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.

Analysis of the Acid/Base Profile of Natural Products from Different Sources.

For many years drug discovery and other areas in chemistry have successfully relied on natural products. Recent advances in computational methods have made possible to study the chemical space of natural products from different sources. Ionizable acidic and basic functional groups heavily influence physicochemical properties and thus a molecule's absorption, distribution, metabolism, excretion, and toxicity characteristics as well as their affinity for biological targets. This work reports the generation and critical comparison of the acid/base profiles of ten chemical databases including seven natural products sets from different origins, a set of semisynthetic compounds, a collection of approved drugs, and a compendium of food chemicals. Similarities were found in the proportion of the main charge state categories among the natural products databases with few differences in their pKa distributions. Clear differences were observed between natural products and the approved drugs and semi-synthetic natural products databases, whereas natural products share some trends with the food chemical database. We noted that the natural products collections comprise around 45 % of neutral compounds. The proportion of single acids was approximately twice that found for FDA drugs, and they demonstrated a similar distribution of pKa values. In contrast to drugs, only 5 % of compounds among the natural products sets had a single basic group. Likewise, simple ampholytes were less prevalent in the natural products databases relative to drugs.

The Acid/Base Profile of a Large Food Chemical Database.

Molecular acid/base properties have a significant influence on membrane permeation, metabolism, absorption, and affinity for biological targets. In particular, ionizable groups are critical in the strength of target-molecule interactions, pharmacokinetics, and toxicity. In this study, we estimated the acid/base properties of the food chemicals from FooDB, a public compound collection with more than 22,000 compounds. It was found that the food chemicals have 40.9 % of neutral compounds, which is twice as many as that found in approved drugs. The most common functional groups among the acid groups in the food chemicals were phenols (16.1 %), phosphates (17.3 %), and carboxylates (17.3 %) while the single-base-containing compounds were of less interest as they accounted for just 5.5 %. To the best of our knowledge, this is the first systematic acid/base profiling of food chemicals and it is part of a continued effort to profile food chemicals for their broad interest in several areas such as nutrition and the food industry in general.