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

Subodh Kumar Mishra,Amit Kumar

doi:10.1093/database/baw002

Abstract

Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php.Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php

Highlights

Nucleic acids are the key macromolecule elements in the cell and it regulates the cellular activities in several ways, at various stages such as replication, transcription, posttranscription, translation and various processes such as host–pathogen interaction, affinity maturation of antibody, regulation of cellular stress, cell metabolism and many more [1,2,3,4,5]
The graphical user interface (GUI) of Nucleic acid ligand database (NALDB) database is available at the web URL http://bsbe.iiti.ac.in/bsbe/naldb/ HOME.php
The NALDB is a collection of nucleic acid binding small molecule with >3500 entries

Summary

Introduction

Nucleic acids are the key macromolecule elements in the cell and it regulates the cellular activities in several ways, at various stages such as replication, transcription, posttranscription, translation and various processes such as host–pathogen interaction, affinity maturation of antibody, regulation of cellular stress, cell metabolism and many more [1,2,3,4,5]. Cellular nucleic acids are majorly classified as DNA or RNA that may fold into different type of structures such as duplex, triplex, quadruplex, hairpin form, etc. The formation of G-quadruplex structure inhibits the translation of RNA sequence found in 50-UTR of Arabidopsis thaliana ATR mRNA [12]. The expression c9orf gene was inhibited due to the formation of G-quadruplex structure in the non-coding region of its mRNA and causes Amyotrophic lateral sclerosis (ALS), a neurodegenerative disease [13]. Apart from inhibiting the gene expression, special structures of nucleic acid have an important role in double-stranded break repair, for example, DSBinduced small RNA [14]

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