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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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Yancoskie MN, Maritz C, van Eijk P, Reed SH, Naegeli H. To incise or not and where: SET-domain methyltransferases know. Trends Biochem Sci 2023; 48:321-330. [PMID: 36357311 DOI: 10.1016/j.tibs.2022.10.003] [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: 07/22/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
The concept of the histone code posits that histone modifications regulate gene functions once interpreted by epigenetic readers. A well-studied case is trimethylation of lysine 4 of histone H3 (H3K4me3), which is enriched at gene promoters. However, H3K4me3 marks are not needed for the expression of most genes, suggesting extra roles, such as influencing the 3D genome architecture. Here, we highlight an intriguing analogy between the H3K4me3-dependent induction of double-strand breaks in several recombination events and the impact of this same mark on DNA incisions for the repair of bulky lesions. We propose that Su(var)3-9, Enhancer-of-zeste and Trithorax (SET)-domain methyltransferases generate H3K4me3 to guide nucleases into chromatin spaces, the favorable accessibility of which ensures that DNA break intermediates are readily processed, thereby safeguarding genome stability.
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Affiliation(s)
- Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Patrick van Eijk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Simon H Reed
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland.
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3
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Razmi M, Yazdanpanah A, Etemad-Moghadam S, Alaeddini M, Angelini S, Eini L. Clinical prognostic value of the SMYD2/3 as new epigenetic biomarkers in solid cancer patients: a systematic review and meta-analysis. Expert Rev Mol Diagn 2022; 22:1-15. [PMID: 36346387 DOI: 10.1080/14737159.2022.2144235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND SET and MYND domain-containing protein (SMYD) family with methyltransferase activity is involved in cancer progression. This novel meta-analysis aimed to evaluate the association of SMYD family with the clinical and survival outcomes in solid cancer patients. METHODS We systematically searched Embase, PubMed, Scopus and Web of Science to select relevant articles. Hazard ratios (HRs), odds ratios (ORs), and 95% confidence intervals were extracted. Heterogeneity was evaluated by chi-square-based Q and I2 tests, while publication bias by funnel plots and Egger's test. RESULTS Thirty-two articles (4,826 patients) met inclusion criteria. SMYD2/3 overexpression was statistically associated with poor overall survival (HR = 1.794, P < 0.001), disease/relapse/progression-free survival (HR = 2.114, P < 0.001), disease/cancer-specific survival (HR = 3.220, P = 0.003), larger tumor size (OR = 1.963, P < 0.001), advanced TNM stage (OR = 2.066, P < 0.001), lymph node metastasis (OR = 2.054, P < 0.001), and distant metastasis (OR = 1.978, P = 0.004). Subgroup analysis showed more significant association between SMYD2 overexpression and reduced survival outcomes than that in SMYD3. Conversely, the relationship between SMYD3 and various clinicopathologic factors was stronger compared to SMYD2. CONCLUSION Enhanced SMYD2/3 expression may be an unfavorable clinical prognostic factor in different solid cancer types.
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Affiliation(s)
- Mahdieh Razmi
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Oncopathology Research Center, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Ayna Yazdanpanah
- Department of Tissue Engineering and Regenerative Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahroo Etemad-Moghadam
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojgan Alaeddini
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sabrina Angelini
- Department of Pharmacy and Biotechnology (Fabit), University of Bologna, Bologna, Italy
| | - Leila Eini
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Division of Histology, Department of Basic Science, Faculty of Veterinary Medicine, Science and Research Branch, Islamic Azad University, Tehran, Iran
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4
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Zeng X, Guo H, Liu Z, Qin Z, Cong Y, Ren N, Zhang Y, Zhang N. S100A11 activates the pentose phosphate pathway to induce malignant biological behaviour of pancreatic ductal adenocarcinoma. Cell Death Dis 2022; 13:568. [PMID: 35752610 PMCID: PMC9233679 DOI: 10.1038/s41419-022-05004-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 05/22/2022] [Accepted: 06/07/2022] [Indexed: 01/21/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most refractory malignancies and has a poor prognosis. In recent years, increasing evidence has shown that an imbalance of metabolism may contribute to unrestricted pancreatic tumour progression and that the pentose phosphate pathway (PPP) plays a pivotal role in cellular metabolism. S100A11 has been shown to regulate multiple biological functions related to the progression and metastasis of various cancer types. However, the exact mechanisms and prognostic value of S100A11 in PDAC remain unclear. Here, we found that S100A11 expression was increased in PDAC and significantly associated with worse prognosis and disease progression. Mechanistically, S100A11 knockdown suppressed the PPP by impairing nascent mRNA synthesis of TKT (transketolase). The current study also demonstrated that H3K4me3 at the -268/+77 region of the TKT promoter was required for its transcriptional activation and S100A11 promoted H3K4me3 loading to the TKT promoter by interacting with SMYD3 protein. Taking these findings together, this study provided new insights into the potential value of S100A11 for treating pancreatic cancer, suggesting that it could be a therapeutic target for PDAC patients.
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Affiliation(s)
- Xue Zeng
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang, 110042, PR China
| | - Hong Guo
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang, 110042, PR China
| | - Zhuang Liu
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang, 110042, PR China
| | - Zilan Qin
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang, 110042, PR China
| | - Yuyang Cong
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang, 110042, PR China
| | - Naihan Ren
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang, 110042, PR China
| | - Yuxiang Zhang
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang, 110042, PR China
| | - Na Zhang
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Cancer Hospital of Dalian University of Technology, Shenyang, 110042, PR China.
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Unique SMYD5 Structure Revealed by AlphaFold Correlates with Its Functional Divergence. Biomolecules 2022; 12:biom12060783. [PMID: 35740908 PMCID: PMC9221539 DOI: 10.3390/biom12060783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
SMYD5 belongs to a special class of protein lysine methyltransferases with an MYND (Myeloid-Nervy-DEAF1) domain inserted into a SET (Suppressor of variegation, Enhancer of Zeste, Trithorax) domain. Despite recent advances in its functional characterization, the lack of the crystal structure has hindered our understanding of the structure-and-function relationships of this most unique member of the SMYD protein family. Here, we demonstrate the reliability of using AlphaFold structures for understanding the structure and function of SMYD5 by comparing the AlphaFold structures to the known crystal structures of SMYD proteins, using an inter-residue distance maps-based metric. We found that the AlphaFold confidence scores are inversely associated with the refined B-factors and can serve as a structural indicator of conformational flexibility. We also found that the N-terminal sequence of SMYD5, predicted to be a mitochondrial targeting signal, contains a novel non-classical nuclear localization signal. This sequence is structurally flexible and does not have a well-defined conformation, which might facilitate its recognition for SMYD5’s cytonuclear transport. The structure of SMYD5 is unique in many aspects. The “crab”-like structure with a large negatively charged cleft provides a potential binding site for basic molecules such as protamines. The less positively charged MYND domain is associated with the undetectable DNA-binding ability. The most surprising feature is an incomplete target lysine access channel that lacks the evolutionarily conserved tri-aromatic arrangement, being associated with the low H3/H4 catalytic activity. This study expands our understanding of the SMYD protein family from a classical two-lobed structure to a structure of its own kind, being as a fundamental determinant of its functional divergence.
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Lee B, Katsushima K, Pokhrel R, Yuan M, Stapleton S, Jallo G, Wechsler-Reya RJ, Eberhart CG, Ray A, Perera RJ. The long non-coding RNA SPRIGHTLY and its binding partner PTBP1 regulate exon 5 skipping of SMYD3 transcripts in group 4 medulloblastomas. Neurooncol Adv 2022; 4:vdac120. [PMID: 36267874 PMCID: PMC9569026 DOI: 10.1093/noajnl/vdac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Although some of the regulatory genes, signaling pathways, and gene regulatory networks altered in medulloblastomas (MB) are known, the roles of non-coding RNAs, particularly long non-coding RNAs (lncRNAs), are poorly described. Here we report that the lncRNA SPRIGHTLY (SPRY4-IT1) gene is upregulated in group 4 medulloblastoma (G4 MB). Methods SPRIGHTLY expression was assessed in MB subgroup patient-derived xenografts, cell lines, and patient samples. The effect of SPRIGHTLY hemizygous deletion on proliferation, invasion, apoptosis, and colony formation were assessed in vitro and on tumor growth in vivo. dChIRP pull-down assays were used to assess SPRIGHTLY-binding partners, confirmed by immunoprecipitation. SMYD3 ΔE5 transcripts were examined in cell lines and publicly available RNA-seq data. Pathway analysis was performed by phospho-kinase profiling and RNA-seq. Results CRISPR/Cas9 deletion of SPRIGHTLY reduced cell viability and invasion and increased apoptosis in G4 MB cell lines in vitro. SPRIGHTLY hemizygous-deleted G4 MB cells injected into mouse cerebellums produced smaller tumors than those derived from parental cells expressing both copies of SPRIGHTLY. SPRIGHTLY lncRNA bound to the intronic region of the SMYD3 pre-mRNA transcript. SPRIGHTLY also interacted with PTPB1 protein to regulate SMYD3 exon skipping to produce an aberrant protein. SPRIGHTLY-driven SMYD3 regulation enhanced the expression of EGFR pathway genes in G4 MB cell lines and activated cell coagulation/hemostasis-related gene expression, suggesting a novel oncogenic role in G4 MB. Conclusions These results demonstrate the importance of SPRIGHTLY lncRNA as a promoter of G4 MB and the role of the SPRIGHTLY-SMYD3-PTPB1 axis as an important oncogenic regulator in MB.
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Affiliation(s)
- Bongyong Lee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Rudramani Pokhrel
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Menglang Yuan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Stacie Stapleton
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - George Jallo
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Robert J Wechsler-Reya
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charles G Eberhart
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Ave – Ross Bldg 558, Baltimore, MD 21205, USA
| | - Animesh Ray
- Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont CA, 91711, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
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7
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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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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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9
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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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10
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Alshiraihi IM, Jarrell DK, Arhouma Z, Hassell KN, Montgomery J, Padilla A, Ibrahim HM, Crans DC, Kato TA, Brown MA. In Silico/In Vitro Hit-to-Lead Methodology Yields SMYD3 Inhibitor That Eliminates Unrestrained Proliferation of Breast Carcinoma Cells. Int J Mol Sci 2020; 21:ijms21249549. [PMID: 33333978 PMCID: PMC7765450 DOI: 10.3390/ijms21249549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/29/2022] Open
Abstract
SMYD3 is a lysine methyltransferase that regulates the expression of over 80 genes and is required for the uncontrolled proliferation of most breast, colorectal, and hepatocellular carcinomas. The elimination of SMYD3 restores normal expression patterns of these genes and halts aberrant cell proliferation, making it a promising target for small molecule inhibition. In this study, we sought to establish a proof of concept for our in silico/in vitro hit-to-lead enzyme inhibitor development platform and to identify a lead small molecule candidate for SMYD3 inhibition. We used Schrodinger® software to screen libraries of small molecules in silico and the five compounds with the greatest predicted binding affinity within the SMYD3 binding pocket were purchased and assessed in vitro in direct binding assays and in breast cancer cell lines. We have confirmed the ability of one of these inhibitors, Inhibitor-4, to restore normal rates of cell proliferation, arrest the cell cycle, and induce apoptosis in breast cancer cells without affecting wildtype cell behavior. Our results provide a proof of concept for this fast and affordable small molecule hit-to-lead methodology as well as a promising candidate small molecule SMYD3 inhibitor for the treatment of human cancer.
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Affiliation(s)
- Ilham M. Alshiraihi
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA; (I.M.A.); (Z.A.); (K.N.H.); (D.C.C.); (T.A.K.)
- Department of Biology, University of Tabuk, Tabuk 47713, Saudi Arabia
| | - Dillon K. Jarrell
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, Aurora, CO 80045-7109, USA;
| | - Zeyad Arhouma
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA; (I.M.A.); (Z.A.); (K.N.H.); (D.C.C.); (T.A.K.)
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
| | - Kelly N. Hassell
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA; (I.M.A.); (Z.A.); (K.N.H.); (D.C.C.); (T.A.K.)
| | - Jaelyn Montgomery
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA; (J.M.); (A.P.)
| | - Alyssa Padilla
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523-1617, USA; (J.M.); (A.P.)
| | - Hend M. Ibrahim
- Department of Medical Biochemistry, Zagazig University, Zagazig 44511, Egypt;
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523-1618, USA
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523-1678, USA
| | - Debbie C. Crans
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA; (I.M.A.); (Z.A.); (K.N.H.); (D.C.C.); (T.A.K.)
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, USA
| | - Takamitsu A. Kato
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA; (I.M.A.); (Z.A.); (K.N.H.); (D.C.C.); (T.A.K.)
- Department of Environmental & Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523-1618, USA
| | - Mark A. Brown
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO 80523-1005, USA; (I.M.A.); (Z.A.); (K.N.H.); (D.C.C.); (T.A.K.)
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523-1678, USA
- Epidemiology Section, Colorado School of Public Health, Fort Collins, CO 80523-1612, USA
- Institute for Learning and Teaching, Colorado State University, Fort Collins, CO 80523-1052, USA
- Department of Ethnic Studies, Colorado State University, Fort Collins, CO 80523-1790, USA
- Correspondence:
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11
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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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12
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Chen J, He Z, Yuan Y, Huang F, Luo B, Zhang J, Pan T, Zhang H, Zhang J. Host factor SMYD3 is recruited by Ebola virus nucleoprotein to facilitate viral mRNA transcription. Emerg Microbes Infect 2020; 8:1347-1360. [PMID: 31516086 PMCID: PMC6758638 DOI: 10.1080/22221751.2019.1662736] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The polymerase complex of Ebola virus (EBOV) is the functional unit for transcription and replication of viral genome. Nucleoprotein (NP) is a multifunctional protein with high RNA binding affinity and recruits other viral proteins to form functional polymerase complex. In our study, we investigated host proteins associated with EBOV polymerase complex using NP as bait in a transcription and replication competent minigenome system by mass spectrometry analysis and identified SET and MYND domain-containing protein 3 (SMYD3) as a novel host protein which was required for the replication of EBOV. SMYD3 specifically interacted with NP and was recruited to EBOV inclusion bodies through NP. The depletion of SMYD3 dramatically suppressed EBOV mRNA production. A mimic of non-phosphorylated VP30, which is a transcription activator, could partially rescue the viral mRNA production downregulated by the depletion of SMYD3. In addition, SMYD3 promoted NP-VP30 interaction in a dose-dependent manner. These results revealed that SMYD3 was a novel host factor recruited by NP to supporting EBOV mRNA transcription through increasing the binding of VP30 to NP. Thus, our study provided a new understanding of mechanism underlying the transcription of EBOV genome, and a novel anti-EBOV drug design strategy by targeting SMYD3.
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Affiliation(s)
- Jingliang Chen
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , People's Republic of China
| | - Zhangping He
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , People's Republic of China
| | - Yaochang Yuan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , People's Republic of China
| | - Feng Huang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , People's Republic of China.,Department of Respiration, Affiliated Guangzhou Women and Children's Hospital, Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , People's Republic of China
| | - Baohong Luo
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , People's Republic of China
| | - Jianhua Zhang
- CAS Key Laboratory for Pathogenic Microbiology, Institute of Microbiology, Chinese Academy of Sciences , Beijing , People's Republic of China
| | - Ting Pan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , People's Republic of China
| | - Hui Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , People's Republic of China
| | - Junsong Zhang
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Sun Yat-Sen University , Guangzhou , People's Republic of China
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13
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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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14
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Sun J, Shi F, Yang N. Exploration of the Substrate Preference of Lysine Methyltransferase SMYD3 by Molecular Dynamics Simulations. ACS OMEGA 2019; 4:19573-19581. [PMID: 31788587 PMCID: PMC6881823 DOI: 10.1021/acsomega.9b01842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 10/31/2019] [Indexed: 06/10/2023]
Abstract
SMYD3, a SET and MYND domain containing lysine methyltransferase, catalyzes the transfer of the methyl group from a methyl donor onto the Nε group of a lysine residue in the substrate protein. Methylation of MAP3 kinase kinase (MAP3K2) by SMYD3 has been implicated in Ras-driven tumorigenesis. The crystal structure of SMYD3 in complex with MAP3K2 peptide reveals a shallow hydrophobic pocket (P-2), which accommodates the binding of a phenylalanine residue at the -2 position of the substrate (F258) is a crucial determinant of substrate specificity of SMYD3. To better understand the substrate preference of SMYD3 at the -2 position, molecular dynamics (MD) simulations and the MM/GBSA method were performed on the crystal structure of SMYD3-MAP3K2 complex (PDB: 5EX0) after substitution of F258 residue of MAP3K2 to each of the other 19 natural residues, respectively. Binding free energy calculations reveal that the P-2 pocket prefers an aromatic hydrophobic group and none of the substitutions behave better than the wild-type phenylalanine residue does. Furthermore, we investigated the structure-activity relationships (SAR) of a series of non-natural phenylalanine derivative substitutions at the -2 position and found that quite a few modifications on the sidechain of F258 residue could strengthen its binding to the P-2 pocket of SMYD3. These explorations provide insights into developing novel SMYD3 inhibitors with high potency and high selectivity against MAP3K2 and cancer.
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Affiliation(s)
| | | | - Na Yang
- E-mail: . Tel/Fax: + 8622 85358193
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15
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Zhang Y, Li C, Yang Z. Is MYND Domain-Mediated Assembly of SMYD3 Complexes Involved in Calcium Dependent Signaling? Front Mol Biosci 2019; 6:121. [PMID: 31737645 PMCID: PMC6837996 DOI: 10.3389/fmolb.2019.00121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/17/2019] [Indexed: 12/17/2022] Open
Abstract
Macromolecular complexes are essential to intracellular signal transduction by creating signaling niches and enabling a chain of reactions that transmit external signals into various cellular responses. Analysis of SMYD3 interactome indicates this protein lysine methyltransferase might be involved in calcium dependent signaling pathways through forming complexes with the phospholipase PLCB3, calcium/calmodulin dependent kinase CAMK2B, or calcineurin inhibitor RCAN3. SMYD3 is well-known as a histone H3K4 methyltransferase involved in epigenetic transcriptional regulation; however, any roles SMYD3 may play in signaling transduction remain unknown. KEGG pathway enrichment analysis reveals the SMYD3 interacting proteins are overrepresented in several signaling pathways such as estrogen signaling pathway, NOD-like receptor signaling pathway, and WNT signaling pathway. Sequence motif scanning reveals a significant enrichment of PXLXP motif in SMYD3 interacting proteins. The MYND domain of SMYD3 is known to bind to the PXLXP motif. The enrichment of the PXLXP motif suggests that the MYND domain is likely to be a key interaction module that mediates formation of some SMYD3 complexes. The presence of the PXLXP motifs in PLCB3 and CAMK2B indicates the potential role of the MYND domain in mediating complex formation in signaling. The structural basis of SMYD3 MYND domain-mediated interactions is unknown. The only available MYND-peptide complex structure suggests the MYND domain-mediated interaction is likely transient and dynamic. The transient nature will make this domain well-suited to mediate signaling transduction processes where it may allow rapid responses to cellular perturbations and changes in environment.
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Affiliation(s)
- Yingxue Zhang
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Chunying Li
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA, United States
| | - Zhe Yang
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, United States
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16
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Whatley KCL, Padalino G, Whiteland H, Geyer KK, Hulme BJ, Chalmers IW, Forde-Thomas J, Ferla S, Brancale A, Hoffmann KF. The repositioning of epigenetic probes/inhibitors identifies new anti-schistosomal lead compounds and chemotherapeutic targets. PLoS Negl Trop Dis 2019; 13:e0007693. [PMID: 31730617 PMCID: PMC6881072 DOI: 10.1371/journal.pntd.0007693] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/27/2019] [Accepted: 10/30/2019] [Indexed: 01/13/2023] Open
Abstract
Background Praziquantel represents the frontline chemotherapy used to treat schistosomiasis, a neglected tropical disease (NTD) caused by infection with macro-parasitic blood fluke schistosomes. While this drug is safe, its inability to kill all schistosome lifecycle stages within the human host often requires repeat treatments. This limitation, amongst others, has led to the search for novel anti-schistosome replacement or combinatorial chemotherapies. Here, we describe a repositioning strategy to assess the anthelmintic activity of epigenetic probes/inhibitors obtained from the Structural Genomics Consortium. Methodology/Principle findings Thirty-seven epigenetic probes/inhibitors targeting histone readers, writers and erasers were initially screened against Schistosoma mansoni schistosomula using the high-throughput Roboworm platform. At 10 μM, 14 of these 37 compounds (38%) negatively affected schistosomula motility and phenotype after 72 hours of continuous co-incubation. Subsequent dose-response titrations against schistosomula and adult worms revealed epigenetic probes targeting one reader (NVS-CECR2-1), one writer (LLY-507 and BAY-598) and one eraser (GSK-J4) to be particularly active. As LLY-507/BAY-598 (SMYD2 histone methyltransferase inhibitors) and GSK-J4 (a JMJD3 histone demethylase inhibitor) regulate an epigenetic process (protein methylation) known to be critical for schistosome development, further characterisation of these compounds/putative targets was performed. RNA interference (RNAi) of one putative LLY-507/BAY-598 S. mansoni target (Smp_000700) in adult worms replicated the compound-mediated motility and egg production defects. Furthermore, H3K36me2, a known product catalysed by SMYD2 activity, was also reduced by LLY-507 (25%), BAY-598 (23%) and siSmp_000700 (15%) treatment of adult worms. Oviposition and packaging of vitelline cells into in vitro laid eggs was also significantly affected by GSK-J4 (putative cell permeable prodrug inhibitor of Smp_034000), but not by the related structural analogue GSK-J1 (cell impermeable inhibitor). Conclusion/Significance Collectively, these results provide further support for the development of next-generation drugs targeting schistosome epigenetic pathway components. In particular, the progression of histone methylation/demethylation modulators presents a tractable strategy for anti-schistosomal control. Human schistosomiasis is caused by infection with parasitic blood fluke worms. Global control of this NTD is currently facilitated by administration of a single drug, praziquantel (PZQ). This mono-chemotherapeutic strategy of schistosomiasis control presents challenges as PZQ is not active against all human-dwelling schistosome lifecycle stages and the evolution of PZQ resistant parasites remains a threat. Therefore, new drugs to be used in combination with or in replacement of PZQ are urgently needed. Here, continuing our studies on Schistosoma mansoni epigenetic processes, we performed anthelmintic screening of 37 epigenetic probes/epigenetic inhibitors obtained from the Structural Genomics Consortium (SGC). The results of these studies highlighted that schistosome protein methylation/demethylation processes are acutely vulnerable. In particular, compounds affecting schistosome SMYD (LLY-507, BAY-598) or JMJD (GSK-J4) homologues are especially active on schistosomula and adult worms during in vitro phenotypic drug screens. The active epigenetic probes identified here as well as their corresponding S. mansoni protein targets offers new starting points for the development of next-generation anti-schistosomals.
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Affiliation(s)
- Kezia C. L. Whatley
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Gilda Padalino
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Helen Whiteland
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Kathrin K. Geyer
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Benjamin J. Hulme
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Iain W. Chalmers
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Josephine Forde-Thomas
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Salvatore Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, United Kingdom
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff, United Kingdom
| | - Karl F. Hoffmann
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail:
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17
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Guo X, Puttabyatappa M, Thompson RC, Padmanabhan V. Developmental Programming: Contribution of Epigenetic Enzymes to Antral Follicular Defects in the Sheep Model of PCOS. Endocrinology 2019; 160:2471-2484. [PMID: 31398247 PMCID: PMC6760338 DOI: 10.1210/en.2019-00389] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/22/2019] [Indexed: 12/27/2022]
Abstract
Prenatal testosterone (T)-treated sheep, similar to women with polycystic ovary syndrome (PCOS), manifest oligo-/anovulation, hyperandrogenism, and polyfollicular ovary. The polyfollicular ovarian morphology, a result of persistence of antral follicles, arises, in part, by transcriptional changes in key mediators of follicular development that, in turn, are driven by epigenetic mechanisms. We hypothesized that prenatal T excess induces, in a cell-specific manner, transcriptional changes in key mediators of follicular development associated with relevant changes in epigenetic machinery. Expression levels of key mediators of follicular development, DNA methyltransferases (DNMTs), and histone de-/methylases and de-/acetylases were determined in laser-capture microdissection-isolated antral follicular granulosa and theca and ovarian stromal cells from 21 months of age control and prenatal T-treated sheep (100 mg IM twice weekly from gestational day 30 to 90; term: 147 days). Changes in histone methylation were determined by immunofluorescence. Prenatal T treatment induced the following: (i) cell-specific changes in gene expression of key mediators of follicular development and steroidogenesis; (ii) granulosa, theca, and stromal cell-specific changes in DNMTs and histone de-/methylases and deacetylases, and (iii) increases in histone 3 trimethylation at lysine 9 in granulosa and histone 3 dimethylation at lysine 4 in theca cells. The pattern of histone methylation was consistent with the expression profile of histone de-/methylases in the respective cells. These findings suggest that changes in expression of key genes involved in the development of the polyfollicular phenotype in prenatal T-treated sheep are mediated, at least in part, by cell-specific changes in epigenetic-modifying enzymes.
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Affiliation(s)
- Xingzi Guo
- Department of Obstetrics and Gynecology, Xiangya Third Hospital, Central South University, Changsha, Hunan, People’s Republic of China
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | | | - Robert C Thompson
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan
| | - Vasantha Padmanabhan
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
- Correspondence: Vasantha Padmanabhan, PhD, Department of Pediatrics, University of Michigan, 7510 MSRB 1, 1500 West Medical Center Drive, Ann Arbor, Michigan 48109. E-mail:
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18
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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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19
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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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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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A chemical biology toolbox to study protein methyltransferases and epigenetic signaling. Nat Commun 2019; 10:19. [PMID: 30604761 PMCID: PMC6318333 DOI: 10.1038/s41467-018-07905-4] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 12/04/2018] [Indexed: 12/11/2022] Open
Abstract
Protein methyltransferases (PMTs) comprise a major class of epigenetic regulatory enzymes with therapeutic relevance. Here we present a collection of chemical probes and associated reagents and data to elucidate the function of human and murine PMTs in cellular studies. Our collection provides inhibitors and antagonists that together modulate most of the key regulatory methylation marks on histones H3 and H4, providing an important resource for modulating cellular epigenomes. We describe a comprehensive and comparative characterization of the probe collection with respect to their potency, selectivity, and mode of inhibition. We demonstrate the utility of this collection in CD4+ T cell differentiation assays revealing the potential of individual probes to alter multiple T cell subpopulations which may have implications for T cell-mediated processes such as inflammation and immuno-oncology. In particular, we demonstrate a role for DOT1L in limiting Th1 cell differentiation and maintaining lineage integrity. This chemical probe collection and associated data form a resource for the study of methylation-mediated signaling in epigenetics, inflammation and beyond. Protein methyltransferases (PMTs) are epigenetic regulatory enzymes with significant therapeutic relevance. Here the authors describe a collection of chemical inhibitors and antagonists to modulate most of the key methylation marks on histones H3 and H4, and use the collection to study of the role of PMTs in mouse and human T cell differentiation.
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22
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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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23
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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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Tracy C, Warren JS, Szulik M, Wang L, Garcia J, Makaju A, Russell K, Miller M, Franklin S. The Smyd Family of Methyltransferases: Role in Cardiac and Skeletal Muscle Physiology and Pathology. CURRENT OPINION IN PHYSIOLOGY 2017; 1:140-152. [PMID: 29435515 DOI: 10.1016/j.cophys.2017.10.001] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein methylation plays a pivotal role in the regulation of various cellular processes including chromatin remodeling and gene expression. SET and MYND domain-containing proteins (Smyd) are a special class of lysine methyltransferases whose catalytic SET domain is split by an MYND domain. The hallmark feature of this family was thought to be the methylation of histone H3 (on lysine 4). However, several studies suggest that the role of the Smyd family is dynamic, targeting unique histone residues associated with both transcriptional activation and repression. Smyd proteins also methylate several non-histone proteins to regulate various cellular processes. Although we are only beginning to understand their specific molecular functions and role in chromatin remodeling, recent studies have advanced our understanding of this relatively uncharacterized family, highlighting their involvement in development, cell growth and differentiation and during disease in various animal models. This review summarizes our current knowledge of the structure, function and methylation targets of the Smyd family and provides a compilation of data emphasizing their prominent role in cardiac and skeletal muscle physiology and pathology.
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Affiliation(s)
- Christopher Tracy
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Junco S Warren
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Marta Szulik
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Li Wang
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - June Garcia
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Aman Makaju
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Kristi Russell
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Mickey Miller
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
| | - Sarah Franklin
- Department of Internal Medicine, Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT
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25
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Wang L, Wang QT, Liu YP, Dong QQ, Hu HJ, Miao Z, Li S, Liu Y, Zhou H, Zhang TC, Ma WJ, Luo XG. ATM Signaling Pathway Is Implicated in the SMYD3-mediated Proliferation and Migration of Gastric Cancer Cells. J Gastric Cancer 2017; 17:295-305. [PMID: 29302370 PMCID: PMC5746651 DOI: 10.5230/jgc.2017.17.e33] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/23/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022] Open
Abstract
Purpose We previously found that the histone methyltransferase suppressor of variegation, enhancer of zeste, trithorax and myeloid-nervy-deformed epidermal autoregulatory factor-1 domain-containing protein 3 (SMYD3) is a potential independent predictive factor or prognostic factor for overall survival in gastric cancer patients, but its roles seem to differ from those in other cancers. Therefore, in this study, the detailed functions of SMYD3 in cell proliferation and migration in gastric cancer were examined. Materials and Methods SMYD3 was overexpressed or suppressed by transfection with an expression plasmid or siRNA, and a wound healing migration assay and Transwell assay were performed to detect the migration and invasion ability of gastric cancer cells. Additionally, an MTT assay and clonogenic assay were performed to evaluate cell proliferation, and a cell cycle analysis was performed by propidium iodide staining. Furthermore, the expression of genes implicated in the ataxia telangiectasia mutated (ATM) pathway and proteins involved in cell cycle regulation were detected by polymerase chain reaction and western blot analyses. Results Compared with control cells, gastric cancer cells transfected with si-SMYD3 showed lower migration and invasion abilities (P<0.05), and the absence of SMYD3 halted cells in G2/M phase and activated the ATM pathway. Furthermore, the opposite patterns were observed when SMYD3 was elevated in normal gastric cells. Conclusions To the best of our knowledge, this study provides the first evidence that the absence of SMYD3 could inhibit the migration, invasion, and proliferation of gastric cancer cells and halt cells in G2/M phase via the ATM-CHK2/p53-Cdc25C pathway. These findings indicated that SMYD3 plays crucial roles in the proliferation, migration, and invasion of gastric cancer cells and may be a useful therapeutic target in human gastric carcinomas.
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Affiliation(s)
- Lei Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Qiu-Tong Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yu-Peng Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Qing-Qing Dong
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Hai-Jie Hu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhi Miao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shuang Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yong Liu
- Department of Gastric Cancer Surgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China.,Tianjin Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Hao Zhou
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Tong-Cun Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Wen-Jian Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Xue-Gang Luo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, China.,Tianjin Industrial Microbiology Key Lab, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
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26
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Huang L, Xu AM. SET and MYND domain containing protein 3 in cancer. Am J Transl Res 2017; 9:1-14. [PMID: 28123630 PMCID: PMC5250700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/21/2016] [Indexed: 06/06/2023]
Abstract
Lysine methylation plays a vital role in histone modification. Deregulations of lysine methyltransferases and demethylases have been frequently observed in human cancers. The SET and MYND domain containing protein 3 (SMYD3) is a novel histone lysine methyltransferase and it functions by regulating chromatin during the development of myocardial and skeletal muscle. It has been recently unveiled to play significant roles in human cancer genesis and progression via regulating various key cancer-associated genes and pathways and promoting cell proliferation and migration. Upregulation of SMYD3 expression is present in multiple cancer types, suggesting it as a potential prognostic marker. Herein the structure, substrates and targets of SMYD3, and its effects on initiation, invasion and metastasis of diverse tumors (e.g., esophageal squamous cell carcinoma, gastric cancer, hepatocellular carcinoma, cholangiocarcinoma, breast cancer, prostate cancer, and leukemia) are systematically reviewed, providing clues for the development of novel SMYD3-specific personalized anti-cancer therapy. SMYD3 inhibitors (e.g., BCI-121 and novobiocin) could hopefully fight against tumors with efficacy.
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Affiliation(s)
- Lei Huang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical UniversityHefei, China
- German Cancer Research Center (DKFZ)Heidelberg, Germany
| | - A-Man Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Anhui Medical UniversityHefei, China
- Department of General Surgery, The Fourth Affiliated Hospital of Anhui Medical UniversityHefei, China
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27
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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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Kudithipudi S, Jeltsch A. Approaches and Guidelines for the Identification of Novel Substrates of Protein Lysine Methyltransferases. Cell Chem Biol 2016; 23:1049-1055. [PMID: 27569752 DOI: 10.1016/j.chembiol.2016.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 06/11/2016] [Accepted: 07/03/2016] [Indexed: 12/18/2022]
Abstract
Protein lysine methylation is emerging as a general post-translational modification (PTM) with essential functions regulating protein stability, activity, and protein-protein interactions. One of the outstanding challenges in this field is linking protein lysine methyltransferases (PKMTs) with specific substrates and lysine methylation events in a systematic manner. Inability to validate reported PKMT substrates delayed progress in the field and cast unnecessary doubt about protein lysine methylation as a truly general PTM. Here, we aim to provide a concise guide to help avoid some of the most common pitfalls in studies searching for new PKMT substrates and propose a set of seven basic biochemical rules: (1) include positive controls; (2) use target lysine mutations of substrate proteins as negative controls; (3) use inactive enzyme variants as negative controls; (4) report quantitative methylation data; (5) consider PKMT specificity; (6) validate methyl lysine antibodies; and (7) connect cellular and in vitro results. We explain the logic behind them and discuss how they should be implemented in the experimental work.
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Affiliation(s)
- Srikanth Kudithipudi
- Faculty of Chemistry, Institute of Biochemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Faculty of Chemistry, Institute of Biochemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany.
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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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