On the mechanism of substrate/non-substrate recognition by P-glycoprotein

P-Glycoprotein (P-gp, multi-drug resistance protein, MDR1) plays a gatekeeper role, interfering delivery of multiple pharmaceuticals to the target tissues and cells. We performed Molecular Dynamics (MD) simulations to generate fifty side-chain variants for P-gp (PDB ID: 4Q9H-L) followed by docking of 31 drugs (0.6≤ER≤22.7) to the whole surface except the ATPase domains and the extracellular part. A selection of the most negative energy complex for each ligand followed. All compounds docked to the two areas - the main binding cavity at the top of P-gp (12.5% of compounds with ER<1; 44.4% of 1≤ER≤2; and 100% of ER>2), and the binding sites in the middle of P-gp (87.5% of ER<1; 55.6% of 1≤ER≤2; and 0% of ER>2). Our results show that anti-substrates (ER<1), intermediate compounds (1≤ER≤2) and strong substrates (ER>2) might behave differently in relation to the P-gp. According to our calculations, the anti-substrates almost do not bind the main binding cavity (MBC) of P-gp and rather approach the other binding sites on the protein; the substrates preferably bind the MBC; the intermediate compounds with 1≤ER≤2 bind both MBC and other binding sites almost equally. The modelling results are in line with the known hypothesis that binding the MBC is prerequisite for the pumping the compound off the P-gp.