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Kudo G, Hirao T, Harada R, Hirokawa T, Shigeta Y, Yoshino R. Prediction of the binding mechanism of a selective DNA methyltransferase 3A inhibitor by molecular simulation. Sci Rep 2024; 14:13508. [PMID: 38866895 PMCID: PMC11169543 DOI: 10.1038/s41598-024-64236-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
DNA methylation is an epigenetic mechanism that introduces a methyl group at the C5 position of cytosine. This reaction is catalyzed by DNA methyltransferases (DNMTs) and is essential for the regulation of gene transcription. The DNMT1 and DNMT3A or -3B family proteins are known targets for the inhibition of DNA hypermethylation in cancer cells. A selective non-nucleoside DNMT3A inhibitor was developed that mimics S-adenosyl-l-methionine and deoxycytidine; however, the mechanism of selectivity is unclear because the inhibitor-protein complex structure determination is absent. Therefore, we performed docking and molecular dynamics simulations to predict the structure of the complex formed by the association between DNMT3A and the selective inhibitor. Our simulations, binding free energy decomposition analysis, structural isoform comparison, and residue scanning showed that Arg688 of DNMT3A is involved in the interaction with this inhibitor, as evidenced by its significant contribution to the binding free energy. The presence of Asn1192 at the corresponding residues in DNMT1 results in a loss of affinity for the inhibitor, suggesting that the interactions mediated by Arg688 in DNMT3A are essential for selectivity. Our findings can be applied in the design of DNMT-selective inhibitors and methylation-specific drug optimization procedures.
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Affiliation(s)
- Genki Kudo
- Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
| | - Takumi Hirao
- Doctoral Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8575, Japan
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yasuteru Shigeta
- Physics Department, Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8571, Japan
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Ryunosuke Yoshino
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
- Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
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Ying H, Zhang B, Cao G, Wang Y, Zhang X. Role for ubiquitin-specific protease 7 (USP7) in the treatment and the immune response to hepatocellular carcinoma: potential mechanisms. Transl Cancer Res 2023; 12:3016-3033. [PMID: 38130306 PMCID: PMC10731377 DOI: 10.21037/tcr-23-153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/19/2023] [Indexed: 12/23/2023]
Abstract
Background Ubiquitin-specific protease 7 (USP7) is a deubiquitinating enzyme that can affect or regulate a variety of cellular activities. The purpose of this study was to investigate therapeutic and immunologic effects of USP7 in hepatocellular carcinoma (HCC), and as well to evaluate potential mechanisms of action. Methods USP7-related gene expression and clinical data were obtained from The Cancer Genome Atlas (TCGA) dataset, International Cancer Genome Consortium (ICGC) dataset, and Gene Expression Omnibus (GEO) dataset. Pathways associated with USP7 were determined by gene set enrichment analysis (GSEA). The relationships among USP7, immunity, and drug therapy were also investigated and potential mechanisms of action were explored. Results TCGA database results demonstrated USP7 mRNA expression levels to be upregulated in HCC tissues. Results were validated with UALCAN, ICGC, and GSE10143 datasets, as well as immunohistochemistry and reverse transcription-polymerase chain reaction (RT-PCR) experiments and were consistent with TCGA database findings (all P<0.05). GSEA analysis demonstrated increased USP7 levels to be associated with CHEMOKINE, Janus kinase/signal transducer and activator of transcription (JAK-STAT), mitogen-activated protein kinase (MAPK), P53, vascular endothelial growth factor (VEGF), and wingless (WNT) signaling pathways. Based on immune correlation analysis, USP7 was dramatically associated with immune cells and immune checkpoint molecules. In terms of drug therapy, USP7 expression levels were significantly related to HCC sensitivity to ciclosporin, talazoparib, dabrafenib, trametinib, paclitaxel, sorafenib, bortezomib, sunitinib, and crizotinib. Based on these results, we mechanistically propose an association between USP7 and these four drug targets: B-Raf proto-oncogene serine/threonine protein kinase (BRAF), mitogen-activated extracellular signal-regulated kinase (MEK), DNA topoisomerase I (TOPOI), and poly ADP-ribose polymerase (PARP). Conclusions USP7 plays a therapeutic and immunological role in HCC. The four drug targets BRAF, MEK, TOPOI, and PARP are implicated in the USP7 mechanism of action.
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Affiliation(s)
- Huiwen Ying
- Department of Infectious Diseases, Affiliated Hospital of Nantong University, Nantong, China
- Department of Infectious Diseases, Xuancheng People’s Hospital, Xuancheng, China
| | - Bin Zhang
- Department of Infectious Diseases, Affiliated Hospital of Nantong University, Nantong, China
| | - Guilian Cao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Yunan Wang
- Department of Rheumatism and Immunology, Affiliated Hospital of Nantong University, Nantong, China
| | - Xian Zhang
- Department of Infectious Diseases, Affiliated Hospital of Nantong University, Nantong, China
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Xu J, Wang Y, Zhang J, Abdelmoneim AA, Liang Z, Wang L, Jin J, Dai Q, Ye F. Elastic network models and molecular dynamic simulations reveal the molecular basis of allosteric regulation in ubiquitin-specific protease 7 (USP7). Comput Biol Med 2023; 162:107068. [PMID: 37290391 DOI: 10.1016/j.compbiomed.2023.107068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/14/2023] [Accepted: 05/27/2023] [Indexed: 06/10/2023]
Abstract
Ubiquitin-specific protease 7 (USP7) is one of the most abundant deubiquitinases and plays an important role in various malignant tumors. However, the molecular mechanisms underlying USP7's structures, dynamics, and biological significance are yet to be investigated. In this study, we constructed the full-length models of USP7 in both the extended and compact state, and applied elastic network models (ENM), molecular dynamics (MD) simulations, perturbation response scanning (PRS) analysis, residue interaction networks as well as allosteric pocket prediction to investigate allosteric dynamics in USP7. Our analysis of intrinsic and conformational dynamics revealed that the structural transition between the two states is characterized by global clamp motions, during which the catalytic domain (CD) and UBL4-5 domain exhibit strong negative correlations. The PRS analysis, combined with the analysis of disease mutations and post-translational modifications (PTMs) further highlighted the allosteric potential of the two domains. The residue interaction network based on MD simulations captured an allosteric communication path which starts at CD domain and ends at UBL4-5 domain. Moreover, we identified a pocket at the TRAF-CD interface as a high-potential allosteric site for USP7. Overall, our studies not only provide molecular insights into the conformational changes of USP7, but also aid in the design of allosteric modulators that target USP7.
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Affiliation(s)
- Jing Xu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Yiran Wang
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Jiali Zhang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Amr Abbas Abdelmoneim
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Lei Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Jia Jin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Qi Dai
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China.
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Sun J, Liu F, Yuan L, Pang NN, Zhu B, Yang N. Mechanism studies of the activation of DNA methyltransferase DNMT1 triggered by histone H3 ubiquitination, revealed by multi-scale molecular dynamics simulations. SCIENCE CHINA. LIFE SCIENCES 2023; 66:313-323. [PMID: 36271982 DOI: 10.1007/s11427-021-2179-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/17/2022] [Indexed: 11/05/2022]
Abstract
DNMT1 is a DNA methyltransferase that catalyzes and maintains methylation in CpG dinucleotides. It blocks the entrance of DNA into the catalytic pocket via the replication foci targeting sequence (RFTS) domain. Recent studies have shown that an H3-tail-conjugated two-mono-ubiquitin mark (H3Ub2) activates DNMT1 by binding to the RFTS domain. However, the activation mechanism of DNMT1 remains unclear. In this work, we combine various sampling methods of extensive simulations, including conventional molecular dynamics, Gaussian-accelerated molecular dynamics, and coarse-grained molecular dynamics, to elucidate the activation mechanism of DNMT1. Geometric and energy analyses show that binding of H3Ub2 to the RFTS domain of DNMT1 results in the bending of the α4-helix in the RFTS domain at approximately 30°-35°, and the RFTS domain rotates ∼20° anti-clockwise and moves ∼3 Å away from the target recognition domain (TRD). The hydrogen-bonding network at the RFTS-TRD interface is significantly disrupted, implying that the RFTS domain is dissociated from the catalytic core, which contributes to activating the auto-inhibited conformation of DNMT1. These results provide structural and dynamic evidence for the role of H3Ub2 in regulating the catalytic activity of DNMT1.
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Affiliation(s)
- Jixue Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China
| | - Fei Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China
| | - Longxiao Yuan
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China
| | - Ning-Ning Pang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Key Laboratory of Medical Data Analysis and Statistical Research of Tianjin, Nankai University, Tianjin, 300353, China.
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Qiu L, Zhang M, Li C, Hou Y, Liu H, Lin J, Yao J, Duan DZ, Zhang YX, Li M, Li YL, Wang P, Li JT, Jin XJ, Liu YQ. Deciphering the active constituents of Dabushen decoction of ameliorating osteoarthritis via PPARγ preservation by targeting DNMT1. Front Pharmacol 2022; 13:993498. [PMID: 36506533 PMCID: PMC9727303 DOI: 10.3389/fphar.2022.993498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 11/01/2022] [Indexed: 11/24/2022] Open
Abstract
Osteoarthritis (OA) is a multifactorial and chronic degenerative joint disease. Due to the adverse effects of currently used drugs, a safer and more effective therapy for treating OA is needed. Peroxisome proliferator-activated receptor-γ (PPARγ) is a key protein protecting cartilage. DNMT1-mediated hypermethylation of PPARγ promoter leads to its suppression. Therefore, DNMT1 might be an effective target for exerting cartilage protective effects by regulating the epigenetic expression of PPARγ. Dabushen decoction (DD) is a representative prescription of Dunhuang ancient medical prescription, which has a potential therapeutic effect on OA. So far, the research of the efficacy and material basis of DD in the treatment of OA remains unclear. In this study, Micro-CT, HE staining, S-O staining, and immunohistochemistry analysis were used to demonstrate that DD increased the expression of PPARγ and collagen synthesis in an OA rat model. Next, the structure of DNMT1 was used to screen the active constituents of DD by molecular docking method for treatment OA. Seven potential active constituents, including isoliquiritigenin, emodin, taxifolin, catalpol, alisol A, zingerone, and schisandrin C were hited. The protective effect of the potential active constituents to chondrocytes were evaluated by protein capillary electrophoresis, immunofluorescence assays, and ex vivo culture of rat knee cartilage. The five constituents, such as alisol A, emodin, taxifolin, isoliquiritigenin, and schisandrin C could promote the expression of PPARγ and ameliorate IL-1β-induced downregulation of collagen II and the production of MMP-13. Alisol A and Emodin could effectively mitigate cartilage damage. At last, molecular dynamics simulations with MM-GBSA method was applied to investigate the interaction pattern of the active constituents and DNMT1 complexes. The five constituents, such as alisol A, emodin, taxifolin, isoliquiritigenin, and schisandrin C achieved a stable binding pattern with DNMT1, in which alisol A has a relatively high binding free energy. In conclusion, this study elucidates that the active constituents of DD (alisol A, emodin, taxifolin, isoliquiritigenin, and schisandrin C) could ameliorate osteoarthritis via PPARγ preservation by targeting DNMT1.These findings facilitated clinical use of DD and provided a valuable strategy for developing natural epigenetic modulators from Chinese herbal formula.
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Affiliation(s)
- Lu Qiu
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou, China
| | - Min Zhang
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China
| | - Chenghao Li
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou, China
| | - Yehu Hou
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou, China
| | - Hao Liu
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jia Lin
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China
| | - Juan Yao
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China
| | - Dong Zhu Duan
- Shaanxi Key Laboratory of Phytochemistry and College of Chemistry and Chemical Engineering, Baoji University of Arts and Sciences, Baoji, China
| | - Yi Xi Zhang
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China
| | - Mi Li
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China
| | - Ya Ling Li
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou, China
| | - Peng Wang
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jin Tian Li
- Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou, China
| | - Xiao Jie Jin
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou, China,College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China,*Correspondence: Xiao Jie Jin, ; Yong Qi Liu,
| | - Yong Qi Liu
- Gansu University Key Laboratory for Molecular Medicine and Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China,Key Laboratory of Dunhuang Medicine, Ministry of Education, Gansu University of Chinese Medicine, Lanzhou, China,*Correspondence: Xiao Jie Jin, ; Yong Qi Liu,
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