Rationalizing the role of SAR tolerance for ligand-based virtual screening.

It is well appreciated that the results of ligand-based virtual screening (LBVS) are much influenced by methodological details, given the generally strong compound class dependence of LBVS methods. It is less well understood to what extent structure-activity relationship (SAR) characteristics might influence the outcome of LBVS. We have assessed the hypothesis that the success of prospective LBVS depends on the SAR tolerance of screening targets, in addition to methodological aspects. In this context, SAR tolerance is rationalized as the ability of a target protein to specifically interact with series of structurally diverse active compounds. In compound data sets, SAR tolerance articulates itself as SAR continuity, i.e., the presence of structurally diverse compounds having similar potency. In order to analyze the role of SAR tolerance for LBVS, activity landscape representations of compounds active against 16 different target proteins were generated for which successful LBVS applications were reported. In all instances, the activity landscapes of known active compounds contained multiple regions of local SAR continuity. When analyzing the location of newly identified LBVS hits and their SAR environments, we found that these hits almost exclusively mapped to regions of distinct local SAR continuity. Taken together, these findings indicate the presence of a close link between SAR tolerance at the target level, SAR continuity at the ligand level, and the probability of LBVS success.