Assessing Connexin-43 Gap Junction Inhibitors through Quantitative Structure-Activity Relationship Modeling

Abstract

The regulation of Cx43 GJ activity could potentially offer therapeutic benefits for cardiac arrhythmias and other related disorders. The search for new agents that can modulate GJ activity involves molecular docking, a method that predicts the binding affinities of ligands. However, these predictions often do not align well with the actual potencies. In this study, we examined the utility of the Quantitative Structure-Activity Relationship (QSAR) modeling in combination with molecular docking for the identification of new potent inhibitors of Cx43 GJs with greater precision. Our QSAR models were based on the structural evaluation of 16 known Cx43 GJ inhibitors with experimentally determined concentrations needed to achieve 50% inhibition of Cx43 GJ conductance (eIC50). Such evaluation allowed us to relate the structure of compounds with their potency and compare their eIC50ies with those predicted by molecular docking and our QSAR models (pIC50). The pIC50 values of Cx43 GJ inhibitors, as determined by 2D-QSAR and 3D-QSAR (compounds with high structural flexibility excluded) models well correlated with their eIC50 values (R = 0.89 and 0.98, respectively) in contrast to the pIC50 values obtained from molecular docking (R = 0.77). Further, using the established QSAR models, we proposed d-limonene, a monocyclic monoterpene, and farnesene, an acyclic sesquiterpene, as potential Cx43 inhibitors and tested them experimentally on cells expressing Cx43. The obtained eIC50ies (30 and 1.3 µM, respectively) were close to their pIC50ies predicted by 2D-QSAR (14 and 0.6 µM) while pIC50ies provided by molecular docking were 66 and 16 µM, respectively. However, 3D-QSAR modeling was inaccurate for farnesene, a compound with a large number of rotational bounds (42 and 50 µM for d-limonene and farnesene, respectively). Our results suggest that QSAR modeling could potentially streamline the discovery and development of potent and specific GJ inhibitors.