Computational study of the lipase-mediated desymmetrisation of 2-substituted-propane-1,3-diamines

ChemBioChem

Volumn 10, Issue 18, 2009, Pages 2875-2883

  García Urdiales, Eduardo ^a   Busto, Eduardo ^a   Ríos Lombardía, Nicolás ^a   Gotor Fernández, Vicente ^a   Gotor, Vicente ^a  

^a UNIVERSITY OF OVIEDO   (Spain)

Author keywords

Catalysis; Desymmetrisation; Diamines; Hydrolases; Molecular dynamics

Indexed keywords

1 NAPHTHYLPROPANE 1,3 DIAMINE DERIVATIVE; 2 BENZYLPROPANE 1,3 DIAMINE DERIVATIVE; 2 METHOXYPHENYLPROPANE 1,3 DIAMINE DERIVATIVE; 2 NAPHTHYLPROPANE 1,3 DIAMINE DERIVATIVE; 2 PHENYLPROPANE 1,3 DIAMINE DERIVATIVE; 3 METHOXYPHENYLPROPANE 1,3 DIAMINE DERIVATIVE; 4 FLUOROPHENYLPROPANE 1,3 DIAMINE DERIVATIVE; 4 METHOXYPHENYLPROPANE 1,3 DIAMINE DERIVATIVE; 4 METHYLPHENYLPROPANE 1,3 DIAMINE DERIVATIVE; 4 TRIFLUOROMETHYLPHENYLPROPANE 1,3 DIAMINE DERIVATIVE; DIAMINE DERIVATIVE; TRIACYLGLYCEROL LIPASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; BURKHOLDERIA CEPACIA; DEACYLATION; ENANTIOSELECTIVITY; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME STRUCTURE; ENZYME SUBSTRATE; HYDROGEN BOND; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; SIMULATION;

BINDING SITES; BURKHOLDERIA CEPACIA; CATALYSIS; CATALYTIC DOMAIN; DIAMINES; LIPASE; MOLECULAR DYNAMICS SIMULATION; STEREOISOMERISM; THERMODYNAMICS;

BURKHOLDERIA CEPACIA;

EID: 72949106483     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.200900412     Document Type: Article

References (52)

1. a) Asymmetric Organic Synthesis with Enzymes (Eds.: V. Gotor, I. Alfonso, E. García-Urdiales), Wiley-VCH, Weinheim, 2008;
2. b) Biocatalysis in the Pharmaceutical and Biotechnology Industries (Ed.: R. N. Patel), CRC Press, Boca Raton, 2007.
3. E. García-Urdiales, I. Alfonso, V. Gotor, Chem. Rev. 2005, 105, 313-354.
4. a) Q. Jing, R. J. Kazlauskas, Chirality 2008, 20, 724-735;
5. b) R. J. Kazlauskas, A. N. E. Weissfloch, A. T. Rappaport, L. A. Cuccia, J. Org. Chem. 1991, 56, 2656-2665.
6. a) F. Hæffner, T. Norin, K. Hult, Biophys. J. 1998, 74, 1251 -1262;
7. b) C. Orrenius, F. Hæffner, D. Rotticci, N. Öhrner, T. Norin, K. Hult, Biocatal. Biotransform. 1998, 16, 1-15.
8. D. L. Ollis, E. Cheah, M. Cygler, B. Dijkstra, F. Frolow, S. M. Franken, M. Harel, S. J. Remington, I. Silman, J. Schrag, J. L. Sussman, K. H. G. Verschueren, A. Goldman, Protein Eng. 1992, 5, 197-211.
9. N. Öhrner, C. Orrenius, A. Mattson, T. Norin, K. Hult, Enzyme Microb. Technol. 1996, 19, 328-331.
10. a) W. V. Tuomi, R. J. Kazlauskas, J. Org. Chem. 1999, 64, 2638-2647;
11. b) J. Zuegg, H. Hönig, J. D. Schrag, M. Cygler, J. Mol. Catal. B Enzym. 1997, 3, 83-98.
12. a) J.-C. Kizirian, Chem. Rev. 2008, 108, 140-205;
13. b)W. P. Hems, M. Groarke, A. Zanotti-Gerosa, G. A. Grasa, Acc. Chem. Res. 2007, 40, 1340-1347;
14. c) T. Ema, D. Tanida, T. Sakai, J. Am. Chem. Soc. 2007, 129, 10591-10596.
15. a) J.-K. Lee, Y.-W. Suh, M. C. Kung, C. M. Downing, H. H. Harold, Tetrahedron Lett. 2007, 48, 4919-4923;
16. b) J. de Abajo, J. G. de La Campa, Plast. Eng. 2005, 70, 541-602.
17. a) M. Sebela, M. Tylichova, P. Pec, J. Neural Transm. 2007, 114, 793-798;
18. b) S. R. Nagarajan, B. Devadas, J. W. Malecha, H.-F. Lu, P. G. Ruminski, J. G. Rico, T. E. Rogers, L. D. Marrufo, J. T. Collins, H. P. Kleine, M. K. Lantz, J. Zhu, N. F. Green, M. A. Russell, B. H. Landis, L. M. Miller, D. M. Meyer, T. D. Duffin, V. W. Engleman, M. B. Finn, S. K. Freeman, D. W. Griggs, M. L. Williams, M. A. Nickols, J. A. Pegg, K. E. Shannon, C. Steininger, M. M. Westlin, G. A. Nickols, J. L. Keene, Bioorg. Med. Chem. 2007, 15, 3783-3800;
19. c) K. Weinhardt, M. B. Wallach, M. Marx, J. Med. Chem. 1985, 28, 694-698.
20. a) J. González-Sabín, F. Rebolledo, V. Gotor, Chem. Soc. Rev. 2009, 38, 1916 -1925;
21. b) G.-Q. Lin, M.-H. Xy, Y.-W. Zhong, X.-W. Sun, Acc. Chem. Res. 2008, 41, 831-840.
22. a) E. Busto, V. Gotor-Fernández, J. Montejo-Bernardo, S. García-Granda, V. Gotor, Tetrahedron 2009, 65, 8393-8401;
23. b) N. Ríos-Lombardía, E. Busto, E. García-Urdiales, V. Gotor-Fernández, V. Gotor, J. Org. Chem. 2009, 74, 2571-2574;
24. c) E. Busto, V. Gotor-Fernández, J. Montejo-Bernardo, S. García-Granda, V. Gotor, Org. Lett. 2007, 9, 4203 - 4206.
25. For a description of the accepted mechanism for serine hydrolases see: J. Kraut, Annu. Rev. Biochem. 1977, 46, 331- 358.
26. J. González-Sabín, I. Lavandera, F. Rebolledo, V. Gotor, Tetrahedron: Asymmetry 2007, 17, 1264-1274.
27. The UniProt Consortium, Nucleic Acids Res. 2007, 35, D193-D197.
28. B. Rubin, Nat. Struct. Biol. 1994, 1, 568-572.
29. a) A. Mezzetti, J. D. Schrag, C. S. Cheong, R. J. Kazlauskas, Chem. Biol. 2005, 12, 427-437;
30. b) M. Luic, S. Tomić, I. Leščić, E. Ljubović, D. Šepac, V. Šunjić, L. Vitale, W. Saenger, B. Kojić-Prodić, Eur. J. Biochem. 2001, 268, 3964-3973;
31. c) D. A. Lang, M. L. M. Mannesse, G. H. De Haas, H. M. Verheij, B. W. Dijkstra, Eur. J. Biochem. 1998, 254, 333-340;
32. d) K. K. Kim, H. K. Song, D. H. Shin, K. Y. Hwang, S. W. Suh, Structure 1997, 5, 173-185;
33. e) J. D. Schrag, Y. Li, M. Cygler, D. Lang, T. Burgdorf, H.-J. Hecht, R. Schmid, D. Schomburg, T. J. Rydel, J. D. Oliver, L. C. Strickland, C. M. Dunaway, S. B. Larson, J. Day, A. McPherson, Structure 1997, 5, 187-202.
34. A. Tafi, A. vanAlmsick, F. Corelli, M. Crusco, K. E. Laumen, M. P. Schneider, M. Botta, J. Org. Chem. 2000, 65, 3659-3665.
35. The binding and mechanistic behaviour of lipases towards primary amines is qualitatively similar to that observed for their isosteric alcohols: R. J. Kazlauskas, A. N. E. Weissfloch, J. Mol. Catal. B Enzym. 1997, 3, 65-72.
36. Average and standard deviation values computed over the first 500 ps of the analysis period of the MDS.
37. E. García-Urdiales, N. Ríos-Lombardía, J. Mangas-Sánchez, V. Gotor-Fernández, V. Gotor, ChemBioChem 2009, 10, 1830-1838.
38. Average and standard deviation values computed over the range 110-610 ps.
39. Average and standard deviation values computed over the range 650-1010 ps.
40. Average and standard deviation values computed over the range 500-1010 ps.
41. 1010 Sherbrooke Street West, Suite 910, Montréal, Québec, Canada; http://www.chemcomp.com
42. J. Wang, P. Cieplak, P. A. Kollman, J. Comput. Chem. 2000, 21, 1049-1074.
43. a) V. Léonard, L. Fransson, S. Lamare, K. Hult, M. Graber, ChemBioChem 2007, 8, 662-667;
44. b) M. Cammenberg, K. Hult, S. Park, ChemBioChem 2006, 7, 1745-1749;
45. c) S. Raza, L. Fransson, K. Hult, Protein Sci. 2001, 10, 329-338.
46. The dielectric constant of 1,4-dioxane at 20°C is 2.22, D. R. Lide, CRC Handbook of Chemistry and Physics, Taylor & Francis, Oxfordshire, 2006.
47. L. Monique, Biochim. Biophys. Acta 1998, 1386, 305-330.
48. W. L. DeLano. The PyMOL molecular graphics system. DeLano Scientific 2002, San Carlos, CA, USA; http://www.pymol.org
49. a) H. M. Berman, K. Henrick, H. Nakamura, Nat. Struct. Biol. 2003, 10, 980;
50. b) H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, Nucl. Acids Res. 2000, 28, 235-242.
51. A. Warshel, G. Naray-Szabo, F. Sussman, J.-K. Hwang, Biochemistry 1989, 28, 3629-3637.
52. An initial cut-off value of 3 Å between donor and acceptor was selected as criterion for the preliminary search for hydrogen bonds. Ambiguous cases were explored in more detail.