The Journal of Nutrition Aromatic Amino Acids and Related Substances: Chemistry, Biology, Medicine, and Application 3-Dimensional Structures of G Protein-Coupled Receptors and Binding Sites of Agonists and Antagonists

We summarize here recent progress in predicting the 3-dimensional (3D) structure of G protein-coupled receptors (GPCR) and in predicting the binding sites for various agonists and antagonists. These receptors play a critical role in cell communications (dopamine, histamine, epinephrine, and serotonin) and in sensing the outside world (vision, smell, taste, and pain). There are no experimental 3D structures available for human GPCR despite their vital function and importance as therapeutic targets. Indeed, considering every form of life, there is an experimental structure for only 1 GPCR: bovine rhodopsin. Consequently, we developed the MembStruk method to predict the 3D structure without using homology. We then validated our predicted structures by using them to predict their binding sites and binding energies for strongly binding agonists and antagonists. The results were in excellent agreement with available binding and mutation experiments. We will summarize the results for adrenergic receptors, dopamine receptors, chemokine receptors, muscarinic acetylcholine receptors, and a tetrapeptide receptor (mas-related gene C11). J. Nutr. 137: 1528S–1538S, 2007. G protein-coupled receptors (GPCR) are intrinsic membrane proteins with 7 transmembrane (TM) helices, also called 7TM proteins. They are the largest superfamily in the human genome with .800 GPCR identified, including ;340 nonolfactory receptors organized in 5 families: glutamate, rhodopsin, adhesion, frizzled, and secretin (1). A variety of bioactive molecules (including biogenic amines, peptides, lipids, nucleotides, and proteins) modulate GPCR activity to affect regulation of essential physiological processes (e.g. neurotransmission, cellular metabolism, secretion, cell growth, immune defense, and differentiation). Thus, many important cell recognition and communication processes involve GPCR (2,3). Due to their mediation of numerous critical physiological functions, GPCR are involved in all major disease areas, including cardiovascular, metabolic, neurodegenerative, psychiatric, cancer, and infectious diseases (4,5). Indeed, GPCR represent 30–50% of the current drug targets for activation (by agonist drugs) or inhibition (by antagonists) (5,6). It is estimated that the ;80 GPCR-targeting drugs currently marketed account for ;$50 billion in annual sales, and many have annual sales .$2 billion. Target evaluation, lead identification, and optimization of GPCR have accelerated progress in identifying subtypes with specific cell and tissue functions. However, progress in developing new drugs with reduced toxicity and side effects has been hampered by the lack of a 3-dimensional (3D) structure for any human GPCR or the common animal surrogate targets. Despite intensive efforts for decades by many protein crystallography groups, the only experimental 3D structure for any GPCR of any form of life is bovine rhodopsin (7). This is due to poor expression levels, difficulties in large-scale receptor purification, the insolubility in media lacking phospholipids, and the difficulty in crystallization. Unfortunately, the homology of bovine rhodopsin with most drug targets is too low (,20%) for use in homology methods to predict structures. To provide the 3D structures needed to understand the function of GPCR and to help design new ligands, we developed the MembStruk method (8) to predict the 3D structure (without using homology to known 3D structures), which we have applied to predict the 3D structures for ;10 GPCR families. We will summarize here the results for b2 adrenergic receptor (AR), D2 1 Published in a supplement to The Journal of Nutrition. Presented at the ‘‘Conference on Aromatic Amino Acids and Related Substances: Chemistry, Biology, Medicine, and Application’’ held July 20–21, 2006 in Vancouver, Canada. The conference was sponsored by Ajinomoto Company, Inc. The organizing committee for the symposium and Guest Editors for the supplement were: Katsuji Takai, Dennis M. Bier, Luc Cynober, Sidney M. Morris, Jr., and Yoshiharu Shimomura. Guest Editor disclosure: Expenses to travel to the meeting were paid by Ajinomoto Company, Inc. for K. Takai, D. M. Bier, L. Cynober, S. M. Morris, Jr., and Y. Shimomura; D. M. Bier has consulted for Ajinomoto Company, Inc. on scientific issues. 2 Supported in part by NIH (R21-MH073910-01-A1) and by the Materials and Process Simulation Center. The original funding for this work was through an ARO-MURI (Dr. R. Campbell) and then by Aventis (now Sanofi-Aventis) and Berlex (now part of Bayer-Schering). 3 Author disclosures: Travel expenses for W. A. Goddard III to attend meeting paid by The Ajinomoto Company, Inc.; R. Abrol, no conflicts of interest. 4 Color versions of Figures 1, 2, 3, 6, 7, 9, 12, 16, and 17 are available with the online posting of this paper at jn.nutrition.org. 5 Abbreviations used: AR, adrenergic receptor; Asn, asparagine; Asp, aspartic acid; 3D, 3-dimensional; DR, dopamine receptor; EC, extracellular; EPI, epinephrine; GPCR, G protein-coupled receptor; His, histidine; IC, intracellular; Ile, isoleucine; MAR, muscarinic acetylcholine receptor; MD, molecular dynamics; Mrg, mas-related gene; Phe, phenylalanine; QNB, quinuclidinyl benzilate; Ser, serine; TM, transmembrane; Trp, tryptophan; Tyr, tyrosine; Val, valine. * To whom correspondence should be addressed. E-mail: [email protected]. 1528S 0022-3166/07 $8.00 a 2007 American Society for Nutrition. by gest on Jauary 6, 2016 jn.nition.org D ow nladed fom DC1.html http://jn.nutrition.org/content/suppl/2007/05/18/137.6.1528S. 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