Computational Study on the modulators binding to human multidrug resistance (MDR) p-Glycoprotein

GABRIEL J. JARA, D. MARIANO A. VERA, ADRIANA B. PIERINI

Los Cocos, Córdoba, Argentina

Conferencia; 9th Latin American Conference on Physical Organic Chemistry; 2007

IUPAC

The human multidrug resistance (MDR) P-glycoprotein (MDR1:ABCB1, hereafter, P-gp) acts as an efflux pump that transports a wide variety of structurally unrelated compounds outside the cell, using ATP hydrolysis as driving force. The P-gp is over-expressed in cancer cells and it promotes the extrusion of chemotherapeutic drugs outside these cells. The so-called MDR modulators are relevant pharmaceutical targets since they are intended to control or to inhibit its pumping activity. Typical P-gp substrates, as rhodamine 123, together with a set of such modulators, with known MDR inhibitory activity1 were calculated with first principles Quantum Mechanics methods (B3LYP/6-31+G**) and further tested by docking them into a structural model of the P-gp, using a genetic algorithm and the AMBER charges model. Three different binding regions were found. The docking energies calculated in one of these binding regions correlate with the experimental activities (inhibitory concentration IC50 against rhodamine). Classical Molecular Dynamics (MD) simulations on selected P-gp/modulator complexes are also introduced in order to understand the nature of the prevalent interactions with these drugs. The computational results confirm the hypothesis that, in contrast to the pattern observed for most modulators under study, verapamil (one of the first and better known modulators) and the rhodamine have different binding sites which do not overlap, as proposed on experimental bases.2 The site which holds the most stable P-gp/modulator conformations overlaps with the rhodamine primary binding site and it is drawn by a hydrophobic pocket containing remarkably conserved residues, G336, L339, F343 and V345 among them.3 The residues involved are located at the 1st, 3rd, 4th and 6th transmembrane -helices segments. Relevant hydrogen bonds with other conserved H-bond donor residues have been identified for a subset of compounds, while the orientation of the phenyl moieties into the pocket are responsible for the main hydrophobic contacts in the whole set of drugs. MD simulations carried out starting from the P-gp/modulator complexes obtained confirm the persistency of these interactions as well as the change in the mobility of the transmembrane segments involved in this site. Preliminary MD simulations including extended models for the P-gp/modulator complex immersed in the lipid bilayer are also discussed. <!-- @page { size: 8.5in 11in; margin: 0.79in } P { margin-bottom: 0.08in } --> 1 G. Ecker, M Huber, D. Schmid, P. Chiba, Mol. Pharm. 1999, 56, 791; Globisch C. et al.Bioorganic & Medicinal Chemistry 2006, 14, 1588. 2 Loo, T. W. ; Bartlett, M. C. Clarke, D. M. J. Biol. Chem. 2003, 278, 50136; Ambudkar et al. Proc. Natl. Acd. Sci 1997, 94, 10594. 3 Chang, G. J. Mol. Biol. 2003, 330, 419.