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Thomas J, Ghosh A, Ranjan S, Satija J. Cheminformatics approach to identify andrographolide derivatives as dual inhibitors of methyltransferases (nsp14 and nsp16) of SARS-CoV-2. Sci Rep 2024; 14:9801. [PMID: 38684706 PMCID: PMC11058777 DOI: 10.1038/s41598-024-58532-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
The Covid-19 pandemic outbreak has accelerated tremendous efforts to discover a therapeutic strategy that targets severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to control viral infection. Various viral proteins have been identified as potential drug targets, however, to date, no specific therapeutic cure is available against the SARS-CoV-2. To address this issue, the present work reports a systematic cheminformatic approach to identify the potent andrographolide derivatives that can target methyltransferases of SARS-CoV-2, i.e. nsp14 and nsp16 which are crucial for the replication of the virus and host immune evasion. A consensus of cheminformatics methodologies including virtual screening, molecular docking, ADMET profiling, molecular dynamics simulations, free-energy landscape analysis, molecular mechanics generalized born surface area (MM-GBSA), and density functional theory (DFT) was utilized. Our study reveals two new andrographolide derivatives (PubChem CID: 2734589 and 138968421) as natural bioactive molecules that can form stable complexes with both proteins via hydrophobic interactions, hydrogen bonds and electrostatic interactions. The toxicity analysis predicts class four toxicity for both compounds with LD50 value in the range of 500-700 mg/kg. MD simulation reveals the stable formation of the complex for both the compounds and their average trajectory values were found to be lower than the control inhibitor and protein alone. MMGBSA analysis corroborates the MD simulation result and showed the lowest energy for the compounds 2734589 and 138968421. The DFT and MEP analysis also predicts the better reactivity and stability of both the hit compounds. Overall, both andrographolide derivatives exhibit good potential as potent inhibitors for both nsp14 and nsp16 proteins, however, in-vitro and in vivo assessment would be required to prove their efficacy and safety in clinical settings. Moreover, the drug discovery strategy aiming at the dual target approach might serve as a useful model for inventing novel drug molecules for various other diseases.
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Affiliation(s)
- Jobin Thomas
- Centre for Nanobiotechnology (CNBT), Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Anupam Ghosh
- NanoBio Research Lab, School of Nano Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721301, India
| | - Shivendu Ranjan
- NanoBio Research Lab, School of Nano Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721301, India
| | - Jitendra Satija
- Centre for Nanobiotechnology (CNBT), Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
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2
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Majrashi TA, El Hassab MA, Mahmoud SH, Mostafa A, Wahsh EA, Elkaeed EB, Hassan FE, Eldehna WM, Abdelgawad SM. In vitro biological evaluation and in silico insights into the antiviral activity of standardized olive leaves extract against SARS-CoV-2. PLoS One 2024; 19:e0301086. [PMID: 38662719 PMCID: PMC11045091 DOI: 10.1371/journal.pone.0301086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/08/2024] [Indexed: 04/28/2024] Open
Abstract
There is still a great global need for efficient treatments for the management of SARS-CoV-2 illness notwithstanding the availability and efficacy of COVID-19 vaccinations. Olive leaf is an herbal remedy with a potential antiviral activity that could improve the recovery of COVID-19 patients. In this work, the olive leaves major metabolites were screened in silico for their activity against SARS-CoV-2 by molecular docking on several viral targets such as methyl transferase, helicase, Plpro, Mpro, and RdRp. The results of in silico docking study showed that olive leaves phytoconstituents exhibited strong potential antiviral activity against SARS-CoV-2 selected targets. Verbacoside demonstrated a strong inhibition against methyl transferase, helicase, Plpro, Mpro, and RdRp (docking scores = -17.2, -20, -18.2, -19.8, and -21.7 kcal/mol.) respectively. Oleuropein inhibited 5rmm, Mpro, and RdRp (docking scores = -15, -16.6 and -18.6 kcal/mol., respectively) respectively. Apigenin-7-O-glucoside exhibited activity against methyl transferase and RdRp (docking score = -16.1 and -19.4 kcal/mol., respectively) while Luteolin-7-O-glucoside inhibited Plpro and RdRp (docking score = -15.2 and -20 kcal/mol., respectively). The in vitro antiviral assay was carried out on standardized olive leaf extract (SOLE) containing 20% oleuropein and IC50 was calculated. The results revealed that 20% SOLE demonstrated a moderate antiviral activity against SARS-CoV-2 with IC50 of 118.3 μg /mL. Accordingly, olive leaf could be a potential herbal therapy against SARS-CoV-2 but more in vivo and clinical investigations are recommended.
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Affiliation(s)
- Taghreed A. Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Asir, Saudi Arabia
| | - Mahmoud A. El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), South Sinai, Egypt
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Engy A. Wahsh
- Clinical Pharmacy Department, Faculty of Pharmacy, October 6 University, Giza Governorate, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Fatma E. Hassan
- Department of Physiology, General Medicine Practice Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Medical Physiology Department, Kasr Alainy, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
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3
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Chen Y, Weng X, Zhang C, Wang S, Wu X, Cheng B. Inhibition of SUV39H1 reduces tumor angiogenesis via Notch1 in oral squamous cell carcinoma. PeerJ 2024; 12:e17222. [PMID: 38650654 PMCID: PMC11034493 DOI: 10.7717/peerj.17222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Targeting tumor angiogenesis is an important approach in advanced tumor therapy. Here we investigated the effect of the suppressor of variegation 3-9 homolog 1 (SUV39H1) on tumor angiogenesis in oral squamous cell carcinoma (OSCC). The GEPIA database was used to analyze the expression of SUV39H1 in various cancer tissues. The expression of SUV39H1 in OSCC was detected by immunohistochemistry, and the correlation between SUV39H1 and Notch1 and microvascular density (MVD) was analyzed. The effect of SUV39H1 inhibition on OSCC was investigated in vivo by chaetocin treatment. The migration and tube formation of vascular endothelial cells by conditioned culture-medium of different treatments of oral squamous cell cells were measured. The transcriptional level of SUV39H1 is elevated in various cancer tissues. The transcription level of SUV39H1 in head and neck squamous cell carcinoma was significantly higher than that in control. Immunohistochemistry result showed increased SUV39H1 expression in OSCC, which was significantly correlated with T staging. The expression of SUV39H1 was significantly correlated with Notch1 and CD31. In vivo experiment chaetocin treatment significantly inhibit the growth of tumor, and reduce SUV39H1, Notch1, CD31 expression. The decreased expression of SUV39H1 in OSCC cells lead to the decreased expression of Notch1 and VEGF proteins, as well as the decreased migration and tube formation ability of vascular endothelial cells. Inhibition of Notch1 further enhance this effect. Our results suggest inhibition of SUV39H1 may affect angiogenesis by regulating Notch1 expression. This study provides a foundation for SUV39H1 as a potential therapeutic target for OSCC.
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MESH Headings
- Humans
- Receptor, Notch1/metabolism
- Receptor, Notch1/genetics
- Mouth Neoplasms/pathology
- Mouth Neoplasms/metabolism
- Mouth Neoplasms/drug therapy
- Mouth Neoplasms/blood supply
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/drug therapy
- Neovascularization, Pathologic/pathology
- Animals
- Repressor Proteins/metabolism
- Repressor Proteins/genetics
- Methyltransferases/metabolism
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/genetics
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/blood supply
- Cell Line, Tumor
- Mice
- Cell Movement/drug effects
- Gene Expression Regulation, Neoplastic/drug effects
- Angiogenesis
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Affiliation(s)
- Yan Chen
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiuhong Weng
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chuanjie Zhang
- Department of Children Health Care, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Simin Wang
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xuechen Wu
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bo Cheng
- Department of Stomatology, Zhongnan Hospital of Wuhan University, Wuhan, China
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4
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Tsukamoto Y, Igarashi M, Kato H. Targeting cap1 RNA methyltransferases as an antiviral strategy. Cell Chem Biol 2024; 31:86-99. [PMID: 38091983 DOI: 10.1016/j.chembiol.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/30/2023] [Accepted: 11/20/2023] [Indexed: 01/21/2024]
Abstract
Methylation is one of the critical modifications that regulates numerous biological processes. Guanine capping and methylation at the 7th position (m7G) have been shown to mature mRNA for increased RNA stability and translational efficiency. The m7G capped cap0 RNA remains immature and requires additional methylation at the first nucleotide (N1-2'-O-Me), designated as cap1, to achieve full maturation. This cap1 RNA with N1-2'-O-Me prevents its recognition by innate immune sensors as non-self. Viruses have also evolved various strategies to produce self-like capped RNAs with the N1-2'-O-Me that potentially evades the antiviral response and establishes an efficient replication. In this review, we focus on the importance of the presence of N1-2'-O-Me in viral RNAs and discuss the potential for drug development by targeting host and viral N1-2'-O-methyltransferases.
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Affiliation(s)
- Yuta Tsukamoto
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hiroki Kato
- Institute of Cardiovascular Immunology, Medical Faculty, University Hospital Bonn, University of Bonn, Bonn, Germany.
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Tao Y, Felber JG, Zou Z, Njomen E, Remsberg JR, Ogasawara D, Ye C, Melillo B, Schreiber SL, He C, Remillard D, Cravatt BF. Chemical Proteomic Discovery of Isotype-Selective Covalent Inhibitors of the RNA Methyltransferase NSUN2. Angew Chem Int Ed Engl 2023; 62:e202311924. [PMID: 37909922 PMCID: PMC10999112 DOI: 10.1002/anie.202311924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/03/2023]
Abstract
5-Methylcytosine (m5 C) is an RNA modification prevalent on tRNAs, where it can protect tRNAs from endonucleolytic cleavage to maintain protein synthesis. The NSUN family (NSUN1-7 in humans) of RNA methyltransferases are capable of installing the methyl group onto the C5 position of cytosines in RNA. NSUNs are implicated in a wide range of (patho)physiological processes, but selective and cell-active inhibitors of these enzymes are lacking. Here, we use cysteine-directed activity-based protein profiling (ABPP) to discover azetidine acrylamides that act as stereoselective covalent inhibitors of human NSUN2. Despite targeting a conserved catalytic cysteine in the NSUN family, the NSUN2 inhibitors show negligible cross-reactivity with other human NSUNs and exhibit good proteome-wide selectivity. We verify that the azetidine acrylamides inhibit the catalytic activity of recombinant NSUN2, but not NSUN6, and demonstrate that these compounds stereoselectively disrupt NSUN2-tRNA interactions in cancer cells, leading to a global reduction in tRNA m5 C content. Our findings thus highlight the potential to create isotype-selective and cell-active inhibitors of NSUN2 with covalent chemistry targeting a conserved catalytic cysteine.
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Affiliation(s)
- Yongfeng Tao
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550N. Torrey Pines Road, La Jolla, CA-92307, USA
| | - Jan G Felber
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550N. Torrey Pines Road, La Jolla, CA-92307, USA
- LMU Munich, Department of Pharmacy, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Zhongyu Zou
- Department of Chemistry, The University of Chicago, 929 East 57th Street, GCIS E319B, Chicago, IL-60637, USA
| | - Evert Njomen
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550N. Torrey Pines Road, La Jolla, CA-92307, USA
| | - Jarrett R Remsberg
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550N. Torrey Pines Road, La Jolla, CA-92307, USA
- Current address: Belharra Therapeutics, 3985 Sorrento Valley Blvd Suite C, San Diego, CA-92121, USA
| | - Daisuke Ogasawara
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550N. Torrey Pines Road, La Jolla, CA-92307, USA
| | - Chang Ye
- Department of Chemistry, The University of Chicago, 929 East 57th Street, GCIS E319B, Chicago, IL-60637, USA
| | - Bruno Melillo
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550N. Torrey Pines Road, La Jolla, CA-92307, USA
- Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA-02142, USA
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA-02142, USA
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, MA-02138, Cambridge, USA
| | - Chuan He
- Department of Chemistry, The University of Chicago, 929 East 57th Street, GCIS E319B, Chicago, IL-60637, USA
- Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, GCIS E319B, Chicago, IL-60637, USA
| | - David Remillard
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550N. Torrey Pines Road, La Jolla, CA-92307, USA
- Current address: Novartis, 10675 John Jay Hopkins Dr, San Diego, CA-92121, USA
| | - Benjamin F Cravatt
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550N. Torrey Pines Road, La Jolla, CA-92307, USA
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6
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高 毅, 王 培, 逯 素, 马 万. [METTL3 inhibitor STM2457 improves metabolic dysfunction-associated fatty liver disease by regulating mitochondrial function in mice]. Nan Fang Yi Ke Da Xue Xue Bao 2023; 43:1689-1696. [PMID: 37933644 PMCID: PMC10630206 DOI: 10.12122/j.issn.1673-4254.2023.10.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Indexed: 11/08/2023]
Abstract
OBJECTIVE To investigate the effect of methyltransferase-like 3 (METTL3) inhibitor STM2457 in metabolic dysfunction-associated fatty liver disease (MAFLD). METHODS C57BL/6J mouse models of MAFLD induced by high-fat diet feeding for 16 weeks were treated with intraperitoneal injections of STM2457 (50 mg/kg) for 2 weeks. The changes in m6A modification level in the liver tissue of the mice were determined with dot-blot hybridization, and the hepatic levels of triglyceride (TG), alanine aminotransferase (ALT) and glutathione aminotransferase (AST) were detected. The histological changes of the liver and changes in insulin resistance and metabolic profile of the mice were evaluated using HE staining, insulin tolerance tests and metabolic cages; transmission electron microscopy (TEM) was employed to examine the changes in mitochondrial morphology. In a HepG2 cell model of steatosis induced by treatment with sodium oleate/sodium palmitate for 48 h, the protective effect of STM2457 (1 μmol/L) on mitochondrial function was assessed by measuring mitochondrial membrane potential using a fluorescence probe (JC-1). RESULTS The mouse models of MAFLD showed significant elevation of m6A modification level in the liver tissues and obviously upregulated mRNA expression of METT3 (P<0.05). Treatment with STM2457 significantly reduced body weight and liver lipid deposition and m6A modification levels, increased glucose tolerance and insulin sensitivity, lowered hepatic TG and serum ALT and AST levels, and increased respiratory entropy (RQ) in the mouse models (all P<0.05). HepG2 cells with steatosis exhibited obvious mitochondrial swelling with decreased mitochondrial membrane potential, but the STM2457-treated cells maintained a normal mitochondrial morphology with a higher membrane potential (P<0.05). CONCLUSION The METTL3 inhibitor STM2457 improves MAFLD by reducing high-fat diet-induced mitochondrial damage in mice.
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Affiliation(s)
- 毅男 高
- />山东第一医科大学第一附属医院(山东省千佛山医院)检验科//山东省医药卫生临床检验诊断学重点实验室,山东 济南 250014Department of Clinical Laboratory Medicine, First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China
| | - 培君 王
- />山东第一医科大学第一附属医院(山东省千佛山医院)检验科//山东省医药卫生临床检验诊断学重点实验室,山东 济南 250014Department of Clinical Laboratory Medicine, First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China
| | - 素梅 逯
- />山东第一医科大学第一附属医院(山东省千佛山医院)检验科//山东省医药卫生临床检验诊断学重点实验室,山东 济南 250014Department of Clinical Laboratory Medicine, First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China
| | - 万山 马
- />山东第一医科大学第一附属医院(山东省千佛山医院)检验科//山东省医药卫生临床检验诊断学重点实验室,山东 济南 250014Department of Clinical Laboratory Medicine, First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China
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7
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Bobileva O, Bobrovs R, Sirma EE, Kanepe I, Bula AL, Patetko L, Ramata-Stunda A, Grinberga S, Jirgensons A, Jaudzems K. 3-(Adenosylthio)benzoic Acid Derivatives as SARS-CoV-2 Nsp14 Methyltransferase Inhibitors. Molecules 2023; 28:molecules28020768. [PMID: 36677825 PMCID: PMC9862586 DOI: 10.3390/molecules28020768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
SARS-CoV-2 nsp14 guanine-N7-methyltransferase plays an important role in the viral RNA translation process by catalyzing the transfer of a methyl group from S-adenosyl-methionine (SAM) to viral mRNA cap. We report a structure-guided design and synthesis of 3-(adenosylthio)benzoic acid derivatives as nsp14 methyltransferase inhibitors resulting in compound 5p with subnanomolar inhibitory activity and improved cell membrane permeability in comparison with the parent inhibitor. Compound 5p acts as a bisubstrate inhibitor targeting both SAM and mRNA-binding pockets of nsp14. While the selectivity of 3-(adenosylthio)benzoic acid derivatives against human glycine N-methyltransferase was not improved, the discovery of phenyl-substituted analogs 5p,t may contribute to further development of SARS-CoV-2 nsp14 bisubstrate inhibitors.
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Affiliation(s)
- Olga Bobileva
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
- Correspondence:
| | - Raitis Bobrovs
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | | | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Anna L. Bula
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Liene Patetko
- Faculty of Biology, University of Latvia, LV-1004 Riga, Latvia
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8
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Li J, Wang L, Hahn Q, Nowak RP, Viennet T, Orellana EA, Roy Burman SS, Yue H, Hunkeler M, Fontana P, Wu H, Arthanari H, Fischer ES, Gregory RI. Structural basis of regulated m 7G tRNA modification by METTL1-WDR4. Nature 2023; 613:391-397. [PMID: 36599985 DOI: 10.1038/s41586-022-05566-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Chemical modifications of RNA have key roles in many biological processes1-3. N7-methylguanosine (m7G) is required for integrity and stability of a large subset of tRNAs4-7. The methyltransferase 1-WD repeat-containing protein 4 (METTL1-WDR4) complex is the methyltransferase that modifies G46 in the variable loop of certain tRNAs, and its dysregulation drives tumorigenesis in numerous cancer types8-14. Mutations in WDR4 cause human developmental phenotypes including microcephaly15-17. How METTL1-WDR4 modifies tRNA substrates and is regulated remains elusive18. Here we show, through structural, biochemical and cellular studies of human METTL1-WDR4, that WDR4 serves as a scaffold for METTL1 and the tRNA T-arm. Upon tRNA binding, the αC region of METTL1 transforms into a helix, which together with the α6 helix secures both ends of the tRNA variable loop. Unexpectedly, we find that the predicted disordered N-terminal region of METTL1 is part of the catalytic pocket and essential for methyltransferase activity. Furthermore, we reveal that S27 phosphorylation in the METTL1 N-terminal region inhibits methyltransferase activity by locally disrupting the catalytic centre. Our results provide a molecular understanding of tRNA substrate recognition and phosphorylation-mediated regulation of METTL1-WDR4, and reveal the presumed disordered N-terminal region of METTL1 as a nexus of methyltransferase activity.
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Affiliation(s)
- Jiazhi Li
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Quentin Hahn
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Radosław P Nowak
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thibault Viennet
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Shourya S Roy Burman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Hong Yue
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Moritz Hunkeler
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pietro Fontana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eric S Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Cambridge, MA, USA.
- Harvard Initiative for RNA Medicine, Boston, MA, USA.
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9
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Liu YT, Romero C, Xiao X, Guo L, Zhou X, Applebaum MA, Xu L, Skapek SX. Methyltransferase Inhibition Enables Tgf β Driven Induction of CDKN2A and B in Cancer Cells. Mol Cell Biol 2023; 43:115-129. [PMID: 36941772 PMCID: PMC10038032 DOI: 10.1080/10985549.2023.2186074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 12/21/2022] [Accepted: 02/20/2023] [Indexed: 03/23/2023] Open
Abstract
CDKN2A/B deletion or silencing is common across human cancer, reinforcing the general importance of bypassing its tumor suppression in cancer formation or progression. In rhabdomyosarcoma (RMS) and neuroblastoma, two common childhood cancers, the three CDKN2A/B transcripts are independently expressed to varying degrees, but one, ARF, is uniformly silenced. Although TGFβ induces certain CDKN2A/B transcripts in HeLa cells, it was unable to do so in five tested RMS lines unless the cells were pretreated with a broadly acting methyltransferase inhibitor, DZNep, or one targeting EZH2. CDKN2A/B induction by TGFβ correlated with de novo appearance of three H3K27Ac peaks within a 20 kb cis element ∼150 kb proximal to CDKN2A/B. Deleting that segment prevented their induction by TGFβ but not a basal increase driven by methyltransferase inhibition alone. Expression of two CDKN2A/B transcripts was enhanced by dCas9/CRISPR activation targeting either the relevant promoter or the 20 kb cis elements, and this "precise" manipulation diminished RMS cell propagation in vitro. Our findings show crosstalk between methyltransferase inhibition and TGFβ-dependent activation of a remote enhancer to reverse CDKN2A/B silencing. Though focused on CDKN2A/B here, such crosstalk may apply to other TGFβ-responsive genes and perhaps govern this signaling protein's complex effects promoting or blocking cancer.
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Affiliation(s)
- Yen-Ting Liu
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Celeste Romero
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Xue Xiao
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Lei Guo
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaoyun Zhou
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mark A. Applebaum
- Section of Hematology/Oncology, Department of Pediatrics, University of Chicago, Chicago, Illinois, USA
| | - Lin Xu
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Population and Data Sciences, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Stephen X. Skapek
- Division of Hematology/Oncology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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10
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Li S, Zou D, Chen W, Britz GW, Liu Z, Weng YL. METTL3 inhibition reduces N 6 -methyladenosine levels and prevents allogeneic CD4 + T-cell responses. Immunol Cell Biol 2022; 100:718-730. [PMID: 36005900 PMCID: PMC9990421 DOI: 10.1111/imcb.12581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 07/24/2022] [Accepted: 08/24/2022] [Indexed: 02/02/2023]
Abstract
Alloreactive CD4+ T cells play a central role in allograft rejection. However, the post-transcriptional regulation of the effector program in alloreactive CD4+ T cells remains unclear. N6 -methyladenosine (m6 A) RNA modification is involved in various physiological and pathological processes. Herein, we investigated whether m6 A methylation plays a role in the allogeneic T-cell effector program. m6 A levels of CD4+ T cells from spleens, draining lymph nodes and skin allografts were determined in a skin transplantation model. The effects of a METTL3 inhibitor (STM2457) on CD4+ T-cell characteristics including proliferation, cell cycle, cell apoptosis and effector differentiation were determined after stimulation of polyclonal and alloantigen-specific (TEa; CD4+ T cells specific for I-Eα52-68 ) CD4+ T cells with α-CD3/α-CD28 monoclonal antibodies and cognate CB6F1 alloantigen, respectively. We found that graft-infiltrating CD4+ T cells expressed high m6 A levels. Administration of STM2457 reduced m6 A levels, inhibited T-cell proliferation and suppressed effector differentiation of polyclonal CD4+ T cells. Alloreactive TEa cells challenged with 40 μm STM2457 exhibited deficits in T-cell proliferation and T helper type 1 cell differentiation, a cell cycle arrest in the G0 phase and elevated cell apoptosis. Moreover, these impaired T-cell responses were associated with the diminished expression levels of transcription factors Ki-67, c-Myc and T-bet. Therefore, METTL3 inhibition reduces the expression of several key transcriptional factors for the T-cell effector program and suppresses alloreactive CD4+ T-cell effector function and differentiation. Targeting m6 A-related enzymes and molecular machinery in CD4+ T cells represents an attractive therapeutic approach to prevent allograft rejection.
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Affiliation(s)
- Shuang Li
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, Texas, USA
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, Texas, USA
| | - Dawei Zou
- Department of Surgery, Immunobiology & Transplant Science Center, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Wenhao Chen
- Department of Surgery, Immunobiology & Transplant Science Center, Houston Methodist Research Institute and Institute for Academic Medicine, Houston Methodist Hospital, Houston, Texas, USA
| | - Gavin W Britz
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, Texas, USA
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, Texas, USA
| | - Zhaoqian Liu
- Department of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, and National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Yi-Lan Weng
- Department of Neurosurgery, Houston Methodist Neurological Institute, Houston, Texas, USA
- Center for Neuroregeneration, Houston Methodist Research Institute, Houston, Texas, USA
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11
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Yazdi AK, Pakarian P, Perveen S, Hajian T, Santhakumar V, Bolotokova A, Li F, Vedadi M. Kinetic Characterization of SARS-CoV-2 nsp13 ATPase Activity and Discovery of Small-Molecule Inhibitors. ACS Infect Dis 2022; 8:1533-1542. [PMID: 35822715 PMCID: PMC9305828 DOI: 10.1021/acsinfecdis.2c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/29/2022]
Abstract
SARS-CoV-2 non-structural protein 13 (nsp13) is a highly conserved helicase and RNA 5'-triphosphatase. It uses the energy derived from the hydrolysis of nucleoside triphosphates for directional movement along the nucleic acids and promotes the unwinding of double-stranded nucleic acids. Nsp13 is essential for replication and propagation of all human and non-human coronaviruses. Combined with its defined nucleotide binding site and druggability, nsp13 is one of the most promising candidates for the development of pan-coronavirus therapeutics. Here, we report the development and optimization of bioluminescence assays for kinetic characterization of nsp13 ATPase activity in the presence and absence of single-stranded DNA. Screening of a library of 5000 small molecules in the presence of single-stranded DNA resulted in the discovery of six nsp13 small-molecule inhibitors with IC50 values ranging from 6 ± 0.5 to 50 ± 6 μM. In addition to providing validated methods for high-throughput screening of nsp13 in drug discovery campaigns, the reproducible screening hits we present here could potentially be chemistry starting points toward the development of more potent and selective nsp13 inhibitors, enabling the discovery of antiviral therapeutics.
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Affiliation(s)
| | - Paknoosh Pakarian
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Sumera Perveen
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Taraneh Hajian
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | | | - Albina Bolotokova
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Fengling Li
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Masoud Vedadi
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
- Department of Pharmacology and Toxicology,
University of Toronto, Toronto, Ontario M5S 1A8,
Canada
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12
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Eissa IH, Alesawy MS, Saleh AM, Elkaeed EB, Alsfouk BA, El-Attar AAMM, Metwaly AM. Ligand and Structure-Based In Silico Determination of the Most Promising SARS-CoV-2 nsp16-nsp10 2'- o-Methyltransferase Complex Inhibitors among 3009 FDA Approved Drugs. Molecules 2022; 27:2287. [PMID: 35408684 PMCID: PMC9000629 DOI: 10.3390/molecules27072287] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/27/2022] [Accepted: 03/28/2022] [Indexed: 12/15/2022] Open
Abstract
As a continuation of our earlier work against SARS-CoV-2, seven FDA-approved drugs were designated as the best SARS-CoV-2 nsp16-nsp10 2'-o-methyltransferase (2'OMTase) inhibitors through 3009 compounds. The in silico inhibitory potential of the examined compounds against SARS-CoV-2 nsp16-nsp10 2'-o-methyltransferase (PDB ID: (6W4H) was conducted through a multi-step screening approach. At the beginning, molecular fingerprints experiment with SAM (S-Adenosylmethionine), the co-crystallized ligand of the targeted enzyme, unveiled the resemblance of 147 drugs. Then, a structural similarity experiment recommended 26 compounds. Therefore, the 26 compounds were docked against 2'OMTase to reveal the potential inhibitory effect of seven promising compounds (Protirelin, (1187), Calcium folinate (1913), Raltegravir (1995), Regadenoson (2176), Ertapenem (2396), Methylergometrine (2532), and Thiamine pyrophosphate hydrochloride (2612)). Out of the docked ligands, Ertapenem (2396) showed an ideal binding mode like that of the co-crystallized ligand (SAM). It occupied all sub-pockets of the active site and bound the crucial amino acids. Accordingly, some MD simulation experiments (RMSD, RMSF, Rg, SASA, and H-bonding) have been conducted for the 2'OMTase-Ertapenem complex over 100 ns. The performed MD experiments verified the correct binding mode of Ertapenem against 2'OMTase exhibiting low energy and optimal dynamics. Finally, MM-PBSA studies indicated that Ertapenem bonded advantageously to the targeted protein with a free energy value of -43 KJ/mol. Furthermore, the binding free energy analysis revealed the essential amino acids of 2'OMTase that served positively to the binding. The achieved results bring hope to find a treatment for COVID-19 via in vitro and in vivo studies for the pointed compounds.
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Affiliation(s)
- Ibrahim H. Eissa
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt; (M.S.A.); (A.M.S.)
| | - Mohamed S. Alesawy
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt; (M.S.A.); (A.M.S.)
| | - Abdulrahman M. Saleh
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt; (M.S.A.); (A.M.S.)
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, Almaarefa University, Riyadh 13713, Saudi Arabia;
| | - Bshra A. Alsfouk
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Abdul-Aziz M. M. El-Attar
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo 11884, Egypt;
| | - Ahmed M. Metwaly
- Pharmacognosy and Medicinal Plants Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo 11884, Egypt
- Biopharmaceutical Products Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), Alexandria 21934, Egypt
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13
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Nencka R, Silhan J, Klima M, Otava T, Kocek H, Krafcikova P, Boura E. Coronaviral RNA-methyltransferases: function, structure and inhibition. Nucleic Acids Res 2022; 50:635-650. [PMID: 35018474 PMCID: PMC8789044 DOI: 10.1093/nar/gkab1279] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/08/2021] [Accepted: 12/20/2021] [Indexed: 02/06/2023] Open
Abstract
Coronaviral methyltransferases (MTases), nsp10/16 and nsp14, catalyze the last two steps of viral RNA-cap creation that takes place in cytoplasm. This cap is essential for the stability of viral RNA and, most importantly, for the evasion of innate immune system. Non-capped RNA is recognized by innate immunity which leads to its degradation and the activation of antiviral immunity. As a result, both coronaviral MTases are in the center of scientific scrutiny. Recently, X-ray and cryo-EM structures of both enzymes were solved even in complex with other parts of the viral replication complex. High-throughput screening as well as structure-guided inhibitor design have led to the discovery of their potent inhibitors. Here, we critically summarize the tremendous advancement of the coronaviral MTase field since the beginning of COVID pandemic.
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Affiliation(s)
- Radim Nencka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Tomas Otava
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Hugo Kocek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Petra Krafcikova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic
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14
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Zhai CT, Tian YC, Tang ZX, Shao LJ. RNA methyltransferase NSUN2 promotes growth of hepatocellular carcinoma cells by regulating fizzy-related-1 in vitro and in vivo. Kaohsiung J Med Sci 2021; 37:991-999. [PMID: 34370374 DOI: 10.1002/kjm2.12430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/16/2021] [Accepted: 06/20/2021] [Indexed: 12/29/2022] Open
Abstract
The aim of the study was to investigate the role of NSUN2 (NOP2/Sun RNA Methyltransferase Family Member 2) in hepatocellular carcinoma (HCC). The expressions of NSUN2 and FZR1 were measured. Cell viability, proliferation, and apoptosis were assessed. HCC xenograft in nude mouse model was established. Tumor weight and volume were examined. Tumor tissues were collected for immunohistochemistry (IHC). TCGA database analysis and clinical sample testing suggested that the transcript levels of NSUN2 and FZR1 were increased in HCC tissues. NSUN2 knockdown inhibited HCC cell viability and proliferation, and promoted cell apoptosis. Moreover, the effects of NSUN2 could be countered by overexpressing FZR1. In animal experiment, NSUN2 silencing suppressed tumor growth in nude mice by downregulating FZR1. In conclusion, NSUN2 has a regulatory effect on HCC cell proliferation and apoptosis. NSUN2 knockout could inhibit cellular processes in HCC and tumor growth, likely via FZR1 inhibition. This finding has not only revealed the role of NSUN2 in HCC growth, but also suggests a promising target for HCC treatment.
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Affiliation(s)
- Chun-Tao Zhai
- Department of General Surgery, The Affiliated Suzhou Science & Technology Town Hospital of Nanjing Medcial University, Jiangsu Province, China
| | - Yi-Cheng Tian
- Department of General Surgery, The Affiliated Suzhou Science & Technology Town Hospital of Nanjing Medcial University, Jiangsu Province, China
| | - Zu-Xiong Tang
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Jiangsu Province, China
| | - Long-Jiang Shao
- Department of General Surgery, The Affiliated Suzhou Science & Technology Town Hospital of Nanjing Medcial University, Jiangsu Province, China
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15
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Moroz‐Omori EV, Huang D, Kumar Bedi R, Cheriyamkunnel SJ, Bochenkova E, Dolbois A, Rzeczkowski MD, Li Y, Wiedmer L, Caflisch A. METTL3 Inhibitors for Epitranscriptomic Modulation of Cellular Processes. ChemMedChem 2021; 16:3035-3043. [PMID: 34237194 PMCID: PMC8518639 DOI: 10.1002/cmdc.202100291] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/29/2021] [Indexed: 12/31/2022]
Abstract
The methylase METTL3 is the writer enzyme of the N6 -methyladenosine (m6 A) modification of RNA. Using a structure-based drug discovery approach, we identified a METTL3 inhibitor with potency in a biochemical assay of 280 nM, while its enantiomer is 100 times less active. We observed a dose-dependent reduction in the m6 A methylation level of mRNA in several cell lines treated with the inhibitor already after 16 h of treatment, which lasted for at least 6 days. Importantly, the prolonged incubation (up to 6 days) with the METTL3 inhibitor did not alter levels of other RNA modifications (i. e., m1 A, m6 Am , m7 G), suggesting selectivity of the developed compound towards other RNA methyltransferases.
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Affiliation(s)
- Elena V. Moroz‐Omori
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | - Danzhi Huang
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | - Rajiv Kumar Bedi
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | | | - Elena Bochenkova
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | - Aymeric Dolbois
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | - Maciej D. Rzeczkowski
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | - Yaozong Li
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | - Lars Wiedmer
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
| | - Amedeo Caflisch
- Department of BiochemistryUniversity of ZurichWinterthurerstrasse 1908057ZurichSwitzerland
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16
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Koumpoura CL, Robert A, Athanassopoulos CM, Baltas M. Antimalarial Inhibitors Targeting Epigenetics or Mitochondria in Plasmodium falciparum: Recent Survey upon Synthesis and Biological Evaluation of Potential Drugs against Malaria. Molecules 2021; 26:molecules26185711. [PMID: 34577183 PMCID: PMC8467436 DOI: 10.3390/molecules26185711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 12/01/2022] Open
Abstract
Despite many efforts, malaria remains among the most problematic infectious diseases worldwide, mainly due to the development of drug resistance by P. falciparum. Over the past decade, new essential pathways have been emerged to fight against malaria. Among them, epigenetic processes and mitochondrial metabolism appear to be important targets. This review will focus on recent evolutions concerning worldwide efforts to conceive, synthesize and evaluate new drug candidates interfering selectively and efficiently with these two targets and pathways. The focus will be on compounds/scaffolds that possess biological/pharmacophoric properties on DNA methyltransferases and HDAC’s for epigenetics, and on cytochrome bc1 and dihydroorotate dehydrogenase for mitochondrion.
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Affiliation(s)
- Christina L. Koumpoura
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France; (C.L.K.); (A.R.)
| | - Anne Robert
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France; (C.L.K.); (A.R.)
| | | | - Michel Baltas
- CNRS, LCC (Laboratoire de Chimie de Coordination), Université de Toulouse, UPS, INPT, Inserm ERL 1289, 205 Route de Narbonne, BP 44099, CEDEX 4, F-31077 Toulouse, France; (C.L.K.); (A.R.)
- Correspondence:
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17
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Secilmis S, Sinan Dal M, Kizil Cakar M, Merdin A, Ahu Baysal N, Altuntas F. Combination of Venetoclax and hypomethylating agents in relapsed/refractory acute myeloid leukemia: A case series from a single center. J BUON 2021; 26:2026-2032. [PMID: 34761613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
PURPOSE Venetoclax (VEN) is an oral selective inhibitor of antiapoptotic protein B-cell leukemia/lymphoma-2 (BCL-2). METHODS We report 7 relapsed/refractory (R/R) acute myeloid leukemia (AML) patients treated with venetoclax and hypomethylating agents (HMA). RESULTS More than half of the patients could go on with venetoclax for only a few months. CONCLUSION Using venetoclax combined with HMA in R/R AML should be kept in mind as an alternative salvage option.
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Affiliation(s)
- Sema Secilmis
- Hematology Clinic and Bone Marrow Transplantation Unit, University of Health Sciences Ankara Dr. Abdurrahman Yurtaslan Oncology Education and Research Hospital, Ankara, Turkey
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18
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Newman JA, Douangamath A, Yadzani S, Yosaatmadja Y, Aimon A, Brandão-Neto J, Dunnett L, Gorrie-Stone T, Skyner R, Fearon D, Schapira M, von Delft F, Gileadi O. Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Nat Commun 2021; 12:4848. [PMID: 34381037 DOI: 10.1101/2021.03.15.435326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/28/2021] [Indexed: 05/25/2023] Open
Abstract
There is currently a lack of effective drugs to treat people infected with SARS-CoV-2, the cause of the global COVID-19 pandemic. The SARS-CoV-2 Non-structural protein 13 (NSP13) has been identified as a target for anti-virals due to its high sequence conservation and essential role in viral replication. Structural analysis reveals two "druggable" pockets on NSP13 that are among the most conserved sites in the entire SARS-CoV-2 proteome. Here we present crystal structures of SARS-CoV-2 NSP13 solved in the APO form and in the presence of both phosphate and a non-hydrolysable ATP analog. Comparisons of these structures reveal details of conformational changes that provide insights into the helicase mechanism and possible modes of inhibition. To identify starting points for drug development we have performed a crystallographic fragment screen against NSP13. The screen reveals 65 fragment hits across 52 datasets opening the way to structure guided development of novel antiviral agents.
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Affiliation(s)
- Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, Oxford, UK.
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Setayesh Yadzani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | | | - Antony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - José Brandão-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Tyler Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Rachael Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Opher Gileadi
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
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19
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Newman JA, Douangamath A, Yadzani S, Yosaatmadja Y, Aimon A, Brandão-Neto J, Dunnett L, Gorrie-Stone T, Skyner R, Fearon D, Schapira M, von Delft F, Gileadi O. Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Nat Commun 2021; 12:4848. [PMID: 34381037 PMCID: PMC8358061 DOI: 10.1038/s41467-021-25166-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022] Open
Abstract
There is currently a lack of effective drugs to treat people infected with SARS-CoV-2, the cause of the global COVID-19 pandemic. The SARS-CoV-2 Non-structural protein 13 (NSP13) has been identified as a target for anti-virals due to its high sequence conservation and essential role in viral replication. Structural analysis reveals two "druggable" pockets on NSP13 that are among the most conserved sites in the entire SARS-CoV-2 proteome. Here we present crystal structures of SARS-CoV-2 NSP13 solved in the APO form and in the presence of both phosphate and a non-hydrolysable ATP analog. Comparisons of these structures reveal details of conformational changes that provide insights into the helicase mechanism and possible modes of inhibition. To identify starting points for drug development we have performed a crystallographic fragment screen against NSP13. The screen reveals 65 fragment hits across 52 datasets opening the way to structure guided development of novel antiviral agents.
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Affiliation(s)
- Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, Oxford, UK.
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Setayesh Yadzani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | | | - Antony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - José Brandão-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Tyler Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Rachael Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Opher Gileadi
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
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20
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Chen S, Lu XT, He TT, Yishake D, Tan XY, Hou MJ, Luo Y, Long JA, Tang ZH, Zhong RH, Fang AP, Zhu HL. Betaine Delayed Muscle Loss by Attenuating Samtor Complex Inhibition for mTORC1 Signaling Via Increasing SAM Level. Mol Nutr Food Res 2021; 65:e2100157. [PMID: 34061446 DOI: 10.1002/mnfr.202100157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/29/2021] [Indexed: 01/26/2023]
Abstract
SCOPE The muscle loss during aging results from the blunt of protein synthesis and poses threat to the elderly health. This study aims to investigate whether betaine affects muscle loss by improving protein synthesis. METHODS AND RESULTS Male C57BL/6J mice are raised from age 12 or 15 months. Mice are fed with AIN-93M diet without or with 2% w/v betaine in distilled water as control group or betaine intervention group (Bet), respectively. Betaine supplementation to mice demonstrates better body composition, grip strength, and motor function. Muscle morphology upregulates expression of myogenic regulate factors, and elevates myosin heavy chain and also improves in Bet group. Betaine promotes muscle protein synthesis via tethering mammalian target of rapamycin complex1 protein kinase (mTORC1) on the lysosomal membrane thereby activating mTORC1 signaling. All these effects aforementioned are time-dependent (p < 0.05). Ultrahigh-performance liquid chromatography results show that betaine increases S-adenosyl-l-methionine (SAM) via methionine cycle. SAM sensor-Samtor-overexpression in C2C12 cells could displace mTORC1 from lysosome thereby inhibiting the mTORC1 signaling. Addition of betaine attenuates this inhibition by increasing SAM level and then disrupting interaction of Samtor complex. CONCLUSIONS These observations indicate that betaine could promisingly promote protein synthesis to delay age-related muscle loss.
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Affiliation(s)
- Si Chen
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Xiao-Ting Lu
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Tong-Tong He
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Dinuerguli Yishake
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Xu-Yin Tan
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Meng-Jun Hou
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Yun Luo
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Jing-An Long
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Zhi-Hong Tang
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Rong-Huan Zhong
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Ai-Ping Fang
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
| | - Hui-Lian Zhu
- Department of Nutrition, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangzhou, 510080, China
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21
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Basu S, Mak T, Ulferts R, Wu M, Deegan T, Fujisawa R, Tan KW, Lim CT, Basier C, Canal B, Curran JF, Drury LS, McClure AW, Roberts EL, Weissmann F, Zeisner TU, Beale R, Cowling VH, Howell M, Labib K, Diffley JFX. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of Nsp14 RNA cap methyltransferase. Biochem J 2021; 478:2481-2497. [PMID: 34198328 PMCID: PMC8286817 DOI: 10.1042/bcj20210219] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022]
Abstract
The COVID-19 pandemic has presented itself as one of the most critical public health challenges of the century, with SARS-CoV-2 being the third member of the Coronaviridae family to cause a fatal disease in humans. There is currently only one antiviral compound, remdesivir, that can be used for the treatment of COVID-19. To identify additional potential therapeutics, we investigated the enzymatic proteins encoded in the SARS-CoV-2 genome. In this study, we focussed on the viral RNA cap methyltransferases, which play key roles in enabling viral protein translation and facilitating viral escape from the immune system. We expressed and purified both the guanine-N7 methyltransferase nsp14, and the nsp16 2'-O-methyltransferase with its activating cofactor, nsp10. We performed an in vitro high-throughput screen for inhibitors of nsp14 using a custom compound library of over 5000 pharmaceutical compounds that have previously been characterised in either clinical or basic research. We identified four compounds as potential inhibitors of nsp14, all of which also showed antiviral capacity in a cell-based model of SARS-CoV-2 infection. Three of the four compounds also exhibited synergistic effects on viral replication with remdesivir.
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Affiliation(s)
- Souradeep Basu
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Tiffany Mak
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Mary Wu
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Tom Deegan
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Kang Wei Tan
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Chew Theng Lim
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Clovis Basier
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Berta Canal
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Joseph F Curran
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Lucy S Drury
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Allison W McClure
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Emma L Roberts
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Florian Weissmann
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Theresa U Zeisner
- Cell Cycle Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Victoria H Cowling
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Michael Howell
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Karim Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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22
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Burgess HM, Depledge DP, Thompson L, Srinivas KP, Grande RC, Vink EI, Abebe JS, Blackaby WP, Hendrick A, Albertella MR, Kouzarides T, Stapleford KA, Wilson AC, Mohr I. Targeting the m 6A RNA modification pathway blocks SARS-CoV-2 and HCoV-OC43 replication. Genes Dev 2021; 35:1005-1019. [PMID: 34168039 PMCID: PMC8247602 DOI: 10.1101/gad.348320.121] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 11/24/2022]
Abstract
N6-methyladenosine (m6A) is an abundant internal RNA modification, influencing transcript fate and function in uninfected and virus-infected cells. Installation of m6A by the nuclear RNA methyltransferase METTL3 occurs cotranscriptionally; however, the genomes of some cytoplasmic RNA viruses are also m6A-modified. How the cellular m6A modification machinery impacts coronavirus replication, which occurs exclusively in the cytoplasm, is unknown. Here we show that replication of SARS-CoV-2, the agent responsible for the COVID-19 pandemic, and a seasonal human β-coronavirus HCoV-OC43, can be suppressed by depletion of METTL3 or cytoplasmic m6A reader proteins YTHDF1 and YTHDF3 and by a highly specific small molecule METTL3 inhibitor. Reduction of infectious titer correlates with decreased synthesis of viral RNAs and the essential nucleocapsid (N) protein. Sites of m6A modification on genomic and subgenomic RNAs of both viruses were mapped by methylated RNA immunoprecipitation sequencing (meRIP-seq). Levels of host factors involved in m6A installation, removal, and recognition were unchanged by HCoV-OC43 infection; however, nuclear localization of METTL3 and cytoplasmic m6A readers YTHDF1 and YTHDF2 increased. This establishes that coronavirus RNAs are m6A-modified and host m6A pathway components control β-coronavirus replication. Moreover, it illustrates the therapeutic potential of targeting the m6A pathway to restrict coronavirus reproduction.
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Affiliation(s)
- Hannah M Burgess
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, New York 10016, USA
| | - Letitia Thompson
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | | | - Rebecca C Grande
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Elizabeth I Vink
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Jonathan S Abebe
- Department of Medicine, New York University School of Medicine, New York, New York 10016, USA
| | | | - Alan Hendrick
- Storm Therapeutics Ltd, Cambridge CB22 3AT, United Kingdom
| | | | - Tony Kouzarides
- The Gurdon Institute, Department of Pathology, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Kenneth A Stapleford
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Angus C Wilson
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
| | - Ian Mohr
- Department of Microbiology, New York University School of Medicine, New York, New York 10016, USA
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23
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Garbo S, Zwergel C, Battistelli C. m6A RNA methylation and beyond - The epigenetic machinery and potential treatment options. Drug Discov Today 2021; 26:2559-2574. [PMID: 34126238 DOI: 10.1016/j.drudis.2021.06.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 05/02/2021] [Accepted: 06/08/2021] [Indexed: 12/14/2022]
Abstract
m6A is emerging as one of the most important RNA modifications because of its involvement in pathological and physiological events. Here, we provide an overview of this epitranscriptomic modification, beginning with a description of the molecular players involved and continuing with a focus on the role of m6A in the maintenance of stemness, induction of the epithelial to mesenchymal transition (EMT), and tumor progression. Finally, we discuss the state of the art regarding the design and validation of inhibitors of m6A writers or erasers to provide a background for future investigations and for the development of specific therapeutics.
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Affiliation(s)
- Sabrina Garbo
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Department of Excellence 2018-2022, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy; Oncohaematology Department, IRCCS Ospedale Pediatrico Bambino Gesù, Viale di San Paolo 15, 00146 Rome, Italy
| | - Clemens Zwergel
- Department of Drug Chemistry and Technologies, Department of Excellence 2018-2022, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Cecilia Battistelli
- Istituto Pasteur Italia, Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Department of Excellence 2018-2022, Sapienza University of Rome, Viale Regina Elena 324, 00161 Rome, Italy.
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24
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Yankova E, Blackaby W, Albertella M, Rak J, De Braekeleer E, Tsagkogeorga G, Pilka ES, Aspris D, Leggate D, Hendrick AG, Webster NA, Andrews B, Fosbeary R, Guest P, Irigoyen N, Eleftheriou M, Gozdecka M, Dias JML, Bannister AJ, Vick B, Jeremias I, Vassiliou GS, Rausch O, Tzelepis K, Kouzarides T. Small-molecule inhibition of METTL3 as a strategy against myeloid leukaemia. Nature 2021; 593:597-601. [PMID: 33902106 PMCID: PMC7613134 DOI: 10.1038/s41586-021-03536-w] [Citation(s) in RCA: 473] [Impact Index Per Article: 157.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/12/2021] [Indexed: 12/22/2022]
Abstract
N6-methyladenosine (m6A) is an abundant internal RNA modification1,2 that is catalysed predominantly by the METTL3-METTL14 methyltransferase complex3,4. The m6A methyltransferase METTL3 has been linked to the initiation and maintenance of acute myeloid leukaemia (AML), but the potential of therapeutic applications targeting this enzyme remains unknown5-7. Here we present the identification and characterization of STM2457, a highly potent and selective first-in-class catalytic inhibitor of METTL3, and a crystal structure of STM2457 in complex with METTL3-METTL14. Treatment of tumours with STM2457 leads to reduced AML growth and an increase in differentiation and apoptosis. These cellular effects are accompanied by selective reduction of m6A levels on known leukaemogenic mRNAs and a decrease in their expression consistent with a translational defect. We demonstrate that pharmacological inhibition of METTL3 in vivo leads to impaired engraftment and prolonged survival in various mouse models of AML, specifically targeting key stem cell subpopulations of AML. Collectively, these results reveal the inhibition of METTL3 as a potential therapeutic strategy against AML, and provide proof of concept that the targeting of RNA-modifying enzymes represents a promising avenue for anticancer therapy.
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Affiliation(s)
- Eliza Yankova
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- Storm Therapeutics Ltd, Cambridge, UK
| | | | | | - Justyna Rak
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Etienne De Braekeleer
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Georgia Tsagkogeorga
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
- Storm Therapeutics Ltd, Cambridge, UK
| | | | - Demetrios Aspris
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- The Center for the Study of Hematological Malignancies/Karaiskakio Foundation, Nicosia, Cyprus
| | | | | | | | | | | | | | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Maria Eleftheriou
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK
| | - Malgorzata Gozdecka
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Joao M L Dias
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge, UK
| | - Andrew J Bannister
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - Binje Vick
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- German Consortium for Translational Cancer Research (DKTK), Munich, Germany
| | - Irmela Jeremias
- Research Unit Apoptosis in Hematopoietic Stem Cells, Helmholtz Zentrum München, German Research Center for Environmental Health (HMGU), Munich, Germany
- German Consortium for Translational Cancer Research (DKTK), Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig Maximilians University München, Munich, Germany
| | - George S Vassiliou
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- The Center for the Study of Hematological Malignancies/Karaiskakio Foundation, Nicosia, Cyprus
| | | | - Konstantinos Tzelepis
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
- Haematological Cancer Genetics, Wellcome Trust Sanger Institute, Cambridge, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Tony Kouzarides
- Milner Therapeutics Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
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25
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Song Y, Kamstra JH, Cao Y, Asselman J, Anglès d'Auriac M, Friberg N. High-throughput analyses and Bayesian network modeling highlight novel epigenetic Adverse Outcome Pathway networks of DNA methyltransferase inhibitor mediated transgenerational effects. J Hazard Mater 2021; 408:124490. [PMID: 33199140 DOI: 10.1016/j.jhazmat.2020.124490] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/26/2020] [Accepted: 11/03/2020] [Indexed: 06/11/2023]
Abstract
A number of epigenetic modulating chemicals are known to affect multiple generations of a population from a single ancestral exposure, thus posing transgenerational hazards. The present study aimed to establish a high-throughput (HT) analytical workflow for cost-efficient concentration-response analysis of epigenetic and phenotypic effects, and to support the development of novel Adverse Outcome Pathway (AOP) networks for DNA methyltransferase (DNMT) inhibitor-mediated transgenerational effects on aquatic organisms. The model DNMT inhibitor 5-azacytidine (5AC) and the model freshwater crustacean Daphnia magna were used to generate new experimental data and served as prototypes to construct AOPs for aquatic organisms. Targeted HT bioassays (DNMT ELISA, MS-HRM and qPCR) in combination with multigenerational ecotoxicity tests revealed concentration-dependent transgenerational (F0-F3) effects of 5AC on total DNMT activity, DNA promoter methylation, gene body methylation, gene transcription and reproduction. Top sensitive toxicity pathways related to 5AC exposure, such as apoptosis and DNA damage responses were identified in both F0 and F3 using Gaussian Bayesian network modeling. Two novel epigenetic AOP networks on DNMT inhibitor mediated one-generational and transgenerational effects were developed for aquatic organisms and assessed for the weight of evidence. The new HT analytical workflow and AOPs can facilitate future ecological hazard assessment of epigenetic modulating chemicals.
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Affiliation(s)
- You Song
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo, Norway.
| | - Jorke H Kamstra
- Institute for Risk Assessment Sciences (IRAS), Utrecht University, PO Box 80177, NL-3508 TD Utrecht, The Netherlands
| | - Yang Cao
- Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | - Jana Asselman
- Blue Growth Research Lab, Ghent University, Bluebridge building, Ostend Science Park 1, 8400 Ostend, Belgium
| | - Marc Anglès d'Auriac
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo, Norway
| | - Nikolai Friberg
- Norwegian Institute for Water Research (NIVA), Gaustadalléen 21, NO-0349 Oslo, Norway; University of Copenhagen, Freshwater Biological Section, Universitetsparken 4, 3rd floor, 2100 Copenhagen, Denmark; University of Leeds, water@leeds, School of Geography, Leeds LS2 9JT UK
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26
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Ahmad S, Waheed Y, Ismail S, Bhatti S, Abbasi SW, Muhammad K. Structure-Based Virtual Screening Identifies Multiple Stable Binding Sites at the RecA Domains of SARS-CoV-2 Helicase Enzyme. Molecules 2021; 26:1446. [PMID: 33800013 PMCID: PMC7962107 DOI: 10.3390/molecules26051446] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023] Open
Abstract
With the emergence and global spread of the COVID-19 pandemic, the scientific community worldwide has focused on search for new therapeutic strategies against this disease. One such critical approach is targeting proteins such as helicases that regulate most of the SARS-CoV-2 RNA metabolism. The purpose of the current study was to predict a library of phytochemicals derived from diverse plant families with high binding affinity to SARS-CoV-2 helicase (Nsp13) enzyme. High throughput virtual screening of the Medicinal Plant Database for Drug Design (MPD3) database was performed on SARS-CoV-2 helicase using AutoDock Vina. Nilotinib, with a docking value of -9.6 kcal/mol, was chosen as a reference molecule. A compound (PubChem CID: 110143421, ZINC database ID: ZINC257223845, eMolecules: 43290531) was screened as the best binder (binding energy of -10.2 kcal/mol on average) to the enzyme by using repeated docking runs in the screening process. On inspection, the compound was disclosed to show different binding sites of the triangular pockets collectively formed by Rec1A, Rec2A, and 1B domains and a stalk domain at the base. The molecule is often bound to the ATP binding site (referred to as binding site 2) of the helicase enzyme. The compound was further discovered to fulfill drug-likeness and lead-likeness criteria, have good physicochemical and pharmacokinetics properties, and to be non-toxic. Molecular dynamic simulation analysis of the control/lead compound complexes demonstrated the formation of stable complexes with good intermolecular binding affinity. Lastly, affirmation of the docking simulation studies was accomplished by estimating the binding free energy by MMPB/GBSA technique. Taken together, these findings present further in silco investigation of plant-derived lead compounds to effectively address COVID-19.
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Affiliation(s)
- Sajjad Ahmad
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan; (S.A.); (S.I.)
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan; (S.A.); (S.I.)
| | - Saba Ismail
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan; (S.A.); (S.I.)
| | - Saadia Bhatti
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 44000, Pakistan;
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, The Mall, Rawalpindi 46000, Pakistan;
| | - Khalid Muhammad
- Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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Harro CM, Perez-Sanz J, Costich TL, Payne KK, Anadon CM, Chaurio RA, Biswas S, Mandal G, Rigolizzo KE, Sprenger KB, Mine JA, Showe LC, Yu X, Liu K, Rodriguez PC, Pinilla-Ibarz J, Sokol L, Conejo-Garcia JR. Methyltransferase inhibitors restore SATB1 protective activity against cutaneous T cell lymphoma in mice. J Clin Invest 2021; 131:135711. [PMID: 33270606 PMCID: PMC7843215 DOI: 10.1172/jci135711] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 11/25/2020] [Indexed: 12/27/2022] Open
Abstract
Cutaneous T cell lymphoma (CTCL) has a poorly understood etiology and no known cure. Using conditional knockout mice, we found that ablation of the genomic organizer special AT-rich sequence-binding protein 1 (Satb1) caused malignant transformation of mature, skin-homing, Notch-activated CD4+ and CD8+ T cells into progressively fatal lymphoma. Mechanistically, Satb1 restrained Stat5 phosphorylation and the expression of skin-homing chemokine receptors in mature T cells. Notably, methyltransferase-dependent epigenetic repression of SATB1 was universally found in human Sézary syndrome, but not in other peripheral T cell malignancies. H3K27 and H3K9 trimethylation occluded the SATB1 promoter in Sézary cells, while inhibition of SUV39H1/2 methyltransferases (unlike EZH2 inhibition) restored protective SATB1 expression and selectively abrogated the growth of primary Sézary cells more effectively than romidepsin. Therefore, inhibition of methyltransferases that silence SATB1 could address an unmet need for patients with mycosis fungoides/Sézary syndrome, a set of incurable diseases.
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Affiliation(s)
- Carly M. Harro
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
- Department of Cell Biology, Microbiology, and Molecular Biology, and
- Cancer Biology PhD Program, College of Arts and Sciences, University of South Florida, Tampa, Florida, and H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Jairo Perez-Sanz
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Tara Lee Costich
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Kyle K. Payne
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Carmen M. Anadon
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Ricardo A. Chaurio
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Subir Biswas
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Gunjan Mandal
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Kristen E. Rigolizzo
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Kimberly B. Sprenger
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Jessica A. Mine
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Louise C. Showe
- Molecular & Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Xiaoqing Yu
- Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia, USA
| | - Paulo C. Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | | | | | - Jose R. Conejo-Garcia
- Department of Immunology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
- Department of Gynecologic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
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28
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Wang L, Song C, Wang N, Li S, Liu Q, Sun Z, Wang K, Yu SC, Yang Q. NADP modulates RNA m 6A methylation and adipogenesis via enhancing FTO activity. Nat Chem Biol 2020; 16:1394-1402. [PMID: 32719557 DOI: 10.1038/s41589-020-0601-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/11/2020] [Accepted: 06/24/2020] [Indexed: 12/28/2022]
Abstract
Metabolism is often regulated by the transcription and translation of RNA. In turn, it is likely that some metabolites regulate enzymes controlling reversible RNA modification, such as N6-methyladenosine (m6A), to modulate RNA. This hypothesis is at least partially supported by the findings that multiple metabolic diseases are highly associated with fat mass and obesity-associated protein (FTO), an m6A demethylase. However, knowledge about whether and which metabolites directly regulate m6A remains elusive. Here, we show that NADP directly binds FTO, independently increases FTO activity, and promotes RNA m6A demethylation and adipogenesis. We screened a set of metabolites using a fluorescence quenching assay and NADP was identified to remarkably bind FTO. In vitro demethylation assays indicated that NADP enhances FTO activity. Furthermore, NADP regulated mRNA m6A via FTO in vivo, and deletion of FTO blocked NADP-enhanced adipogenesis in 3T3-L1 preadipocytes. These results build a direct link between metabolism and RNA m6A demethylation.
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MESH Headings
- 3T3-L1 Cells
- Adenosine/analogs & derivatives
- Adenosine/metabolism
- Adipocytes/cytology
- Adipocytes/drug effects
- Adipocytes/enzymology
- Adipogenesis/drug effects
- Adipogenesis/genetics
- AlkB Homolog 5, RNA Demethylase/antagonists & inhibitors
- AlkB Homolog 5, RNA Demethylase/genetics
- AlkB Homolog 5, RNA Demethylase/metabolism
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics
- Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolism
- Animals
- Binding Sites
- Cell Differentiation/drug effects
- Demethylation
- Enzyme Assays
- Gene Deletion
- Gene Expression Regulation
- HEK293 Cells
- High-Throughput Screening Assays
- Humans
- Kinetics
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/genetics
- Methyltransferases/metabolism
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- NADP/metabolism
- NADP/pharmacology
- Protein Binding
- Protein Structure, Secondary
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
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Affiliation(s)
- Lina Wang
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, Liaoning, China
| | - Chengli Song
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, Liaoning, China
| | - Na Wang
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, Liaoning, China
| | - Songyu Li
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, Liaoning, China
| | - Qiaoling Liu
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, Liaoning, China
| | - Zhen Sun
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, Liaoning, China
| | - Kai Wang
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, Liaoning, China
| | - Shi-Cang Yu
- Department of Stem Cell and Regenerative Medicine, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China.
| | - Qingkai Yang
- Institute of Cancer Stem Cell, DaLian Medical University, Dalian, Liaoning, China.
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Ugurel OM, Mutlu O, Sariyer E, Kocer S, Ugurel E, Inci TG, Ata O, Turgut-Balik D. Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). Int J Biol Macromol 2020; 163:1687-1696. [PMID: 32980406 PMCID: PMC7513821 DOI: 10.1016/j.ijbiomac.2020.09.138] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 has caused COVID-19 outbreak with nearly 2 M infected people and over 100K death worldwide, until middle of April 2020. There is no confirmed drug for the treatment of COVID-19 yet. As the disease spread fast and threaten human life, repositioning of FDA approved drugs may provide fast options for treatment. In this aspect, structure-based drug design could be applied as a powerful approach in distinguishing the viral drug target regions from the host. Evaluation of variations in SARS-CoV-2 genome may ease finding specific drug targets in the viral genome. In this study, 3458 SARS-CoV-2 genome sequences isolated from all around the world were analyzed. Incidence of C17747T and A17858G mutations were observed to be much higher than others and they were on Nsp13, a vital enzyme of SARS-CoV-2. Effect of these mutations was evaluated on protein-drug interactions using in silico methods. The most potent drugs were found to interact with the key and neighbor residues of the active site responsible from ATP hydrolysis. As result, cangrelor, fludarabine, folic acid and polydatin were determined to be the most potent drugs which have potency to inhibit both the wild type and mutant SARS-CoV-2 helicase. Clinical data supporting these findings would be important towards overcoming COVID-19.
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Affiliation(s)
- Osman Mutluhan Ugurel
- Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa Campus, 34210 Esenler, Istanbul, Turkey; Altinbas University, School of Engineering and Natural Science, Department of Basic Science, 34217 Bagcilar, Istanbul, Turkey
| | - Ozal Mutlu
- Marmara University, Faculty of Arts and Sciences, Department of Biology, Goztepe Campus, 34722 Kadikoy, Istanbul, Turkey
| | - Emrah Sariyer
- Artvin Coruh University, Vocational School of Health Services, Medical Laboratory Techniques, Artvin, Turkey
| | - Sinem Kocer
- Istanbul Yeni Yuzyil University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, 34010 Cevizlibag, Istanbul, Turkey
| | - Erennur Ugurel
- Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa Campus, 34210 Esenler, Istanbul, Turkey
| | - Tugba Gul Inci
- Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa Campus, 34210 Esenler, Istanbul, Turkey
| | - Oguz Ata
- Altinbas University, School of Engineering and Natural Science, Department of Software Engineering, 34217 Bagcilar, Istanbul, Turkey
| | - Dilek Turgut-Balik
- Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa Campus, 34210 Esenler, Istanbul, Turkey.
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30
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Yan W, Guo Y, Xu F, Saxena D, Li X. Identification of Differentially Methylated Regions Associated with a Knockout of SUV39H1 in Prostate Cancer Cells. Genes (Basel) 2020; 11:genes11101188. [PMID: 33066102 PMCID: PMC7601968 DOI: 10.3390/genes11101188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/29/2020] [Accepted: 10/09/2020] [Indexed: 12/11/2022] Open
Abstract
Epigenetic alterations, such as histone methylations, affect the pathogenesis of tumors including prostate cancer (PCa). Previously, we reported that metformin reduced SUV39H1, a histone methyltransferase of H3 Lys9, to inhibit the migration of PCa cells. Since histone methylation is functionally linked to DNA methylation, we speculate that the knockout of the SUV39H1 gene will affect the genomic DNA methylation profile to regulate PCa cell migration and invasion. The genome-wide DNA methylation level is lower in SUV39H1 knockout (KO) cells than wild-type (WT) ones. However, the methylation levels in functional regions of CpG Islands (CGI), 5' untranslated region (UTR5), and exon regions are higher in KO cells than WT cells. Analysis of differentially methylated regions (DMRs) identified 1241 DMR genes that have differential methylation on CG sites when comparing the KO and WT samples. Gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes Pathways analysis showed that knockout of SUV39H1 affects gene sets and pathways that are heavily involved in cell shapes, cell recognition, adhesion, motility, and migration. Our study suggests that SUV39H1 plays an important role in PCa migration via the epigenetic regulation of methylation on CG sites, and is a novel and legitimate target to inhibit PCa cell migration.
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Affiliation(s)
- Wenbo Yan
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; (W.Y.); (Y.G.); (F.X.); (D.S.)
| | - Yuqi Guo
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; (W.Y.); (Y.G.); (F.X.); (D.S.)
| | - Fangxi Xu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; (W.Y.); (Y.G.); (F.X.); (D.S.)
| | - Deepak Saxena
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; (W.Y.); (Y.G.); (F.X.); (D.S.)
| | - Xin Li
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY 10010, USA; (W.Y.); (Y.G.); (F.X.); (D.S.)
- Perlmutter Cancer Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Urology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Correspondence: ; Tel.: +1-2129927009; Fax: +1-2129984087
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31
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Wu H, Xu Z, Wang Z, Ren Z, Li L, Ruan Y. Exosomes from dendritic cells with Mettl3 gene knockdown prevent immune rejection in a mouse cardiac allograft model. Immunogenetics 2020; 72:423-430. [PMID: 33009922 DOI: 10.1007/s00251-020-01180-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
We have previously demonstrated that Mettl3-silencing dendritic cells (DCs) exhibited immature properties and prolonged allograft survival in a murine heart transplantation model. Exosomes derived from donor DCs (Dex) are involved in the immune rejection of organ transplantation, and blocking Dex transfer may suppress immune rejection. Herein, this study aimed to investigate whether Mettl3 knockdown inhibits the secretion and activity of donor Dex, thereby inhibiting donor Dex-mediated immune rejection. The imDex, mDex, shCtrl-mDex, and shMettl3-mDex were obtained from the culture supernatant of DCs (immature DCs, mature DCs, shCtrl-infected mature DCs, shMettl3-infected mature DCs) derived from donor BALB/c mouse bone marrow and then co-cultured with splenic T cell lymphocyte suspension from recipient C57BL/6 mice in vitro or injected into recipient C57BL/6 mice before the cardiac transplantation. Donor shMettl3-mDex expressed lower concentration of exosomes and lower expression of Mettl3, Dex markers (ICAM-1, MHC-I, MHC-II), as well as lower ability to activate T cell immune response than shCtrl-mDex. Administration of donor shMettl3-mDex attenuated immune rejection after mouse heart transplantation and prolonged the allograft survival. In summary, Mettl3 knockdown inhibits the immune rejection of Dex in a mouse cardiac allograft model.
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Affiliation(s)
- Hongbing Wu
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University; Hubei Cardiovascular Medicine Clinical Research Center & Hubei Key Laboratory of Cardiology, 238# Jiefang Road, Wuchang District, Hubei Province, Wuhan, China
| | - Zhaojia Xu
- Department of Critical Care Medicine, Jin Yin-tan Hospital, 1# Yin-Tan Road, Dongxihu District, Hubei Province, Wuhan, China
| | - Zhiwei Wang
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University; Hubei Cardiovascular Medicine Clinical Research Center & Hubei Key Laboratory of Cardiology, 238# Jiefang Road, Wuchang District, Hubei Province, Wuhan, China.
| | - Zongli Ren
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University; Hubei Cardiovascular Medicine Clinical Research Center & Hubei Key Laboratory of Cardiology, 238# Jiefang Road, Wuchang District, Hubei Province, Wuhan, China
| | - Luocheng Li
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University; Hubei Cardiovascular Medicine Clinical Research Center & Hubei Key Laboratory of Cardiology, 238# Jiefang Road, Wuchang District, Hubei Province, Wuhan, China
| | - Yongle Ruan
- Department of Cardiovascular Surgery, Renmin Hospital of Wuhan University; Hubei Cardiovascular Medicine Clinical Research Center & Hubei Key Laboratory of Cardiology, 238# Jiefang Road, Wuchang District, Hubei Province, Wuhan, China
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32
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Rosas-Lemus M, Minasov G, Shuvalova L, Inniss NL, Kiryukhina O, Brunzelle J, Satchell KJF. High-resolution structures of the SARS-CoV-2 2'- O-methyltransferase reveal strategies for structure-based inhibitor design. Sci Signal 2020; 13:eabe1202. [PMID: 32994211 PMCID: PMC8028745 DOI: 10.1126/scisignal.abe1202] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
There are currently no antiviral therapies specific for SARS-CoV-2, the virus responsible for the global pandemic disease COVID-19. To facilitate structure-based drug design, we conducted an x-ray crystallographic study of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase complex, which methylates Cap-0 viral mRNAs to improve viral protein translation and to avoid host immune detection. We determined the structures for nsp16-nsp10 heterodimers bound to the methyl donor S-adenosylmethionine (SAM), the reaction product S-adenosylhomocysteine (SAH), or the SAH analog sinefungin (SFG). We also solved structures for nsp16-nsp10 in complex with the methylated Cap-0 analog m7GpppA and either SAM or SAH. Comparative analyses between these structures and published structures for nsp16 from other betacoronaviruses revealed flexible loops in open and closed conformations at the m7GpppA-binding pocket. Bound sulfates in several of the structures suggested the location of the ribonucleic acid backbone phosphates in the ribonucleotide-binding groove. Additional nucleotide-binding sites were found on the face of the protein opposite the active site. These various sites and the conserved dimer interface could be exploited for the development of antiviral inhibitors.
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Affiliation(s)
- Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ludmilla Shuvalova
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Nicole L Inniss
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Olga Kiryukhina
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Joseph Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL 60439, USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA.
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
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33
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An M, Wang H, Zhu Y. Mutations in m6A consensus motifs are suppressed in the m6A modified genes in human cancer cells. PLoS One 2020; 15:e0236882. [PMID: 32790688 PMCID: PMC7425885 DOI: 10.1371/journal.pone.0236882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/15/2020] [Indexed: 01/22/2023] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent type of RNA modification. METTL3 in the methyltransferase complex is the core enzyme responsible for methylation. METTL3 selectively catalyzes the adenosines centered in the RRAC motif. Functional studies established that m6A could enhance the translation efficiency (TE) of modified genes by recruiting reader protein YTHDF1 and other initiation factors. We downloaded the m6A peaks in HeLa cells from a previous study and defined the m6A modified genes and sites. Ancestral mutations in the genic region fixed in the HeLa cell samples were defined using their mRNA-Seq data and the alignment between human and mouse genomes. Furthermore, in the small interfering (si)-METTL3 sample, the calculated TE foldchange of all genes was compared to that in the negative control. The TE of m6A genes was globally down-regulated in si-METTL3 versus control compared to the non-m6A genes. In m6A modified genes, RRAC motif mutations were suppressed compared to mutations in non-motif regions or non-m6A genes. Among the m6A genes, a fraction RRAC motif mutations negatively correlated with the TE foldchange (si-METTL3 versus control). The TE of m6A modified genes was enhanced in HeLa cells. RRAC motif mutations could potentially prevent methylation of adenosines and consequently abolish the enhanced translation. Such mutations in the RRAC motif might be deleterious. Accordingly, we observed lower fractions of mutations in RRAC motifs than in other regions. This prevention of mutations in the RRAC motif could be a strategy adopted by cancer cells to maintain the elevated translation of particular genes.
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Affiliation(s)
- Mingzi An
- Department of Gynaecology, Chengyang People's Hospital, Qingdao, Shandong, China
| | - Huiyun Wang
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yingqian Zhu
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
- * E-mail:
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Dong G, Yasgar A, Peterson DL, Zakharov A, Talley D, Cheng KCC, Jadhav A, Simeonov A, Huang R. Optimization of High-Throughput Methyltransferase Assays for the Discovery of Small Molecule Inhibitors. ACS Comb Sci 2020; 22:422-432. [PMID: 32525297 PMCID: PMC7429283 DOI: 10.1021/acscombsci.0c00077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Methyltransferases (MTases) play diverse roles in cellular processes. Aberrant methylation levels have been implicated in many diseases, indicating the need for the identification and development of small molecule inhibitors for each MTase. Specific inhibitors can serve as probes to investigate the function and validate therapeutic potential for the respective MTase. High-throughput screening (HTS) is a powerful method to identify initial hits for further optimization. Here, we report the development of a fluorescence-based MTase assay and compare this format with the recently developed MTase-Glo luminescence assay for application in HTS. Using protein N-terminal methyltransferase 1 (NTMT1) as a model system, we miniaturized to 1536-well quantitative HTS format. Through a pilot screen of 1428 pharmacologically active compounds and subsequent validation, we discovered that MTase-Glo produced lower false positive rates than the fluorescence-based MTase assay. Nevertheless, both assays displayed robust performance along with low reagent requirements and can potentially be employed as general HTS formats for the discovery of inhibitors for any MTase.
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Affiliation(s)
- Guangping Dong
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Adam Yasgar
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Darrell L. Peterson
- Department of Biochemistry, Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
| | - Alexey Zakharov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Daniel Talley
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Ken Chih-Chien Cheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Medicinal Chemistry, Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23219, United States
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35
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Paço A, de Bessa Garcia SA, Freitas R. Methylation in HOX Clusters and Its Applications in Cancer Therapy. Cells 2020; 9:cells9071613. [PMID: 32635388 PMCID: PMC7408435 DOI: 10.3390/cells9071613] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 02/08/2023] Open
Abstract
HOX genes are commonly known for their role in embryonic development, defining the positional identity of most structures along the anterior–posterior axis. In postembryonic life, HOX gene aberrant expression can affect several processes involved in tumorigenesis such as proliferation, apoptosis, migration and invasion. Epigenetic modifications are implicated in gene expression deregulation, and it is accepted that methylation events affecting HOX gene expression play crucial roles in tumorigenesis. In fact, specific methylation profiles in the HOX gene sequence or in HOX-associated histones are recognized as potential biomarkers in several cancers, helping in the prediction of disease outcomes and adding information for decisions regarding the patient’s treatment. The methylation of some HOX genes can be associated with chemotherapy resistance, and its identification may suggest the use of other treatment options. The use of epigenetic drugs affecting generalized or specific DNA methylation profiles, an approach that now deserves much attention, seems likely to be a promising weapon in cancer therapy in the near future. In this review, we summarize these topics, focusing particularly on how the regulation of epigenetic processes may be used in cancer therapy.
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Affiliation(s)
- Ana Paço
- Centre Bio: Bioindustries, Biorefineries and Bioproducts, BLC3 Association—Technology and Innovation Campus, 3405-169 Oliveira do Hospital, Portugal;
| | | | - Renata Freitas
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal;
- ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Correspondence:
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Abstract
G-Quadruplexes (G4s) are non-canonical secondary structures formed within guanine-rich regions of DNA or RNA. G4 sequences/structures have been detected in human and in viral genomes, including Coronaviruses Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and SARS-CoV-2. Here, we outline the existing evidence indicating that G4 ligands and inhibitors of SARS-CoV-2 helicase may exert some antiviral activity reducing viral replication and can represent a potential therapeutic approach to tackle the COVID-19 pandemic due to SARS-CoV-2 infection. We also discuss how repositioning of FDA-approved drugs against helicase activity of other viruses, could represent a rapid strategy to limit deaths associated with COVID-19 pandemic.
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Affiliation(s)
- Nadia Panera
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, 4, Piazza Sant'Onofrio, 00165, Rome, Italy
| | - Alberto Eugenio Tozzi
- Multifactorial Disease and Complex Phenotype Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Anna Alisi
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, 4, Piazza Sant'Onofrio, 00165, Rome, Italy.
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37
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Ahmed-Belkacem R, Sutto-Ortiz P, Guiraud M, Canard B, Vasseur JJ, Decroly E, Debart F. Synthesis of adenine dinucleosides SAM analogs as specific inhibitors of SARS-CoV nsp14 RNA cap guanine-N7-methyltransferase. Eur J Med Chem 2020; 201:112557. [PMID: 32563813 PMCID: PMC7291971 DOI: 10.1016/j.ejmech.2020.112557] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/26/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022]
Abstract
The spreading of new viruses is known to provoke global human health threat. The current COVID-19 pandemic caused by the recently emerged coronavirus SARS-CoV-2 is one significant and unfortunate example of what the world will have to face in the future with emerging viruses in absence of appropriate treatment. The discovery of potent and specific antiviral inhibitors and/or vaccines to fight these massive outbreaks is an urgent research priority. Enzymes involved in the capping pathway of viruses and more specifically RNA N7- or 2′O-methyltransferases (MTases) are now admitted as potential targets for antiviral chemotherapy. We designed bisubstrate inhibitors by mimicking the transition state of the 2′-O-methylation of the cap RNA in order to block viral 2′-O MTases. This work resulted in the synthesis of 16 adenine dinucleosides with both adenosines connected by various nitrogen-containing linkers. Unexpectedly, all the bisubstrate compounds were barely active against 2′-O MTases of several flaviviruses or SARS-CoV but surprisingly, seven of them showed efficient and specific inhibition against SARS-CoV N7-MTase (nsp14) in the micromolar to submicromolar range. The most active nsp14 inhibitor identified is as potent as but particularly more specific than the broad-spectrum MTase inhibitor, sinefungin. Molecular docking suggests that the inhibitor binds to a pocket formed by the S-adenosyl methionine (SAM) and cap RNA binding sites, conserved among SARS-CoV nsp14. These dinucleoside SAM analogs will serve as starting points for the development of next inhibitors for SARS-CoV-2 nsp14 N7-MTase.
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Affiliation(s)
| | - Priscila Sutto-Ortiz
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | - Mathis Guiraud
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France
| | - Bruno Canard
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France
| | | | - Etienne Decroly
- AFMB, CNRS, Aix-Marseille University, UMR 7257, 163 Avenue de Luminy, Marseille, France.
| | - Françoise Debart
- IBMM, CNRS, University of Montpellier, ENSCM, Montpellier, France.
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38
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Wang Z, Hausmann S, Lyu R, Li TM, Lofgren SM, Flores NM, Fuentes ME, Caporicci M, Yang Z, Meiners MJ, Cheek MA, Howard SA, Zhang L, Elias JE, Kim MP, Maitra A, Wang H, Bassik MC, Keogh MC, Sage J, Gozani O, Mazur PK. SETD5-Coordinated Chromatin Reprogramming Regulates Adaptive Resistance to Targeted Pancreatic Cancer Therapy. Cancer Cell 2020; 37:834-849.e13. [PMID: 32442403 PMCID: PMC8187079 DOI: 10.1016/j.ccell.2020.04.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/11/2020] [Accepted: 04/22/2020] [Indexed: 12/18/2022]
Abstract
Molecular mechanisms underlying adaptive targeted therapy resistance in pancreatic ductal adenocarcinoma (PDAC) are poorly understood. Here, we identify SETD5 as a major driver of PDAC resistance to MEK1/2 inhibition (MEKi). SETD5 is induced by MEKi resistance and its deletion restores refractory PDAC vulnerability to MEKi therapy in mouse models and patient-derived xenografts. SETD5 lacks histone methyltransferase activity but scaffolds a co-repressor complex, including HDAC3 and G9a. Gene silencing by the SETD5 complex regulates known drug resistance pathways to reprogram cellular responses to MEKi. Pharmacological co-targeting of MEK1/2, HDAC3, and G9a sustains PDAC tumor growth inhibition in vivo. Our work uncovers SETD5 as a key mediator of acquired MEKi therapy resistance in PDAC and suggests a context for advancing MEKi use in the clinic.
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Affiliation(s)
- Zhentian Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Simone Hausmann
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruitu Lyu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Tie-Mei Li
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Shane M Lofgren
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Natasha M Flores
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mary E Fuentes
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marcello Caporicci
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ze Yang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | | | | | - Michael P Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anirban Maitra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huamin Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Cory Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Julien Sage
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Pawel K Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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39
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Bedi RK, Huang D, Eberle SA, Wiedmer L, Śledź P, Caflisch A. Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer. ChemMedChem 2020; 15:744-748. [PMID: 32159918 DOI: 10.1002/cmdc.202000011] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/28/2020] [Indexed: 12/14/2022]
Abstract
The RNA methylase METTL3 catalyzes the transfer of a methyl group from the cofactor S-adenosyl-L-methionine (SAM) to the N6 atom of adenine. We have screened a library of 4000 analogues and derivatives of the adenosine moiety of SAM by high-throughput docking into METTL3. Two series of adenine derivatives were identified in silico, and the binding mode of six of the predicted inhibitors was validated by protein crystallography. Two compounds, one for each series, show good ligand efficiency. We propose a route for their further development into potent and selective inhibitors of METTL3.
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Affiliation(s)
- Rajiv K Bedi
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Danzhi Huang
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Stefanie A Eberle
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
- Current address: Department of Biomedical Sciences Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, 2200, Copenhagen, Denmark
| | - Lars Wiedmer
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Pawel Śledź
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
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40
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Spizzichino S, Mattedi G, Lauder K, Valle C, Aouadi W, Canard B, Decroly E, Kaptein SJF, Neyts J, Graham C, Sule Z, Barlow DJ, Silvestri R, Castagnolo D. Design, Synthesis and Discovery of N,N'-Carbazoyl-aryl-urea Inhibitors of Zika NS5 Methyltransferase and Virus Replication. ChemMedChem 2020; 15:385-390. [PMID: 31805205 PMCID: PMC7106487 DOI: 10.1002/cmdc.201900533] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/05/2019] [Indexed: 12/18/2022]
Abstract
The recent outbreaks of Zika virus (ZIKV) infection worldwide make the discovery of novel antivirals against flaviviruses a research priority. This work describes the identification of novel inhibitors of ZIKV through a structure-based virtual screening approach using the ZIKV NS5-MTase. A novel series of molecules with a carbazoyl-aryl-urea structure has been discovered and a library of analogues has been synthesized. The new compounds inhibit ZIKV MTase with IC50 between 23-48 μM. In addition, carbazoyl-aryl-ureas also proved to inhibit ZIKV replication activity at micromolar concentration.
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Affiliation(s)
- Sharon Spizzichino
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
- Department of Drug Chemistry and TechnologiesSapienza University of RomeLaboratory Affiliated to Instituto Pasteur Italia – Fondazione Cenci BolognettiPiazzale Aldo Moro 500185RomaItaly
| | - Giulio Mattedi
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - Kate Lauder
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - Coralie Valle
- AFMB, CNRSAix-Marseille University UMR 7257, Case 925163 Avenue de Luminy13288Marseille Cedex 09France
| | - Wahiba Aouadi
- AFMB, CNRSAix-Marseille University UMR 7257, Case 925163 Avenue de Luminy13288Marseille Cedex 09France
| | - Bruno Canard
- AFMB, CNRSAix-Marseille University UMR 7257, Case 925163 Avenue de Luminy13288Marseille Cedex 09France
| | - Etienne Decroly
- AFMB, CNRSAix-Marseille University UMR 7257, Case 925163 Avenue de Luminy13288Marseille Cedex 09France
| | - Suzanne J. F. Kaptein
- Department of Microbiology, Immunology and Transplantation Rega Institute for Medical Research Laboratory of Virology and ChemotherapyKU LeuvenMinderbroedersstraat 103000LeuvenBelgium
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation Rega Institute for Medical Research Laboratory of Virology and ChemotherapyKU LeuvenMinderbroedersstraat 103000LeuvenBelgium
| | - Carl Graham
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - Zakary Sule
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - David J. Barlow
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
| | - Romano Silvestri
- Department of Drug Chemistry and TechnologiesSapienza University of RomeLaboratory Affiliated to Instituto Pasteur Italia – Fondazione Cenci BolognettiPiazzale Aldo Moro 500185RomaItaly
| | - Daniele Castagnolo
- School of Cancer and Pharmaceutical SciencesKing's College LondonLondonSE1 9NHUK
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Wang Q, Zheng J, Zou JX, Xu J, Han F, Xiang S, Liu P, Chen HW, Wang J. S-adenosylhomocysteine (AdoHcy)-dependent methyltransferase inhibitor DZNep overcomes breast cancer tamoxifen resistance via induction of NSD2 degradation and suppression of NSD2-driven redox homeostasis. Chem Biol Interact 2020; 317:108965. [PMID: 32001260 DOI: 10.1016/j.cbi.2020.108965] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 02/05/2023]
Abstract
Endocrine therapies (e.g. tamoxifen and aromatase inhibitors) targeting estrogen action are effective in decreasing mortality of breast cancer. However, their efficacy is limited by intrinsic and acquired resistance. Our previous study demonstrated that overexpression of a histone methyltransferase NSD2 drives tamoxifen resistance in breast cancer cells and that NSD2 is a potential biomarker of tamoxifen resistant breast cancer. Here, we found that DZNep, an indirect inhibitor of histone methyltransferases, potently induces the degradation of NSD2 protein and inhibits the expression of NSD2 target genes (HK2, G6PD, GLUT1 and TIGAR) involved in the pentose phosphate pathway (PPP). DZNep treatment of tamoxifen-resistant breast cancer cells and xenograft tumors also strongly inhibits tumor growth and the cancer cell survival through decreasing cell production of NADPH and glutathione (GSH) and invoking elevated ROS to cause apoptosis. These findings suggest that DZNep-like agents can be developed to target NSD2 histone methyltransferase for effective treatment of tamoxifen-resistant breast cancer.
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Affiliation(s)
- Qianqian Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, PR China
| | - Jianwei Zheng
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, PR China
| | - June X Zou
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Sacramento, CA, USA; Comprehensive Cancer Center, University of California, Davis, Sacramento, CA, USA
| | - Jianzhen Xu
- Shantou University Medical College, No. 22 Xinling Road, Shantou, China
| | - Fanghai Han
- Department of Gastrointestinal Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120, PR China
| | - Songtao Xiang
- Department of Urology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510120, PR China
| | - Peiqing Liu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, PR China; National-Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, Guangdong, 510006, PR China
| | - Hong-Wu Chen
- Department of Biochemistry and Molecular Medicine, University of California, Davis, School of Medicine, Sacramento, CA, USA; Comprehensive Cancer Center, University of California, Davis, Sacramento, CA, USA.
| | - Junjian Wang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510006, PR China; National-Local Joint Engineering Laboratory of Druggability and New Drugs Evaluation, Sun Yat-sen University, Guangzhou, Guangdong, 510006, PR China.
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42
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Jaiwal A, Natarajaswamy K, Venkat Rajam M. RNA silencing of hormonal biosynthetic genes impairs larval growth and development in cotton bollworm, Helicoverpa armigera. J Biosci 2020; 45:109. [PMID: 32975236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The cotton bollworm, Helicoverpa armigera, is a highly polyphagous pest, causing enormous losses to various economically important crops. The identification and in vitro functional validation of target genes of a pest is a prerequisite to combat pest via host-mediated RNA interference (RNAi). In the present study, six hormonal biosynthesis genes of H. armigera were chosen and evaluated by feeding insect larvae with dsRNAs corresponding to each target gene, viz., juvenile hormone acid methyltransferase (HaJHAMT), prothoracicotropic hormone (HaPTTH), pheromone biosynthesis-activating peptide (HaPBAP), molt regulating transcription factor (HaHR3), activated protein 4 (HaAP-4) and eclosion hormone precursor (HaEHP). The loss of function phenotypes for these hormonal genes were observed by releasing second instar larvae on to artificial diet containing target gene-specific dsRNAs. Ingestion of dsRNAs resulted in mortality ranging from 60% to 90%, reduced larval weight, phenotypic deformities and delayed pupation. The quantitative real-time PCR (qRT-PCR) analysis showed that the target gene transcript levels were decreased drastically (31% to 77%) as compared to control or unrelated control (GFP-dsRNA), and correlated well with the mortality and developmental defects of larvae. Also, a comparison of the silencing efficacy of un-diced long HaPTTH -dsRNAwith RNase III diced HaPTTH-dsRNA (siRNAs) revealed that long dsRNAs were more efficient in silencing the target gene. These results indicated that the hormonal biosynthesis genes have varied sensitivity towards RNAi and could be the vital targets for insect resistance in crop plants like cotton which are infested by H. armigera.
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Affiliation(s)
- Anjali Jaiwal
- Department of Genetics, University of Delhi - South Campus, Benito Juarez Road, New Delhi 110021, India
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43
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Ferreira de Freitas R, Ivanochko D, Schapira M. Methyltransferase Inhibitors: Competing with, or Exploiting the Bound Cofactor. Molecules 2019; 24:E4492. [PMID: 31817960 PMCID: PMC6943651 DOI: 10.3390/molecules24244492] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/11/2022] Open
Abstract
Protein methyltransferases (PMTs) are enzymes involved in epigenetic mechanisms, DNA repair, and other cellular machineries critical to cellular identity and function, and are an important target class in chemical biology and drug discovery. Central to the enzymatic reaction is the transfer of a methyl group from the cofactor S-adenosylmethionine (SAM) to a substrate protein. Here we review how the essentiality of SAM for catalysis is exploited by chemical inhibitors. Occupying the cofactor binding pocket to compete with SAM can be hindered by the hydrophilic nature of this site, but structural studies of compounds now in the clinic revealed that inhibitors could either occupy juxtaposed pockets to overlap minimally, but sufficiently with the bound cofactor, or induce large conformational remodeling leading to a more druggable binding site. Rather than competing with the cofactor, other inhibitors compete with the substrate and rely on bound SAM, either to allosterically stabilize the substrate binding site, or for direct SAM-inhibitor interactions.
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Affiliation(s)
- Renato Ferreira de Freitas
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Rua Arcturus 3, São Bernardo do Campo, SP 09606-070, Brazil
| | - Danton Ivanochko
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON M5G 1L7, Canada
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 2M9, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, MaRS Centre, South Tower, 101 College St., Suite 700, Toronto, ON M5G 1L7, Canada
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
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44
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Myoung J, Lee JY, Min KS. Methyltransferase of a cell culture-adapted hepatitis E inhibits the MDA5 receptor signaling pathway. J Microbiol 2019; 57:1126-1131. [PMID: 31758397 PMCID: PMC7090864 DOI: 10.1007/s12275-019-9478-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 12/14/2022]
Abstract
Hepatitis E virus (HEV) is a causative agent of acute hepatitis and jaundice. The number of human infections is approximated to be over 20 million cases per year. The transmission is mainly via the fecal-oral route and contaminated water and food are considered to be a major source of infection. As a mouse model is not available, a recent development of a cell culture-adapted HEV strain (47832c) is considered as a very important tools for molecular analysis of HEV pathogenesis in cells. Previously, we demonstrated that HEV-encoded methyltransferase (MeT) encoded by the 47832c strain inhibits MDA5- and RIG-I-mediated activation of interferon β (IFN-β) promoter. Here, we report that MeT impairs the phosphorylation and activation of interferon regulatory factor 3 and the p65 subunit of NF-κB in a dose-dependent manner. In addition, the MeT encoded by the 47832c, but not that of HEV clinical or field isolates (SAR-55, Mex-14, KC-1, and ZJ-1), displays the inhibitory effect. A deeper understanding of MeTmediated suppression of IFN-β expression would provide basis of the cell culture adaptation of HEV.
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Affiliation(s)
- Jinjong Myoung
- Korea Zoonosis Research Institute, Genetic Engineering Research Institute and Department of Bioactive Material Science, Jeonbuk National University, Jeonju, 54896, Republic of Korea.
| | - Jeong Yoon Lee
- Korea Zoonosis Research Institute, Genetic Engineering Research Institute and Department of Bioactive Material Science, Jeonbuk National University, Jeonju, 54896, Republic of Korea
| | - Kang Sang Min
- Korea Zoonosis Research Institute, Genetic Engineering Research Institute and Department of Bioactive Material Science, Jeonbuk National University, Jeonju, 54896, Republic of Korea
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45
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Barve A, Vega A, Shah PP, Ghare S, Casson L, Wunderlich M, Siskind LJ, Beverly LJ. Perturbation of Methionine/S-adenosylmethionine Metabolism as a Novel Vulnerability in MLL Rearranged Leukemia. Cells 2019; 8:cells8111322. [PMID: 31717699 PMCID: PMC6912509 DOI: 10.3390/cells8111322] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022] Open
Abstract
Leukemias bearing mixed lineage leukemia (MLL) rearrangement (MLL-R) resulting in expression of oncogenic MLL fusion proteins (MLL-FPs) represent an especially aggressive disease subtype with the worst overall prognoses and chemotherapeutic response. MLL-R leukemias are uniquely dependent on the epigenetic function of the H3K79 methyltransferase DOT1L, which is misdirected by MLL-FPs activating gene expression, driving transformation and leukemogenesis. Given the functional necessity of these leukemias to maintain adequate methylation potential allowing aberrant activating histone methylation to proceed, driving leukemic gene expression, we investigated perturbation of methionine (Met)/S-adenosylmethionine (SAM) metabolism as a novel therapeutic paradigm for MLL-R leukemia. Disruption of Met/SAM metabolism, by either methionine deprivation or pharmacologic inhibition of downstream metabolism, reduced overall cellular methylation potential, reduced relative cell numbers, and induced apoptosis selectively in established MLL-AF4 cell lines or MLL-AF6-expressing patient blasts but not in BCR-ABL-driven K562 cells. Global histone methylation dynamics were altered, with a profound loss of requisite H3K79 methylation, indicating inhibition of DOT1L function. Relative occupancy of the repressive H3K27me3 modification was increased at the DOT1L promoter in MLL-R cells, and DOT1L mRNA and protein expression was reduced. Finally, pharmacologic inhibition of Met/SAM metabolism significantly prolonged survival in an advanced, clinically relevant patient–derived MLL-R leukemia xenograft model, in combination with cytotoxic induction chemotherapy. Our findings provide support for further investigation into the development of highly specific allosteric inhibitors of enzymatic mediators of Met/SAM metabolism or dietary manipulation of methionine levels. Such inhibitors may lead to enhanced treatment outcomes for MLL-R leukemia, along with cytotoxic chemotherapy or DOT1L inhibitors.
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Affiliation(s)
- Aditya Barve
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA; (A.B.); (L.J.S.)
| | - Alexis Vega
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY 40202, USA;
| | - Parag P. Shah
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA;
| | - Smita Ghare
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (S.G.); (L.C.)
| | - Lavona Casson
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (S.G.); (L.C.)
| | - Mark Wunderlich
- Department of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
| | - Leah J. Siskind
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA; (A.B.); (L.J.S.)
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA;
| | - Levi J. Beverly
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40202, USA; (A.B.); (L.J.S.)
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA;
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA; (S.G.); (L.C.)
- Correspondence: ; Tel.: +01-502-852-8968
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Gaillard SL, Zahurak M, Sharma A, Reiss KA, Sartorius-Mergenthaler S, Downs M, Anders NM, Ahuja N, Rudek MA, Azad N. A phase 1 trial of the oral DNA methyltransferase inhibitor CC-486 and the histone deacetylase inhibitor romidepsin in advanced solid tumors. Cancer 2019; 125:2837-2845. [PMID: 31012962 PMCID: PMC6663621 DOI: 10.1002/cncr.32138] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND Epigenetic abnormalities are manifold in all solid tumors and include changes in chromatin configuration and DNA methylation. The authors designed a phase 1 study to evaluate the oral DNA methyltransferase inhibitor CC-486 combined with the histone deacetylase inhibitor romidepsin in advanced solid tumors with dose expansion to further evaluate pharmacodynamics and possible clinical benefit of the recommended phase 2 dose (RP2D). METHODS This was a phase 1 study with a 3 + 3 dose-escalation design and an expansion phase for patients with virally mediated cancers. The disease control rate (DCR) was the primary outcome for the expansion cohort. Correlative studies included long interspersed nucleotide element 1 (LINE-1) methylation and drug exposure in blood samples (clinicaltrials.gov identifier NCT01537744). RESULTS Fourteen patients were enrolled in the dose-escalation portion at 3 dose levels. Three patients experienced dose-limiting toxicities; the RP2D was oral CC-486 300 mg daily on days 1 through 14 and romidepsin 8 mg/m2 on days 8 and 15. Because of slow accrual into the expansion phase, the trial was closed after 4 patients enrolled. Common toxicities of the combination included nausea (83.3%), anorexia (72.2%), fatigue (61.1%), and constipation (55.6%). There were 12 patients evaluable for response, 5 with stable disease, of whom 2 received >4 cycles; there were no responses. Exposure to CC-486 and romidepsin was consistent with prior data. LINE-1 methylation on C1D8 was significantly reduced (mean, -6.23; 95% CI, -12.23, -0.24; P = .04). CONCLUSIONS Although, at the RP2D, the combination of CC-486 and romidepsin was tolerable, no significant anticancer activity was observed. Significant demethylation in post-treatment circulating tumor DNA and biopsies provided proof of target acquisition.
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Affiliation(s)
- Stéphanie L. Gaillard
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Gynecology and Obstetrics Division of Gynecologic Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Marianna Zahurak
- Department of Oncology Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD
| | - Anup Sharma
- Department of Surgery Division of Surgical Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Kim A. Reiss
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | | | - Melinda Downs
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Nicole M. Anders
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Nita Ahuja
- Department of Surgery Division of Surgical Oncology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Michelle A. Rudek
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Medicine Division of Clinical Pharmacology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Nilofer Azad
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD
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Oerum S, Catala M, Atdjian C, Brachet F, Ponchon L, Barraud P, Iannazzo L, Droogmans L, Braud E, Ethève-Quelquejeu M, Tisné C. Bisubstrate analogues as structural tools to investigate m 6A methyltransferase active sites. RNA Biol 2019; 16:798-808. [PMID: 30879411 PMCID: PMC6546350 DOI: 10.1080/15476286.2019.1589360] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/24/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022] Open
Abstract
RNA methyltransferases (MTases) catalyse the transfer of a methyl group to their RNA substrates using most-often S-adenosyl-L-methionine (SAM) as cofactor. Only few RNA-bound MTases structures are currently available due to the difficulties in crystallising RNA:protein complexes. The lack of complex structures results in poorly understood RNA recognition patterns and methylation reaction mechanisms. On the contrary, many cofactor-bound MTase structures are available, resulting in well-understood protein:cofactor recognition, that can guide the design of bisubstrate analogues that mimic the state at which both the substrate and the cofactor is bound. Such bisubstrate analogues were recently synthesized for proteins monomethylating the N6-atom of adenine (m6A). These proteins include, amongst others, RlmJ in E. coli and METLL3:METT14 and METTL16 in human. As a proof-of-concept, we here test the ability of the bisubstrate analogues to mimic the substrate:cofactor bound state during catalysis by studying their binding to RlmJ using differential scanning fluorimetry, isothermal titration calorimetry and X-ray crystallography. We find that the methylated adenine base binds in the correct pocket, and thus these analogues could potentially be used broadly to study the RNA recognition and catalytic mechanism of m6A MTases. Two bisubstrate analogues bind RlmJ with micro-molar affinity, and could serve as starting scaffolds for inhibitor design against m6A RNA MTases. The same analogues cause changes in the melting temperature of the m1A RNA MTase, TrmK, indicating non-selective protein:compound complex formation. Thus, optimization of these molecular scaffolds for m6A RNA MTase inhibition should aim to increase selectivity, as well as affinity.
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Affiliation(s)
- Stephanie Oerum
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Marjorie Catala
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Franck Brachet
- Institut de Biologie Physico-Chimique, IBPC, CNRS, Paris, France
| | - Luc Ponchon
- Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris, France
| | - Pierre Barraud
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Louis Droogmans
- Laboratoire de Microbiologie, Université libre de Bruxelles (ULB), Gosselies, Belgium
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS, Université Paris Descartes, Paris, France
| | - Carine Tisné
- Laboratoire d’Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS, Université Paris Diderot, Paris, France
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48
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Lu C, Yang D, Klement JD, Oh IK, Savage NM, Waller JL, Colby AH, Grinstaff MW, Oberlies NH, Pearce CJ, Xie Z, Kulp SK, Coss CC, Phelps MA, Albers T, Lebedyeva IO, Liu K. SUV39H1 Represses the Expression of Cytotoxic T-Lymphocyte Effector Genes to Promote Colon Tumor Immune Evasion. Cancer Immunol Res 2019; 7:414-427. [PMID: 30610059 DOI: 10.1158/2326-6066.cir-18-0126] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 08/07/2018] [Accepted: 12/18/2018] [Indexed: 01/23/2023]
Abstract
Despite the presence of CTLs in the tumor microenvironment, the majority of immunogenic human colon cancer does not respond to immune checkpoint inhibitor immunotherapy, and microsatellite instable (MSI) tumors are not naturally eliminated. The molecular mechanism underlying the inactivity of tumor-infiltrating CTLs is unknown. We report here that CTLs were present in both MSI and microsatellite stable colon tumors. The expression of the H3K9me3-specific histone methyltransferase SUV39H1 was significantly elevated in human colon carcinoma compared with normal colon tissues. Using a mouse colon carcinoma model, we further determined that tumor-infiltrating CTLs in the colon tumor microenvironment have high expression of SUV39H1. To target SUV39H1 in the tumor microenvironment, a virtual chemical library was screened on the basis of the SET (suppressor of variegation 3-9, enhancer of zeste and trithorax) domain structure of the human SUV39H1 protein. Functional enzymatic activity assays identified a small molecule that inhibits SUV39H1 enzymatic activity. On the basis of the structure of this small molecule, we modified it and chemically synthesized a small molecule, termed F5446, which has an EC50 of 0.496 μmol/L for SUV39H1 enzymatic activity. H3K9me3 was enriched in the promoters of GZMB, PRF1, FASLG, and IFNG in quiescent T cells. F5446 inhibited H3K9me3, thereby upregulating expression of these effectors in tumor-infiltrating CTLs and suppressing colon carcinoma growth in a CD8+ CTL-dependent manner in vivo Our data indicate that SUV39H1 represses CTL effector gene expression and, in doing so, confers colon cancer immune escape.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Cell Line, Tumor
- Colonic Neoplasms/drug therapy
- Colonic Neoplasms/immunology
- Colonic Neoplasms/metabolism
- Disease Models, Animal
- Enzyme Inhibitors/pharmacology
- Enzyme Inhibitors/therapeutic use
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/immunology
- Histones/metabolism
- Humans
- Lymphocytes, Tumor-Infiltrating/drug effects
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Methyltransferases/antagonists & inhibitors
- Methyltransferases/immunology
- Methyltransferases/metabolism
- Mice
- Repressor Proteins/antagonists & inhibitors
- Repressor Proteins/immunology
- Repressor Proteins/metabolism
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
- Tumor Escape
- Tumor Microenvironment/drug effects
- Tumor Microenvironment/immunology
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Affiliation(s)
- Chunwan Lu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia.
- Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia
- Charlie Norwood VA Medical Center, Augusta, Georgia
| | - Dafeng Yang
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia
- Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia
- Charlie Norwood VA Medical Center, Augusta, Georgia
| | - John D Klement
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia
- Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia
- Charlie Norwood VA Medical Center, Augusta, Georgia
| | - Il Kyu Oh
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia
| | - Natasha M Savage
- Department of Pathology, Medical College of Georgia, Augusta, Georgia
| | - Jennifer L Waller
- Department of Population Health Sciences, Medical College of Georgia, Augusta, Georgia
| | - Aaron H Colby
- Ionic Pharmaceuticals, Brookline, Massachusetts
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Mark W Grinstaff
- Ionic Pharmaceuticals, Brookline, Massachusetts
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, North Carolina
| | | | - Zhiliang Xie
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Samuel K Kulp
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Christopher C Coss
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Mitch A Phelps
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Thomas Albers
- Department of Chemistry and Physics, Augusta University, Augusta, Georgia
| | - Iryna O Lebedyeva
- Department of Chemistry and Physics, Augusta University, Augusta, Georgia
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta, Georgia.
- Georgia Cancer Center, Medical College of Georgia, Augusta, Georgia
- Charlie Norwood VA Medical Center, Augusta, Georgia
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49
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Ruang-Rit K, Park Y. Endocrine system in supernumerary molting of the flour beetle, Tribolium freemani, under crowded conditions. Insect Biochem Mol Biol 2018; 101:76-84. [PMID: 30149057 DOI: 10.1016/j.ibmb.2018.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/17/2018] [Accepted: 08/21/2018] [Indexed: 06/08/2023]
Abstract
In the flour beetle, Tribolium freemani, a crowded environment in the last larval instar delays the development into a pupa, but the beetle continues to engage in larval-larval molting, which is an adaptive response to avoid being the victim of cannibalism as an immobile pupa. To understand the endocrine mechanism involved in this developmental process, we investigated the components of the juvenile hormone and ecdysone signaling systems. We examined whether elevated juvenile hormone levels in the crowded condition is the sole causal factor for the supernumerary molting. RNA interference (RNAi) of the JH acid methyltransferase (TfMT3) for lowering juvenile hormone titer in the crowded condition could not rescue pupation and instead resulted in lethality with developmental arrest at the prepupal stage. Kruppel-homolog 1 (TfKr-h1), the immediate downstream JH signal, was highly upregulated even in the RNAi of TfMT3 in a crowded condition. RNAi of TfKr-h1 resulted in a phenocopy of the lethal TfMT3 RNAi in a crowded condition. In addition, RNAi of TfMT3 in a crowded condition resulted in lack of the major ecdysone peak in the prepupal stage. We conclude that while a crowded condition induces supernumerary molts by elevating juvenile hormone levels, it can also inhibit metamorphosis by disrupting additional endocrine processes. The current study suggests that crowded conditions affect multiple independent factors in the endocrine and the downstream signaling systems.
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Affiliation(s)
- Krissana Ruang-Rit
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, United States
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, United States.
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50
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Zhou W, Debnath A, Jennings G, Hahn HJ, Vanderloop BH, Chaudhuri M, Nes WD, Podust LM. Enzymatic chokepoints and synergistic drug targets in the sterol biosynthesis pathway of Naegleria fowleri. PLoS Pathog 2018; 14:e1007245. [PMID: 30212566 PMCID: PMC6136796 DOI: 10.1371/journal.ppat.1007245] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/27/2018] [Indexed: 11/29/2022] Open
Abstract
Naegleria fowleri is a free-living amoeba that can also act as an opportunistic pathogen causing severe brain infection, primary amebic meningoencephalitis (PAM), in humans. The high mortality rate of PAM (exceeding 97%) is attributed to (i) delayed diagnosis, (ii) lack of safe and effective anti-N. fowleri drugs, and (iii) difficulty of delivering drugs to the brain. Our work addresses identification of new molecular targets that may link anti-Naegleria drug discovery to the existing pharmacopeia of brain-penetrant drugs. Using inhibitors with known mechanism of action as molecular probes, we mapped the sterol biosynthesis pathway of N. fowleri by GC-MS analysis of metabolites. Based on this analysis, we chemically validated two enzymes downstream to CYP51, sterol C24-methyltransferase (SMT, ERG6) and sterol Δ8-Δ7 -isomerase (ERG2), as potential therapeutic drug targets in N. fowleri. The sterol biosynthetic cascade in N. fowleri displayed a mixture of canonical features peculiar to different domains of life: lower eukaryotes, plants and vertebrates. In addition to the cycloartenol→ergosterol biosynthetic route, a route leading to de novo cholesterol biosynthesis emerged. Isotopic labeling of the de novo-synthesized sterols by feeding N. gruberi trophozoites on the U13C-glucose-containing growth medium identified an exogenous origin of cholesterol, while 7-dehydrocholesterol (7DHC) had enriched 13C-content, suggesting a dual origin of this metabolite both from de novo biosynthesis and metabolism of scavenged cholesterol. Sterol homeostasis in Naegleria may be orchestrated over the course of its life-cycle by a "switch" between ergosterol and cholesterol biosynthesis. By demonstrating the growth inhibition and synergistic effects of the sterol biosynthesis inhibitors, we validated new, potentially druggable, molecular targets in N. fowleri. The similarity of the Naegleria sterol Δ8-Δ7 -isomerase to the human non-opioid σ1 receptor, implicated in human CNS conditions such as addiction, amnesia, pain and depression, provides an incentive to assess structurally diverse small-molecule brain-penetrant drugs targeting the human receptor for anti-Naegleria activity.
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Affiliation(s)
- Wenxu Zhou
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Anjan Debnath
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Gareth Jennings
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Hye Jee Hahn
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Boden H. Vanderloop
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Minu Chaudhuri
- Department of Microbiology and Immunology, Meharry Medical College, Nashville, Tennessee, United States of America
| | - W. David Nes
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas, United States of America
| | - Larissa M. Podust
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
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