Introduction

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]. Currently, there are at least four types of epigenetic regulation: DNA methylation, post-translational modifications of histones (from relatively small groups such as methyl, acetyl, and phosphoryl groups to the attachment of larger moieties such as poly (ADP-ribose) and small ubiquitin-like modifier (SUMO)), ATP-dependent chromatin remodeling (eviction, deposition, or sliding of nucleosomes along DNA), and non-coding RNA regulation (microRNA, small interfering RNA, piwi-interacting 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].

Epigenetic enzyme-mediated control of gene transcription is a critical aspect of embryonic development and continues to play a role in gene regulation and genome stability throughout the lifespan of an organism [7]. The mechanism is often dysregulated with aberrant gene expression and repression in human diseases (e.g. cancer, depression, diabetes mellitus, and inflammatory disease) 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. Therefore, identifying the most appropriate enzymes that should be targeted in the cases of different diseases is a fundamental prerequisite for epigenetic therapeutics.

In recent years, remarkable progress has been made in target identification, drug discovery, and clinical validation for epigenetic therapeutics [10]. Three classes of epigenetic enzymes have been successfully targeted by small chemical modulators that have reached clinical trials for specific therapeutics: the DNA methyltransferases (e.g., Azacitidine, Decitabine), histone deacetylases (e.g., Vorinostat, Romidepsin), and Aurora-B kinases (e.g., Tozasertib, Danusertib) [6]. Some epigenetic enzyme classes have been demonstrated to have strong disease association and are currently being targeted by small molecular modulators in preclinical discovery programs at a number of academic, industry, and government laboratories [11]–[14]. With substantial enthusiasm for the development and implementation of epigenetic therapies, more and more modulators emerged one after another for orphan epigenetic enzymes; on the other hand, known epigenetic modulators may not just work as single agents but rather as components of combination therapies. Therefore, a complete understanding of the chemical epigenomic landscape for chemical-enzyme pairs is necessary for the commencement of more specific and effective therapeutic strategies.

Nowadays, most of the existing resources devoted to epigenetics focus mainly on detailed information about epigenetic features in methylated DNAs [15], [16], modified chromatin proteins [17]–[19], and associated phenotypes [20]–[22] but less on their therapeutics―epigenetic enzymes and modulators. Specialized databases and analysis systems dedicated to epigenetic enzymes and modulators are becoming crucial for a better understanding epigenetic mechanisms of enzymes and designing modulators for therapeutics. To fill this gap, we have developed HEMD, an integrated database of human epigenetic enzymes and their modulators focused on epigenetic therapeutics. This is the first online database, to our knowledge, that focuses on exhaustive information from epigenetic regulation, related disorders to therapeutics in the context of relationship between 269 human enzymes and 4377 modulators, together with their statistical evaluation, references to the scientific literature, and cross-links to other associated databases, such as Enzyme Nomenclature [23], NCBI Epigenomics [15], DAnCER [20], GenBank [24], Uniprot [25], etc. Furthermore, BLAST (basic local alignment search tool) search engine for enzymes and a chemical structure search engine for small modulators are available as web-based tools for epigenetic molecule recognition. Taken together, HEMD is a comprehensive resource that could provide useful information and tool for the investigation of epigenetic mechanisms and novel drug design.

Materials and Methods

First, abstracts of PubMed were automatically filtered for relevant articles in the “DNA methylation”, “histones modification”, “chromatin remodeling”, and “non-coding RNA”. The names of proteins were then extracted from the abstracts to clusters by a protein name dictionary constructed from UniProt [25], retrieving ∼400 distinct biological proteins in human. A team of scientists manually processed the papers with respect to the clustered names. With at least three cases of experimental evidence in biochemistry, crystal structure complex and domain analysis, 269 proteins supporting their functional regulation of gene expression by epigenetic manner, were verified as epigenetic enzymes for deposition into the HEMD. All proteins in the HEMD were annotated with gene information, biological function, natural mutations, and related diseases extracted from GenBank [24], Uniprot [25], Enzyme Nomenclature [23] and original literature. An up-to-date synchronization on available structures of epigenetic enzymes from PDB [26] is present and their structural classification SCOP [27] and CATH [28] based on the PDB ID are also labeled. Theoretical models of epigenetic enzymes without structures were generated with I-TASSER [29] or built manually using Modeller [30] when C-score of the best I-TASSER model is below −1.5 or high-homologous oligomeric templates are available in PDB. All structures are downloadable as PDB files. Notably, extensive descriptions of binding sites on both substrates and modulators were separately summarized from literature and the sites were always highlighted in the diagram of protein topologies [31], [32] if they have been explicitly validated by biochemistry or structural biology.

Second, after all epigenetic enzymes with relevant annotation information were collected, we further searched for epigenetic modulators for the 269 epigenetic enzymes. All the abstracts from PubMed, United States Patent and European Patent files containing “modulator/effector/activator/inhibitor/agonist/antagonist” in combination with the name of the collected epigenetic enzymes were curated and then manually identified as the final set, resulting in the collection of 4377 chemical epigenetic modulators with respective references. Meanwhile, publicly available binding affinities and test methods of the epigenetic modulators to their epigenetic targets were also obtained from the references. Among the epigenetic modulators in the HEMD, those that increase a particular protein function, for example, catalytic rate, are classified as “epigenetic activator” or “A”. Those that decrease a particular protein function are classified as “epigenetic inhibitor” or “I”. The remaining modulators, which have dual effects on activation and inhibition in a concentration-dependent manner, are classified to the “epigenetic regulator” or “R” category. Since epigenetic modulators were initially identified from endogenous ligands and then widely accepted for the development of novel types of drugs, the tags “Endogenous” and “Druggable” in the HEMD differentiate epigenetic modulators produced in vivo and designed for drug use, respectively. In addition, important physicochemical properties used in drug discovery, such as logP, PSA, the number of rotatable bonds, etc., were calculated on the epigenetic modulators by Filter Program from Openeye (http://www.eyesopen.com). Each modulator in the HEMD is downloadable as 2D mol and 3D mol2 files.

Results

The HEMD database

HEMD is an integrated repository on epigenetic enzymes and chemical modulators for therapeutics, which was manually curated from original literature. In total, 269 epigenetic enzymes and 4377 chemical modulators identified from in vitro binding to the epigenetic enzymes were deposited and fully annotated by the database developers and experts in the field (Figure 1).

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Figure 1. Web interface and back-end database in HEMD.

Key interface screenshots showing the interrelation of tools and user can directly view from “Browse” menu or start search by “Search” menu. All recorders are deposited in MySQL and some kind of important data for epigenetic therapeutics has been summarized in the lower part of the diagram.

https://doi.org/10.1371/journal.pone.0039917.g001

Epigenetic enzymes in HEMD cover four parts, of which 19 of the epigenetic proteins are from DNA methylation, 219 from histone modification, 28 from chromatin remodeling and 3 from non-coding RNA (Figure 2). Crystal structures of 929 redundant proteins were extracted from PDB and 142 epigenetic enzymes have been resolved. Based on the known structures, theoretical 3D models of the remaining 127 enzymes without crystal structures are constructed and downloadable from HEMD. Ninety-two modulator binding sites of the enzymes were identified from crystal complexes. By analyzing the occurrence of structural domains in the epigenetic enzymes represented in Pfam [31], two kinds of known domains, DNA/RNA/Histone binding domain and catalytic domain, which are the structural basis for epigenetic function are found in 43% and 74% of the 269 epigenetic enzymes, respectively. In addition, success in developing epigenetic therapeutics relies heavily on identifying the most relevant diseases to target, therefore 317 diseases from abnormal epigenetic enzymes have been carefully referenced and exhaustively described in HEMD, including 113 types of cancer and 204 non-oncology disorders.

Download:

• PPT
  PowerPoint slide
• PNG
  larger image
• TIFF
  original image

Figure 2. Statistics on the epigenetic enzymes and modulators.

(A) Class distribution of epigenetic enzymes. (B) The classification of epigenetic enzymes related disease by WHO codes. A00–B99: Certain infectious and parasitic diseases, C00–D48: Neoplasms, D50–D89: Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism, E00–E90: Endocrine, nutritional and metabolic diseases, F00–F99: Mental and behavioural disorders, G00–G99: Diseases of the nervous system, H00–H59: Diseases of the eye and adnexa, H60–H95: Diseases of the ear and mastoid process, I00–I99: Diseases of the circulatory system, J00–J99: Diseases of the respiratory system, K00–K93: Diseases of the digestive system, L00–L99: Diseases of the skin and subcutaneous tissue, M00–M99: Diseases of the musculoskeletal system and connective tissue, N00–N99: Diseases of the genitourinary system, O00–O99: Pregnancy, childbirth and the puerperium, P00–P96: Certain conditions originating in the perinatal period, Q00–Q99: Congenital malformations, deformations and chromosomal abnormalities, R00–R99: Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified, S00–T98: Injury, poisoning and certain other consequences of external causes, U00–U99: Codes for special purposes. (C) Category distribution of epigenetic modulators. (D) History of discovering epigenetic modulators.

https://doi.org/10.1371/journal.pone.0039917.g002

Among 4377 epigenetic chemical modulators in current HEMD, 241 activators, 4148 inhibitors, and 2 regulators were revealed to bind to corresponding epigenetic enzymes, and only 14 modulators (0.32%) have multiple effects on different epigenetic systems (Figure 2), finally resulting in 7016 epigenetic interactions between the enzymes and chemical modulators in HEMD. The chemical modulators range from organic small molecules (4053, 92.60%), peptides (249, 5.69%), nucleotides (61, 1.39%), to salts (14, 0.32%). Since almost all epigenetic hits/leads/drugs were initially derived from endogenous molecules and then screened and modified in drug discovery, HEMD now holds 176 endogenous epigenetic seeds and 4199 compounds in the pipeline of drug discovery.

Discussion

HEMD is a manually curated database dedicated to epigenetic therapeutics involving enzymes and chemical modulators. It is the first online resource of this kind and the data in HEMD are freely available to all potential users. We harvested verified epigenetic enzymes and modulators from scientific articles. Of the 269 epigenetic enzymes in HEMD, 240 (89.22%) proteins have been associated with diseases and 107 (39.78%) proteins can be targeted for therapeutics by chemical modulators. Remarkably, >45% epigenetic modulators in HEMD are not covered by two important bioactive small molecule databases viz, Drugbank [38] and ChEMBL [39]. Even compared with the largest chemical collection PubChem (http://pubchem.ncbi.nlm.nih.gov), there are still 23% unique compounds in HEMD and a great number of compounds deposited in PubChem have no epigenetic annotations, revealing the potential utilities of HEMD in the epigenetic therapeutics.

Our initial collection mainly focused on epigenetic therapeutics by enzymes and their chemical modulators, which have been widely studied in recent 20 years. More than 200 proteins were found as epigenetic regulators in the area of DNA methylation, histones modifications, chromatin remodeling, and non-coding RNA. The formation and regulation of higher-order chromatin architecture derives from various integrants like DNA methylation, histone modifications, histone variants, and architectural proteins [40], which also could be decomposed into the functions from four types of enzymes curated in HMED. In future, we will continue updating the database every six months and respond to “Expert” request within one week.

HEMD provides users with both chemical and biological tools for information mining on epigenetic molecules. We believe such integrative epigenetic data and tools will not only help scientists to find novel relationships for epigenetic therapeutics, but also provide a starting point for biologists and chemists who have interests in entering the field. HEMD is freely available at http://mdl.shsmu.edu.cn/HEMD/.