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Lanka G, Banerjee S, Adhikari N, Ghosh B. Fragment-based discovery of new potential DNMT1 inhibitors integrating multiple pharmacophore modeling, 3D-QSAR, virtual screening, molecular docking, ADME, and molecular dynamics simulation approaches. Mol Divers 2024:10.1007/s11030-024-10837-5. [PMID: 38637479 DOI: 10.1007/s11030-024-10837-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
DNA methyl transferases (DNMTs) are one of the crucial epigenetic modulators associated with a wide variety of cancer conditions. Among the DNMT isoforms, DNMT1 is correlated with bladder, pancreatic, and breast cancer, as well as acute myeloid leukemia and esophagus squamous cell carcinoma. Therefore, the inhibition of DNMT1 could be an attractive target for combating cancers and other metabolic disorders. The disadvantages of the existing nucleoside and non-nucleoside DNMT1 inhibitors are the main motive for the discovery of novel promising inhibitors. Here, pharmacophore modeling, 3D-QSAR, and e-pharmacophore modeling of DNMT1 inhibitors were performed for the large fragment database screening. The resulting fragments with high dock scores were combined into molecules. The current study revealed several constitutional pharmacophoric features that can be essential for selective DNMT1 inhibition. The fragment docking and virtual screening identified 10 final hit molecules that exhibited good binding affinities in terms of docking score, binding free energies, and acceptable ADME properties. Also, the modified lead molecules (GL1b and GL2b) designed in this study showed effective binding with DNMT1 confirmed by their docking scores, binding free energies, 3D-QSAR predicted activities and acceptable drug-like properties. The MD simulation studies also suggested that leads (GL1b and GL2b) formed stable complexes with DNMT1. Therefore, the findings of this study can provide effective information for the development/identification of novel DNMT1 inhibitors as effective anticancer agents.
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Affiliation(s)
- Goverdhan Lanka
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
- Computer Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata, West Bengal, 700032, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, P. O. Box 17020, Kolkata, West Bengal, 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India.
- Computer Aided Drug Design Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, 500078, India.
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Subaramaniyam U, Ramalingam D, Balan R, Paital B, Sar P, Ramalingam N. Annonaceous acetogenins as promising DNA methylation inhibitors to prevent and treat leukemogenesis - an in silico approach. J Biomol Struct Dyn 2023:1-14. [PMID: 38149859 DOI: 10.1080/07391102.2023.2297010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/10/2023] [Indexed: 12/28/2023]
Abstract
Leukemia is a haematological malignancy affecting blood and bone marrow, ranking 10th among the other common cancers. DNA methylation is an epigenetic dysregulation that plays a critical role in leukemogenesis. DNA methyltransferases (DNMTs) such as DNMT1, DNMT3A and DNMT3B are the key enzymes catalysing DNA methylation. Inhibition of DNMT1 with secondary metabolites from medicinal plants helps reverse DNA methylation. The present study focuses on inhibiting DNMT1 protein (PDB ID: 3PTA) with annonaceous acetogenins through in-silico studies. The docking and molecular dynamic (MD) simulation study was carried out using Schrödinger Maestro and Desmond, respectively. These compounds' drug likeliness, ADMET properties and bioactivity scores were analysed. About 76 different acetogenins were chosen for this study, among which 17 showed the highest binding energy in the range of -8.312 to -10.266 kcal/mol. The compounds with the highest negative binding energy were found to be annohexocin (-10.266 kcal/mol), isoannonacinone (-10.209 kcal/mol) and annonacin (-9.839 kcal/mol). MD simulation results reveal that annonacin remains stable throughout the simulation time of 100 ns and also binds to the catalytic domain of DNMT1 protein. From the above results, it can be concluded that annonacin has the potential to inhibit the DNA methylation process and prevent leukemogenesis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Udayadharshini Subaramaniyam
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, India
| | - Divya Ramalingam
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, India
| | - Ranjini Balan
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, India
| | - Biswaranjan Paital
- Redox Regulation Laboratory, Department of Zoology, College of Basic Science and Humanities, Odisha University of Agriculture and Technology, Bhubaneswar, India
| | - Pranati Sar
- Biotechnology Department, Silver Oak Institute of Science, Silver Oak University, Ahmedabad, India
| | - Nirmaladevi Ramalingam
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, India
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Zhou S, Ou H, Wu Y, Qi D, Pei X, Yu X, Hu X, Wu E. Targeting tumor endothelial cells with methyltransferase inhibitors: Mechanisms of action and the potential of combination therapy. Pharmacol Ther 2023:108434. [PMID: 37172786 DOI: 10.1016/j.pharmthera.2023.108434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/30/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023]
Abstract
Tumor endothelial cells (TECs) reside in the inner lining of blood vessels and represent a promising target for targeted cancer therapy. DNA methylation is a chemical process that involves the transfer of a methyl group to a specific base in the DNA strand, catalyzed by DNA methyltransferase (DNMT). DNMT inhibitors (DNMTis) can inhibit the activity of DNMTs, thereby preventing the transfer of methyl groups from s-adenosyl methionine (SAM) to cytosine. Currently, the most viable therapy for TECs is the development of DNMTis to release cancer suppressor genes from their repressed state. In this review, we first outline the characteristics of TECs and describe the development of tumor blood vessels and TECs. Abnormal DNA methylation is closely linked to tumor initiation, progression, and cell carcinogenesis, as evidenced by numerous studies. Therefore, we summarize the role of DNA methylation and DNA methyltransferase and the therapeutic potential of four types of DNMTi in targeting TECs. Finally, we discuss the accomplishments, challenges, and opportunities associated with combination therapy with DNMTis for TECs.
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Affiliation(s)
- Shu Zhou
- State Key Laboratory of Biosensing, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Hailong Ou
- State Key Laboratory of Biosensing, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Yatao Wu
- State Key Laboratory of Biosensing, College of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Dan Qi
- Texas A & M University Schools of Medicine and Pharmacy, College Station, TX 77843, USA
| | - Xiaming Pei
- Department of Urology, Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, Hunan 410013, China
| | - Xiaohui Yu
- Department of Urology, Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, Hunan 410013, China
| | - Xiaoxiao Hu
- State Key Laboratory of Biosensing, College of Biology, Hunan University, Changsha, Hunan 410082, China; Research Institute of Hunan University in Chongqing, Chongqing 401120, China.
| | - Erxi Wu
- Department of Neurosurgery, Neuroscience Institute, Baylor Scott & White Health, Temple, TX 78508, USA; Texas A & M University Schools of Medicine and Pharmacy, College Station, TX 77843, USA; LIVESTRONG Cancer Institutes, Department of Oncology, Dell Medical School, the University of Texas at Austin, Austin, TX 78712, USA.
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Asim A, Kiani YS, Saeed MT, Jabeen I. Decoding the Role of Epigenetics in Breast Cancer Using Formal Modeling and Machine-Learning Methods. Front Mol Biosci 2022; 9:882738. [PMID: 35898303 PMCID: PMC9309526 DOI: 10.3389/fmolb.2022.882738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Breast carcinogenesis is known to be instigated by genetic and epigenetic modifications impacting multiple cellular signaling cascades, thus making its prevention and treatments a challenging endeavor. However, epigenetic modification, particularly DNA methylation-mediated silencing of key TSGs, is a hallmark of cancer progression. One such tumor suppressor gene (TSG) RUNX3 (Runt-related transcription factor 3) has been a new insight in breast cancer known to be suppressed due to local promoter hypermethylation mediated by DNA methyltransferase 1 (DNMT1). However, the precise mechanism of epigenetic-influenced silencing of the RUNX3 signaling resulting in cancer invasion and metastasis remains inadequately characterized. In this study, a biological regulatory network (BRN) has been designed to model the dynamics of the DNMT1–RUNX3 network augmented by other regulators such as p21, c-myc, and p53. For this purpose, the René Thomas qualitative modeling was applied to compute the unknown parameters and the subsequent trajectories signified important behaviors of the DNMT1–RUNX3 network (i.e., recovery cycle, homeostasis, and bifurcation state). As a result, the biological system was observed to invade cancer metastasis due to persistent activation of oncogene c-myc accompanied by consistent downregulation of TSG RUNX3. Conversely, homeostasis was achieved in the absence of c-myc and activated TSG RUNX3. Furthermore, DNMT1 was endorsed as a potential epigenetic drug target to be subjected to the implementation of machine-learning techniques for the classification of the active and inactive DNMT1 modulators. The best-performing ML model successfully classified the active and least-active DNMT1 inhibitors exhibiting 97% classification accuracy. Collectively, this study reveals the underlined epigenetic events responsible for RUNX3-implicated breast cancer metastasis along with the classification of DNMT1 modulators that can potentially drive the perception of epigenetic-based tumor therapy.
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Jiang W, Block ME, Boosani CS. Short communication: TNF-α and IGF-1 regulates epigenetic mechanisms of HDAC2 and HDAC10. PLoS One 2022; 17:e0263190. [PMID: 35143520 PMCID: PMC8830685 DOI: 10.1371/journal.pone.0263190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/13/2022] [Indexed: 11/19/2022] Open
Abstract
Vascular restenosis often presents as a consequence of injury to the vessel wall, resulting from stenting and other interventional procedures. Such injury to the arteries induces proliferation of Vascular Smooth Muscle Cells (VSMCs), resulting in cellular hyperplasia and restenosis. We and others have previously reported de-novo production of different cytokines and growth factors such as Tumor Necrosis Factor Alpha (TNF-α) and Insulin like Growth Factor 1 (IGF-1), after vascular injury. As complex as it is, the profuse proliferation of VSMCs appears to be occurring due to several induced factors which initiate molecular mechanisms and exacerbate disease conditions. In many pathological events, the deleterious effects of TNF-α and IGF-1 in initiating disease mechanisms was reported. In the present work, we explored whether TNF-α and IGF-1 can regulate epigenetic mechanisms that promote proliferation of VSMCs. We investigated the mechanistic roles of proteins which can structurally interact with DNMT1 and initiate cellular pathways that promote proliferation of VSMCs. Our findings here, identify a novel molecular mechanism that is initiated by TNF-α and IGF-1. It was previously reported that DNMT1 expression is directly induced by TNF-α and IGF-1 treatment and increased/induced expression of DNMT1 causes silencing of genes that are essential to maintaining cellular homeostasis such as the tumor suppressor genes. We have earlier reported that TNF-α and IGF-1 treatment elevates DNMT1 expression in VSMCs and causes increased VSMC proliferation. However, the molecular mechanisms involved were not fully deciphered. Interestingly, in the present study we found that TNF-α and IGF-1 treatment failed to elevate DNMT1 expression levels in absence of HDAC2 and HDAC10. Also, while HDAC2 expression was not affected by HDAC10 knockdown, HDAC2 is essentially required for HDAC10 expression. Further, in TNF-α and IGF-1 induced epigenetic signaling mechanism, the expression of two important proteins EZH2 and PCNA seem to be regulated in an HDAC2-HDAC10 dependent manner. Our results show an inter-dependence of epigenetic mediators in inducing proliferation in VSMCs. To our knowledge, this is the first report that shows HDAC2 dependent expression of HDAC10, and suggests a novel mechanistic link between DNMT1, HDAC10 and HDAC2 that regulates EZH2 and PCNA to enhance cell proliferation of VSMCs which is the underlying cause for neointimal hyperplasia and restenosis.
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Affiliation(s)
- Wanlin Jiang
- Department of Clinical and Translational Science, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Megan E. Block
- Department of Clinical and Translational Science, Creighton University School of Medicine, Omaha, Nebraska, United States of America
| | - Chandra S. Boosani
- Department of Clinical and Translational Science, Creighton University School of Medicine, Omaha, Nebraska, United States of America
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Therapeutical interference with the epigenetic landscape of germ cell tumors: a comparative drug study and new mechanistical insights. Clin Epigenetics 2022; 14:5. [PMID: 34996497 PMCID: PMC8742467 DOI: 10.1186/s13148-021-01223-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/18/2021] [Indexed: 12/18/2022] Open
Abstract
Background Type II germ cell tumors (GCT) are the most common solid cancers in males of age 15 to 35 years. Treatment of these tumors includes cisplatin-based therapy achieving high cure rates, but also leading to late toxicities. As mainly young men are suffering from GCTs, late toxicities play a major role regarding life expectancy, and the development of therapy resistance emphasizes the need for alternative therapeutic options. GCTs are highly susceptible to interference with the epigenetic landscape; therefore, this study focuses on screening of drugs against epigenetic factors as a treatment option for GCTs.
Results We present seven different epigenetic inhibitors efficiently decreasing cell viability in GCT cell lines including cisplatin-resistant subclones at low concentrations by targeting epigenetic modifiers and interactors, like histone deacetylases (Quisinostat), histone demethylases (JIB-04), histone methyltransferases (Chaetocin), epigenetic readers (MZ-1, LP99) and polycomb-repressive complexes (PRT4165, GSK343). Mass spectrometry-based analyses of the histone modification landscape revealed effects beyond the expected mode-of-action of each drug, suggesting a wider spectrum of activity than initially assumed. Moreover, we characterized the effects of each drug on the transcriptome of GCT cells by RNA sequencing and found common deregulations in gene expression of ion transporters and DNA-binding factors. A kinase array revealed deregulations of signaling pathways, like cAMP, JAK-STAT and WNT. Conclusion Our study identified seven drugs against epigenetic modifiers to treat cisplatin-resistant GCTs. Further, we extensively analyzed off-target effects and modes-of-action, which are important for risk assessment of the individual drugs. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01223-1.
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7
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DNAzymes, Novel Therapeutic Agents in Cancer Therapy: A Review of Concepts to Applications. J Nucleic Acids 2021; 2021:9365081. [PMID: 34760318 PMCID: PMC8575636 DOI: 10.1155/2021/9365081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/06/2021] [Indexed: 11/17/2022] Open
Abstract
The past few decades have witnessed a rapid evolution in cancer drug research which is aimed at developing active biological interventions to regulate cancer-specific molecular targets. Nucleic acid-based therapeutics, including ribozymes, antisense oligonucleotides, small interference RNA (siRNA), aptamer, and DNAzymes, have emerged as promising candidates regulating cancer-specific genes at either the transcriptional or posttranscriptional level. Gene-specific catalytic DNA molecules, or DNAzymes, have shown promise as a therapeutic intervention against cancer in various in vitro and in vivo models, expediting towards clinical applications. DNAzymes are single-stranded catalytic DNA that has not been observed in nature, and they are synthesized through in vitro selection processes from a large pool of random DNA libraries. The intrinsic properties of DNAzymes like small molecular weight, higher stability, excellent programmability, diversity, and low cost have brought them to the forefront of the nucleic acid-based therapeutic arsenal available for cancers. In recent years, considerable efforts have been undertaken to assess a variety of DNAzymes against different cancers. However, their therapeutic application is constrained by the low delivery efficiency, cellular uptake, and target detection within the tumour microenvironment. Thus, there is a pursuit to identify efficient delivery methods in vivo before the full potential of DNAzymes in cancer therapy is realized. In this light, a review of the recent advances in the use of DNAzymes against cancers in preclinical and clinical settings is valuable to understand its potential as effective cancer therapy. We have thus sought to firstly provide a brief overview of construction and recent improvements in the design of DNAzymes. Secondly, this review stipulates the efficacy, safety, and tolerability of DNAzymes developed against major hallmarks of cancers tested in preclinical and clinical settings. Lastly, the recent advances in DNAzyme delivery systems along with the challenges and prospects for the clinical application of DNAzymes as cancer therapy are also discussed.
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Hu J, Yang Y, Lv X, Lao Z, Yu L. Dichlorodiphenyltrichloroethane metabolites inhibit DNMT1 activity which confers methylation-specific modulation of the sex determination pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 279:116828. [PMID: 33765505 DOI: 10.1016/j.envpol.2021.116828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 02/11/2021] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
Dichlorodiphenyltrichloroethane (DDT) poses a significant health risk to humans which is associated with genomic DNA hypomethylation. However, the mechanism and biological consequences remain poorly understood. In vitro assays confirmed that the DDT metabolites 2,2-bis(p-chlorophenyl)-acetic acid (DDA) and 1-chloro-2,2-bis-(p-chlorophenyl)ethylene (DDMU), but not other DDT metabolites, significantly inhibited DNA methyltransferase 1 (DNMT1) activity, leading to genomic hypomethylation in cell culture assays. DNMT1 as a target for DNA hypomethylation induced by DDT metabolites was also confirmed using cell cultures in which DNMT1 was silenced or highly expressed. DDA and DDMU can modify methylation markers in the promoter regions of sexual development-related genes, and change the expression of Sox9 and Oct4 in embryonic stem cells. Molecular docking indicated that DDA and DDMU bound to DNMT1 with high binding affinity. Molecular dynamic simulation revealed that DDA and DDMU acted as allosteric modulators that reshaped the conformation of the catalytic domain of DNMT1. These findings provide a new insight into DDT-induced abnormalities in sexual development and demonstrate that selective binding to DNMT1 by DDA and DDMU can interfere with human DNMT1 activity and regulate the expression of the Sox9 and Oct4 genes.
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Affiliation(s)
- Junjie Hu
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Yan Yang
- Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou, 510006, PR China; Synergy Innovation Institute of GDUT, Shantou, 515041, China
| | - Xiaomei Lv
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Zhilang Lao
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Lili Yu
- Translational Medicine Collaborative Innovation Center, The First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, 1017 Dongmen North Road, Luohu District, Shenzhen, 518020, Guangdong, China.
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Juárez-Mercado KE, Prieto-Martínez FD, Sánchez-Cruz N, Peña-Castillo A, Prada-Gracia D, Medina-Franco JL. Expanding the Structural Diversity of DNA Methyltransferase Inhibitors. Pharmaceuticals (Basel) 2020; 14:ph14010017. [PMID: 33375520 PMCID: PMC7824300 DOI: 10.3390/ph14010017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
Inhibitors of DNA methyltransferases (DNMTs) are attractive compounds for epigenetic drug discovery. They are also chemical tools to understand the biochemistry of epigenetic processes. Herein, we report five distinct inhibitors of DNMT1 characterized in enzymatic inhibition assays that did not show activity with DNMT3B. It was concluded that the dietary component theaflavin is an inhibitor of DNMT1. Two additional novel inhibitors of DNMT1 are the approved drugs glyburide and panobinostat. The DNMT1 enzymatic inhibitory activity of panobinostat, a known pan inhibitor of histone deacetylases, agrees with experimental reports of its ability to reduce DNMT1 activity in liver cancer cell lines. Molecular docking of the active compounds with DNMT1, and re-scoring with the recently developed extended connectivity interaction features approach, led to an excellent agreement between the experimental IC50 values and docking scores.
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Affiliation(s)
- K. Eurídice Juárez-Mercado
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
| | - Fernando D. Prieto-Martínez
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
| | - Norberto Sánchez-Cruz
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
| | - Andrea Peña-Castillo
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
| | - Diego Prada-Gracia
- Research Unit on Computational Biology and Drug Design, Children’s Hospital of Mexico Federico Gomez, Mexico City 06720, Mexico;
| | - José L. Medina-Franco
- DIFACQUIM Research Group, Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Avenida Universidad 3000, Mexico City 04510, Mexico; (K.E.J.-M.); (F.D.P.-M.); (N.S.-C.); (A.P.-C.)
- Correspondence:
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Li M, Qi L, Xu JB, Zhong LY, Chan S, Chen SN, Shao XR, Zheng LY, Dong ZX, Fang TL, Mai ZY, Li J, Zheng Y, Zhang XD. Methylation of the Promoter Region of the Tight Junction Protein-1 by DNMT1 Induces EMT-like Features in Multiple Myeloma. MOLECULAR THERAPY-ONCOLYTICS 2020; 19:197-207. [PMID: 33251332 PMCID: PMC7666313 DOI: 10.1016/j.omto.2020.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/07/2020] [Indexed: 11/19/2022]
Abstract
The molecular alterations that initiate the development of multiple myeloma (MM) are not fully understood. Our results revealed that TJP1 was downregulated in MM and positively related to the overall survival of MM patients in The Cancer Genome Atlas (TCGA) database and patient samples. In parallel, cell adhesion capacity representing MM metastasis was decreased in MM patients compared with healthy samples, together with the significantly activated epithelial-to-mesenchymal transition (EMT) transcriptional-like patterns of MM cells. Further analyses demonstrated that TJP1 negatively regulated EMT and consequently positively regulated cell adhesion in MM from TCGA database and MM1s cells. Furthermore, the methylation level of each CpG site on the TJP1 promoter was negatively correlated with TJP1 expression levels. Quantitative real-time PCR and western blot assays demonstrated that methylase DNMT1 regulated the methylation of TJP1. Finally, treatment with a combination of the MM clinical medicine bortezomib, methylation inhibitor, or TJP1 overexpression significantly suppressed the viability and progression of tumor cells of MM orthotopic models. In summary, our results indicate that DNMT1 promotes the methylation of TJP1 promoter, thereby decreasing its expression and regulating the development of EMT-inhibited MM cell adhesion. Therefore, methylation of TJP1 is a potential therapeutic agent to prevent the progression of MM disease.
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Affiliation(s)
- Miao Li
- Department of Hematology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
| | - Lin Qi
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
- Corresponding author: Lin Qi, Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China.
| | - Jing-Bo Xu
- Department of Hematology, Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Li-Ye Zhong
- Department of Hematology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510000, China
| | - Szehoi Chan
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
| | - Shu-Na Chen
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
| | - Xin-Rong Shao
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
| | - Li-Yuan Zheng
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
| | - Zhao-Xia Dong
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
| | - Tian-Liang Fang
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
| | - Zhi-Ying Mai
- Department of Hematology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
| | - Juan Li
- Department of Hematology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510000, China
| | - Yongjiang Zheng
- Department of Hematology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
- Corresponding author: Yongjiang Zheng, Department of Hematology, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Xing-Ding Zhang
- Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
- Corresponding author: Xing-Ding Zhang, Department of Pharmacology, Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen 518107, China.
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Identification of aurintricarboxylic acid as a potent allosteric antagonist of P2X1 and P2X3 receptors. Neuropharmacology 2019; 158:107749. [PMID: 31461640 DOI: 10.1016/j.neuropharm.2019.107749] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/14/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022]
Abstract
The homotrimeric P2X3 receptor, one of the seven members of the ATP-gated P2X receptor family, plays a crucial role in sensory neurotransmission. P2X3 receptor antagonists have been identified as promising drugs to treat chronic cough and are suggested to offer pain relief in chronic pain such as neuropathic pain. Here, we analysed whether compounds affect P2X3 receptor activity by high-throughput screening of the Spectrum Collection of 2000 approved drugs, natural products and bioactive substances. We identified aurintricarboxylic acid (ATA) as a nanomolar-potency antagonist of P2X3 receptor-mediated responses. Two-electrode voltage clamp electrophysiology-based concentration-response analysis and selectivity profiling revealed that ATA strongly inhibits the rP2X1 and rP2X3 receptors (with IC50 values of 8.6 nM and 72.9 nM, respectively) and more weakly inhibits P2X2/3, P2X2, P2X4 or P2X7 receptors (IC50 values of 0.76 μM, 22 μM, 763 μM or 118 μM, respectively). Patch-clamp analysis of mouse DRG neurons revealed that ATA inhibited native P2X3 and P2X2/3 receptors to a similar extent than rat P2X3 and P2X2/3 receptors expressed in Xenopus oocytes. In a radioligand binding assay, up to 30 μM ATA did not compete with [3H]-ATP for rP2X3 receptor binding, indicating a non-competitive mechanism of action. Molecular docking studies, site-directed mutagenesis and concentration-response analysis revealed that ATA binds to the negative allosteric site of the hP2X3 receptor. In summary, ATA as a drug-like pharmacological tool compound is a nanomolar-potency, allosteric antagonist with selectivity towards αβ-methylene-ATP-sensitive P2X1 and P2X3 receptors.
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12
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Wallbach M, Tampe B, Dihazi H, Koziolek MJ. [Acute kidney injury: from creatinine to KIM‑1?]. Internist (Berl) 2019; 60:578-586. [PMID: 31001671 DOI: 10.1007/s00108-019-0602-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In addition to the early detection of an acute kidney injury (AKI), several problems or questions have to be addressed. These include the identification of the etiology, the severity (functional or structural), the prognosis (recovery or transition to chronic renal failure), the course of the disease (dialysis or not), and the identification of specific treatment options for AKI. The following article provides an overview of established and new AKI biomarkers as well as an outlook on the potential of future biomarker-associated models of AKI.
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Affiliation(s)
- M Wallbach
- Klinik für Nephrologie und Rheumatologie, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland
| | - B Tampe
- Klinik für Nephrologie und Rheumatologie, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland
| | - H Dihazi
- Klinik für Nephrologie und Rheumatologie, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland
| | - M J Koziolek
- Klinik für Nephrologie und Rheumatologie, Universitätsmedizin Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Deutschland.
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13
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Gomes LR, Low JN, Turner AB, Watson GJ, Baddeley TC, Wardell JL. Crystal structures and Hirshfeld surface analyses of seven 7-aryl-4,7-dioxoheptanoic acids: differing carboxylic acid interactions leading to dimers, chains and three-dimensional arrays. Z KRIST-CRYST MATER 2018. [DOI: 10.1515/zkri-2017-2144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Crystal structures and Hirshfeld surface analysis are reported of seven aryl-CO–CH2CH2COCH2CH2CO2H derivatives, namely aryl=4-ClC6H4, 1: 2-HOC6H4, 2: (2,4-(MeO)2C6H3, 3: 3,5-Me2-4-MeOC6H2, 4: 4-MeC6H4, 5: C6H5, 6: 2,4-(HO)2C6H3, 7. There are significant differences in their molecular conformations and their crystal packing. Within the group of compounds, three different types of carboxylic acid intermolecular interactions are exhibited, all involving O–H···O hydrogen bonds. These three types are (i) symmetric R2
2(8) dimers formed from pairs of O–H···O hydrogen bonds in compounds 1–5, (ii) infinite 1D homo-assemblies of carboxylic groups (homo-AA,A catemers), and (iii), a 3-D array, in which there are no direct carboxylic acid–carboxylic acid interactions, generated from O–H···O interactions of each carboxylic acid group with the hydroxyl and carbonyl groups of other molecules in 7. Each of the carboxylic acid groups in the catemer exhibit anti arrangements with all the carboxylic acid oxygen atoms lying in a plane. Disorder is exhibited in the carboxylic acid groups in 2 and 6. With the variety of oxygen substituents present in 1–7, a large number of O–H···O and C–H···O hydrogen bonds are exhibited, resulting in all cases in three dimension assemblies. In 1–5, interlayer contacts between the carboxylic acid R2
2(8) dimers in rows, with differing sets of weaker C–H···O and/or C–H···π interactions, result in the formation of two-molecular wide columns and/or infinite sheets. While column and sheet sub structures can also be designated in compound 6, on linking the carboxylic acid groups with other substituents via C–H···O, C–H···π and C=O···π interactions, these differ from those in 1–5 due to the different arrangements of the CO2H groups.
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Affiliation(s)
- Ligia R. Gomes
- FP-ENAS-Faculdade de Ciências de Saúde, Escola Superior de Saúde da UFP, Universidade Fernando Pessoa , Rua Carlos da Maia, 296 , P-4200-150 Porto , Portugal
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 687 , P-4169-007 Porto , Portugal
| | - John N. Low
- Department of Chemistry , University of Aberdeen, Meston Walk, Old Aberdeen , AB24 3UE , Scotland , UK
| | - Alan B. Turner
- Department of Chemistry , University of Aberdeen, Meston Walk, Old Aberdeen , AB24 3UE , Scotland , UK
| | - Graeme J.R. Watson
- Department of Chemistry , University of Aberdeen, Meston Walk, Old Aberdeen , AB24 3UE , Scotland , UK
| | - Thomas C. Baddeley
- Department of Chemistry , University of Aberdeen, Meston Walk, Old Aberdeen , AB24 3UE , Scotland , UK
| | - James L. Wardell
- Department of Chemistry , University of Aberdeen, Meston Walk, Old Aberdeen , AB24 3UE , Scotland , UK
- Instituto de Tecnologia em Fármacos e Farmanguinhos , Fundação Oswaldo Cruz , 21041-250 Rio de Janeiro, RJ , Brazil
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Saldívar-González FI, Gómez-García A, Chávez-Ponce de León DE, Sánchez-Cruz N, Ruiz-Rios J, Pilón-Jiménez BA, Medina-Franco JL. Inhibitors of DNA Methyltransferases From Natural Sources: A Computational Perspective. Front Pharmacol 2018; 9:1144. [PMID: 30364171 PMCID: PMC6191485 DOI: 10.3389/fphar.2018.01144] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/21/2018] [Indexed: 12/15/2022] Open
Abstract
Naturally occurring small molecules include a large variety of natural products from different sources that have confirmed activity against epigenetic targets. In this work we review chemoinformatic, molecular modeling, and other computational approaches that have been used to uncover natural products as inhibitors of DNA methyltransferases, a major family of epigenetic targets with therapeutic interest. Examples of computational approaches surveyed in this work are docking, similarity-based virtual screening, and pharmacophore modeling. It is also discussed the chemoinformatic-guided exploration of the chemical space of naturally occurring compounds as epigenetic modulators which may have significant implications in epigenetic drug discovery and nutriepigenetics.
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Affiliation(s)
| | - Alejandro Gómez-García
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | | | - Norberto Sánchez-Cruz
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - Javier Ruiz-Rios
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - B Angélica Pilón-Jiménez
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
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15
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Chromatin dynamics at the core of kidney fibrosis. Matrix Biol 2018; 68-69:194-229. [DOI: 10.1016/j.matbio.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/16/2018] [Accepted: 02/17/2018] [Indexed: 02/06/2023]
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Li Y, Wang Y, Li D, Zhang Y, Zhao T, Li C. Procaine is a specific DNA methylation inhibitor with anti‐tumor effect for human gastric cancer. J Cell Biochem 2017; 119:2440-2449. [PMID: 28926119 DOI: 10.1002/jcb.26407] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 09/12/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Yong‐Chao Li
- Department of Gastrointestinal SurgeryChina‐Japan Union Hospital of Jilin UniversityChangchunJilinP.R. China
| | - Yun Wang
- Department of MedicineLiver and Biliary Disease Hospital of Jilin ProvinceChangchunP.R. China
| | - Dan‐Dan Li
- Department of Endoscopy CenterChina‐Japan Union Hospital of Jilin UniversityChangchunJilinP.R. China
| | - Ying Zhang
- Department of Endoscopy CenterChina‐Japan Union Hospital of Jilin UniversityChangchunJilinP.R. China
| | - Tian‐Cheng Zhao
- Department of Endoscopy CenterChina‐Japan Union Hospital of Jilin UniversityChangchunJilinP.R. China
| | - Chang‐Feng Li
- Department of Endoscopy CenterChina‐Japan Union Hospital of Jilin UniversityChangchunJilinP.R. China
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Ma SC, Hao YJ, Jiao Y, Wang YH, Xu LB, Mao CY, Yang XL, Yang AN, Tian J, Zhang MH, Jin SJ, Xu H, Jiang YD, Zhang HP. Homocysteine‑induced oxidative stress through TLR4/NF‑κB/DNMT1‑mediated LOX‑1 DNA methylation in endothelial cells. Mol Med Rep 2017; 16:9181-9188. [PMID: 29039510 DOI: 10.3892/mmr.2017.7753] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 08/22/2017] [Indexed: 11/05/2022] Open
Abstract
Atherosclerosis (AS) is a progressive disease of multifactorial origin, which occurs in response to endothelial injury. Increased homocysteine (Hcy) is considered a major cause of endothelial dysfunction, oxidative stress and DNA methylation; however, the mechanisms remain to be fully elucidated. The aim of the present study was to investigate whether Hcy causes injury to endothelial cells (ECs) by the effect of lectin‑like oxidized‑low density lipoprotein receptor‑1 (LOX‑1) DNA methylation through toll‑like receptor 4(TLR4)/nuclear factor (NF)‑κB/DNA methyltransferase (DNMT)1. The ECs were treated with different concentrations of Hcy, and it was found that Hcy promoted the expression of TLR4, leading to EC injury. The effect of oxidative stress was analyzed by measuring superoxide dismutase, malondialdehyde and hydrogen peroxide in the ECs. In addition, the association between NF‑κB and DNMT1 was examined by treatment of the ECs with pyrrolidine dithiocarbamate (PDTC). The results suggested that Hcy induced LOX‑1 DNA hypomethyaltion to promote the expression levels of LOX‑1. Taken together, Hcy injured the ECs through the effect of methylation and trans‑sulfuration metabolism of LOX‑1 through TLR4/NF‑κB/DNMT1. Following injury to the ECs, lipids, particularly ox‑LDL, accumulated in the sub‑endothelial layer to promote the formation of AS.
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Affiliation(s)
- Sheng-Chao Ma
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Yin-Ju Hao
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Yun Jiao
- Department of Infectious Diseases, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Yan-Hua Wang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Ling-Bo Xu
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Cai-Yan Mao
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Xiao-Ling Yang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - An-Ning Yang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Jue Tian
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Ming-Hao Zhang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Shao-Ju Jin
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Hua Xu
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Yi-Deng Jiang
- School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
| | - Hui-Ping Zhang
- Department of Prenatal Diagnosis Center, General Hospital of Ningxia Medical University, Yinchuan, Ningxia 750004, P.R. China
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The potential role of in silico approaches to identify novel bioactive molecules from natural resources. Future Med Chem 2017; 9:1665-1686. [PMID: 28841048 DOI: 10.4155/fmc-2017-0124] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In recent years, integration of in silico approaches to natural product (NP) research reawakened the declined interest in NP-based drug discovery efforts. In particular, advancements in cheminformatics enabled comparison of NP databases with contemporary small-molecule libraries in terms of molecular properties and chemical space localizations. Virtual screening and target fishing approaches were successful in recognizing the untold macromolecular targets for NPs to exploit the unmet therapeutic needs. Developments in molecular docking and scoring methods along with molecular dynamics enabled to predict the target-ligand interactions more accurately taking into consideration the remarkable structural complexity of NPs. Hence, innovative in silico strategies have contributed valuably to the NP research in drug discovery processes as reviewed herein. [Formula: see text].
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Krishna S, Shukla S, Lakra AD, Meeran SM, Siddiqi MI. Identification of potent inhibitors of DNA methyltransferase 1 (DNMT1) through a pharmacophore-based virtual screening approach. J Mol Graph Model 2017; 75:174-188. [PMID: 28582695 DOI: 10.1016/j.jmgm.2017.05.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 02/06/2023]
Abstract
DNA methylation is an epigenetic change that results in the addition of a methyl group at the carbon-5 position of cytosine residues. DNA methyltransferase (DNMT) inhibitors can suppress tumour growth and have significant therapeutic value. However, the established inhibitors are limited in their application due to their substantial cytotoxicity. Additionally, the standard drugs for DNMT inhibition are non-selective cytosine analogues with considerable cytotoxic side-effects. In the present study, we have designed a workflow by integrating various ligand-based and structure-based approaches to discover new agents active against DNMT1. We have derived a pharmacophore model with the help of available DNMT1 inhibitors. Utilising this model, we performed the virtual screening of Maybridge chemical library and the identified hits were then subsequently filtered based on the Naïve Bayesian classification model. The molecules that have returned from this classification model were subjected to ensemble based docking. We have selected 10 molecules for the biological assay by inspecting the interactions portrayed by these molecules. Three out of the ten tested compounds have shown DNMT1 inhibitory activity. These compounds were also found to demonstrate potential inhibition of cellular proliferation in human breast cancer MDA-MB-231 cells. In the present study, we have utilized a multi-step virtual screening protocol to identify inhibitors of DNMT1, which offers a starting point to develop more potent DNMT1 inhibitors as anti-cancer agents.
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Affiliation(s)
- Shagun Krishna
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Samriddhi Shukla
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Amar Deep Lakra
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Syed Musthapa Meeran
- Endocrinology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India
| | - Mohammad Imran Siddiqi
- Molecular & Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 260031, India.
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20
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Cheray M, Pacaud R, Nadaradjane A, Oliver L, Vallette FM, Cartron PF. Specific Inhibition of DNMT3A/ISGF3γ Interaction Increases the Temozolomide Efficiency to Reduce Tumor Growth. Am J Cancer Res 2016; 6:1988-1999. [PMID: 27698935 PMCID: PMC5039338 DOI: 10.7150/thno.9150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 07/16/2015] [Indexed: 11/28/2022] Open
Abstract
DNA methylation is a fundamental feature of genomes and is a candidate for pharmacological manipulation that might have important therapeutic advantage. Thus, DNA methyltransferases (DNMTs) appear to be ideal targets for drug intervention. By focusing on interactions existing between DNMT3A and DNMT3A-binding protein (D3A-BP), our work identifies the DNMT3A/ISGF3γ interaction such as a biomarker whose the presence level is associated with a poor survival prognosis and with a poor prognosis of response to the conventional chemotherapeutic treatment of glioblastoma multiforme (radiation plus temozolomide). Our data also demonstrates that the disruption of DNMT3A/ISGF3γ interactions increases the efficiency of chemotherapeutic treatment on established tumors in mice. Thus, our data opens a promising and innovative alternative to the development of specific DNMT inhibitors.
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21
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Chen YT, Liao JW, Tsai YC, Tsai FJ. Inhibition of DNA methyltransferase 1 increases nuclear receptor subfamily 4 group A member 1 expression and decreases blood glucose in type 2 diabetes. Oncotarget 2016; 7:39162-39170. [PMID: 27322146 PMCID: PMC5129922 DOI: 10.18632/oncotarget.10043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/29/2016] [Indexed: 12/30/2022] Open
Abstract
Our previous genome-wide association studies showed that DNA methyltransferase 1 (DNMT1) is associated with increased susceptibility to type 2 diabetes (T2D) in Han Chinese individuals. Here, we aimed to further evaluate the role of DNMT1 in T2D. We performed a genome-wide DNA methylation array and found that the nuclear receptor subfamily 4 group A member 1 (NR4A1) promoter was hypermethylated in patients with T2D and in a mouse model of T2D. Moreover, DNA hypermethylation of the NR4A1 promoter reduced NR4A1 mRNA expression. Transient transfection of human NR4A1 into RIN-m5F and 293T cells caused DNMT1 inhibition and induced insulin receptor activation. NR4A1knockdown by shRNA resulted in overexpression of DNMT1 and inhibition of insulin receptor, suggesting that the NR4A1 gene is involved in the epigenetics pathway. Furthermore, T2D model mice treated with the DNMT1 inhibitor aurintricarboxylic acid (ATA) showed reduced activation of DNMT1 in pancreatic β cells; this effect reversed the changes in NR4A1 expression and decreased blood glucose in T2D model mice. Thus, our results showed for the first time that DNMT1 caused NR4A1 DNA hypermethylation and blocked insulin signaling in patients with T2D. Importantly, ATA therapy may be useful for decreasing blood glucose levels by reversing NR4A1-dependent insulin signaling. These findings improve our understanding of the crucial roles of these regulatory elements in human T2D.
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Affiliation(s)
- Yng-Tay Chen
- Human Genetic Center, Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Jiunn-Wang Liao
- Graduate Institute of Veterinary Pathobiology, Research Center for Animal Medicine, Animal Disease Diagnostic Center, National Chung Hsing University, Taichung, Taiwan
| | - Ya-Ching Tsai
- Human Genetic Center, Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Human Genetic Center, Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
- Graduate Institute of China Medical Science, China Medical University, Taichung, Taiwan
- Department of Medical Genetics, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Department of Health and Nutrition Biotechnology, Asia University, Taichung, Taiwan
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Molecular Modeling and Chemoinformatics to Advance the Development of Modulators of Epigenetic Targets: A Focus on DNA Methyltransferases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 105:1-26. [PMID: 27567482 DOI: 10.1016/bs.apcsb.2016.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In light of the emerging field of Epi-informatics, ie, computational methods applied to epigenetic research, molecular docking, and dynamics, pharmacophore and activity landscape modeling and QSAR play a key role in the development of modulators of DNA methyltransferases (DNMTs), one of the major epigenetic target families. The increased chemical information available for modulators of DNMTs has opened up the avenue to explore the epigenetic relevant chemical space (ERCS). Herein, we discuss recent progress on the identification and development of inhibitors of DNMTs as potential epi-drugs and epi-probes that have been driven by molecular modeling and chemoinformatics methods. We also survey advances on the elucidation of their structure-activity relationships and exploration of ERCS. Finally, it is illustrated how computational approaches can be applied to identify modulators of DNMTs in food chemicals.
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Wang N, Wang Z, Wang Y, Xie X, Shen J, Peng C, You J, Peng F, Tang H, Guan X, Chen J. Dietary compound isoliquiritigenin prevents mammary carcinogenesis by inhibiting breast cancer stem cells through WIF1 demethylation. Oncotarget 2016; 6:9854-76. [PMID: 25918249 PMCID: PMC4496402 DOI: 10.18632/oncotarget.3396] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 02/15/2015] [Indexed: 02/07/2023] Open
Abstract
Breast cancer stem cells (CSCs) are considered as the root of mammary tumorigenesis. Previous studies have demonstrated that ISL efficiently limited the activities of breast CSCs. However, the cancer prevention activities of ISL and its precise molecular mechanisms remain largely unknown. Here, we report a novel function of ISL as a natural demethylation agent targeting WIF1 to prevent breast cancer. ISL administration suppressed in vivo breast cancer initiation and progression, accompanied by reduced CSC-like populations. A global gene expression profile assay further identified WIF1 as the main response gene of ISL treatment, accompanied by the simultaneous downregulation of β-catenin signaling and G0/G1 phase arrest in breast CSCs. In addition, WIF1 inhibition significantly relieved the CSC-limiting effects of ISL and methylation analysis further revealed that ISL enhanced WIF1 gene expression via promoting the demethylation of its promoter, which was closely correlated with the inhibition of DNMT1 methyltransferase. Molecular docking analysis finally revealed that ISL could stably dock into the catalytic domain of DNMT1. Taken together, our findings not only provide preclinical evidence to demonstrate the use of ISL as a dietary supplement to inhibit mammary carcinogenesis but also shed novel light on WIF1 as an epigenetic target for breast cancer prevention.
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Affiliation(s)
- Neng Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Zhiyu Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong.,Department of Mammary Disease, Guangdong Provincial Hospital of Chinese Medicine, The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangdong, China
| | - Yu Wang
- Department of Pharmacology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Xiaoming Xie
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Jiangang Shen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Cheng Peng
- School of Pharmaceutical Science, Chengdu University of Traditional Chinese Medicine, Sichuan, Chengdu, China
| | - Jieshu You
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Fu Peng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Hailin Tang
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Xinyuan Guan
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong
| | - Jianping Chen
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, the University of Hong Kong, Hong Kong.,School of Pharmaceutical Science, Chengdu University of Traditional Chinese Medicine, Sichuan, Chengdu, China
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24
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Joshi M, Rajpathak SN, Narwade SC, Deobagkar D. Ensemble-Based Virtual Screening and Experimental Validation of Inhibitors Targeting a Novel Site of Human DNMT1. Chem Biol Drug Des 2016; 88:5-16. [PMID: 26850820 DOI: 10.1111/cbdd.12741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 01/16/2016] [Accepted: 01/31/2016] [Indexed: 12/29/2022]
Abstract
Human DNA methyltransferase1 (hDNMT1) is responsible for preserving DNA methylation patterns that play important regulatory roles in differentiation and development. Misregulation of DNA methylation has thus been linked to many syndromes, life style diseases, and cancers. Developing specific inhibitors of hDNMT1 is an important challenge in the area since the currently targeted cofactor and substrate binding site share structural features with various proteins. In this work, we generated a structural model of the active form of hDNMT1 and identified that the 5-methylcytosine (5-mC) binding site of the hDNMT1 is structurally unique to the protein. This site has been previously demonstrated to be critical for methylation activity. We further performed multiple nanosecond time scale atomistic molecular dynamics simulations of the structural model followed by virtual screening of the Asinex database to identify inhibitors targeting the 5-mC site. Two compounds were discovered that inhibited hDNMT1 in vitro, one of which also showed inhibition in vivo corroborating the screening procedure. This study thus identifies and attempts to validate for the first time a unique site of hDNMT1 that could be harnessed for rationally designing highly selective and potent hypomethylating agents.
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Affiliation(s)
- Manali Joshi
- Bioinformatics Centre, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Shriram N Rajpathak
- Center of Advanced Studies, Department of Zoology, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Santosh C Narwade
- Center of Advanced Studies, Department of Zoology, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
| | - Deepti Deobagkar
- Bioinformatics Centre, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India.,Center of Advanced Studies, Department of Zoology, S. P. Pune University, Ganeshkhind Road, Pune, Maharashtra, 411007, India
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Duenas-Gonzalez A, Medina-Franco JL, Chavez-Blanco A, Dominguez-Gomez G, Fernández-de Gortari E. Developmental DNA methyltransferase inhibitors in the treatment of gynecologic cancers. Expert Opin Pharmacother 2015; 17:323-38. [PMID: 26559668 DOI: 10.1517/14656566.2016.1118053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION DNA methylation has become an attractive target for the treatment of cancer. DNA methyltransferase inhibitors have proven useful for the treatment of myelodysplastic syndrome and are being evaluated in gynecological neoplasias. AREAS COVERED We provide an overview of the current knowledge on DNA methylation and cancer and the role of DNA methylation in cervical, ovarian and endometrial carcinomas. The results of recent clinical trials with demethylating agents for cervical and ovarian cancer treatment are also discussed. EXPERT OPINION There are few studies of DNA demethylating agents for cervical and ovarian cancer treatment; nevertheless, the results are promising. To accelerate these advances, there are at least two actions that can be simultaneously pursued. One is to greatly increase the number of small clinical exploratory trials with existing demethylating drugs and using methylome analyses to identify predictive factors for response and/or toxicity. The second is finding out epigenetic 'drivers' unique to gynecological cancers and their subtypes, and then proceed to clinical trials in a highly selected population of patients. It is expected that in the future, DNA demethylation could have a role in the treatment of gynecologic cancers.
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Affiliation(s)
- Alfonso Duenas-Gonzalez
- a Instituto de Investigaciones Biomédicas , Universidad Nacional Autónoma de México/Instituto Nacional de Cancerología , Mexico City , Mexico
| | - José L Medina-Franco
- b Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México City , México
| | - Alma Chavez-Blanco
- c Division of Basic Research , Instituto Nacional de Cancerología , Mexico City , México
| | | | - Eli Fernández-de Gortari
- b Facultad de Química, Departamento de Farmacia , Universidad Nacional Autónoma de México , México City , México
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Naselli F, Belshaw NJ, Gentile C, Tutone M, Tesoriere L, Livrea MA, Caradonna F. Phytochemical Indicaxanthin Inhibits Colon Cancer Cell Growth and Affects the DNA Methylation Status by Influencing Epigenetically Modifying Enzyme Expression and Activity. JOURNAL OF NUTRIGENETICS AND NUTRIGENOMICS 2015; 8:114-27. [PMID: 26439130 DOI: 10.1159/000439382] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/10/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Recently, we have shown anti-proliferative and pro-apoptotic effects of indicaxanthin associated with epigenetic modulation of the onco-suppressor p16INK4a in the human colon cancer cell line CACO2. In the present study, the epigenetic activity of indicaxanthin and the mechanisms involved were further investigated in other colorectal cancer cell lines. METHODS LOVO1, CACO2, HT29, HCT116, and DLD1 cells were used to evaluate the potential influence of consistent dietary concentrations of indicaxanthin on DNA methylation, and the epigenetic mechanisms involved were researched. RESULTS Indicaxanthin exhibited anti-proliferative activity in all cell lines but HT29, induced demethylation in the promoters of some methylation-silenced onco-suppressor genes involved in colorectal carcinogenesis (p16INK4a, GATA4, and ESR1), and left unchanged others which were basally hypermethylated (SFRP1 and HPP1). In apparent contrast, cell exposure to indicaxanthin increased DNMT gene expression, although indicaxanthin appeared to be an inhibitor of DNMT activity. Indicaxanthin also increased the expression of genes involved in DNA demethylation. Finally, an in silico molecular modelling approach suggested stable binding of indicaxanthin at the DNMT1 catalytic site. CONCLUSIONS Our findings contribute to new knowledge in the field of phytochemicals and specifically suggest dietary indicaxanthin as a potential epigenetic agent to protect colon cells against tumoral alterations.
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Affiliation(s)
- Flores Naselli
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Universitx00E0; di Palermo, Palermo, Italy
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Wang X, Zhang L, Ding N, Yang X, Zhang J, He J, Li Z, Sun LQ. Identification and characterization of DNAzymes targeting DNA methyltransferase I for suppressing bladder cancer proliferation. Biochem Biophys Res Commun 2015; 461:329-33. [DOI: 10.1016/j.bbrc.2015.04.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 04/07/2015] [Indexed: 10/23/2022]
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Cheray M, Nadaradjane A, Bonnet P, Routier S, Vallette FM, Cartron PF. Specific inhibition of DNMT1/CFP1 reduces cancer phenotypes and enhances chemotherapy effectiveness. Epigenomics 2015; 6:267-75. [PMID: 25111481 DOI: 10.2217/epi.14.18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
AIM DNA methylation is a fundamental biologic process of genomes and is a candidate for pharmacological manipulation that might have important therapeutic advantages. Thus, DNA methyltransferases (DNMTs) appear to be ideal targets for drug intervention. MATERIALS & METHODS To develop a new generation of DNMT inhibitor, we analyzed the ability of peptides to selectively inhibit certain DNMT1-incuding complexes. RESULTS Our study demonstrates that the disruption of DNMT1/CFP1-including complexes increases the efficiency of chemotherapeutic treatment on established tumors in mice. CONCLUSION Our data opens a promising and innovative alternative to the development of DNMT inhibitors.
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Shilpi A, Parbin S, Sengupta D, Kar S, Deb M, Rath SK, Pradhan N, Rakshit M, Patra SK. Mechanisms of DNA methyltransferase-inhibitor interactions: Procyanidin B2 shows new promise for therapeutic intervention of cancer. Chem Biol Interact 2015; 233:122-38. [PMID: 25839702 DOI: 10.1016/j.cbi.2015.03.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Revised: 03/17/2015] [Accepted: 03/22/2015] [Indexed: 12/20/2022]
Abstract
DNA methyltransferases (DNMTs) is a key epigenetic enzyme for pharmacological manipulation and is employed in cancer reprogramming. During past few years multiple strategies have been implemented to excavate epigenetic compounds targeting DNMTs. In light of the emerging concept of chemoinformatics, molecular docking and simulation studies have been employed to accelerate the development of DNMT inhibitors. Among the DNMT inhibitors known till date, epigallocathechin-3-gallate (EGCG) was identified to be effective in reducing DNMT activity. However, the broad spectrum of EGCG to other diseases and variable target enzymes offers some limitations. In view of this, 32 EGCG analogues were screened at S-Adnosyl-L-homocysteine (SAH) binding pocket of DNMTs and procyanidin B2-3, 3'-di-O-gallate (procyanidin B2) was obtained as potent inhibitor having medicinally relevant chemical space. Further, in vitro analysis demonstrates the efficiency of procyanidin B2 in attenuating DNMT activity at IC50 of 6.88±0.647 μM and subsequently enhancing the expression of DNMT target genes, E-cadherin, Maspin and BRCA1. Moreover, the toxic property of procyanidin B2 towards triple negative breast cancer cells to normal cells offers platform for pre-clinical trial and an insight to the treatment of cancer.
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Affiliation(s)
- Arunima Shilpi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Sabnam Parbin
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Dipta Sengupta
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Moonmoon Deb
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Sandip Kumar Rath
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Nibedita Pradhan
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Madhumita Rakshit
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India.
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Medina-Franco JL, Méndez-Lucio O, Dueñas-González A, Yoo J. Discovery and development of DNA methyltransferase inhibitors using in silico approaches. Drug Discov Today 2014; 20:569-77. [PMID: 25526932 DOI: 10.1016/j.drudis.2014.12.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/19/2014] [Accepted: 12/10/2014] [Indexed: 01/08/2023]
Abstract
Multiple strategies have evolved during the past few years to advance epigenetic compounds targeting DNA methyltransferases (DNMTs). Significant progress has been made in HTS, lead optimization and determination of 3D structures of DNMTs. In light of the emerging concept of epi-informatics, computational approaches are employed to accelerate the development of DNMT inhibitors helping to screen chemical databases, mine the DNMT-relevant chemical space, uncover SAR and design focused libraries. Computational methods also synergize with natural-product-based drug discovery and drug repurposing. Herein, we survey the latest developments of in silico approaches to advance epigenetic drug and probe discovery targeting DNMTs.
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Affiliation(s)
- José L Medina-Franco
- Facultad de Química, Departamento de Farmacia, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City 04510, Mexico.
| | - Oscar Méndez-Lucio
- Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Alfonso Dueñas-González
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Av. San Fernando 22, Mexico City 14080, Mexico
| | - Jakyung Yoo
- Life Science Research Institute, Daewoong Pharmaceutical Co. Ltd., 72 Dugye-Ro, Pogok-Eup, Gyeonggi-do 449-814, Republic of Korea
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Larabi R, Abtouche S, Brahimi M. Theoretical study of methyl group transfer assisted by proton transfer reaction in the N-acylated imidates. J Mol Model 2014; 20:2302. [DOI: 10.1007/s00894-014-2302-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/12/2014] [Indexed: 11/28/2022]
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Falk SP, Weisblum B. Aptamer Displacement Screen for Flaviviral RNA Methyltransferase Inhibitors. ACTA ACUST UNITED AC 2014; 19:1147-53. [PMID: 24793430 DOI: 10.1177/1087057114533147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/02/2014] [Indexed: 01/08/2023]
Abstract
RNA-protein interactions are vital to the replication of the flaviviral genome. Discovery focused on small molecules that disrupt these interactions represent a viable path for identification of new inhibitors. The viral RNA (vRNA) cap methyltransferase (MTase) of the flaviviruses has been validated as a suitable drug target. Here we report the development of a high-throughput screen for the discovery of compounds that target the RNA binding site of flaviviral protein NS5A. The assay described here is based on displacement of an MT-bound polynucleotide aptamer, decathymidylate derivatized at its 5' end with fluorescein (FL-dT10). Based on the measurement of fluorescence polarization, FL-dT10 bound to yellow fever virus (YFV) MTase in a saturable manner with a Kd= 231 nM. The binding was reversed by a 250-nucleotide YFV messenger RNA (mRNA) transcript and by the triphenylmethane dye aurintricarboxylic acid (ATA). The EC50for ATA displacement was 1.54 µM. The MTase cofactors guanosine-5'-triphosphate and S-adenosyl-methionine failed to displace FL-dT10. Analysis by electrophoretic mobility shift assay (EMSA) suggests that ATA binds YFV MTase so as to displace the vRNA. The assay was determined to have a Z' of 0.83 and was successfully used to screen a library of known bioactives.
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Affiliation(s)
- Shaun P Falk
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Bernard Weisblum
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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Rilova E, Erdmann A, Gros C, Masson V, Aussagues Y, Poughon-Cassabois V, Rajavelu A, Jeltsch A, Menon Y, Novosad N, Gregoire JM, Vispé S, Schambel P, Ausseil F, Sautel F, Arimondo PB, Cantagrel F. Design, synthesis and biological evaluation of 4-amino-N- (4-aminophenyl)benzamide analogues of quinoline-based SGI-1027 as inhibitors of DNA methylation. ChemMedChem 2014; 9:590-601. [PMID: 24678024 PMCID: PMC4506529 DOI: 10.1002/cmdc.201300420] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Quinoline derivative SGI-1027 (N-(4-(2-amino-6-methylpyrimidin-4-ylamino)phenyl)-4-(quinolin-4-ylamino)benzamide) was first described in 2009 as a potent inhibitor of DNA methyltransferase (DNMT) 1, 3A and 3B. Based on molecular modeling studies, performed using the crystal structure of Haemophilus haemolyticus cytosine-5 DNA methyltransferase (MHhaI C5 DNMT), which suggested that the quinoline and the aminopyridimine moieties of SGI-1027 are important for interaction with the substrates and protein, we designed and synthesized 25 derivatives. Among them, four compounds—namely the derivatives 12, 16, 31 and 32—exhibited activities comparable to that of the parent compound. Further evaluation revealed that these compounds were more potent against human DNMT3A than against human DNMT1 and induced the re-expression of a reporter gene, controlled by a methylated cytomegalovirus (CMV) promoter, in leukemia KG-1 cells. These compounds possessed cytotoxicity against leukemia KG-1 cells in the micromolar range, comparable with the cytotoxicity of the reference compound, SGI-1027. Structure–activity relationships were elucidated from the results. First, the presence of a methylene or carbonyl group to conjugate the quinoline moiety decreased the activity. Second, the size and nature of the aromatic or heterocycle subsitutents effects inhibition activity: tricyclic moieties, such as acridine, were found to decrease activity, while bicyclic substituents, such as quinoline, were well tolerated. The best combination was found to be a bicyclic substituent on one side of the compound, and a one-ring moiety on the other side. Finally, the orientation of the central amide bond was found to have little effect on the biological activity. This study provides new insights in to the structure-activity relationships of SGI-1027 and its derivative.
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Affiliation(s)
- Elodie Rilova
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Alexandre Erdmann
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Christina Gros
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Véronique Masson
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Yannick Aussagues
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Valérie Poughon-Cassabois
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Arumugam Rajavelu
- Institute of Biochemistry, Faculty of Chemistry, University StuttgartPfaffenwaldring 55, 70569 Stuttgart (Germany)
| | - Albert Jeltsch
- Institute of Biochemistry, Faculty of Chemistry, University StuttgartPfaffenwaldring 55, 70569 Stuttgart (Germany)
| | - Yoann Menon
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Natacha Novosad
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Jean-Marc Gregoire
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Stéphane Vispé
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Philippe Schambel
- Institut de Recherches Pierre Fabre17 Rue Jean Moulin, 81106 Castres Cedex (France)
| | - Fréderic Ausseil
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - François Sautel
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Paola B Arimondo
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
| | - Frédéric Cantagrel
- USR CNRS-Pierre Fabre No. 3388 ETaC, Centre de Recherche et de Développement Pierre Fabre (CRDPF)3 Ave Hubert Curien, 31035 Toulouse Cedex 01 (France) E-mail:
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Rationalization of activity cliffs of a sulfonamide inhibitor of DNA methyltransferases with induced-fit docking. Int J Mol Sci 2014; 15:3253-61. [PMID: 24566147 PMCID: PMC3958909 DOI: 10.3390/ijms15023253] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 02/12/2014] [Accepted: 02/14/2014] [Indexed: 12/04/2022] Open
Abstract
Inhibitors of human DNA methyltransferases (DNMT) are of increasing interest to develop novel epi-drugs for the treatment of cancer and other diseases. As the number of compounds with reported DNMT inhibition is increasing, molecular docking is shedding light to elucidate their mechanism of action and further interpret structure–activity relationships. Herein, we present a structure-based rationalization of the activity of SW155246, a distinct sulfonamide compound recently reported as an inhibitor of human DNMT1 obtained from high-throughput screening. We used flexible and induce-fit docking to develop a binding model of SW155246 with a crystallographic structure of human DNMT1. Results were in excellent agreement with experimental information providing a three-dimensional structural interpretation of ‘activity cliffs’, e.g., analogues of SW155246 with a high structural similarity to the sulfonamide compound, but with no activity in the enzymatic assay.
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Méndez-Lucio O, Tran J, Medina-Franco JL, Meurice N, Muller M. Toward Drug Repurposing in Epigenetics: Olsalazine as a Hypomethylating Compound Active in a Cellular Context. ChemMedChem 2014; 9:560-5. [DOI: 10.1002/cmdc.201300555] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Indexed: 11/09/2022]
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Medina-Franco JL, Méndez-Lucio O, Martinez-Mayorga K. The Interplay Between Molecular Modeling and Chemoinformatics to Characterize Protein–Ligand and Protein–Protein Interactions Landscapes for Drug Discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 96:1-37. [DOI: 10.1016/bs.apcsb.2014.06.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Cheray M, Pacaud R, Nadaradjane A, Vallette FM, Cartron PF. Specific inhibition of one DNMT1-including complex influences tumor initiation and progression. Clin Epigenetics 2013; 5:9. [PMID: 23809695 PMCID: PMC3727981 DOI: 10.1186/1868-7083-5-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/03/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reactivation of silenced tumor suppressor genes by DNMT inhibitors has provided an alternative approach to cancer therapy. However, DNMT inhibitors have also been shown to induce or enhance tumorigenesis via DNA hypomethylation-induced oncogene activation and chromosomal instability. To develop more specific DNMT inhibitors for efficient cancer therapy, we compared the effects of peptides designed to specifically disrupt the interaction of DNMT1 with different proteins. FINDINGS Our data indicated that the use of an unspecific DNMT inhibitor (5aza-2deoxycytidine), a DNMT1 inhibitor (procainamide) or peptides disrupting the DNMT1/PCNA, DNMT1/EZH2, DNMT1/HDAC1, DNMT1/DNMT3b and DNMT1/HP1 interactions promoted or enhanced in vivo tumorigenesis in a mouse glioma model. In contrast, a peptide disrupting the DNMT1/DMAP1 interaction, which per se did not affect tumor growth, sensitized cancer cells to chemotherapy/irradiation-induced cell death. Finally, our data indicated that the peptide disrupting the DNMT1/DMAP1 interaction increased the efficiency of temozolomide treatment. CONCLUSION Our data suggest that the DNMT1/DMAP1 interaction could be an effective anti-cancer target and opens a new avenue for the development of new strategies to design DNMT inhibitors.
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Affiliation(s)
- Mathilde Cheray
- Centre de Recherche en Cancérologie Nantes-Angers, INSERM, U892, Equipe Apoptose et progression tumorale, Equipe labellisée Ligue Nationale Contre le Cancer, 8 quai moncousu, BP7021, Nantes, 44007, France.
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Yoo J, Choi S, Medina-Franco JL. Molecular modeling studies of the novel inhibitors of DNA methyltransferases SGI-1027 and CBC12: implications for the mechanism of inhibition of DNMTs. PLoS One 2013; 8:e62152. [PMID: 23637988 PMCID: PMC3636198 DOI: 10.1371/journal.pone.0062152] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Accepted: 03/18/2013] [Indexed: 12/05/2022] Open
Abstract
DNA methylation is an epigenetic modification that regulates gene expression by DNA methyltransferases (DNMTs). Inhibition of DNMTs is a promising approach for cancer therapy. Recently, novel classes of the quinolone-based compound, SGI-1027, and RG108-procainamide conjugates, CBC12, have been identified as potent DNMT inhibitors. In this work, we report comprehensive studies using induced-fit docking of SGI-1027 and CBC12 with human DNMT1 and DNMT3A. The docking was performed in the C-terminal MTase catalytic domain, which contains the substrate and cofactor binding sites, in the presence and absence of other domains. Induced-fit docking predicts possible binding modes of the ligands through the appropriate structural changes in the receptor. This work suggests a hypothesis of the inhibitory mechanisms of the new inhibitors which is in agreement with the reported autoinhibitory mechanism. The insights obtained in this work can be used to design DNMT inhibitors with novel scaffolds.
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Affiliation(s)
- Jakyung Yoo
- National Leading Research Lab of Molecular Modeling & Drug Design, College of Pharmacy, Division of Life and Pharmaceutical Sciences, and Global Top5 Research Program, Ewha Womans University, Seoul, Korea
| | - Sun Choi
- National Leading Research Lab of Molecular Modeling & Drug Design, College of Pharmacy, Division of Life and Pharmaceutical Sciences, and Global Top5 Research Program, Ewha Womans University, Seoul, Korea
- * E-mail: (SC) (SC); (JLMF) (JM)
| | - José L. Medina-Franco
- Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
- * E-mail: (SC) (SC); (JLMF) (JM)
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Popovic R, Shah MY, Licht JD. Epigenetic therapy of hematological malignancies: where are we now? Ther Adv Hematol 2013; 4:81-91. [PMID: 23610616 DOI: 10.1177/2040620712466864] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
A growing amount of evidence points towards alterations in epigenetic machinery as a leading cause in disease initiation and progression. Like genetic alterations, misregulation of the epigenetic regulators can lead to abnormal gene expression. However, unlike genetic events, the epigenetic machinery may be targeted pharmacologically, potentially resulting in the reversal of a particular epigenetic state. The success of DNA methyltransferase and histone deacetylase inhibitors represents a proof of concept for the use of therapies intended to target the epigenome in the treatment of hematological malignancies. Nevertheless, the molecular mechanisms underlying the efficacy of these agents have not been completely elucidated. Recently, a large number of studies sequencing cancer cell genomes identified recurring mutations of epigenetic regulators, providing new insights into the molecular underpinnings of cancer. Consequently, the efforts to identify specific epigenetic inhibitors have been expanded in order to target particular subsets of patients. This review will summarize the progress made using the currently available epigenetic therapies and discuss some of the more recently identified targets whose inhibition may present potential avenues for the treatment of hematologic malignancies.
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Affiliation(s)
- Relja Popovic
- Division of Hematology/Oncology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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Medina-Franco JL, Yoo J. Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: insights to unveil inhibitors in chemical databases. Mol Divers 2013; 17:337-44. [PMID: 23447100 DOI: 10.1007/s11030-013-9428-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2012] [Accepted: 02/07/2013] [Indexed: 12/21/2022]
Abstract
Inhibitors of DNA methyltransferase (DNMT) are attractive compounds not only as potential therapeutic agents for the treatment of cancer and other diseases, but also as research tools to investigate the role of DNMTs in epigenetic events. Recent advances in high-throughput screening (HTS) for epigenetic targets and the availability of the first crystallographic structure of human DNMT1 encourage the integration of research strategies to uncover and optimize the activity of DNMT inhibitors. Herein, we present a binding model of a novel small-molecule DNMT1 inhibitor obtained by HTS, recently released in a public database. The docking model is in agreement with key interactions previously identified for established inhibitors using extensive computational studies including molecular dynamics and structure-based pharmacophore modeling. Based on the chemical structure of the novel inhibitor, a sequential computational screening of five chemical databases was performed to identify candidate compounds for testing. Similarity searching followed by molecular docking of chemical databases such as approved drugs, natural products, a DNMT-focused library, and a general screening collection, identified at least 108 molecules with promising DNMT inhibitory activity. The chemical structures of all hit compounds are disclosed to encourage the research community working on epigenetics to test experimentally the enzymatic and demethylating activity in vivo. Five candidate hits are drugs approved for other indications and represent potential starting points of a drug repurposing strategy.
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Affiliation(s)
- José L Medina-Franco
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, 04510 México, D.F., Mexico.
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Plitta B, Adamska E, Giel-Pietraszuk M, Fedoruk-Wyszomirska A, Naskręt-Barciszewska M, Markiewicz WT, Barciszewski J. New cytosine derivatives as inhibitors of DNA methylation. Eur J Med Chem 2012; 55:243-54. [DOI: 10.1016/j.ejmech.2012.07.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 07/11/2012] [Accepted: 07/16/2012] [Indexed: 12/31/2022]
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