Molecular dynamics simulation of the P2Y14 receptor. Ligand docking and identification of a putative binding site of the distal hexose moiety

Bioorganic and Medicinal Chemistry Letters

Volumn 17, Issue 3, 2007, Pages 761-766

  Ivanov, Andrei A ^a   Fricks, Ingrid ^b   Kendall Harden, T ^b   Jacobson, Kenneth A ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

G protein coupled receptor; Homology modeling; Monte Carlo; Nucleotide; Pyrimidine; UDP glucose

Indexed keywords

ANION; ARGININE; CATION; GLUTAMIC ACID; HEXOSE; LIGAND; LYSINE; NUCLEIC ACID BASE; PHOSPHATE; PURINE P2Y RECEPTOR; PURINE P2Y14 RECEPTOR; PYROPHOSPHATE; RHODOPSIN; RIBOSE; UNCLASSIFIED DRUG; URIDINE DIPHOSPHATE GLUCOSE;

ARTICLE; BINDING SITE; HUMAN; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; MONTE CARLO METHOD; PHOSPHOLIPID BILAYER; PROTEIN CARBOHYDRATE INTERACTION; SIMULATION;

BINDING SITES; HEXOSES; HUMANS; HYDROGEN BONDING; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MONTE CARLO METHOD; RECEPTORS, PURINERGIC P2; RHODOPSIN; URIDINE DIPHOSPHATE;

EID: 33846191194     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bmcl.2006.10.081     Document Type: Article

References (26)

1. Ford S.M., Bonner T.I., Neubig R.R., Rosser E.M., Pin J.-P., Davenport A.P., Spedding M., and Harmar A.J. Pharmacol. Rev. 57 (2005) 279
2. Costanzi S., Mamedova L., Gao Z.-G., and Jacobson K.A. J. Med. Chem. 47 (2004) 5393
3. Brunschweiger A., and Müller C.E. Curr. Med. Chem. 13 (2006) 289
4. Abbracchio M.P., Boeynaems J.-M., Barnard E.A., Boyer J.L., Kennedy C., Miras-Portugal M.T., King B.F., Gachet C., Jacobson K.A., Weisman G.A., and Burnstock G. Trends Pharmacol. Sci. 24 (2003) 52
5. Jacobson K.A., Costanzi S., Ohno M., Joshi B.V., Besada P., Xu B., and Tchilibon S. Curr. Top. Med. Chem. 4 (2004) 671
6. Shaver S.R., Rideout J.L., Pendergast W., Douglas J.G., Brown E.G., Boyer J.L., Patel R.I., Redick C.C., Jones A.C., Picher M., and Yerxa B.R. Purinergic Signaling 1 (2005) 183
7. Chambers J.K., Macdonald L.E., Sarau H.M., Ames R.S., Freeman K., Foley J.J., Zhu Y., McLaughlin M.M., Murdock P., McMillan L., Trill J., Swift A., Aiyar N., Taylor P., Vawter L., Naheed S., Szekeres P., Hervieu G., Scott C., Watson J.M., Murphy A.J., Duzic E., Klein C., Bergsma D.J., Wilson S., and Livi G.P. J. Biol. Chem. 275 (2000) 10767
8. Lazarowski E.R., Shea D.A., Boucher R.C., and Harden T.K. Mol. Pharmacol. 63 (2003) 1190
9. Ault A.D., and Broach J.R. Protein Eng. 19 (2006) 1
10. Mehler E.L., Periole X., Hassan S.A., and Weinstein H. J. Comput. Aided Mol. Des. 16 (2002) 841
11. Woolf T.B., and Roux B. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 11631
12. Woolf T.B., and Roux B. Proteins 24 (1996) 92
13. Allen T.W., Andersen O.S., and Roux B. J. Am. Chem. Soc. 125 (2003) 9868
14. http://thallium.med.cornell.edu/RouxLab/.
15. Costanzi S., Joshi B.V., Maddileti S., Mamedova L., Gonzalez-Moa M.J., Marquez V.E., Harden T.K., and Jacobson K.A. J. Med. Chem. 48 (2005) 8108
16. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. J. Comput. Chem. 4 (1983) 187
17. Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., and Olson A.J. J. Comput. Chem. 19 (1998) 1639
18. Jacobson K.A., Costanzi S., Ivanov A.A., Tchilibon S., Besada P., Gao Z.-G., Maddileti S., and Harden T.K. Biochem. Pharmacol. 71 (2006) 540
19. Mohamadi F.N., Richards G.J., Guida W.C., Liskamp R., Lipton M., Caufield C., Chang G., Hendrickson T., and Still W.C. J. Comput. Chem. 11 (1990) 440
20. Kim H.S., Ravi R.G., Marquez V.E., Maddileti S., Wihlborg A.-K., Erlinge D., Malmsjö M., Boyer J.L., Harden T.K., and Jacobson K.A. J. Med. Chem. 45 (2002) 208
21. Erb L., Garrad R., Wang Y., Quinn T., Turner J.T., and Weisman G.A. J. Biol. Chem. 270 (1995) 4185
22. Moro S., Hoffmann C., and Jacobson K.A. Biochemistry 38 (1999) 3498
23. Major D.T., and Fischer B. J. Med. Chem. 47 (2004) 4391
24. Hoffmann C., Moro S., Nicholas R.A., Harden K.A., and Jacobson K.A. J. Biol. Chem. 274 (1999) 14639
25. Ray K., Ghosh S.P., and Northup J.K. Endocrinology 145 (2004) 3892
26. Perlman J.H., Colson A.-O., Jain R., Czyzewski B., Cohen L.A., Osman R., and Gershengorn M.C. Biochemistry 36 (1997) 15670