HDACiDB: a database for histone deacetylase inhibitors

Kasi Murugan,1 Shanmugasamy Sangeetha,2 Shanmugasamy Ranjitha,2 Antony Vimala,2 Saleh Al-Sohaibani,1 Gopal Rameshkumar21Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia; 2Bioinformatics Laboratory, Anna University K. Balachander Research Centre, MIT Campus of Anna University Chennai, Chennai, IndiaAbstract: An histone deacetylase (HDAC) inhibitor database (HDACiDB) was constructed to enable rapid access to data relevant to the development of epigenetic modulators (HDAC inhibitors [HDACi]), helping bring precision cancer medicine a step closer. Thousands of HDACi targeting HDACs are in various stages of development and are being tested in clinical trials as monotherapy and in combination with other cancer agents. Despite the abundance of HDACi, information resources are limited. Tools for in silico experiments on specific HDACi prediction, for designing and analyzing the generated data, as well as custom-made specific tools and interactive databases, are needed. We have developed an HDACiDB that is a composite collection of HDACi and currently comprises 1,445 chemical compounds, including 419 natural and 1,026 synthetic ones having the potential to inhibit histone deacetylation. Most importantly, it will allow application of Lipinski’s rule of five drug-likeness and other physicochemical property-based screening of the inhibitors. It also provides easy access to information on their source of origin, molecular properties, drug likeness, as well as bioavailability with relevant references cited. Being the first comprehensive database on HDACi that contains all known natural and synthetic HDACi, the HDACiDB may help to improve our knowledge concerning the mechanisms of actions of available HDACi and enable us to selectively target individual HDAC isoforms and establish a new paradigm for intelligent epigenetic cancer drug design. The database is freely available on the http://hdacidb.bioinfo.au-kbc.org.in/hdacidb/ website.Keywords: cancer, drug likeness, histone deacetylase inhibitors, epigenetics, Lipinski’s rule, molecular propertie