Structure based drug design and LIE models for GPCRs

CINF 52

Peter Kolb, kolb@blur.compbio.ucsf.edu1, Daniel M. Rosenbaum, drosenb1@stanford.edu2, Anne Marie Jorgensen, anmj@lundbeck.com3, John J. Irwin, jji@cgl.ucsf.edu1, Brian K Shoichet, shoichet@cgl.ucsf.edu1, and Brian K. Kobilka2. (1) Department of Pharmaceutical Chemistry, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, (2) Department of Molecular and Cellular Physiology, Stanford University, 157 Beckman Center, Stanford, CA 94305, (3) Department of Computational Chemistry, H. Lundbeck A/S, Ottiliavej 9, Dk 2500 Valby, Denmark
Aminergic GPCRs have been in the focus of pharmaceutical research for the past decades. Due to the lack of crystal structures, all efforts had to be limited to ligand- and homology model-based methods, however. The recently solved structure of the ß2-adrenergic receptor now offers the opportunity to use structure-based design approaches. Consequently, we carried out a virtual screening campaign using the program DOCK and the 1 M molecules of the "lead-like" subset of the ZINC library. Upon testing of 31 selected molecules, six were found to be active with binding affinities below 7 µM, with the best compound binding with a Kd of 17 nM.

In order to evaluate routes for improving the ranking and investigate the energetic contributions for binding to ß2-adrenergic, we calculated Linear Interaction Energy (LIE) models based on binding data obtained from literature. Specifially, we used the LIECE (Linear Interaction Energy with Continuum Electrostatics) approach that has been developed by Huang and Caflisch. The resulting model with good predictivity was used to reevaluate the six hits of the primary screening as well as an in-house data set. Interestingly, the coefficients for the energy terms differ significantly from previously published LIECE models for proteases and kinases, which demonstrates the distinctness of GPCR binding sites.

 

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2:00 PM-5:15 PM, Tuesday, March 24, 2009 Salt Palace Convention Center -- 254 A, Oral

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The 237th ACS National Meeting, Salt Lake City, UT, March 22-26, 2009