Total Syntheses and Initial Evaluation of [Ψ[C(=S)NH]Tpg4]vancomycin, [Ψ[=NH)NH]Tpg4]vancomycin, [Ψ[CH2NH]Tpg4]vancomycin, and Their (4-Chlorobiphenyl)methyl Derivatives: Synergistic Binding Pocket and Peripheral Modifications for the Glycopeptide Antibiotics

Journal of the American Chemical Society

Volumn 137, Issue 10, 2015, Pages 3693-3704

  Okano, Akinori ^a   Nakayama, Atsushi ^a   Wu, Kejia ^a   Lindsey, Erick A ^a   Schammel, Alex W ^a   Feng, Yiqing ^a   Collins, Karen C ^a   Boger, Dale L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SYNTHESIS (CHEMICAL);

ANTI-MICROBIAL ACTIVITY; ANTIBIOTIC ACTIVITY; CLINICAL RESISTANCE; FUNCTIONALIZATIONS; GLYCOPEPTIDE ANTIBIOTICS; METHYL DERIVATIVES; RESISTANT BACTERIA; SYNERGISTIC MECHANISM;

ANTIBIOTICS;

AGLYCONE; BIPHENYL DERIVATIVE; POLYPEPTIDE ANTIBIOTIC AGENT; VANCOMYCIN DERIVATIVE; 4-CHLOROBIPHENYL; ANTIINFECTIVE AGENT; VANCOMYCIN;

ANTIBACTERIAL ACTIVITY; ARTICLE; CHEMICAL MODIFICATION; DRUG BINDING; DRUG POTENCY; DRUG POTENTIATION; DRUG SYNTHESIS; ENTEROCOCCUS FAECALIS; ENTEROCOCCUS FAECIUM; ESCHERICHIA COLI; METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS; NONHUMAN; ANTIBIOTIC RESISTANCE; BACTERIUM; BINDING SITE; CHEMISTRY; DRUG EFFECTS; METABOLISM; MICROBIAL SENSITIVITY TEST; STRUCTURE ACTIVITY RELATION; SYNTHESIS;

ANTI-BACTERIAL AGENTS; BACTERIA; BINDING SITES; BIPHENYL COMPOUNDS; CHEMISTRY TECHNIQUES, SYNTHETIC; DRUG RESISTANCE, BACTERIAL; MICROBIAL SENSITIVITY TESTS; STRUCTURE-ACTIVITY RELATIONSHIP; VANCOMYCIN;

EID: 84925249755     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/jacs.5b01008     Document Type: Article

References (115)

1. Cooper, G. L.; Given, D. B. In Vancomycin: A Comprehensive Review of 30 Years of Clinical Experience; Park Row Publications: Indianapolis, IN, 1986; pp 1-5.
2. Glycopeptide Antibiotics; Nagarajan, R., Ed.; Marcel Dekker: New York, 1994.
3. Kahne, D.; Leimkuhler, C.; Lu, W.; Walsh, C. T. Chem. Rev. 2005, 105, 425
4. McCormick, M. H.; Stark, W. M.; Pittenger, G. E.; Pittenger, R. C.; McGuire, J. M. Antibiot. Annu. 1955-1956, 606
5. Parenti, F.; Beretta, G.; Berti, M.; Arioli, V. J. Antibiot. 1978, 31, 276
6. Nicas, T. I.; Mullen, D. L.; Flokowitsch, J. E.; Preston, D. A.; Snyder, N. J.; Zweifel, M. J.; Wilkie, S. C.; Rodriguez, M. J.; Thompson, R. C.; Cooper, R. D. Antimicrob. Agents Chemother. 1996, 40, 2194
7. Nagarajan, R.; Schabel, A. A.; Occolowitz, J. L.; Counter, F. T.; Ott, J. L.; Felty-Duckworth, A. M. J. Antibiot. 1989, 42, 63
8. Markham, A. Drugs 2014, 74, 1823
9. Candiani, G.; Abbondi, M.; Borgonovi, M.; Romano, G.; Parenti, F. J. Antimicrob. Chemother. 1999, 44, 179
10. Anderson, V. R.; Keating, G. M. Drugs 2008, 68, 639
11. Judice, J. K.; Pace, J. L. Bioorg. Med. Chem. Lett. 2003, 13, 4165
12. Corey, G. R.; Stryjewski, M. E.; Weyenberg, W.; Yasothan, U.; Kirkpatrick, P. Nat. Rev. Drug Discovery 2009, 8, 929
13. Harris, C. M.; Kopecka, H.; Harris, T. M. J. Am. Chem. Soc. 1983, 105, 6915
14. Williamson, M. P.; Williams, D. H. J. Am. Chem. Soc. 1981, 103, 6580
15. Leclercq, R.; Derlot, E.; Duval, J.; Courvalin, P. N. Engl. J. Med. 1988, 319, 157
16. Courvalin, P. Clin. Infect. Dis. 2006, 42, S25
17. Weigel, L. M.; Clewell, D. B.; Gill, S. R.; Clark, N. C.; McDougal, L. K.; Flannagan, S. E.; Kolonay, J. F.; Shetty, J.; Killgore, G. E.; Tenover, F. C. Science 2003, 302, 1569
18. Howden, B. P.; Davies, J. K.; Johnson, P. D.; Stinear, T. P.; Grayson, M. L. Clin. Microbiol. Rev. 2010, 23, 99
19. Walsh, T. R.; Howe, R. A. Annu. Rev. Microbiol. 2002, 56, 657
20. Brickner, S. J. Curr. Pharm. Des. 1996, 2, 175
21. Scheetz, M. H.; Knechtel, S. A.; Malczynski, M.; Postelnick, M. J.; Qi, C. Antimicrob. Agents Chemother. 2008, 52, 2256
22. Brickner, S. J.; Barbachyn, M. R.; Hutchinson, D. K.; Manninen, P. R. J. Med. Chem. 2008, 51, 1981
23. Baltz, R. H.; Miao, V.; Wrigley, S. K. Nat. Prod. Rep. 2005, 22, 717
24. Baltz, R. H. Curr. Opin. Chem. Biol. 2009, 13, 144
25. Malabarba, A.; Nicas, T. I.; Thompson, R. C. Med. Res. Rev. 1997, 17, 69
26. Najarajan, R. J. Antibiot. 1993, 46, 1181
27. Van Bambeke, F. V.; Laethem, Y. V.; Courvalin, P.; Tulkens, P. M. Drugs 2004, 64, 913
28. Butler, M. S.; Hansford, K. A.; Blaskovich, M. A.; Halai, R.; Cooper, M. A. J. Antibiot. 2014, 67, 631
29. Fowler, B. S.; Laemmerhold, K. M.; Miller, S. J. J. Am. Chem. Soc. 2012, 134, 9755
30. Griffith, B. R.; Krepel, C.; Fu, X.; Blanchard, S.; Ahmed, A.; Edmiston, C. E.; Thorson, J. S. J. Am. Chem. Soc. 2007, 129, 8150
31. Jain, R. K.; Trias, J.; Ellman, J. A. J. Am. Chem. Soc. 2003, 125, 8740
32. Weist, S.; Kittel, C.; Bischoff, D.; Bister, B.; Pfeifer, V.; Nicholson, G. J.; Wohlleben, W.; Süssmuth, R. D. J. Am. Chem. Soc. 2004, 126, 5942
33. Süssmuth, R. D. ChemBioChem 2002, 3, 295
34. von Nussbaum, F.; Brands, M.; Hinzen, B.; Weigand, S.; Häbich, D. Angew. Chem., Int. Ed. 2006, 45, 5072
35. James, R. C.; Pierce, J. G.; Okano, A.; Xie, J.; Boger, D. L. ACS Chem. Biol. 2012, 7, 797
36. Wright, G. D. Chem. Commun. 2011, 47, 4055
37. Walsh, C. T. Nature 2000, 406, 775
38. Marshall, C. G.; Lessard, I. A.; Park, I.; Wright, G. D. Antimicrob. Agents Chemother. 1998, 42, 2215
39. Courvalin, P. Clin. Infect. Dis. 2006, 42, S25
40. Allen, N. E.; Hobbs, J. N., Jr.; Nicas, T. I. Antimicrob. Agents Chemother. 1996, 40, 2356
41. Sharman, G. J.; Try, A. C.; Dancer, R. J.; Cho, Y. R.; Staroske, T.; Bardsley, B.; Maguire, A. J.; Cooper, M. A.; O'Brien, D. P.; Williams, D. H. J. Am. Chem. Soc. 1997, 119, 12041
42. Allen, N. E.; Nicas, T. I. FEMS Microbiol. Rev. 2003, 26, 511
43. Hong, H.-J.; Hutchings, M. I.; Buttner, M. J. Adv. Exp. Med. Biol. 2008, 631, 200
44. Koteva, K.; Hong, H.-J.; Wang, X. D.; Nazi, I.; Hughes, D.; Naldrett, M. J.; Buttner, M. J.; Wright, G. D. Nat. Chem. Biol. 2010, 6, 327
45. Ikeda, S.; Hanaki, H.; Yanagisawa, C.; Ikeda-Dantsuji, Y.; Matsui, H.; Iwatsuki, M.; Shiomi, K.; Nakae, T.; Sunakawa, K.; Omura, S. J. Antibiot. 2010, 63, 533
46. Kwun, M. J.; Novotna, G.; Hesketh, A. R.; Hill, L.; Hong, H. Antimicrob. Agents Chemother. 2013, 57, 4470
47. Higgins, D. L.; Chang, R.; Debabov, D. V.; Leung, J.; Wu, T.; Krause, K. M.; Sandvik, E.; Hubbard, J. M.; Kaniga, K.; Schmidt, D. E., Jr.; Gao, Q.; Cass, R. T.; Karr, D. E.; Benton, B. M.; Humphrey, P. P. Antimicrob. Agents Chemother. 2005, 49, 1127
48. Cooper, R. D. G.; Snyder, N. J.; Zweifel, M. J.; Staszak, M. A.; Wilkie, S. C.; Nicas, T. I.; Mullen, D. L.; Butler, T. F.; Rodriguez, M. J.; Huff, B. E.; Thompson, R. C. J. Antibiot. 1996, 49, 575
49. Ge, M.; Chen, Z.; Onishi, H. R.; Kohler, J.; Silver, L. L.; Kerns, R.; Fukuzawa, S.; Thompson, C.; Kahne, D. Science 1999, 284, 507
50. Chen, L.; Walker, D.; Sun, B.; Hu, Y.; Walker, S.; Kahne, D. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 5658
51. Goldman, R. C.; Baizman, E. R.; Longley, C. B.; Branstrom, A. A. FEMS Microbiol. Lett. 2000, 183, 209
52. Boger, D. L.; Miyazaki, S.; Kim, S. H.; Wu, J. H.; Castle, S. L.; Loiseleur, O.; Jin, Q. J. Am. Chem. Soc. 1999, 121, 10004
53. Boger, D. L.; Kim, S. H.; Mori, Y.; Weng, J.-H.; Rogel, O.; Castle, S. L.; McAtee, J. J. J. Am. Chem. Soc. 2001, 123, 1862
54. Crowley, B. M.; Mori, Y.; McComas, C. C.; Tang, D.; Boger, D. L. J. Am. Chem. Soc. 2004, 126, 4310
55. Shimamura, H.; Breazzano, S. P.; Garfunkle, J.; Kimball, F. S.; Trzupek, J. D.; Boger, D. L. J. Am. Chem. Soc. 2010, 132, 7776
56. Evans, D. A.; Wood, M. R.; Trotter, B. W.; Richardson, T. I.; Barrow, J. C.; Katz, J. L. Angew. Chem., Int. Ed. 1998, 37, 2700
57. Evans, D. A.; Dinsmore, C. J.; Watson, P. S.; Wood, M. R.; Richardson, T. I.; Trotter, B. W.; Katz, J. L. Angew. Chem., Int. Ed. 1998, 37, 2704
58. Evans, D. A.; Barrow, J. C.; Watson, P. S.; Ratz, A. M.; Dinsmore, C. J.; Evrard, D. A.; DeVries, K. M.; Ellman, J. A.; Rychnovsky, S. D.; Lacour, J. J. Am. Chem. Soc. 1997, 119, 3419
59. Evans, D. A.; Dinsmore, C. J.; Ratz, A. M.; Evrard, D. A.; Barrow, J. C. J. Am. Chem. Soc. 1997, 119, 3417
60. Nicolaou, K. C.; Takayanagi, M.; Jain, N. F.; Natarajan, S.; Koumbis, A. E.; Bando, T.; Ramanjulu, J. M. Angew. Chem., Int. Ed. 1998, 37, 2717
61. Nicolaou, K. C.; Natarajan, S.; Li, H.; Jain, N. F.; Hughes, R.; Solomon, M. E.; Ramanjulu, J. M.; Boddy, C. N. C.; Takayanagi, M. Angew. Chem., Int. Ed. 1998, 37, 2708
62. Nicolaou, K. C.; Jain, N. F.; Natarajan, S.; Hughes, R.; Solomon, M. E.; Li, H.; Ramanjulu, J. M.; Takayanagi, M.; Koumbis, A. E.; Bando, T. Angew. Chem., Int. Ed. 1998, 37, 2714
63. Boger, D. L. Med. Res. Rev. 2001, 21, 356
64. Nicolaou, K. C.; Boddy, C. N. C.; Brase, S.; Winssinger, N. Angew. Chem., Int. Ed. 1999, 38, 2096
65. Evans, D. A.; DeVries, K. M. Drugs Pharm. Sci. 1994, 63, 63
66. Bugg, T. D. H.; Wright, G. D.; Dutka-Malen, S.; Arthur, M.; Courvalin, P.; Walsh, C. T. Biochemistry 1991, 30, 10408
67. Walsh, C. T. Science 1993, 261, 308
68. Walsh, C. T.; Fisher, S. L.; Park, I.-S.; Prahalad, M.; Wu, Z. Chem. Biol. 1996, 3, 21
69. Lessard, I. A.; Walsh, C. T. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 11028
70. Healy, V. L.; Lessard, I. A.; Roper, D. I.; Knox, J. R.; Walsh, C. T. Chem. Biol. 2000, 7, R109
71. Perkins, H. R. Pharmacol. Ther. 1982, 16, 181
72. Williams, D. H.; Williamson, M. P.; Butcher, D. W.; Hammond, S. J. J. Am. Chem. Soc. 1983, 105, 1332
73. Schaefer, M.; Schneider, T. R.; Sheldrick, G. M. Structure 1996, 4, 1509
74. McComas, C. C.; Crowley, B. M.; Boger, D. L. J. Am. Chem. Soc. 2003, 125, 9314
75. Crowley, B. M.; Boger, D. L. J. Am. Chem. Soc. 2006, 128, 2885
76. Xie, J.; Pierce, J. G.; James, R. C.; Okano, A.; Boger, D. L. J. Am. Chem. Soc. 2011, 133, 13946
77. Xie, J.; Okano, A.; Pierce, J. G.; James, R. C.; Stamm, S.; Crane, C. M.; Boger, D. L. J. Am. Chem. Soc. 2012, 134, 1284
78. Okano, A.; James, R. C.; Pierce, J. G.; Xie, J.; Boger, D. L. J. Am. Chem. Soc. 2012, 134, 8790
79. Okano, A.; Nakayama, A.; Schammel, A. W.; Boger, D. L. J. Am. Chem. Soc. 2014, 136, 13522
80. Bowden, K.; Heilbron, I. M.; Jones, E. R. H.; Weedon, B. C. L. J. Chem. Soc. 1946, 39
81. Bowers, A.; Halsall, T. G.; Jones, E. R. H.; Lemin, A. J. J. Chem. Soc. 1953, 2548
82. Corey, E. J.; Suggs, J. W. Tetrahedron Lett. 1975, 16, 2647
83. Corey, E. J.; Boger, D. L. Tetrahedron Lett. 1978, 19, 2461
84. Corey, E. J.; Schmidt, G. Tetrahedron Lett. 1979, 20, 399
85. Moorthy, J. N.; Singhal, N. J. Org. Chem. 2005, 70, 1926
86. 3 was mandatory to prevent oxidation of the thioamide when EtOAc was used as either an extraction or chromatography solvent.
87. Ge, M.; Thompson, C.; Kahne, D. J. Am. Chem. Soc. 1998, 120, 11014
88. Thompson, C.; Ge, M.; Kahne, D. J. Am. Chem. Soc. 1999, 121, 1237
89. Leimkuhler, C.; Chen, Z.; Kruger, R. G.; Oberthur, M.; Lu, W.; Walsh, C. T.; Kahne, D. Tetrahedron: Asymmetry 2005, 16, 599
90. Nicolaou, K. C.; Mitchell, H. J.; Jain, N. F.; Winssinger, N.; Hughes, R.; Bando, T. Angew. Chem., Int. Ed. 1999, 38, 240
91. Nicolaou, K. C.; Mitchell, H. J.; Jain, N. F.; Bando, T.; Hughes, R.; Winssinger, N.; Natarajan, S.; Koumbis, A. E. Chem.-Eur. J. 1999, 5, 2648
92. Ritter, T. K.; Mong, K.-K. T.; Liu, T.; Nakatani, T.; Wong, C. H. Angew. Chem., Int. Ed. 2003, 42, 4657
93. Losey, H. C.; Peczuh, M. W.; Chen, Z.; Eggert, U. S.; Dong, S. D.; Pelczer, I.; Kahne, D.; Walsh, C. T. Biochemistry 2001, 40, 4745
94. Oberthur, M.; Leimkuhler, C.; Kruger, R. G.; Lu, W.; Walsh, C. T.; Kahne, D. J. Am. Chem. Soc. 2005, 127, 10747
95. Losey, H. C.; Jiang, J.; Biggins, J. B.; Oberthur, M.; Ye, X.; Dong, S. D.; Kahne, D.; Thorson, J. S.; Walsh, C. T. Chem. Biol. 2002, 9, 1305
96. Dong, S. D.; Oberthur, M.; Losey, H. C.; Anderson, J. W.; Eggert, U. S.; Peczuh, M. W.; Walsh, C. T.; Kahne, D. J. Am. Chem. Soc. 2002, 124, 9064
97. Kruger, R. G.; Lu, W.; Oberthur, M.; Tao, J.; Kahne, D.; Walsh, C. T. Chem. Biol. 2005, 12, 131
98. Thayer, D. A.; Wong, C. H. Chem.-Asian J. 2006, 1, 445
99. Thayer, D. A.; Yu, H. N.; Galan, M. C.; Wong, C. H. Angew. Chem., Int. Ed. 2005, 44, 4596
100. Solenberg, P. J.; Matsushima, P.; Stack, D. R.; Wilkie, S. C.; Thompson, R. C.; Baltz, R. H. Chem. Biol. 1997, 4, 195
101. Oh, T.-J.; Kim, D. H.; Kang, S. Y.; Yamaguchi, T.; Sohng, J. K. J. Antibiot. 2011, 64, 103
102. Fu, X.; Albermann, C.; Zhang, C. S.; Thorson, J. S. Org. Lett. 2005, 7, 1513
103. Fu, X.; Albermann, C.; Jiang, J. Q.; Liao, J. C.; Zhang, C. S.; Thorson, J. S. Nat. Biotechnol. 2003, 21, 1467
104. Nakayama, A.; Okano, A.; Feng, Y.; Collins, J. C.; Collins, K. C.; Walsh, C. T.; Boger, D. L. Org. Lett. 2014, 16, 3572
105. Presently there are four commercial suppliers of UMP morpholidate. We employed material obtained from Sigma-Aldrich ($176/g)
106. Oberthur, M.; Leimkuhler, C.; Kahne, D. Org. Lett. 2004, 6, 2873
107. Commercially available (Sigma-Aldrich)
108. Corey, E. J.; Boger, D. L. Tetrahedron Lett. 1978, 19, 5
109. Chen, Z.; Eggert, U. S.; Dong, S. D.; Shaw, S. J.; Sun, B.; LaTour, J. V.; Kahne, D. Tetrahedron 2002, 58, 6585
110. Kerns, R.; Dong, S. D.; Fukuzawa, S.; Carbeck, J.; Kohler, J.; Silver, L.; Kahne, D. J. Am. Chem. Soc. 2000, 122, 12608
111. The sequence was conducted only twice on a preparative scale and consequently is not yet optimized
112. Vancomycin-sensitive S. aureus (VSSA, ATCC 25923): sensitive to vancomycin, teicoplanin, oritavancin, daptomycin, linezolid, quinupristin-dalfopristin, fussidic acid, azithromycin, telithromycin, gentamycin, penicillin V, nafcillin, ampicillin, oxacillin, ciprofloxacin, levofloxacin, garenoxacin, and moxifloxacin. Methicillin-resistant S. aureus (MRSA, ATCC 43300): sensitive to vancomycin, teicoplanin, daptomycin, linezolid, tigecycline, and ciprofloxacin; resistant to methicillin, amoxicillin, amoxicillin with clavulanic acid, cephalexin, enrofloxacin, erythromycin, azithromycin, gentamycin, clindamycin, lincomycin-spectinomycin, neomycin, oxacillin, penicillin G, streptomycin, trimethoprim-sulfamethoxazole, and tetracycline. VanA E.faecalis (VanA VRE, BM 4166): resistant to erythromycin, gentamicin, chloramphenicol, and ciprofloxacin as well as vancomycin and teicoplanin; sensitive to daptomycin. VanA E. faecium (VanA VRE,ATCC BAA-2317): resistant to ampicillin, benzylpenicillin, ciprofloxacin, erythromycin, levofloxacin, nitrofurantoin, and tetracycline as well as vancomycin and teicoplanin; insensitive to linezolid; sensitive to tigecycline and dalfopristine. VanB E. faecalis (VanB VRE, ATCC 51299): resistant to vancomycin, streptomycin, gentamicin; sensitive to teicoplanin, ampicillin, tetracycline, and ciprofloxacin
113. Cardo, D.; Horan, T.; Andrus, M.; Dembinski, M.; Edwards, J.; Peavy, G.; Tolson, J.; Wagner, D. Am. J. Infect. Control 2004, 32, 470
114. Laxminarayan, R. Antibiotic Resistance: The Unfolding Crisis. In Extending the Cure: Policy Responses to the Growing Threat of Antibiotic Resistance; Laxminarayan, R.; Malani, A.; Howard, D.; Smith, D. L., Eds.; Resources for the Future: Washington, DC, 2007; Chapter 1, pp 25-37
115. Walsh, C. T.; Fischbach, M. A. Sci. Am. 2009, 301 (1) 44