Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach

Journal of Computer-Aided Molecular Design

Volumn 24, Issue 12, 2010, Pages 1023-1033

  Neves, Marco A C ^a   Simões, Sérgio ^b   Luisa Sa E Melo M ^a  

^a UNIVERSITY OF COIMBRA   (Portugal)

^b UNIVERSITY OF COIMBRA   (Portugal)

Author keywords

CXCR4; CXCR4 antagonists; Drug discovery; Homology modeling; Virtual screening

Indexed keywords

CRYSTAL STRUCTURE; DISEASES; VIRTUAL REALITY; VIRUSES;

CHEMOTYPES; CXCR4; CXCR4 ANTAGONIST; DRUG DISCOVERY; G PROTEIN COUPLED RECEPTORS; HOMOLOGY MODELING; HUMAN IMMUNODEFICIENCY VIRUS INFECTIONS; MODELING APPROACH; OPTIMISATIONS; VIRTUAL SCREENING;

LIGANDS;

8 [(4 AMINOBUTYL)(2 BENZIMIDAZOLYLMETHYL)AMINO] 1,2,3,4 TETRAHYDROQUINOLINE; CHEMOCENTRIX COMPOUND; CHEMOKINE RECEPTOR CXCR4; CHEMOKINE RECEPTOR CXCR4 ANTAGONIST; MSX 122; N [1,4,8,11 TETRAAZACYCLOTETRADECANYL 1,4 PHENYLENEBIS(METHYLENE)] 2 (AMINOMETHYL)PYRIDINE; PLERIXAFOR; PSEUDOTHIOUREA DERIVATIVE; THIOUREA DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; LIGAND BINDING; MOLECULAR BIOLOGY; MOLECULAR MODEL; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

EID: 78651281188     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-010-9393-x     Document Type: Article

References (56)

1. Baggiolini M (1998) Nature 392:565
2. Zou YR, Kottmann AH, Kuroda M, Taniuchi I, Littman DR (1998) Nature 393:595
3. Tachibana K, Hirota S, Iizasa H, Yoshida H, Kawabata K, Kataoka Y, Kitamura Y, Matsushima K, Yoshida N, Nishikawa S, Kishimoto T, Nagasawa T (1998) Nature 393:591
4. Doranz BJ, Berson JF, Rucker J, Doms RW (1997) Immunol Res 16:15
5. Muller A, Homey B, Soto H, Ge NF, Catron D, Buchanan ME, McClanahan T, Murphy E, Yuan W, Wagner SN, Barrera JL, Mohar A, Verastegui E, Zlotnik A (2001) Nature 410:50
6. Taichman RS, Cooper C, Keller ET, Pienta KJ, Taichman NS, McCauley LK (2002) Cancer Res 62:1832
7. Nanki T, Hayashida K, El-Gabalawy HS, Suson S, Shi KR, Girschick HJ, Yavuz S, Lipsky PE (2000) J Immunol 165:6590
8. Abi-Younes S, Sauty A, Mach F, Sukhova GK, Libby P, Luster AD (2000) Circ Res 86:131
9. Steen A, Schwartz TW, Rosenkilde MM (2009) Mini-Rev Med Chem 9:1605
10. Burger JA, Peled A (2009) Leukemia 23:43
11. Lukacs NW, Berlin A, Schols D, Skerlj RT, Bridger GJ (2002) Am J Pathol 160:1353
12. Hernandez PA, Gorlin RJ, Lukens JN, Taniuchi S, Bohinjec J, Francois F, Klotman ME, Diaz GA (2003) Nature Genet 34:70
13. Balabanian K, Lagane B, Pablos JL, Laurent L, Planchenault T, Verola O, Lebbe C, Kerob D, Dupuy A, Hermine O, Nicolas JF, Latger-Cannard W, Bensoussan D, Bordigoni P, Baleux F, Le Deist F, Virelizier JL, Arenzana-Seisdedos F, Bachelerie F (2005) Blood 105:2449
14. Bridger GJ, Skerlj RT, Padmanabhan S, Martellucci SA, Henson GW, Struyf S, Witvrouw M, Schols D, De Clercq E (1999) J Med Chem 42:3971
15. Este JA, Cabrera C, De Clercq E, Struyf S, Van Damme J, Bridger G, Skerlj RT, Abrams MJ, Henson G, Gutierrez A, Clotet B, Schols D (1999) Mol Pharmacol 55:67
16. Rosenkilde MM, Gerlach LO, Jakobsen JS, Skerlj RT, Bridger GJ, Schwartz TW (2004) J Biol Chem 279:3033
17. Gerlach LO, Skerlj RT, Bridger GJ, Schwartz TW (2001) J Biol Chem 276:14153
18. Hendrix CW, Flexner C, MacFarland RT, Giandomenico C, Fuchs EJ, Redpath E, Bridger G, Henson GW (2000) Antimicrob Agents Chemother 44:1667
19. Hendrix CW, Collier AC, Lederman MM, Schols D, Pollard RB, Brown S, Jackson JB, Coombs RW, Gleshy MJ, Flexner CW, Bridger GJ, Badel K, MacFarland RT, Henson GW, Calandra G (2004) JAIDS 37:1253
20. Rosenkilde MM, Gerlach LO, Hatse S, Skerlj RT, Schols D, Bridger GJ, Schwartz TW (2007) J Biol Chem 282:27354
21. Skerlj RT, Bridger GJ, Caller A, McEachern EJ, Crawford JB, Zhou YX, Atsma B, Langille J, Nan S, Veale D, Wilson T, Harwig C, Hatse S, Princen K, De Clercq E, Schols D (2010) J Med Chem 53:3376
22. Gudmundsson KS, Sebahar PR, Richardson LD, Miller JF, Turner EM, Catalano JG, Spaltenstein A, Lawrence W, Thomson M, Jenkinson S (2009) Bioorg Med Chem Lett 19:5048
23. Gudmundsson KS, Boggs SD, Catalano JG, Svolto A, Spaltenstein A, Thomson M, Wheelan P, Jenkinson S (2009) Bioorg Med Chem Lett 19:6399
24. Moyle G, DeJesus E, Boffito M, Wong RS, Gibney C, Badel K, MacFarland R, Calandra G, Bridger G, Becker S (2009) Clin Infect Dis 48:798
25. Zhan WQ, Liang ZX, Zhu AZ, Kurtkaya S, Shim H, Snyder JP, Liotta DC (2007) J Med Chem 50:5655
26. Pettersson S, Perez-Nueno VI, Ros-Blanco L, de la Bellacasa RP, Rabal MO, Batllori X, Clotet B, Clotet-Codina I, Armand-Ugon M, Este J, Borrell JI, Teixido J (2008) Chem Med Chem 3:1549
27. Thoma G, Streiff MB, Kovarik J, Glickman F, Wagner T, Beerli C, Zerwes HG (2008) J Med Chem 51:7915
28. Thomas WD, Leleti MR, Pennell AMK (2007) US Patent 2007/0275965
29. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Science 289:739
30. Park JH, Scheerer P, Hofmann KP, Choe HW, Ernst OP (2008) Nature 454:183
31. Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, Stevens RC (2007) Science 318:1258
32. Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AGW, Tate CG, Schertler GFX (2008) Nature 454:486
33. Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EYT, Lane JR, I'Jzerman AP, Stevens RC (2008) Science 322:1211
34. Cavasotto CN, Orry AJW, Murgolo NJ, Czarniecki MF, Kocsi SA, Hawes BE, O'Neill KA, Hine H, Burton MS, Voigt JH, Abagyan RA, Bayne ML, Monsma FJ (2008) J Med Chem 51:581
35. Evers A, Klabunde T (2005) J Med Chem 48:1088
36. Evers A, Klebe G (2004) J Med Chem 47:5381
37. Katritch V, Rueda M, Lam PCH, Yeager M, Abagyan R (2010) Proteins 78:197
38. Abagyan RA, Batalov S (1997) J Mol Biol 273:355
39. Rosenbaum DM, Rasmussen SGF, Kobilka BK (2009) Nature 459:356
40. Cardozo T, Totrov M, Abagyan R (1995) Proteins 23:403
41. Wong RSY, Bodart V, Metz M, Labrecque J, Bridger G, Fricker SP (2008) Mol Pharmacol 74:1485
42. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283
43. Huang N, Shoichet BK, Irwin JJ (2006) J Med Chem 49:6789
44. Okuno Y, Tamon A, Yabuuchi H, Niijima S, Minowa Y, Tonomura K, Kunimoto R, Feng CL (2008) Nucleic Acids Res 36: D907
45. Halgren TA (1996) J Comput Chem 17:490
46. Hinsen K (1998) Proteins 33:417
47. Rueda M, Bottegoni G, Abagyan R (2009) J Chem Inf Model 49:716
48. Totrov M, Abagyan R (1997) Proteins 215
49. Triballeau N, Acher F, Brabet I, Pin JP, Bertrand HO (2005) J Med Chem 48:2534
50. Truchon JF, Bayly CI (2007) J Chem Inf Model 47:488
51. Strader CD, Fong TM, Tota MR, Underwood D, Dixon RAF (1994) Annu Rev Biochem 63:101
52. Reynolds KA, Katritch V, Abagyan R (2009) J Comput-Aided Mol des 23:273
53. Perez-Nueno VI, Ritchie DW, Rabal O, Pascual R, Borrell JI, Teixido J (2008) J Chem Inf Model 48:509
54. Liang XY, Parkinson JA, Weishaupl M, Gould RO, Paisey SJ, Park HS, Hunter TM, Blindauer CA, Parsons S, Sadler PJ (2002) J Am Chem Soc 124:9105
55. Morra G, Genoni A, Neves MAC, Merz KM, Colombo G (2010) Curr Med Chem 17:25
56. Rueda M, Bottegoni G, Abagyan R (2010) J Chem Inf Model 50:186