Ligand Binding to the Pregnane X Receptor by Geometric Matching of Hydrogen Bonds

Hydrogen bonds are important in protein-ligand interactions. We describe a geometric modelof hydrogen bonds, which we useto study ligand binding to the pregnane X recept or (PXR). PXR binds drug ligands promiscuously. Therecently determinedstructureof PXR in humans(hPXR)revealsthat its binding pocket is large, smooth,anduniformly hydrophobic [5], leading to thehypothesisthathydrogenbondsarethemain determinant of binding conformations. Our objective in this work is to identify potential ligand binding conformations to PXRbased on hydrogenbond geometryandusethemasastarting point for ranking ligands in termsof thebinding affinity to humanandmouseversions of PXR. In humans, PXRregulatesthegeneexpressionof cytochromeP450-3A, which metabol izesmany foreign subst ancesin the body, including an estimated60% of prescription drugs, such asthe cholesterol-lowering drug SR12813andantiretroviral drug indinavir. PXR hasalsobeenimplicated in potentially harmful drugdruginteractions with theover-the-counterherbal antidepresantSt.John’s wort. PXR is activated by many exogenouschemical s. Although the binding affinities of several ligands are known for both the humanand the mousePXR, the binding conformations are not known. PXR in mice (mPXR)has77%sequenceidentity with hPXR.Thestructureof mPXRis notyetknown, but its behaviorcan be“humanized” by replacing four aminoacidsin thebinding pocket of mPXRwith thecorresponding onesin hPXR[5]. Weundertook this work to seewhetherwe canexplain binding affiniti esby finding ligand-protein complexesthatsupport theformation of hydrogenbonds. General -purposedocking programs(e.g., [2, 4]) search for favorable binding conformationsby minimizing a complex energy function usingsimulated annealing or genet ic algorithms,andthusareoftenslow. Due to theobservedcharacteristics of thebinding pocket of hPXR,we have explored a minimalist approachthat focuseson only oneaspect of theenergyfunction, thehydrogenbonds,in orderto identify thediscriminating factor in ligand binding to PXR. Our approachis a fast, directed search that avoids local minima. It can alsoaid the general-purposeprogramsby providing good starting conformations, thusdrastically reducing thesearchspace. Hydrogenbondshave beenusedin FlexX [3] aspartof a morecompleteenergy function. Our geometricmodelof hydrogenbonds(consisting of raysandwedges)is morecompactthantheoneused in FlexX, andcanprovide moreefficient andmoreaccuratematchingwithout discretization.