Docking and Free Energy Perturbation Studies of Ligand Binding in the Kappa Opioid Receptor

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• 作者：Dahlia A. Goldfeld ; Robert Murphy ; Byungchan Kim ; Lingle Wang ; Thijs Beuming ; Robert Abel ; Richard A. Friesner
• 刊名：Journal of Physical Chemistry B
• 出版年：2015
• 出版时间：January 22, 2015
• 年：2015
• 卷：119
• 期：3
• 页码：824-835
• 全文大小：442K
• ISSN：1520-5207

文摘

The kappa opioid receptor (KOR) is an important target for pain and depression therapeutics that lack harmful and addictive qualities of existing medications. We present a model for the binding of morphinan ligands and JDTic to the JDTic/KOR crystal structure based on an atomic level description of the water structure within its active site. The model contains two key interaction motifs that are supported by experimental evidence. The first is the formation of a salt bridge between the ligand and Asp 138^3.32 in transmembrane domain (TM) 3. The second is the stabilization by the ligand of two high energy, isolated, and ice-like waters near TM5 and TM6. This model is incorporated via energetic terms into a new empirical scoring function, WScore, designed to assess interactions between ligands and localized water in a binding site. Pairing WScore with the docking program Glide discriminates known active KOR ligands from large sets of decoy molecules much better than Glide鈥檚 older generation scoring functions, SP and XP. We also use rigorous free energy perturbation calculations to provide evidence for the proposed mechanism of interaction between ligands and KOR. The molecular description of ligand binding in KOR should provide a good starting point for future drug discovery efforts for this receptor.