Structure-based prediction of subtype selectivity of histamine H 3 receptor selective antagonists in clinical trials

Journal of Chemical Information and Modeling

Volumn 51, Issue 12, 2011, Pages 3262-3274

  Kim, Soo Kyung ^a   Fristrup, Peter ^b   Abrol, Ravinder ^a   Goddard, William A ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG INTERACTIONS; FORECASTING; HYDROPHOBICITY; MONTE CARLO METHODS; NEURODEGENERATIVE DISEASES; PROTEINS;

ALZHEIMER'S DISEASE; ATTENTION DEFICIT HYPERACTIVITY DISORDER; HYDROPHOBIC INTERACTIONS; MEMBRANE BILAYERS; PHARMACOPHORE MODELING; PROTEIN STRUCTURES; THERAPEUTIC APPLICATION; THREE-DIMENSIONAL STRUCTURE;

STRUCTURAL OPTIMIZATION;

HISTAMINE AGONIST; HISTAMINE H3 RECEPTOR; HISTAMINE H3 RECEPTOR ANTAGONIST; HISTAMINE RECEPTOR;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; HUMAN; METABOLISM; MOLECULAR GENETICS; MONTE CARLO METHOD; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; STRUCTURE ACTIVITY RELATION;

AMINO ACID SEQUENCE; DRUG DESIGN; HISTAMINE AGONISTS; HISTAMINE H3 ANTAGONISTS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PROTEIN CONFORMATION; RECEPTORS, HISTAMINE; RECEPTORS, HISTAMINE H3; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84555177517     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200435b     Document Type: Article

References (43)

1. Lorenzi, S.; Mor, M.; Bordi, F.; Rivara, S.; Rivara, M.; Morini, G.; Bertoni, S.; Ballabeni, V.; Barocelli, E.; Plazzi, P. V. Validation of a histamine H3 receptor model through structure-activity relationships for classical H3 antagonists Bioorg. Med. Chem. 2005, 13, 5647-5657
2. Abrol, R.; Bray, J. K.; Goddard, W. A., III BiHelix: Towards de novo Structure Prediction of an Ensemble of G-Protein Coupled Receptor Conformations. Proteins 2011, DOI: 10.1002/prot.23216.
3. Nissinen, M. J.; Karlstedt, K.; Castren, E.; Panula, P. Expression of histidine decarboxylase and cellular histamine-like immunoreactivity in rat embryogenesis J. Histochem. Cytochem. 1995, 43, 1241-1252
4. Hough, L. B. Genomics meets histamine receptors: New subtypes, new receptors Mol. Pharmacol. 2001, 59, 415-419
5. Berlin, M.; Boyce, C. W.; de Lera Ruiz, M. Histamine H3 Receptor as a Drug Discovery Target J. Med. Chem. 2010, 54, 26-53
6. Kiss, R.; Kiss, B.; Konczol, A.; Szalai, F.; Jelinek, I.; Laszlo, V.; Noszal, B.; Falus, A.; Keseru, G. M. Discoovery of Novel Human Histamine H4 Receptor Ligands by Large-Scale Structure-Based Virtual Screening J. Med. Chem. 2008, 51, 3145-3153
7. Carballo, F. Efficiency of potent gastric acid inhibition Drugs 2005, 65, 105-111
8. Pettit, M. Treatment of gastroesophageal reflux disease Pharm. World Sci. 2005, 27, 432-435
9. Schneider, E. H.; Strasser, A.; Thurmond, R. L.; Seifert, R. Structural requirements for inverse agonism and neutral antagonism of indole-, benzimidazole-, and thienopyrrole-derived histamine H4 receptor ligands J. Pharmacol. Exp. Ther. 2010, 334, 513-521
10. Ligneau, X.; Morisset, S.; Tardivel-Lacombe, J.; Gbahou, F.; Ganellin, C. R.; Stark, H.; Schunack, W.; Schwartz, J.-C.; Arrang, J.-M. Distinct Pharmacology of rat and human histamine H3 receptors: role of two amino acids in the third transmembrane domain Br. J. Pharmacol. 2000, 131, 1247-1250
11. Shimamura, T.; Shiroishi, M.; Weyand, S.; Tsujimoto, H.; Winter, G.; Katritch, V.; Abagyan, R.; Cherezov, V.; Liu, W.; Han, G. W.; Kobayashi, T.; Stevens, R. C.; Iwata, S. Structure of the human histamine H1 receptor complex with doxepin Nature 2011, 475, 65-70
12. Katoh, K.; Kuma, K.; Toh, H.; Miyata, T. MAFFT version 5: improvement in accuracy of multiple sequence alignment Nucleic Acid Res. 2005, 33, 511-518
13. Wimley, W. C.; Creamer, T. P.; White, S. H. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides Biochemistry 1996, 35, 5109-5124
14. Hessa, T. M.-B.; Bernsel, A.; Kim, H.; Sato, Y.; Lerch-Bader, M.; Nilsson, I.; White, S. H.; von Heijne, G. Molecular code for transmembrane-helix recognition by the Sec61 translocon Nature 2007, 450, 1026-1030
15. Cherezov, V.; Rosenbaum, D. M.; Hanson, M. A.; Rasmussen, S. G. F.; Thian, F. S.; Kobilka, T. S.; Choi, H.-J.; Kuhn, P.; Weis, W. I.; Kobilka, B. K.; Stevens, R. C. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor Science 2007, 318, 1258-1265
16. Warne, T.; Serrano-Vega, M. J.; Baker, J. G.; Moukhametzianov, R.; Edwards, P. C.; Henderson, R.; Leslie, A. G. W.; Tate, C. G.; Schertler, G. F. X. Structure of a β1-adrenergic G-protein coupled receptor Nature 2008, 454, 486-491
17. Kam, V. W. T.; Goddard, W. A., III Flat-Bottom Strategy for Improved Accuracy in Protein Side-Chain Placements J. Chem. Theory Comput. 2008, 4, 2160-2169
18. Bray, J. K.; Goddard, W. A., III The structure of human serotonin 2c G-protein-coupled receptor bound to agonists and antagonists J. Mol. Graphics Modell. 2008, 27, 66-81
19. Venable, J. D.; Thurmond, R. L. Development and chemistry of histamine H4 receptor ligands as potential modulators of inflamationary and allergic diseases Anti-Inflammatory Anti-Allergy Agents Med. Chem. 2006, 5, 307-322
20. Stark, H.; Kathmann, M.; Schlicker, E.; Schunack, W.; Schlegel, B.; Sippl, W. Medicinal chemical and pharmacological aspects of imidazole-containing histamine H3 receptor antagonists Mini Rev. Med. Chem. 2004, 4, 965-977
21. Letavic, M. A. Recent medicinal chemistry of the histmine H3 receptor Prog. Med. Chem. 2006, 44, 181-206
22. Brioni, J. D.; Esbenshade, T. A.; Garrison, T. R.; Bitner, S. R.; Cowart, M. D. Discovery of Histamine H3 Antagonists for the Treatment of Cognitive Discorders and Alzheimer's Disease J. Pharmacol. Exp. Ther. 2011, 336, 38-46
23. Esbenshade, T. A.; Fox, G. B. K.; Miller, K. M.; Kang, T. R.; Denny, C. H.; Witte, L. I.; Yao, D. G.; Pan, B. B.; Wetter, L.; Marsh, J.; Bennani, K.; Cowart, Y. L.; Sullivan, M. D.; Hancock, J. P. A. A. Pharmacological properties of ABT-239 [4-(2-{2-[(2R)-2-Methylpyrrolidinyl]ethyl}-benzofuran-5-yl) benzonitrile]: I. Potent and selective histamine H3 receptor antagonist with drug-like properties J. Pharmacol. Exp. Ther. 2005, 313, 165-175
24. Medhurst, A. D.; Atkins, A. R.; Beresford, I. J.; Brackenborough, K.; Briggs, M. A.; Calver, A. R.; Cilia, J.; Cluderay, J. E.; Crook, B.; Davis, J. B.; Davis, R. K.; Davis, R. P.; Dawson, L. A.; Foley, A. G.; Gartlon, J.; Gonzalez, M. I.; Heslop, T.; Hirst, W. D.; Jennings, C.; Jones, D. N.; Lacroix, L. P.; Martyn, A.; Ociepka, S.; Ray, A.; Regan, C. M.; Roberts, J. C.; Schogger, J.; Southam, E.; Stean, T. O.; Trail, B. K.; Upton, N.; Wadsworth, G.; Wald, J. A.; White, T.; Witherington, J.; Woolley, M. L.; Worby, A.; Wilson, D. M. GSK189254, a novel H3 receptor antagonist that binds to histamine H3 receptors in Alzheimer's disease brain and improves cognitive performance in preclinical models J. Pharmacol. Exp. Ther. 2007, 321, 1032-1045
25. Ligneau, X.; Perrin, D.; Landais, L.; Camelin, J. C.; Calmels, T. P.; I., B.-B.; Lecomte, J. M.; Parmentier, R.; Anaclet, C.; Lin, J. S.; Bertaina-Anglade, V.; la Rochelle, C. D.; d'Aniello, F.; Rouleau, A.; Gbahou, F.; Arrang, J. M.; Ganellin, C. R.; Stark, H.; Schunack, W.; Schwartz, J. C. BF2.649 [1-{3-[3-(4-Chlorophenyl)propoxy]propyl}piperidine, Hydrochloride], a Nonimidazole Inverse Agonist/Antagonist at the Human Histamine H3 Receptor: Preclinical Pharmacology J. Pharmacol. Exp. Ther. 2007, 320, 365-375
26. Uveges, A. J.; Kowal, D.; Zhang, Y.; Spangler, T. B.; Dunlop, J.; Semus, S.; Jones, P. G. The role of transmembnane Helix 5 in agonist binding to the human H3 receptor J. Pharmacol. Exp. Ther. 2002, 301, 451-458
27. Shin, N.; Coates, E.; Murgolo, N. J.; Morse, K. L.; Bayne, M.; Strader, C. D.; Monsma, F. J., Jr. Moledular modeling and site-specific mutagenesis of the histamine-binding site of the histamine H4 receptor Mol. Pharmacol. 2002, 62, 38-47
28. Jongejan, A.; Lim, H. D.; Smits, R. A.; de Esch, I. J. P.; Haaksma, E.; Leurs, R. Delineation of agonist binding to the human histamine H4 receptor using mutational analysis, homology modeling, and ab initio calculations J. Chem. Inf. Model. 2008, 48, 1455-1463
29. Lim, H. D.; van Rijn, R. M.; Ling, P.; Bakker, R. A.; Thurmond, R. L.; Leurs, R. Evaluation of Histamine H1-,H2-, and H3-Receptor Ligands at the Human Histamine H4 Receptor: Identification of 4-Methylhistamine as the First Potent and Selective H4 Receptor Agonist J. Pharmacol. Exp. Ther. 2005, 314, 1310-1321
30. Esbenshade, T. A.; Krueger, K. M.; Miller, T. R.; Kang, C. H.; Denny, L. I.; Witte, D. G.; Yao, B. B.; Fox, G. B.; Faghih, R.; Bennani, Y. L.; Williams, M.; Hancock, A. A. Two novel and selective nonimidazole histamine H3 receptor antagonists A-304121 and A-317920: I. In vitro pharmacological effects J. Pharmacol. Exp. Ther. 2003, 305, 887-896
31. Vaidehi, N.; Floriano, W. B.; Trabanino, R.; Hall, S. E.; Freddolino, P.; Choi, E. J.; Goddard, W. A., III Structure and Function of GPCRs Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12622-12627
32. Cho, A. E.; Wendel, J. A.; Vaidehi, N.; Kekenes-Huskey, P. M.; Floriano, W. B.; Maiti, P. K.; Goddard, W. A., III The MPSim-Dock Hierarchical Docking Algorithm: Application to the eight trypsin Inhibitor co-crystals J. Comput. Chem. 2005, 26, 48-71
33. Kalani, Y.; Vaidehi, N.; Hall, S. E.; Floriano, W. B.; Trabanino, R. J.; Freddolino, P. L.; Kam, V.; Goddard, W. A., III Three-dimensional structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 3815-3820
34. Freddolino, P. L.; Kalani, M. Y.; Vaidehi, N.; Floriano, W. B.; Trabanino, R. J.; Freddolino, P. L.; Kam, V.; Goddard, W. A., III Structure and function prediction for human b2- adrenergic receptor Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 2736-2741
35. Spijker, P.; Vaidehi, N.; Freddolino, P. L.; Hilbers, P. A.; Goddard, W. A., III Dynamic behavior of fully solvated b2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist Proc. Natl. Acad. Sci., U.S.A. 2006, 103, 4882-4887
36. Peng, J. Y.; Vaidehi, N.; Hall, S. E.; Goddard, W. A., III The Predicted 3D Structures of the Human M1Muscarinic Acetylcholine Receptor with Agonist or Antagonist Bound Chem. Med. Chem. 2006, 1, 878-890
37. Vaidehi, N.; Schlyer, S.; Trabanino, R. J.; Floriano, W. B.; R., A.; Sharma, S.; Kochanny, M.; Koovakat, S.; Dunning, L.; Liang, M.; Fox, J. M.; de Mendonca, F. L.; Pease, J. E.; Goddard, W. A., III; Horuk, R. Predictions of CCR1 Chemokine Receptor Structure and BX 471 Antagonist Binding Followed by Experimental Validation J. Biol. Chem. 2006, 281, 27613-27620
38. Heo, J.; Han, S.-K.; Vaidehi, N.; Wendel, J.; Kekenes-Huskey, P.; Goddard, W. A., III Prediction of the 3D Structure of FMRF-amide Neutopeptides Bound to the Mouse MrgC11 GPCR and Experimental Validation Chem. Bio. Chem. 2007, 8, 1527-1539
39. Heo, J.; Vaidehi, N.; Wendel, J.; Goddard, W. A., III Prediction of the 3-D structure of rat MrgA G protein-coupled receptor and identification of its binding site J. Mol. Graphics Modell. 2007, 26, 800-812
40. Li, Y.; Zhu, F.; Vaidehi, N.; Goddard, W. A., III; Sheinerman, F.; Reiling, S.; Morize, I.; Mu, L.; Harris, K.; Ardati, A.; Laoui, A. Prediction of the 3D structure and dynamics of human DP G-protein coupled receptor bound to an agonist and an antagonist J. Am. Chem. Soc. 2007, 129, 10720-10731
41. Goddard, W. A., III; Kim, S.-K.; Li, Y.; Trzaskowski, B.; Griffith, A. R.; Abrol, R. Predicted 3D structures for adenosine receptors bound to ligands: Comparison to the crystal structure J. Struct. Biol. 2010, 170, 10-20
42. Mayo, S. L.; Olafson, B. D.; Goddard, W. A., III DREIDING-a generic force field for molecular simulations J. Phys. Chem. 1990, 94, 8897-8909
43. Jaakola, V. P.; Griffith, M. T.; Hanson, M. A.; Cherezov, V.; Chien, E. Y.; Lane, J. R.; Ijzerman, A. P.; Stevens, R. C. The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist Science 2008, 322, 1211-1277