Molecular Modeling of the Antitumor Agents Azinomycins A and B: Force-Field Parametrization and DNA Cross-Linking-Based Filtering

Journal of Organic Chemistry

Volumn 63, Issue 14, 1998, Pages 4620-4625

  Alcaro, Stefano ^a   Coleman, Robert S ^b  

^a UNIVERSITY MAGNA GRAECIA OF CATANZARO   (Italy)

^b OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AZINOMYCIN A; AZINOMYCIN B; UNCLASSIFIED DRUG;

ANTINEOPLASTIC ACTIVITY; ARTICLE; DNA CROSS LINKING; DRUG DNA INTERACTION; DRUG ISOLATION; STREPTOMYCES; TUMOR;

EID: 0032504073     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo972274j     Document Type: Article

References (37)

1. Nagaoka, K.; Matsumoto, M.; Oono, J.; Yokoi, K.; Ishizeki, S.; Nakashima, T. J. Antibiot. 1986, 39, 1527. Yokoi, K.; Nagaoka, K.; Nakashima, T. Chem. Pharm. Bull. 1986, 34, 4554.
2. Nagaoka, K.; Matsumoto, M.; Oono, J.; Yokoi, K.; Ishizeki, S.; Nakashima, T. J. Antibiot. 1986, 39, 1527. Yokoi, K.; Nagaoka, K.; Nakashima, T. Chem. Pharm. Bull. 1986, 34, 4554.
3. 50 = 0.07 μg/mL (1a) and 0.11 μg/mL (1b) against L5178Y cells. In vivo antitumor activity: 193% ILS at 16 μg/kg 1b (3/7 survivors) against P388 leukemia; 161% ILS at 32 μg/kg 1b (5/8 survivors) against Erlich carcinoma. In the same system, mitomycin C exhibited a 204% ILS at 1 mg/kg against P388 leukemia.
4. Azinomycin B is apparently identical to carzinophilin A, an antitumor agent isolated in 1954 from Streptomyces sahachiroi: Hata, T.; Koga, F.; Sano, Y.; Kanamori, K.; Matsumae, A.; Sugawara, R.; Hoshi, T.; Shimi, T.; Ito, S.; Tomizawa, S. J. Antibiot. Ser. A. 1954, 7, 107.
5. Tomasz, M.; Lipman, R.; McGuinness, B. F.; Nakanishi, K. J. Am. Chem. Soc. 1988, 110, 5892 and references therein. For a recent review, see: Tomasz, M. Chem. Biol. 1995, 2, 575.
6. Tomasz, M.; Lipman, R.; McGuinness, B. F.; Nakanishi, K. J. Am. Chem. Soc. 1988, 110, 5892 and references therein. For a recent review, see: Tomasz, M. Chem. Biol. 1995, 2, 575.
7. Lown, J. W.; Majumdar, K. C. Can. J. Biochem. 1977, 55, 630.
8. Armstrong, R. W.; Salvati, M. E.; Nguyen, M. J. Am. Chem. Soc. 1992, 114, 3144.
9. For synthetic studies on the azinomycins, see: Coleman, R. S.; Carpenter, A. J. J. Org. Chem. 1992, 57, 5813. Coleman, R. S.; Carpenter, A. J. Tetrahedron 1997, 53, 16313. Coleman, R. S.; Kong, J.-S. J. Am. Chem. Soc. 1998, 120, 3538.
10. For synthetic studies on the azinomycins, see: Coleman, R. S.; Carpenter, A. J. J. Org. Chem. 1992, 57, 5813. Coleman, R. S.; Carpenter, A. J. Tetrahedron 1997, 53, 16313. Coleman, R. S.; Kong, J.-S. J. Am. Chem. Soc. 1998, 120, 3538.
11. For synthetic studies on the azinomycins, see: Coleman, R. S.; Carpenter, A. J. J. Org. Chem. 1992, 57, 5813. Coleman, R. S.; Carpenter, A. J. Tetrahedron 1997, 53, 16313. Coleman, R. S.; Kong, J.-S. J. Am. Chem. Soc. 1998, 120, 3538.
12. All calculations were preformed on Silicon Graphics Indigo Impact R10000 computers using the programs MacroModel version 5.5 (Columbia University, New York, 1996) and Spartan version 4.0 (Wavefunction, Inc., Irvine, CA, 1995).
13. Gundertofte, K.; Liljefors, T.; Norrby, P.-O.; Pettersson, I. J. Comput. Chem. 1996, 17, 429.
14. MacroModel: Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440. MM2: Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127. MM3: Allinger, N. L.; Yuh, Y. H.; Lii, J.H. J. Am. Chem. Soc. 1989, 111, 8551. AMBER: Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Nguyen, D. T. J. Comput. Chem. 1986, 7, 230. OPLS: Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657. AMBER*: McDonald, D. Q.; Still, W. C. Tetrahedron Lett. 1992, 33, 7743. MMFF: Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
15. MacroModel: Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440. MM2: Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127. MM3: Allinger, N. L.; Yuh, Y. H.; Lii, J.H. J. Am. Chem. Soc. 1989, 111, 8551. AMBER: Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Nguyen, D. T. J. Comput. Chem. 1986, 7, 230. OPLS: Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657. AMBER*: McDonald, D. Q.; Still, W. C. Tetrahedron Lett. 1992, 33, 7743. MMFF: Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
16. MacroModel: Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440. MM2: Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127. MM3: Allinger, N. L.; Yuh, Y. H.; Lii, J.H. J. Am. Chem. Soc. 1989, 111, 8551. AMBER: Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Nguyen, D. T. J. Comput. Chem. 1986, 7, 230. OPLS: Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657. AMBER*: McDonald, D. Q.; Still, W. C. Tetrahedron Lett. 1992, 33, 7743. MMFF: Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
17. MacroModel: Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440. MM2: Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127. MM3: Allinger, N. L.; Yuh, Y. H.; Lii, J.H. J. Am. Chem. Soc. 1989, 111, 8551. AMBER: Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Nguyen, D. T. J. Comput. Chem. 1986, 7, 230. OPLS: Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657. AMBER*: McDonald, D. Q.; Still, W. C. Tetrahedron Lett. 1992, 33, 7743. MMFF: Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
18. MacroModel: Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440. MM2: Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127. MM3: Allinger, N. L.; Yuh, Y. H.; Lii, J.H. J. Am. Chem. Soc. 1989, 111, 8551. AMBER: Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Nguyen, D. T. J. Comput. Chem. 1986, 7, 230. OPLS: Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657. AMBER*: McDonald, D. Q.; Still, W. C. Tetrahedron Lett. 1992, 33, 7743. MMFF: Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
19. MacroModel: Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440. MM2: Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127. MM3: Allinger, N. L.; Yuh, Y. H.; Lii, J.H. J. Am. Chem. Soc. 1989, 111, 8551. AMBER: Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Nguyen, D. T. J. Comput. Chem. 1986, 7, 230. OPLS: Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657. AMBER*: McDonald, D. Q.; Still, W. C. Tetrahedron Lett. 1992, 33, 7743. MMFF: Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
20. MacroModel: Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440. MM2: Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127. MM3: Allinger, N. L.; Yuh, Y. H.; Lii, J.H. J. Am. Chem. Soc. 1989, 111, 8551. AMBER: Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Nguyen, D. T. J. Comput. Chem. 1986, 7, 230. OPLS: Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657. AMBER*: McDonald, D. Q.; Still, W. C. Tetrahedron Lett. 1992, 33, 7743. MMFF: Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
21. MacroModel: Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440. MM2: Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127. MM3: Allinger, N. L.; Yuh, Y. H.; Lii, J.H. J. Am. Chem. Soc. 1989, 111, 8551. AMBER: Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Nguyen, D. T. J. Comput. Chem. 1986, 7, 230. OPLS: Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657. AMBER*: McDonald, D. Q.; Still, W. C. Tetrahedron Lett. 1992, 33, 7743. MMFF: Halgren, T. A. J. Comput. Chem. 1996, 17, 490.
22. For the structurally related natural product ficellomycin, see: Kuo, M.-S.; Yurek, D. A.; Mizsak, S. A. J. Antibiot. 1989, 42, 357.
23. Brockman, R. W.; Shaddix, S. C.; Williams, M.; Struck, R. F. Cancer Treatment Rep. 1976, 60, 1317. Schnabel, F. M., Jr.; Trader, M. W.; Laster, W. R., Jr.; Shaddix, S. C.; Brockman, R. W. Cancer Treatment Rep. 1976, 60, 1325. Hammer, C. F.; Heller, S. R.; Craig, J. H. Tetrahedron 1972, 28, 239. Gassman, P. G.; Fentiman, A. F., Jr. J. Org. Chem. 1967, 32, 2388. For a review of 1-azabicyclo[3.1.0]hexanes, see: Black, D. S. C.; Doyle, J. E. Adv. Heterocycl. Chem. 1980, 27, 1.
24. Brockman, R. W.; Shaddix, S. C.; Williams, M.; Struck, R. F. Cancer Treatment Rep. 1976, 60, 1317. Schnabel, F. M., Jr.; Trader, M. W.; Laster, W. R., Jr.; Shaddix, S. C.; Brockman, R. W. Cancer Treatment Rep. 1976, 60, 1325. Hammer, C. F.; Heller, S. R.; Craig, J. H. Tetrahedron 1972, 28, 239. Gassman, P. G.; Fentiman, A. F., Jr. J. Org. Chem. 1967, 32, 2388. For a review of 1-azabicyclo[3.1.0]hexanes, see: Black, D. S. C.; Doyle, J. E. Adv. Heterocycl. Chem. 1980, 27, 1.
25. Brockman, R. W.; Shaddix, S. C.; Williams, M.; Struck, R. F. Cancer Treatment Rep. 1976, 60, 1317. Schnabel, F. M., Jr.; Trader, M. W.; Laster, W. R., Jr.; Shaddix, S. C.; Brockman, R. W. Cancer Treatment Rep. 1976, 60, 1325. Hammer, C. F.; Heller, S. R.; Craig, J. H. Tetrahedron 1972, 28, 239. Gassman, P. G.; Fentiman, A. F., Jr. J. Org. Chem. 1967, 32, 2388. For a review of 1-azabicyclo[3.1.0]hexanes, see: Black, D. S. C.; Doyle, J. E. Adv. Heterocycl. Chem. 1980, 27, 1.
26. Brockman, R. W.; Shaddix, S. C.; Williams, M.; Struck, R. F. Cancer Treatment Rep. 1976, 60, 1317. Schnabel, F. M., Jr.; Trader, M. W.; Laster, W. R., Jr.; Shaddix, S. C.; Brockman, R. W. Cancer Treatment Rep. 1976, 60, 1325. Hammer, C. F.; Heller, S. R.; Craig, J. H. Tetrahedron 1972, 28, 239. Gassman, P. G.; Fentiman, A. F., Jr. J. Org. Chem. 1967, 32, 2388. For a review of 1-azabicyclo[3.1.0]hexanes, see: Black, D. S. C.; Doyle, J. E. Adv. Heterocycl. Chem. 1980, 27, 1.
27. Brockman, R. W.; Shaddix, S. C.; Williams, M.; Struck, R. F. Cancer Treatment Rep. 1976, 60, 1317. Schnabel, F. M., Jr.; Trader, M. W.; Laster, W. R., Jr.; Shaddix, S. C.; Brockman, R. W. Cancer Treatment Rep. 1976, 60, 1325. Hammer, C. F.; Heller, S. R.; Craig, J. H. Tetrahedron 1972, 28, 239. Gassman, P. G.; Fentiman, A. F., Jr. J. Org. Chem. 1967, 32, 2388. For a review of 1-azabicyclo[3.1.0]hexanes, see: Black, D. S. C.; Doyle, J. E. Adv. Heterocycl. Chem. 1980, 27, 1.
28. Rauk, A.; Yang, D.; Tsankov, D.; Wieser, H.; Koltypin, Yu.; Gedanken, A.; Shustov, G. V. J. Am. Chem. Soc. 1995, 117, 4160.
29. Alagona, G.; Ghio, C.; Pratesi, C. J. Comput. Chem. 1991, 12, 934. Alemán, C.; Perez, J. J. Biopolymers 1993, 33, 1811. Palmer, D. E.; Pattaroni, C.; Nunami, K.; Chadha, R. K.; Goodman, M.; Wakamiya, T.; Fukase, K.; Horimoto, S.; Kitazawa, M.; Fujita, H.; Kubo, A.; Shiba, T. J. Am. Chem. Soc. 1992, 114, 5634.
30. Alagona, G.; Ghio, C.; Pratesi, C. J. Comput. Chem. 1991, 12, 934. Alemán, C.; Perez, J. J. Biopolymers 1993, 33, 1811. Palmer, D. E.; Pattaroni, C.; Nunami, K.; Chadha, R. K.; Goodman, M.; Wakamiya, T.; Fukase, K.; Horimoto, S.; Kitazawa, M.; Fujita, H.; Kubo, A.; Shiba, T. J. Am. Chem. Soc. 1992, 114, 5634.
31. Alagona, G.; Ghio, C.; Pratesi, C. J. Comput. Chem. 1991, 12, 934. Alemán, C.; Perez, J. J. Biopolymers 1993, 33, 1811. Palmer, D. E.; Pattaroni, C.; Nunami, K.; Chadha, R. K.; Goodman, M.; Wakamiya, T.; Fukase, K.; Horimoto, S.; Kitazawa, M.; Fujita, H.; Kubo, A.; Shiba, T. J. Am. Chem. Soc. 1992, 114, 5634.
32. References to these structures are available in the Supporting Information.
33. Konda, Y.; Machida, T.; Sasaki, T.; Takeda, K.; Takayanagi, H.; Harigaya, Y. Chem. Pharm. Bull. 1994, 42, 285.
34. Chang, G.; Guida, W. C.; Still, W. C. J. Am. Chem. Soc. 1989, 111, 4379.
35. Ponder, J. W.; Richards, F. M. J. Comput. Chem. 1987, 8, 1016.
36. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127.
37. These values are based on the standard model of B-DNA as proposed by Arnott and implemented in MacroModel. See: Arnott, S.; Campbell-Smith, P.; Chandresekharan, P. CRC Handbook of Biochemistry; CRC Press: Boca Raton, FL, 1976; Vol. 2.