Cancer Res 2016; 5:330-333. [PMID: 30713830 DOI: 10.21037/tcr.2016.06.26] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Pawel K Mazur
- Departments of Pediatrics, Stanford University School of Medicine, CA 94305, USA.,Departments of Genetics, Stanford University School of Medicine, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, CA 94305, USA
| | - Julien Sage
- Departments of Pediatrics, Stanford University School of Medicine, CA 94305, USA.,Departments of Genetics, Stanford University School of Medicine, CA 94305, USA
| | - Nicolas Reynoird
- Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble Cedex, France
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