title: What is the likelihood of an active compound to be promiscuous? Systematic assessment of compound promiscuity on the basis of PubChem confirmatory bioassay data.
abstract: Compound promiscuity refers to the ability of small molecules to specifically interact with multiple targets, which represents the origin of polypharmacology. Promiscuity is thought to be a widespread characteristic of pharmaceutically relevant compounds. Yet, the degree of promiscuity among active compounds from different sources remains uncertain. Here, we report a thorough analysis of compound promiscuity on the basis of more than 1,000 PubChem confirmatory bioassays, which yields an upper-limit assessment of promiscuity among active compounds. Because most PubChem compounds have been tested in large numbers of assays, data sparseness has not been a limiting factor for the current analysis. We have determined that there is an overall likelihood of ∼50% of an active PubChem compound to interact with two or more targets. The probability to interact with more than five targets is reduced to 7.6%. On average, an active PubChem compound was found to interact with ∼2.5 targets. Moreover, if only activities consistently detected in all assays available for a given target were considered, this ratio was further reduced to ∼2.3 targets per compound. For comparison, we have also analyzed high-confidence activity data from ChEMBL, the major public repository of compounds from medicinal chemistry, and determined that an active ChEMBL compound interacted on average with only ∼1.5 targets. Taken together, our results indicate that the degree of compound promiscuity is lower than often assumed.
authors.affiliation: Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität Bonn, Dahlmannstr. 2, 53113, Bonn, Germany.
authors.forename: Ye
authors.initials: Y
authors.lastname: Hu
authors.forename: Jürgen
authors.initials: J
authors.lastname: Bajorath
mesh_terms: D001681:Biological Assay / Q000706:statistics & numerical data; D062126:Databases, Chemical / Q000706:statistics & numerical data; D016208:Databases, Factual / Q000706:statistics & numerical data; D004364:Pharmaceutical Preparations / Q000737:chemistry*; D011336:Probability; D013329:Structure-Activity Relationship
chemical_list: D004364:Pharmaceutical Preparations