NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

Area of Science:

• Biochemistry
• Medicinal Chemistry
• Bioinformatics

Background:

• Nucleic acids are crucial targets for drug discovery.
• Existing databases lack comprehensive ligand information for all nucleic acid types.
• Developing novel ligands for nucleic acids is essential for treating diseases.

Purpose of the Study:

• To introduce the Nucleic Acid Ligand Database (NALDB), a novel resource for small molecules targeting nucleic acids.
• To provide a centralized platform for experimental data on nucleic acid-targeting ligands.
• To facilitate drug discovery research by offering detailed ligand and target information.

Main Methods:

• Compilation of over 3500 ligand entries with detailed experimental data.
• Inclusion of pharmacokinetic and pharmacodynamic properties, chemical structures (2D/3D), and biological activity (Ki, Kd, IC50).
• Development of web-based search tools, including text and structure queries, and a multi-dimensional advanced search.

Main Results:

• NALDB is the first database to cover all types of nucleic acid ligands.
• The database includes multi-conformer ligand entries (up to 255 per ligand) to support virtual screening.
• Features include 3D structure visualization and comprehensive pharmacological information.

Conclusions:

• NALDB serves as a valuable, freely accessible resource for accelerating nucleic acid-based drug discovery.
• The database supports virtual screening and modeling processes for novel ligand development.
• It aids researchers in identifying potential therapeutic agents for cancers and neurological disorders.