A Cheminformatics Analysis of Substituents in Bioactive Molecules and Their Bioisosteric Replacement Network

Abstract Substituents, decorating the central molecule core, play a key role in medicinal chemistry, where they are modified during lead optimization to improve biological activity, physicochemical properties, selectivity, and other drug properties. The selection of appropriate substituents, guided by the bioisosteric principle, is one of the most effective strategies for optimizing molecular properties while preserving affinity for the biological target. Despite the widespread application of bioisosteric replacement in drug discovery, systematic analyses of bioisosteric relationships among substituents derived from large collections of bioactive molecules remain limited. In this work, we present a comprehensive analysis of substituents occurring in bioactive molecules and investigate their bioisosteric relationships using data extracted from medicinal chemistry literature. Bioisosteric pairs are identified from substitution patterns observed in related compounds with activity on the same target, enabling the construction of a network of frequently interchangeable substituents. Because the analysis is based on the observed co-occurrence of substituents within the same molecular environments rather than on structural similarity or physicochemical descriptors, it captures experimentally validated substitution patterns and uncovers not only well-established bioisosteric pairs but also less well-known relationships. The resulting bioisosteric substituent network is made available through a free web application at https://ertlmolecular.com/tools.html, providing a practical resource for medicinal chemists engaged in lead optimization, analog design, and library development.