Use of molecular recognition to drive chemical evolution: Mechanisms of an automated genetic algorithm implementation

Chemistry - A European Journal

Volumn 4, Issue 5, 1998, Pages 825-834

  Eliseev, Alexey V ^a   Nelen, Marina I ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

Combinatorial chemistry; Genetic algorithms; Molecular recognition; Photochemistry; Template synthesis

Indexed keywords

ALGORITHM; GENETICS; GUANIDINIUM DERIVATIVE; ISOMERIZATION; REGENERATION; SILICA GEL;

EID: 0031750811     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-3765(19980515)4:5<825::AID-CHEM825>3.0.CO;2-7     Document Type: Article

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31. For representative reviews on combinatorial chemistry and the principles of library design, see: a) M. A. Gallop, R. W. Barrett, W. J. Dower, S. P. A. Fodor, E. M. Gordon, J. Med. Chem. 1994, 37, 1233-1251; b) E. M. Gordon, R. W. Barrett, W. J. Dower, S. P. A. Fodor, M. A. Gallop, ibid, 1994, 37, 1385-1401; c) N. K. Terrett, M. Gardner, D. W. Gordon, R. J. Kobylecki, J. Steele, Tetrahedron 1995, 57, 8135-8173; d) J. Eichler, R. A. Houghten, Mol. Med. Today 1995, 1, 174-180; e) G. Lowe, Chem. Soc. Rev. 1995, 24, 309; f) L. A. Thompson, J. A. Ellman, Chem. Rev. 1996, 96, 555-600; g) X. Williard, I. Pop, L. Bourel, D. Horvath, R. Baudelle, P. Melnyk, B. Deprez, A. Tartar, Eur. J. Med. Chem., 1996, 37, 87-98; h) F. Balkenhohl, C. von dem Bussche-Hünnefeld, A. Lansky, C. Zechel, Angew. Chem. 1996, 108, 2436-2487; Angew. Chem. Int. Ed. Engl. 1996, 55, 2288-2337.
32. For representative reviews on combinatorial chemistry and the principles of library design, see: a) M. A. Gallop, R. W. Barrett, W. J. Dower, S. P. A. Fodor, E. M. Gordon, J. Med. Chem. 1994, 37, 1233-1251; b) E. M. Gordon, R. W. Barrett, W. J. Dower, S. P. A. Fodor, M. A. Gallop, ibid, 1994, 37, 1385-1401; c) N. K. Terrett, M. Gardner, D. W. Gordon, R. J. Kobylecki, J. Steele, Tetrahedron 1995, 57, 8135-8173; d) J. Eichler, R. A. Houghten, Mol. Med. Today 1995, 1, 174-180; e) G. Lowe, Chem. Soc. Rev. 1995, 24, 309; f) L. A. Thompson, J. A. Ellman, Chem. Rev. 1996, 96, 555-600; g) X. Williard, I. Pop, L. Bourel, D. Horvath, R. Baudelle, P. Melnyk, B. Deprez, A. Tartar, Eur. J. Med. Chem., 1996, 37, 87-98; h) F. Balkenhohl, C. von dem Bussche-Hünnefeld, A. Lansky, C. Zechel, Angew. Chem. 1996, 108, 2436-2487; Angew. Chem. Int. Ed. Engl. 1996, 55, 2288-2337.
33. For representative reviews on combinatorial chemistry and the principles of library design, see: a) M. A. Gallop, R. W. Barrett, W. J. Dower, S. P. A. Fodor, E. M. Gordon, J. Med. Chem. 1994, 37, 1233-1251; b) E. M. Gordon, R. W. Barrett, W. J. Dower, S. P. A. Fodor, M. A. Gallop, ibid, 1994, 37, 1385-1401; c) N. K. Terrett, M. Gardner, D. W. Gordon, R. J. Kobylecki, J. Steele, Tetrahedron 1995, 57, 8135-8173; d) J. Eichler, R. A. Houghten, Mol. Med. Today 1995, 1, 174-180; e) G. Lowe, Chem. Soc. Rev. 1995, 24, 309; f) L. A. Thompson, J. A. Ellman, Chem. Rev. 1996, 96, 555-600; g) X. Williard, I. Pop, L. Bourel, D. Horvath, R. Baudelle, P. Melnyk, B. Deprez, A. Tartar, Eur. J. Med. Chem., 1996, 37, 87-98; h) F. Balkenhohl, C. von dem Bussche-Hünnefeld, A. Lansky, C. Zechel, Angew. Chem. 1996, 108, 2436-2487; Angew. Chem. Int. Ed. Engl. 1996, 55, 2288-2337.
34. For representative reviews on combinatorial chemistry and the principles of library design, see: a) M. A. Gallop, R. W. Barrett, W. J. Dower, S. P. A. Fodor, E. M. Gordon, J. Med. Chem. 1994, 37, 1233-1251; b) E. M. Gordon, R. W. Barrett, W. J. Dower, S. P. A. Fodor, M. A. Gallop, ibid, 1994, 37, 1385-1401; c) N. K. Terrett, M. Gardner, D. W. Gordon, R. J. Kobylecki, J. Steele, Tetrahedron 1995, 57, 8135-8173; d) J. Eichler, R. A. Houghten, Mol. Med. Today 1995, 1, 174-180; e) G. Lowe, Chem. Soc. Rev. 1995, 24, 309; f) L. A. Thompson, J. A. Ellman, Chem. Rev. 1996, 96, 555-600; g) X. Williard, I. Pop, L. Bourel, D. Horvath, R. Baudelle, P. Melnyk, B. Deprez, A. Tartar, Eur. J. Med. Chem., 1996, 37, 87-98; h) F. Balkenhohl, C. von dem Bussche-Hünnefeld, A. Lansky, C. Zechel, Angew. Chem. 1996, 108, 2436-2487; Angew. Chem. Int. Ed. Engl. 1996, 55, 2288-2337.
35. For representative reviews on combinatorial chemistry and the principles of library design, see: a) M. A. Gallop, R. W. Barrett, W. J. Dower, S. P. A. Fodor, E. M. Gordon, J. Med. Chem. 1994, 37, 1233-1251; b) E. M. Gordon, R. W. Barrett, W. J. Dower, S. P. A. Fodor, M. A. Gallop, ibid, 1994, 37, 1385-1401; c) N. K. Terrett, M. Gardner, D. W. Gordon, R. J. Kobylecki, J. Steele, Tetrahedron 1995, 57, 8135-8173; d) J. Eichler, R. A. Houghten, Mol. Med. Today 1995, 1, 174-180; e) G. Lowe, Chem. Soc. Rev. 1995, 24, 309; f) L. A. Thompson, J. A. Ellman, Chem. Rev. 1996, 96, 555-600; g) X. Williard, I. Pop, L. Bourel, D. Horvath, R. Baudelle, P. Melnyk, B. Deprez, A. Tartar, Eur. J. Med. Chem., 1996, 37, 87-98; h) F. Balkenhohl, C. von dem Bussche-Hünnefeld, A. Lansky, C. Zechel, Angew. Chem. 1996, 108, 2436-2487; Angew. Chem. Int. Ed. Engl. 1996, 55, 2288-2337.
36. For representative reviews on combinatorial chemistry and the principles of library design, see: a) M. A. Gallop, R. W. Barrett, W. J. Dower, S. P. A. Fodor, E. M. Gordon, J. Med. Chem. 1994, 37, 1233-1251; b) E. M. Gordon, R. W. Barrett, W. J. Dower, S. P. A. Fodor, M. A. Gallop, ibid, 1994, 37, 1385-1401; c) N. K. Terrett, M. Gardner, D. W. Gordon, R. J. Kobylecki, J. Steele, Tetrahedron 1995, 57, 8135-8173; d) J. Eichler, R. A. Houghten, Mol. Med. Today 1995, 1, 174-180; e) G. Lowe, Chem. Soc. Rev. 1995, 24, 309; f) L. A. Thompson, J. A. Ellman, Chem. Rev. 1996, 96, 555-600; g) X. Williard, I. Pop, L. Bourel, D. Horvath, R. Baudelle, P. Melnyk, B. Deprez, A. Tartar, Eur. J. Med. Chem., 1996, 37, 87-98; h) F. Balkenhohl, C. von dem Bussche-Hünnefeld, A. Lansky, C. Zechel, Angew. Chem. 1996, 108, 2436-2487; Angew. Chem. Int. Ed. Engl. 1996, 55, 2288-2337.
37. For representative reviews on combinatorial chemistry and the principles of library design, see: a) M. A. Gallop, R. W. Barrett, W. J. Dower, S. P. A. Fodor, E. M. Gordon, J. Med. Chem. 1994, 37, 1233-1251; b) E. M. Gordon, R. W. Barrett, W. J. Dower, S. P. A. Fodor, M. A. Gallop, ibid, 1994, 37, 1385-1401; c) N. K. Terrett, M. Gardner, D. W. Gordon, R. J. Kobylecki, J. Steele, Tetrahedron 1995, 57, 8135-8173; d) J. Eichler, R. A. Houghten, Mol. Med. Today 1995, 1, 174-180; e) G. Lowe, Chem. Soc. Rev. 1995, 24, 309; f) L. A. Thompson, J. A. Ellman, Chem. Rev. 1996, 96, 555-600; g) X. Williard, I. Pop, L. Bourel, D. Horvath, R. Baudelle, P. Melnyk, B. Deprez, A. Tartar, Eur. J. Med. Chem., 1996, 37, 87-98; h) F. Balkenhohl, C. von dem Bussche-Hünnefeld, A. Lansky, C. Zechel, Angew. Chem. 1996, 108, 2436-2487; Angew. Chem. Int. Ed. Engl. 1996, 55, 2288-2337.
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48. For recent studies on synthetic receptors involved in recognition, transport, and sensing of guanidinium and amidinium derivatives, see: a) T. W. Bell, J. Liu, Angew. Chem. 1990, 702, 931-933; Angew. Chem. Int. Ed. Engl. 1990, 29, 923-925; b) T. W. Bell, V. J. Santora, J. Am. Chem. Soc. 1992, 774, 8300-8302; c) T. W. Bell, Z. Hou, S. C. Zimmerman, P. A. Thiessen, Angew. Chem. 1995, 107, 2321-2324; Angew. Chem. Int. Ed. Engl. 1995, 34, 2163-2165; d) A. Casnati, P. Minari, A. Pochini, R. Ungaro, W. F. Nijenhuis, F. De long, D. N. Reinhoudt, Israel J. Chem. 1992, 32, 79-87; e) F. J. B. Kremer, G. Chiosis, J. F. J. Engbersen, D. N. Reinhoudt, J. Chem. Soc. Perkin Trans. 2 1994, 677-681; f) M. Takeshita, S. Shinkai, Chem. Lett. 1994, 1349-1352.
49. For recent studies on synthetic receptors involved in recognition, transport, and sensing of guanidinium and amidinium derivatives, see: a) T. W. Bell, J. Liu, Angew. Chem. 1990, 702, 931-933; Angew. Chem. Int. Ed. Engl. 1990, 29, 923-925; b) T. W. Bell, V. J. Santora, J. Am. Chem. Soc. 1992, 774, 8300-8302; c) T. W. Bell, Z. Hou, S. C. Zimmerman, P. A. Thiessen, Angew. Chem. 1995, 107, 2321-2324; Angew. Chem. Int. Ed. Engl. 1995, 34, 2163-2165; d) A. Casnati, P. Minari, A. Pochini, R. Ungaro, W. F. Nijenhuis, F. De long, D. N. Reinhoudt, Israel J. Chem. 1992, 32, 79-87; e) F. J. B. Kremer, G. Chiosis, J. F. J. Engbersen, D. N. Reinhoudt, J. Chem. Soc. Perkin Trans. 2 1994, 677-681; f) M. Takeshita, S. Shinkai, Chem. Lett. 1994, 1349-1352.
50. For recent studies on synthetic receptors involved in recognition, transport, and sensing of guanidinium and amidinium derivatives, see: a) T. W. Bell, J. Liu, Angew. Chem. 1990, 702, 931-933; Angew. Chem. Int. Ed. Engl. 1990, 29, 923-925; b) T. W. Bell, V. J. Santora, J. Am. Chem. Soc. 1992, 774, 8300-8302; c) T. W. Bell, Z. Hou, S. C. Zimmerman, P. A. Thiessen, Angew. Chem. 1995, 107, 2321-2324; Angew. Chem. Int. Ed. Engl. 1995, 34, 2163-2165; d) A. Casnati, P. Minari, A. Pochini, R. Ungaro, W. F. Nijenhuis, F. De long, D. N. Reinhoudt, Israel J. Chem. 1992, 32, 79-87; e) F. J. B. Kremer, G. Chiosis, J. F. J. Engbersen, D. N. Reinhoudt, J. Chem. Soc. Perkin Trans. 2 1994, 677-681; f) M. Takeshita, S. Shinkai, Chem. Lett. 1994, 1349-1352.
51. For recent studies on synthetic receptors involved in recognition, transport, and sensing of guanidinium and amidinium derivatives, see: a) T. W. Bell, J. Liu, Angew. Chem. 1990, 702, 931-933; Angew. Chem. Int. Ed. Engl. 1990, 29, 923-925; b) T. W. Bell, V. J. Santora, J. Am. Chem. Soc. 1992, 774, 8300-8302; c) T. W. Bell, Z. Hou, S. C. Zimmerman, P. A. Thiessen, Angew. Chem. 1995, 107, 2321-2324; Angew. Chem. Int. Ed. Engl. 1995, 34, 2163-2165; d) A. Casnati, P. Minari, A. Pochini, R. Ungaro, W. F. Nijenhuis, F. De long, D. N. Reinhoudt, Israel J. Chem. 1992, 32, 79-87; e) F. J. B. Kremer, G. Chiosis, J. F. J. Engbersen, D. N. Reinhoudt, J. Chem. Soc. Perkin Trans. 2 1994, 677-681; f) M. Takeshita, S. Shinkai, Chem. Lett. 1994, 1349-1352.
52. For recent studies on synthetic receptors involved in recognition, transport, and sensing of guanidinium and amidinium derivatives, see: a) T. W. Bell, J. Liu, Angew. Chem. 1990, 702, 931-933; Angew. Chem. Int. Ed. Engl. 1990, 29, 923-925; b) T. W. Bell, V. J. Santora, J. Am. Chem. Soc. 1992, 774, 8300-8302; c) T. W. Bell, Z. Hou, S. C. Zimmerman, P. A. Thiessen, Angew. Chem. 1995, 107, 2321-2324; Angew. Chem. Int. Ed. Engl. 1995, 34, 2163-2165; d) A. Casnati, P. Minari, A. Pochini, R. Ungaro, W. F. Nijenhuis, F. De long, D. N. Reinhoudt, Israel J. Chem. 1992, 32, 79-87; e) F. J. B. Kremer, G. Chiosis, J. F. J. Engbersen, D. N. Reinhoudt, J. Chem. Soc. Perkin Trans. 2 1994, 677-681; f) M. Takeshita, S. Shinkai, Chem. Lett. 1994, 1349-1352.
53. For recent studies on synthetic receptors involved in recognition, transport, and sensing of guanidinium and amidinium derivatives, see: a) T. W. Bell, J. Liu, Angew. Chem. 1990, 702, 931-933; Angew. Chem. Int. Ed. Engl. 1990, 29, 923-925; b) T. W. Bell, V. J. Santora, J. Am. Chem. Soc. 1992, 774, 8300-8302; c) T. W. Bell, Z. Hou, S. C. Zimmerman, P. A. Thiessen, Angew. Chem. 1995, 107, 2321-2324; Angew. Chem. Int. Ed. Engl. 1995, 34, 2163-2165; d) A. Casnati, P. Minari, A. Pochini, R. Ungaro, W. F. Nijenhuis, F. De long, D. N. Reinhoudt, Israel J. Chem. 1992, 32, 79-87; e) F. J. B. Kremer, G. Chiosis, J. F. J. Engbersen, D. N. Reinhoudt, J. Chem. Soc. Perkin Trans. 2 1994, 677-681; f) M. Takeshita, S. Shinkai, Chem. Lett. 1994, 1349-1352.
54. In a few cases, the receptors isolated after synthesis contained up to 10% of the corresponding cis,trans isomers.
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58. For a description of the mechanisms of photochemical cis-trans isomerization, see: a) G. S. Hammond, J. Saltiel, A. A. Lamola, N. J. Turro, J. S. Bradshaw, D. O. Cowan, R. C. Counsell, V. Vogt, C. Dalton, J. Am. Chem. Soc. 1964, 86, 3197-3217; b) N. J. Turro, Photochem. Photobiol. 1969, 9, 555-563. For the isomerization of chalcones, see: c) M. Reinkhardt, V. G. Mitina, N. S. Pivenko, V. F. Lavrushin, Zh. Obshch. Knim. 1980, 50, 2770-2776.
59. For a description of the mechanisms of photochemical cis-trans isomerization, see: a) G. S. Hammond, J. Saltiel, A. A. Lamola, N. J. Turro, J. S. Bradshaw, D. O. Cowan, R. C. Counsell, V. Vogt, C. Dalton, J. Am. Chem. Soc. 1964, 86, 3197-3217; b) N. J. Turro, Photochem. Photobiol. 1969, 9, 555-563. For the isomerization of chalcones, see: c) M. Reinkhardt, V. G. Mitina, N. S. Pivenko, V. F. Lavrushin, Zh. Obshch. Knim. 1980, 50, 2770-2776.
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63. The limited solubility of arginine derivatives in ethanol and other organic solvents prevented us from using them directly for the solution equilibrium studies. However, a derivative of the authentic biological compound was used for immobilization on the solid support.
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68. The technique of multiple isomerization-isolation steps has been used previously, in a system of porphyrin isomers, to increase the yield of the desired form: a) J. Lindsey, J. Org. Chem. 1980, 42, 5215; b) C. M. Elliott, Anal. Chem. 1980, 52, 666-668. We thank Prof. Lindsey for making us aware of this work. Our approach, however, aims at the generation of molecular entities capable of strong and specific binding to target compounds in solution, for which the similarity of binding between the immobilized and the free ligand is essential.
69. Apparently, the smaller the degree of isomerization, the more cycles are necessary for achieving the macroequilibrium. The total time for macroequilibration is, however, comparable with the time necessary to reach a similar solution equilibrium and can be estimated from straightforward kinetic studies in solution.
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