Modeling of Substrates and Inhibitors Binding to an ABC Multidrug Resistance Transporter

JARA, G. E.; PIERINI, A. B.; VERA, D. M. A.

Córdoba

Congreso; 2do Congreso Argentino de Bioinformática y Biología Computacional; 2011

Background. Multidrug resistance (MDR) promoted by ABC protein transporters is a mechanism which spans from both antimicrobial resistance in bacterial and fungal cells to cancer cells that resist chemotherapy.[1] The P-glycoprotein (MDR1:ABCB1, hereafter, P-gp), an ABC transporter that is over-expressed in cancer cells, catalyzes the extrusion of anti-tumoral drugs outside these cells, using ATP hydrolysis as driving force. Due to its relevance in cancer therapy, P-gp became one of the best known ABC transporters and a model for other proteins of this family. MDR inhibitors for these transporters are relevant pharmaceutical targets, although the lack of structure-activity relationships for inhibitors is the main problem for their design (the protein recognizes a wide variety of structurally unrelated compounds).[1] Therefore, it is important to understand which are the most relevant physical-chemical features of an inhibitor and the kind of interactions with the protein. Computational Methods. We tested a set of P-gp substrates and inhibitors by ab initio calculations together with molecular docking and molecular dynamics (MD) simulations. The compounds tested were well known substrates and inhibitors in combination with novel inhibitors recently proposed ([2], collaboration work). In addition to the study concerning the inhibitors binding, we are setting up a structural model of the protein immersed into a lipid bilayer of palmitoyloleoyl-phosphatidyl-choline (POPC) in order to do long simulations of P-gp into a more realistic environment. The lipids were parameterized using RESP charges and GAFF force field. Results and Discussion. The results reveal the importance of two binding regions, i) one involving transmembrane domains (TM) 4 and 6, the latter being the a-helix which connects the binding region with the ATP hydrolysis domain, and ii) the interface between TMs 2 and 11, one of the “gates” between the lipid membrane and the transmembrane chamber of the protein. Recently, a crystallographic P-gp structure of mouse (Mus musculus) was obtained by X-rays.[3] The binding patterns found with a homology model of the human P-gp and the novel experimental structure are compared Preliminary results on the transporter immersed in the lipid bilayer showed that our model predicts physical properties of th bilayer like the deuterium order parameter and the area pre lipid in good agreement with their experimental valuesConclusions. The docking showed that exists common sites for substrates and modulators and the docking energy found for the modulators correlated with the inhibition activity of the best and with the worst ones. Bneo´s show a docking energy and site similar to Tariquidar, supporting the idea of its potential inhibitory activity. The docking energies were compare against the free energies of binding obtained by MD. We found same energy order observed by docking. Acknowledgement. This study is part of a collaborative project with Prof. George P. Tegos (Univeristy of Ioanina, Greece). References [1] a) Borger-Walmsley M. I. et al (2003) Biochem J, 376: 313; b) Reese, D.C; Johnson, E; Lewinson, O; Nature Rev. (2009), 10:218-227. [2] Ball A, Jara,, G E, Vera D.M.A., Higginbotham A., Stermitz F.R.,Lewis K.,, Pierini A.B., Hamblin M.R., Tegos G. P. 2009, "The case forversatile inhibitors of microbial multidrug resistance pumps; Neohesperidosides from Geraniumcaespitosum" to be sent. [3] S.G. Aller, J. Yu, A. Ward, Y. Weng, S. Chittaboina, R. Zhuo, P.M. Harrell, Y.T. Trinh, Q. Zhang, I.L. Urbatsch and G. Chang, Structure of P-Glycoprotein reveals a molecular basis for poly-specific drug binding, Science 323 (2009) 1718-1722 <!-- @page { margin: 2cm } P { margin-bottom: 0.21cm } -->