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Bioorg Med Chem Lett. 2008 Sep 15;18(18):4963-7. doi: 10.1016/j.bmcl.2008.08.030. Epub 2008 Aug 14.

Molecular modeling aided design of nicotinic acid receptor GPR109A agonists.

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Department of Molecular Systems, Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, USA.


A homology model of the nicotinic acid receptor GPR109A was constructed based on the X-ray crystal structure of bovine rhodopsin. An HTS hit was docked into the homology model. Characterization of the binding pocket by a grid-based surface calculation of the docking model suggested that a larger hydrophobic body plus a polar tail would improve interaction between the ligand and the receptor. The designed compounds were synthesized, and showed significantly improved binding affinity and activation of GPR109A.

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