Are there physicochemical differences between allosteric and competitive ligands?

Previous studies have compared the physicochemical properties of allosteric compounds to non-allosteric compounds. Those studies have found that allosteric compounds tend to be smaller, more rigid, more hydrophobic, and more drug-like than non-allosteric compounds. However, previous studies have not properly corrected for the fact that some protein targets have much more data than other systems. This generates concern regarding the possible skew that can be introduced by the inherent bias in the available data. Hence, this study aims to determine how robust the previous findings are to the addition of newer data. This study utilizes the Allosteric Database (ASD v3.0) and ChEMBL v20 to systematically obtain large datasets of both allosteric and competitive ligands. This dataset contains 70,219 and 9,511 unique ligands for the allosteric and competitive sets, respectively. Physically relevant compound descriptors were computed to examine the differences in their chemical properties. Particular attention was given to removing redundancy in the data and normalizing across ligand diversity and varied protein targets. The resulting distributions only show that allosteric ligands tend to be more aromatic and rigid and do not confirm the increase in hydrophobicity or difference in drug-likeness. These results are robust across different normalization schemes.Author summary: We investigated the differences between allosteric and competitive ligands. Competitive ligands bind in the active site of a protein while allosteric ligands exhibit their effect from a remote location on the protein. Traditionally, drugs take advantage of competitive binding; however when this is not possible, an allosteric site may be a potential target. We used comprehensive, large datasets containing allosteric and competitive ligands curated from publicly available data. We carefully removed redundancy using clustering of both proteins and ligands. Here, we find allosteric ligands tend to be more rigid and aromatic than competitive ligands. However, we contradict previous studies which had indicated allosteric ligands to be more hydrophobic and drug-like. Our study provides insight into chemical traits biochemists should potential consider when designing allosteric ligands.