Structural Mapping of Inhibitors Binding Sites on P-glycoprotein: Mechanism of Inhibition of P-Glycoprotein by Herbal Isoflavones

Aims: Understanding the pattern of inhibitors binding to p-glycoprotein (Pgp).

Study Design: Pgp is an ATP dependent transporter protein, responsible for multi-drug resistance in metastatic tumors. It removes toxins by exporting a variety of structurally unrelated compounds outside the cells, which make Pgp a promising target for designing anti cancer supplementary therapeutic molecules. Isoflavones are present in soyabean and other herbal extracts. The idea was to explore inhibitor binding sites on Pgp to find hotspots which eventually may prove useful in designing compounds with higher specificity and affinity.

Place and Duration of Study: School of Biotechnology, Gautam Buddha University, Greater Noida, between February 2012 and December 2012.

Methodology: The biochemical nature of binding of isoflavones to Pgp has been extensively studied, but the atomic details of their interactions were not understood. Therefore, we have used in silico methods to study binding of eleven isoflavones to Pgp. The docking studies were performed using grid-based ligand docking with energetic (GLIDE).

Results: Isoflavones binds at two slightly distinct sites perpendicular to each other, present in the large hydrophobic cavity of Pgp. Three isoflavones bind to site 1, whereas eight isoflavones bind to site 2 by forming van der Waals and H-bonded interactions. Both the sites are highly hydrophobic in nature and are contributed mainly by side chain of non polar residues present on twelve transmembrane a-helices. Site 1 has minimum dimension of 7.5Å and maximum as 22Å whereas, site 2 is wider and deeper than site1. One sidewall of the site 2 is formed by polar amino acid residues of helix H12, which makes several hydrogen bonds with ligands.

Conclusion: Structure analysis revealed that addition of polar group to hydrophobic ligand may enhance its binding affinity for Pgp, which may be used for designing potent inhibitors to find lead compounds for drug design.