Abstract
BackgroundEpigenetic mechanisms mainly include DNA methylation, post-translational modifications of histones, chromatin remodeling and non-coding RNAs. All of these processes are mediated and controlled by enzymes. Abnormalities of the enzymes are involved in a variety of complex human diseases. Recently, potent natural or synthetic chemicals are utilized to establish the quantitative contributions of epigenetic regulation through the enzymes and provide novel insight for developing new therapeutics. However, the development of more specific and effective epigenetic therapeutics requires a more complete understanding of the chemical epigenomic landscape.DescriptionHere, we present a human epigenetic enzyme and modulator database (HEMD), the database which provides a central resource for the display, search, and analysis of the structure, function, and related annotation for human epigenetic enzymes and chemical modulators focused on epigenetic therapeutics. Currently, HEMD contains 269 epigenetic enzymes and 4377 modulators in three categories (activators, inhibitors, and regulators). Enzymes are annotated with detailed description of epigenetic mechanisms, catalytic processes, and related diseases, and chemical modulators with binding sites, pharmacological effect, and therapeutic uses. Integrating the information of epigenetic enzymes in HEMD should allow for the prediction of conserved features for proteins and could potentially classify them as ideal targets for experimental validation. In addition, modulators curated in HEMD can be used to investigate potent epigenetic targets for the query compound and also help chemists to implement structural modifications for the design of novel epigenetic drugs.ConclusionsHEMD could be a platform and a starting point for biologists and medicinal chemists for furthering research on epigenetic therapeutics. HEMD is freely available at http://mdl.shsmu.edu.cn/HEMD/.
Highlights
Epigenetics is the study of any potentially stable and heritable change in gene expression or cellular phenotype that occurs without changes in DNA [1,2]
The mechanism is often dysregulated with aberrant gene expression and repression in human diseases and the abnormalities have been found to be associated with amplification, mutation, and other alterations of epigenetic enzymes [8,9], indicating that specific classes of diseases might benefit from epigenetic-targeting therapies
We have developed human epigenetic enzyme and modulator database (HEMD), an integrated database of human epigenetic enzymes and their modulators focused on epigenetic therapeutics
Summary
Epigenetics is the study of any potentially stable and heritable change in gene expression or cellular phenotype that occurs without changes in DNA [1,2]. Epigenetic regulation of gene expression can significantly alter the cellular phenotype due to their ability to activate/silence genes and is mediated through chromatin composed of DNA, histones, non-histone proteins, and non-coding RNA [3]. RNA regulation (microRNA, small interfering RNA, piwiinteracting RNA, etc) [2,4,5] These modifications are mediated and controlled by a group of enzymes, which define as epigenetic enzymes by Copeland et al [6]. Potent natural or synthetic chemicals are utilized to establish the quantitative contributions of epigenetic regulation through the enzymes and provide novel insight for developing new therapeutics. Enzymes are annotated with detailed description of epigenetic mechanisms, catalytic processes, and related diseases, and chemical modulators with binding sites, pharmacological effect, and therapeutic uses. Modulators curated in HEMD can be used to investigate potent epigenetic targets for the query compound and help chemists to implement structural modifications for the design of novel epigenetic drugs
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