Enantioselective proteins: Selection, binding studies and molecular modeling of antibodies with affinity towards hydrophobic BINOL derivatives

ChemBioChem

Volumn 8, Issue 16, 2007, Pages 1974-1980

  Rasmussen, Brian Schou ^a   Pedersen, Jan Mondrup ^a   Sørensen, Jesper ^a   Egebjerg, Janni ^a   Schiøtt, Birgit ^a   Mortensen, Kim Kusk ^a   Skrydstrup, Troels ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

Antibodies; Artificial enzymes; Hydrophobic interactions; Ligand docking; Molecular recognition

Indexed keywords

2,2' DIHYDROXY 1,1' BINAPHTHYL;

ANTIBODY AFFINITY; ARTICLE; BINDING AFFINITY; CATALYSIS; COMPUTER ANALYSIS; ENANTIOMER; ENANTIOSELECTIVITY; ENZYME LINKED IMMUNOSORBENT ASSAY; HYDROPHOBICITY; MOLECULAR MODEL; PRIORITY JOURNAL;

ANTIBODIES; BINDING SITES; BINDING, COMPETITIVE; ENZYME-LINKED IMMUNOSORBENT ASSAY; HYDROGEN BONDING; HYDROPHOBICITY; LIGANDS; METALLOPROTEASES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NAPHTHOLS; STEREOISOMERISM;

EID: 37549051390     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.200700295     Document Type: Article

References (44)

1. K. Faber, Biotransformations in Organic Chemistry, 5th ed., Springer, Berlin, 2004.
2. a) T. M. Penning, J. M. Jez, Chem. Rev. 2001, 101, 3027-3046;
3. b) D. Qi, C.-M. Tann, D. Haring, M. D. Distefano, Chem. Rev. 2001, 101, 3081-3111;
4. c) Y. Lu, S. M. Berry, T. D. Pfister, Chem. Rev. 2001, 101, 3047-3080;
5. d) M. T. Reetz, Tetrahedron 2002, 58, 6595-6602;
6. e) M. T. Reetz, K.-E. Jaeger, Chem. Eur. J. 2000, 6, 407-412;
7. f) M. T. Reetz, Proc. Natl. Acad. Sci. USA 2004, 101, 5716-5722.
8. For recent reviews see a) C. M. Thomas, T. R. Ward, Chem. Soc. Rev. 2005, 34, 337-346;
9. b) R. Krämer, Angew. Chem. 2006, 118, 872-874;
10. Angew. Chem. Int. Ed. 2006, 45, 858-860.
11. R. R. Davies, H. Kuang, D. Qi, A. Mazhary, E. Mayaan, M. D. Distefano, Bioorg. Med. Chem. Lett. 1999, 9, 79-84.
12. G. Roelfes, B. L. Feringa, Angew. Chem. 2005, 117, 3294-3296;
13. Angew. Chem. Int. Ed. 2005, 44, 3230-3232.
14. a) M. E. Wilson, G. M. Whitesides, J. Am. Chem. Soc. 1978, 100, 306-307;
15. b) J. Collot, J. Gradinaru, N. Humbert, M. Skander, A. Zocchi, T. R. Ward, J. Am. Chem. Soc. 2003, 125, 9030-9031;
16. c) M. Skander, N. Humbert, J. Collot, J. Gradinaru, G. Klein, A. Loosli, J. Sauser, A. Zocchi, F. Gilardoni, T. R. Ward, J. Am. Chem. Soc. 2004, 126, 14411-14418;
17. d) C. Letondor, A. Pordea, N. Humbert, A. Ivanova, S. Mazurek, M. Novic, T. R. Ward, J. Am. Chem. Soc. 2006, 128, 8320-8328;
18. e) A. Loosli, U. E. Rusband, J. Gradinaru, K. Bernauer, C. W. Schlaepfer, M. Meyer, S. Mazurek, M. Novic, T. R. Ward, Inorg. Chem. 2006, 45, 660-668.
19. H. Yamaguchi, T. Hirano, H. Kiminami, D. Taura, A. Harada, Org. Biomol. Chem. 2006, 4, 3571-3573.
20. a) M. McCarthy, P. J. Guiry, Tetrahedron 2001, 57, 3809-3844;
21. b) M. Berthod, G. Mignani, G. Woodward, M. Lemaire, Chem. Rev. 2005, 105, 1801-1836.
22. a) M. D. Savage, G. Mattson, S. Deasi, G. Nielander, S. Morgensen, E. J. Conklin, Avidin-Biotin Chemistry: A Handbook, Pierce, Rockford, 1992.
23. A. D. Griffiths, S. C. Williams, O. Hartley, I. M. Tomlinson, P. Waterhouse, W. L. Crosby, R. E. Kontermann, P. T. Jones, N. M. Low, T. J. Allison, T. D. Prospero, H. R. Hoogenboom, A. Nissim, J. P. L. Cox, J. L. Harrison, M. Zaccolo, E. Gherardi, G. Winter, EMBO J. 1994, 13, 3245-3260.
24. We have made no attempts to quantify the ELISA scores into binding constants or energies. However, the ELISA scores are internally comparable and proportional to the binding affinity.
25. While in reality 1 and 3 are diastereomers due to the chiral biotin moiety, they will be described as enantiomers, as the biotin moiety is buried in the streptavidin and not involved in binding. See P. C. Weber, M. W. Pantoliano, F. R. Salemme, Acta Crystallogr. Sect. D Biol. Crystallogr. 1995, 51, 590-596.
26. A large number of antibodies (44 of 96) were found to have a low affinity for all of the antigens. The relatively large number of phages showing low affinity towards 1 might arise from loss or death of the phage upon its transfer during the experiments. A few antibodies (five out of 96) were found to be completely unspecific and exhibit high affinity towards even the smallest hapten, 2.
27. a) R. A. Friesner, J. L. Banks, R. B. Murphy, T. A. Halgren, J. J. Klicic, D. T. Mainz, M. P. Repasky, E. H. Knoll, M. Shelly, J. K. Perry, D. E. Shaw, P. Francis, P. S. Shenkin, J. Med. Chem. 2004, 47, 1739-1749;
28. b) T. A. Halgren, R. B. Murphy, R. A. Friesner, H. S. Beard, L. L. Frye, W. T. Pollard, J. L. Banks, J. Med. Chem. 2004, 47, 1750-1759.
29. a) H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, Nucleic Acids Res. 2000, 28, 235-242;
30. b) H. Berman, K. Henrick, H. Nakamura, Nat. Struct. Biol. 2003, 10, 980.
31. A. T. Brünger, D. J. Leahy, T. R. Hynes, R. O. Fox, J. Mol. Biol. 1991, 221, 239-256.
32. R. A. Friesner, R. B. Murphy, M. P. Repasky, L. L. Frye, J. R. Greenwood, T. A. Halgren, P. C. Sanschagrin, D. T. Mainz, J. Med. Chem. 2006, 49, 6177-6196.
33. J. C. Cole, C. W. Murray, J. W. M. Nissink, R. D. Taylor, R. Taylor, Proteins 2005, 60, 325-332.
34. For a recent review of homology modeling see; A. Hillisch, L. F. Pineda, R. Hilgenfeld, Drug Discovery Today 2004, 9, 659-669.
35. For an example of correlating experimental ELISA values with docking studies on homology-modeled antibodies see: S. J. Chambers, G. M. Wyatt, S. D. Garrett, M. R. A. Morgan, Food Agric. Immunol. 1999, 11, 219-228.
36. N. R. J. Whitelegg, A. R. Rees, Protein. Eng. 2000, 13, 819-824.
37. Maestro 7.5, Macromodel 9.1, Impact 4.0, Glide 4.0, Qsite 4.0, Jaguar 6.5 and QM-Polarized Ligand Docking protocol are all part of the Schrödinger Suite 2006, Schrödinger LLC, New York, NY, 2005.
38. a) Molegro Virtual Docker version 1.5, Molegro ApS, 2006;
39. b) R. Thornsen, M. H. Christensen, J. Med. Chem. 2006, 49, 3315-3321.
40. All residues are numbered according to the sequences given in the Supporting Information.
41. See for example: a) O. Hofstetter, H. Hofstetter, V. Schurig, M. Wilchek, B. S. Green, J. Am. Chem. Soc. 1998, 120, 3251-3252;
42. b) O. Hofstetter, H. Hofstetter, M. Wilchek, V. Schurig, B. S. Green, Chem. Commun. 2000, 1581-1582;
43. c) F. Taran, C. Gauchet, B. Mohar, S. Meunier, A. Valleix, P. Y. Renard, C. Créminon, J. Grassi, A. Wagner, C. Mioskowski, Angew. Chem. 2002, 114, 132-135;
44. Angew. Chem. Int. Ed. 2002, 41, 124-127.