Exhaustive Sampling of Docking Poses Reveals Binding Hypotheses for Propafenone Type Inhibitors of P-Glycoprotein

Abstract

Overexpression of the xenotoxin transporter P-glycoprotein (P-gp) represents one major reason for the development of multidrug resistance (MDR), leading to the failure of antibiotic and cancer therapies. Inhibitors of P-gp have thus been advocated as promising candidates for overcoming the problem of MDR. However, due to lack of a high-resolution structure the concrete mode of interaction of both substrates and inhibitors is still not known. Therefore, structure-based design studies have to rely on protein homology models. In order to identify binding hypotheses for propafenone-type P-gp inhibitors, five different propafenone derivatives with known structure-activity relationship (SAR) pattern were docked into homology models of the apo and the nucleotide-bound conformation of the transporter. To circumvent the uncertainty of scoring functions, we exhaustively sampled the pose space and analyzed the poses by combining information retrieved from SAR studies with common scaffold clustering. The results suggest propafenone binding at the transmembrane helices 5, 6, 7 and 8 in both models, with the amino acid residue Y307 playing a crucial role. The identified binding site in the non-energized state is overlapping with, but not identical to, known binding areas of cyclic P-gp inhibitors and verapamil. These findings support the idea of several small binding sites forming one large binding cavity. Furthermore, the binding hypotheses for both catalytic states were analyzed and showed only small differences in their protein-ligand interaction fingerprints, which indicates only small movements of the ligand during the catalytic cycle.

Homology modelling of human P-glycoprotein

“…They found in each case that these drugs bind in similar locations to known P-gp inhibitors such as QZ59-RRR [28] and verapamil [29]. Klepsch et al [30] explored the binding mode of propafenone derivatives in homology models derived from the Sav1866 and mouse crystal structures to capture the differences between the conformational states [30]. The binding modes were similar in both models; propafenone binding occurred on the TMH 5-8 interface, overlapping part of the known cyclic inhibitor and verapamil-binding site.…”

P-glycoprotein induction in Caco-2 cells by newly synthetized thioxanthones prevents paraquat cytotoxicity

“…Computational methods, in particular ligand-protein docking programs, have become essential in any drug discovery program, including in the search for new P-gp modulators (Klepsch et al 2011;Kothandan et al 2011;Palmeira et al 2012b). Estimating binding affinities of ligands within a receptor allows the identification of the energetically most favorable poses, based on its complementarity to the target in terms of shape and properties (Meng et al 2011;Mohan et al 2005).…”

Binding of modulators to mouse and human multidrug resistance P-glycoprotein. A computational study

“…3G61) as a template ([66]), and the other is based on a structure free of ligand and nucleotide (PDB code: 3G5U) ([67]). By comparing the average distance between Cα of residues involved in cystein crosslinking (Error!…”