Quantitative Structure-Epigenetic Activity Relationships

The Acid/Base Characterization of Molecules with Epigenetic Activity

The acidic and basic functional groups in a molecule strongly influence its physicochemical properties, affinity for a macromolecule, pharmacokinetics, and toxicity. For instance, basicity has been correlated with molecular promiscuity, hERG blockade, and phospholipidosis. Nonetheless, no systematic characterization of the acid/base profile of epigenomic databases has been reported. This study describes an analysis of the acidic ionization constant distribution of a library of 7820 compounds with reported activity against epigenetic targets. Furthermore, the epigenomics database's acid/base profile was compared to the reference libraries of food chemicals, natural products, and approved drugs. It was found that the acid/base profile of histone lysine demethylase ligands is more similar to previously approved drugs, and histone acetyltransferase ligands have acidic and basic functional groups largely found in food chemicals and natural products; this support the potential of these libraries for finding new epigenetic inhibitors.

Recent progress on cheminformatics approaches to epigenetic drug discovery

The ability of epigenetic markers to affect genome function has enabled transformative changes in drug discovery, especially in cancer and other emerging therapeutic areas. Concordant with the introduction of the term 'epi-informatics', the size of the epigenetically relevant chemical space has grown substantially and so did the number of applications of cheminformatic methods to epigenetics. Recent progress in epi-informatics has improved our understanding of the structure-epigenetic activity relationships and boosted the development of models predicting novel epigenetic agents. Herein, we review the advances in computational approaches to drug discovery of small molecules with epigenetic modulation profiles, summarize the current chemogenomics data available for epigenetic targets, and provide a perspective on the greater utility of biomedical knowledge mining as a means to advance the epigenetic drug discovery.

Chemoinformatics: a perspective from an academic setting in Latin America

This perspective discusses the current progress of a chemoinformatics group in a major university in Latin America. Three major aspects are discussed in a critical manner: research, education, and collaboration with industry and other public research networks. It is also presented an overview of the progress in applied research and development of research concepts. Efforts to teach chemoinformatics at the undergraduate and graduate levels are discussed. It is addressed how the partnership with industry and other not-for-profit research institutions not only brings additional sources of funding but, more importantly, increases the impact of the multidisciplinary work and offers the students to be exposed to other research environments. We also discuss the main perspectives and challenges that remain to be addressed in these settings.