A New Metric Quantifying Chemical and Biological Property of Small Molecule Metabolites and Drugs

Abstract

One prominent class of drugs is chemical small molecules (CSMs), but the majority of CSMs are of very low druggable potential. Therefore, it is quite important to predict drug-related properties (druggable properties) for candidate CSMs. Currently, a number of druggable properties (e.g., logP and pKa) can be calculated by in silico methods; still the identification of druggable CSMs is a high-risk task, and new quantitative metrics for the druggable potential of CSMs are increasingly needed. Here, we present normalized bond energy (NBE), a new metric for the above purpose. By applying NBE to the DrugBank CSMs whose properties are largely known, we revealed that NBE is able to describe a number of critical druggable properties including logP, pKa, membrane permeability, blood–brain barrier penetration, and human intestinal absorption. Moreover, given that the human endogenous metabolites can serve as important resources for drug discovery, we applied NBE to the metabolites in the Human Metabolome Database. As a result, NBE showed a significant difference in metabolites from various body fluids and was correlated with some important properties, including melting point and water solubility.