ArticleJournal of computer-aided molecular design2011
Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase.
Article in Journal of computer-aided molecular design, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 77 citations in OpenAlex.
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- Decoding the Role of Epigenetics in Breast Cancer Using Formal Modeling and Machine-Learning Methods.Frontiers in molecular biosciences · 2022Article
- The Impact of EGCG and RG108 on SOCS1 Promoter DNA Methylation and Expression in U937 Leukemia Cells.Reports of biochemistry & molecular biology · 2021Article
- Natural Products Impacting DNA Methyltransferases and Histone Deacetylases.Frontiers in pharmacology · 2020Review
- Structure and function insights garnered from in silico modeling of the thrombospondin type-1 domain-containing 7A antigen.Proteins · 2019Article
- Inhibitors of DNA Methyltransferases From Natural Sources: A Computational Perspective.Frontiers in pharmacology · 2018Review
- – (-) Menthol Induces Reversal of Promoter Hypermethylation and Associated Up-Regulation of the FANCF Gene in the SiHa Cell LineAsian Pacific journal of cancer prevention : APJCP · 2017Article
- Bringing Curcumin to the Clinic in Cancer Prevention: a Review of Strategies to Enhance Bioavailability and Efficacy.The AAPS journal · 2017Review
- Is It Reliable to Use Common Molecular Docking Methods for Comparing the Binding Affinities of Enantiomer Pairs for Their Protein Target?International journal of molecular sciences · 2016Article
- Flavonoids as CDK1 Inhibitors: Insights in Their Binding Orientations and Structure-Activity Relationship.PloS one · 2016Article
- DNA cytosine and methylcytosine deamination by APOBEC3B: enhancing methylcytosine deamination by engineering APOBEC3B.The Biochemical journal · 2015Article
- Epigenetic DNA Methylation Linked to Social Dominance.PloS one · 2015Article
- Design, synthesis and biological evaluation of 4-amino-N- (4-aminophenyl)benzamide analogues of quinoline-based SGI-1027 as inhibitors of DNA methylation.ChemMedChem · 2014Article
- Accurate structure prediction of peptide-MHC complexes for identifying highly immunogenic antigens.Molecular immunology · 2013Article
- Docking of a novel DNA methyltransferase inhibitor identified from high-throughput screening: insights to unveil inhibitors in chemical databases.Molecular diversity · 2013Article
- Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.Current pharmaceutical design · 2013Review
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- Curcumin causes promoter hypomethylation and increased expression of FANCF gene in SiHa cell line.Molecular and cellular biochemistry · 2012Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methyltransferase 1 (DNMT1) is an emerging epigenetic target for the treatment of cancer and other diseases. To date, several inhibitors from different structural classes have been published. In this work, we report a comprehensive molecular modeling study of 14 established DNTM1 inhibitors with a herein developed homology model of the catalytic domain of human DNTM1. The geometry of the homology model was in agreement with the proposed mechanism of DNA methylation. Docking results revealed that all inhibitors studied in this work have hydrogen bond interactions with a glutamic acid and arginine residues that play a central role in the mechanism of cytosine DNA methylation. The binding models of compounds such as curcumin and parthenolide suggest that these natural products are covalent blockers of the catalytic site. A pharmacophore model was also developed for all DNMT1 inhibitors considered in this work using the most favorable binding conformations and energetic terms of the docked poses. To the best of our knowledge, this is the first pharmacophore model proposed for compounds with inhibitory activity of DNMT1. The results presented in this work represent a conceptual advance for understanding the protein-ligand interactions and mechanism of action of DNMT1 inhibitors. The insights obtained in this work can be used for the structure-based design and virtual screening for novel inhibitors targeting DNMT1.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.