EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape

Area of Science:

• Chemical Biology
• Bioinformatics
• Drug Discovery

Background:

• Epigenetic protein families regulate gene expression.
• Small molecule ligands are crucial for modulating epigenetic targets.
• Existing resources lack integrated experimental, structural, and chemoinformatic data for epigenetic ligands.

Purpose of the Study:

• To develop EpiDBase, an interactive database consolidating data on small molecule ligands for epigenetic proteins.
• To provide a comprehensive resource for researchers in epigenetic drug discovery.

Main Methods:

• Integrated experimental (IC50), structural, and chemoinformatic data for 5,784 unique ligands.
• Curated unique molecular scaffolds by filtering complex structures and applying drug-likeness rules (ZINC, Lilly MedChem).
• Utilized OpenBabel for physicochemical property analysis and clustering (hierarchical, partitioning, multidimensional scaling).

Main Results:

• EpiDBase contains 11,422 entries of small molecule ligands targeting epigenetic writers, erasers, and readers.
• Includes detailed ligand properties: molecular weight, XlogP, H-bond counts, 2D/3D structures, and InChIKey.
• Offers integrated search (text, disease-specific, advanced) and analysis tools (substructure, similarity).

Conclusions:

• EpiDBase serves as a valuable, integrated resource for the design and development of small molecule epigenetic modulators.
• Facilitates advanced analysis and identification of novel molecular scaffolds for epigenetic targets.