Lessons from natural molecules (original) (raw)

References

  1. Newman, D. J., Cragg, G. M. & Snader, K. M. The influence of natural products upon drug discovery. Nat. Prod. Rep. 17, 215–234 (2000).
    Article CAS Google Scholar
  2. Newman, D. J., Cragg, G. M., Holbeck, S. & Sausville, E. A. Natural products and derivatives as leads to cell cycle pathway targets in cancer chemotherapy. Curr. Cancer Drug Targets 2, 279–308 (2002).
    Article CAS Google Scholar
  3. Newman, D. J., Cragg, G. M. & Snader, K. M. Natural products as sources of new drugs over the period 1981–2002. J. Nat. Prod. 66, 1022–1037 (2003).
    Article CAS Google Scholar
  4. Altmann, K. -H. Microtubule-stabilizing agents: a growing class of important anticancer drugs. Curr. Opin. Chem. Biol. 5, 424–431 (2001).
    Article CAS Google Scholar
  5. Mickel, S. J. et al. Large-scale synthesis of the anti-cancer marine natural product (+)–discodermolide. Part 1: Synthetic strategy and preparation of a common precursor. Org. Proc. Res. Dev. 8, 92–100 (2004).
    Article CAS Google Scholar
  6. Sheldrick, G. M., Jones, P. G., Kennard, O., Williams, D. H. & Smith, G. A. Structure of vancomycin and its complex with acetyl-D-alanyl-D-alanine. Nature 271, 223–225 (1978).
    Article ADS CAS Google Scholar
  7. Williamson, M. P. & Williams, D. H. Structure revision of the antibiotic vancomycin. Use of nuclear Overhauser effect difference spectroscopy. J. Am. Chem. Soc. 103, 6580–6585 (1981).
    Article CAS Google Scholar
  8. Furasaki, A. et al. The crystal and molecular structure of staurosporine, a new alkaloid from a Streptomyces strain. J. Chem. Soc. Chem. Commun. 800–801 (1978).
  9. Sehgal, S. N., Baker, H. & Vezina, C. Rapamycin (AY-22,989), a new antifungal antibiotic. II. Fermentation, isolation and characterization. J. Antibiot. 28, 727–732 (1975).
    Article CAS Google Scholar
  10. Wani, M. C., Taylor, H. L., Wall, M. E., Coggon, P. & McPhail, A. T. The isolation and structure of taxol, a novel antileukemic and antitumor agent. J. Am. Chem. Soc. 93, 2325–2327 (1971).
    Article CAS Google Scholar
  11. Pindur, U., Kim, Y. S. & Mehrabani, F. Advances in indolo[2,3-a]carbazole chemistry: design and synthesis of protein kinase C and topoisomerase I inhibitors. Curr. Med. Chem. 6, 29–69 (1999).
    CAS PubMed Google Scholar
  12. Carson, C. C. 3rd Sildenafil: a 4-year update in the treatment of 20 million erectile dysfunction patients. Curr. Urol. Rep. 4, 488–496 (2003).
    Article Google Scholar
  13. Wong, D. T. & Bymaster, F. P. Development of antidepressant drugs. Fluoxetine (Prozac) and other selective serotonin uptake inhibitors. Adv. Exp. Med. Biol. 363, 77–95 (1995).
    Article CAS Google Scholar
  14. Roth, B. D. The discovery and development of atorvastatin, a potent novel hypolipidemic agent. Prog. Med. Chem. 40, 1–22 (2002).
    Article CAS Google Scholar
  15. Kurzrock, R., Kantarjian, H. M., Druker, B. J. & Talpaz, M. Philadelphia chromosome-positive leukemias: from basic mechanisms to molecular therapeutics. Ann. Intern. Med. 138, 819–830 (2003).
    Article CAS Google Scholar
  16. Lee, M. D., Dunne, T. M., Chang, C. C., Morton, G. O. & Borders, D. B. Calicheamicins, a novel family of antitumor antibiotics. J. Am. Chem. Soc. 109, 3464–3466 (1987).
    Article CAS Google Scholar
  17. Konishi, M. et al. Crystal and molecular structure of dynemicin A: a novel 1,5-diyn-3-ene antitumor antibiotic. J. Am. Chem. Soc. 112, 3715–3716 (1990).
    Article CAS Google Scholar
  18. Thorson, J. S. et al. Understanding and exploiting nature's chemical arsenal: the past, present and future of calicheamicin research. Curr. Pharm. Des. 6, 1841–1879 (2000).
    Article CAS Google Scholar
  19. Scotto, K. W. ET-743: more than an innovative mechanism of action. Anticancer Drugs 13 (Suppl. 1), S3–6 (2002).
    MathSciNet CAS PubMed Google Scholar
  20. Aune, G. J., Furuta, T. & Pommier, Y. Ecteinascidin 743: a novel anticancer drug with a unique mechanism of action. Anticancer Drugs 13, 545–555 (2002).
    Article CAS Google Scholar
  21. Liu, S., Widom, J., Kemp, C. W., Crews, C. M. & Clardy, J. Structure of human methionine aminopeptidase-2 complexed with fumagillin. Science 282, 1324–1327 (1998).
    Article ADS CAS Google Scholar
  22. Meng, L., Kwok, B. H., Sin, N. & Crews, C. M. Eponemycin exerts its antitumor effect through the inhibition of proteasome function. Cancer Res. 59, 2798–2801 (1999).
    CAS PubMed Google Scholar
  23. Fenteany, G. et al. Inhibition of proteasome activities and subunit-specific amino-terminal threonine modification by lactacystin. Science 268, 726–731 (1995).
    Article ADS CAS Google Scholar
  24. Feling, R. H. et al. Salinosporamide A: a highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus salinospora. Angew. Chem. Int. Edn Engl. 42, 355–357 (2003).
    Article CAS Google Scholar
  25. Kim, M. Y., Gleason-Guzman, M., Izbicka, E., Nishioka, D. & Hurley, L. H. The differential biological effects of telomestatin and TMPPyP4 can be attributed to their selectivity for interaction with intramolecular and intermolecular G-quadruplex structures. Cancer Res. 63, 3247–3256 (2003).
    CAS PubMed Google Scholar
  26. Choi, J., Chen, J., Schreiber, S. L. & Clardy, J. Structure of the FKBP12-rapamycin complex interacting with the binding domain of human FRAP. Science 273, 239–242 (1996).
    Article ADS CAS Google Scholar
  27. Gunasekera, S. P., Gunasekera, M., Longley, R. E. & Schulte, G. K. Discodermolide: a new bioactive polyhydroxylated lactone from the marine sponge Discodermia dissoluta. J. Org. Chem. 55, 4912–4915 (1991).
    Article Google Scholar
  28. Talpir, R., Benayahu, Y., Kashman, Y., Pannell, L. & Schleyer, M. Hemiasterlin and geodiamolide TA: two new cytotoxic peptides from the marine sponge Hemiasterella minor. Tetrahedron Lett. 35, 4453–4456 (1994).
    Article CAS Google Scholar
  29. Anderson, R. J., Coleman, J. E., Andersen, R. J. & Roberge, M. Cytotoxic peptides hemiasterlin, hemiasterlin A and hemiasterlin B induce mitotic arrest and abnormal spindle formation. Cancer Chemother. Pharmacol. 39, 223–226 (1997).
    Article CAS Google Scholar
  30. Schantz, E. J. et al. The structure of saxitoxin. J. Am. Chem. Soc. 93, 7344–7345 (1975).
    Google Scholar
  31. Yotsu-Yamashita, M. et al. The structure of zetekitoxin AB, a saxitoxin analog from the Panamanian golden frog Atelopus zeteki: a potent sodium-channel blocker. Proc. Natl Acad. Sci. USA 101, 4346–4351 (2004).
    Article ADS CAS Google Scholar
  32. Rinehart, K. L. et al. Ecteinascidins 729, 743, 745, 759A, 759B and 770: potent antitumor agents from the Caribbean tunicate Ecteinascidia turbinata. J. Org. Chem. 55, 4512–4515 (1990).
    Article CAS Google Scholar
  33. Boghaert, E. R. et al. Antibody-targeted chemotherapy with the calicheamicin conjugate hu3S193-N-acetyl gamma calicheamicin dimethyl hydrazide targets Lewisy and eliminates Lewisy-positive human carcinoma cells and xenografts. Clin. Cancer Res. 10, 4538–4549 (2004).
    Article CAS Google Scholar
  34. DiJoseph, J. F. et al. Antibody-targeted chemotherapy with CMC-544: a CD22-targeted immunoconjugate of calicheamicin for the treatment of B-lymphoid malignancies. Blood 103, 1807–1814 (2004).
    Article CAS Google Scholar
  35. Boldi, A. M. Libraries from natural product-like scaffolds. Curr. Opin. Chem. Biol. 8, 281–286 (2004).
    Article CAS Google Scholar
  36. Gunasekera, S. P., McCarthy, P. J., Kelly-Borges, M., Lobkovsky, E. & Clardy, J. Dysidiolide: a novel protein phosphatase inhibitor from the Caribbean sponge Dysidea etheria de Laubenfels. J. Am. Chem. Soc. 118, 8759–8760 (1996).
    Article CAS Google Scholar
  37. Brohm, D. et al. Natural products are biologically validated starting points in structural space for compound library development: solid-phase synthesis of dysidiolide-derived phosphatase inhibitors. Angew. Chem. Int. Edn Engl. 41, 307–311 (2002).
    Article CAS Google Scholar
  38. Schreiber, S. L. Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 287, 1964–1969 (2000).
    Article ADS CAS Google Scholar
  39. Burke, M. D. & Schreiber, S. L. A planning strategy for diversity-oriented synthesis. Angew. Chem. Int. Edn Engl. 43, 46–58 (2004).
    Article Google Scholar
  40. Burke, M. D., Berger, E. M., Schreiber, S. L. Generating diverse skeletons of small molecules combinatorially. Science 302, 613–618 (2004).
    Article ADS Google Scholar
  41. Walsh, C. Antibiotics: Actions, Origins, Resistance (ASM, Washington, 2003).
    Book Google Scholar
  42. Hubbard, B., Walsh, C. Vancomycin assembly: Nature's way. Angew. Chem. Int. Edn Engl. 730–765 (2003).
  43. Schwarzer, D., Firking, R., Marahiel, M. A. Nonribosomal peptides: from genes to products. Nat. Prod. Rep. 20, 275–287 (2003).
    Article CAS Google Scholar
  44. Walsh, C., Freel Meyers, C. L., Losey, H. C. Antibiotic glycosyltransferases: antibiotic maturation and prospects for reprogramming. J. Med. Chem. 46, 3425–3436 (2003).
    Article CAS Google Scholar
  45. Wendt, K. U., Schulz, G. E., Corey, E. J., Liu, D. R. Enzyme mechanisms for polycyclic triterpene formation. Angew. Chem. Int. Edn Engl. 39, 2812–2833 (2000).
    Article CAS Google Scholar
  46. Whittington, D. A. et al. Bornyl diphosphate synthase: structure and strategy for carbocation manipulation by a terpenoid cyclase. Proc. Natl. Acad. Sci. USA 99, 15375–15380 (2002).
    Article ADS CAS Google Scholar
  47. Rawlings, B. J. Type I polyketide biosynthesis in bacteria (part A). Nat. Prod. Rep. 18, 190–230 (2001).
    Article CAS Google Scholar
  48. Rawlings, B. J. Type I polyketide biosynthesis in bacteria (part B). Nat. Prod. Rep. 18, 231–281 (2001).
    Article CAS Google Scholar
  49. Kohli, R. & Walsh, C. Enzymology of acyl chain macrocyclization in natural product biosynthesis. Chem. Commun. 297–307 (2003).
  50. Schwecke, T. et al. The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin. Proc. Natl Acad. Sci. USA 92, 7839–7843 (1995).
    Article ADS CAS Google Scholar
  51. Ahlert, J. et al. The calicheamycin gene cluster and its iterative type I enediyne PKS. Science 297, 1173–1176 (2002).
    Article ADS CAS Google Scholar
  52. Liu, W., Christensen, S. D., Standage, S. & Shen, B. Biosynthesis of the enediyne antitumor antibiotic C-1027. Science 297, 1170–1173 (2002).
    Article ADS CAS Google Scholar
  53. Shen, B., Liu, W. & Nonaka, K. Enediyne natural products: biosynthesis and prospects towards engineering novel antitumor agents. Curr. Med. Chem. 10, 2317–2325 (2003).
    Article CAS Google Scholar
  54. Zerbe, K. et al. Crystal structure of OxyB, a cytochrome P450 implicated in an oxidative phenol coupling reaction during vancomycin biosynthesis. J. Biol. Chem. 277, 47476–47485 (2002).
    Article CAS Google Scholar
  55. Pylypenko, O., Vitali, F., Zerbe, K., Robinson, J. A. & Schlichting, I. Crystal structure of OxyC, a cytochrome P450 implicated in an oxidative C–C coupling reaction during vancomycin biosynthesis. J. Biol. Chem. 278, 46727–46733 (2003).
    Article CAS Google Scholar
  56. Walker, K. & Croteau, R. Taxol biosynthetic genes. Phytochemistry 58, 1–7 (2001).
    Article CAS Google Scholar
  57. Chau, M., Jennewein, S., Walker, K. & Croteau, R. Taxol biosynthesis: molecular cloning and characterization of a cytochrome P450 taxoid 7 beta-hydroxylase. Chem. Biol. 11, 663–672 (2004).
    CAS PubMed Google Scholar
  58. Jennewein, S., Long, R. M., Williams, R. M. & Croteau, R. Cytochrome p450 taxadiene 5 alpha-hydroxylase, a mechanistically unusual monooxygenase catalyzing the first oxygenation step of taxol biosynthesis. Chem. Biol. 11, 379–387 (2004).
    Article CAS Google Scholar
  59. Yadav, G., Ghokale, R. S. & Mohanty, D. Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. J. Mol. Biol. 328, 335–363 (2003).
    Article CAS Google Scholar
  60. Eppelman, K., Stachelhaus, T. & Marahiel, M. A. Exploitation of the selectivity-conferring code of nonribosomal peptide synthetases for the rational design of novel peptide antibiotics. Biochemistry 42, 9718–9716 (2002).
    Article Google Scholar
  61. Lu, W., Leimkuhler, C., Oberthur, M., Kahne, D. & Walsh, C. AknK is an L-2-deoxyfucosyltransferase in the biosynthesis of the anthracycline aclacinomycin. Biochemistry 43, 4548–4558 (2004).
    Article CAS Google Scholar
  62. Losey, H. C. et al. Incorporation of glucose analogs by glycosyltransferases GtfE and GtfD from the vancomycin biosynthetic pathway to generate variant glycopeptides. Chem. Biol. 9, 1305–1314 (2002).
    Article CAS Google Scholar
  63. Mende, Z. C. & Salas, J. A. Altering the glycosylation pattern of bioactive compounds. Trends Biotechnol. 19, 449–456 (2001).
    Article Google Scholar
  64. McDaniel, R. et al. Multiple genetic modifications of the erythromycin gene cluster to produce a library of novel ‘unnatural’ natural products. Proc. Natl Acad. Sci. USA 96, 1846–1851 (1999).
    Article ADS CAS Google Scholar
  65. Tang, L. & McDaniel, R. Construction of desosamine containing polyketide libraries using a glycosyltransferase with broad substrate specificity. Chem. Biol. 8, 547–555 (2001).
    Article CAS Google Scholar
  66. Wohlleben, W. & Pelzer, S. New compounds by combining modern genomics and old-fashioned mutasysnthesis. Chem. Biol. 9, 1163–1166 (2002).
    Article CAS Google Scholar
  67. Huang, Q., Roessner, C. A., Croteau, R. & Scott, A. I. Engineering E. coli for the synthesis of taxadiene, a key intermediate in the biosynthesis of taxol. Biorg. Med. Chem. 9, 2237–2242 (2001).
    Article CAS Google Scholar
  68. Martin, V. J., Pitera, D. J., Withers, S. T., Newman, J. D. & Keasling, J. D. Engineering a mevalonate pathway in E. coli for production of terpenoids. Nature Biotechnol. 21, 796–802 (2003).
    Article CAS Google Scholar
  69. Ondeyka, J. G. et al. Nodulisporic acids C, C1, and C2: a series of D-ring-opened nodulisporic acids from the fungus Nodulisporium sp. J. Nat. Prod. 66, 121–124 (2003).
    Article CAS Google Scholar
  70. Brady, S. F., Bondi, S. M. & Clardy, J. The guanacastepenes: a highly diverse family of secondary metabolites produced by an endophytic fungus. J. Am. Chem. Soc. 123, 9900–9901 (2001).
    Article CAS Google Scholar
  71. Fuller, R. W. et al. A pentahalogenated monoterpene from the red alga Portieria hornemanni produces a novel cytotoxicity profile against a diverse panel of human tumor cell lines. J. Med. Chem. 35, 3007–3011 (1992).
    Article CAS Google Scholar
  72. Piel, J. Metabolites from symbiotic bacteria. Nat. Prod. Rep. 21, 519–538 (2004).
    Article CAS Google Scholar
  73. Luesch, H., Yoshida, W. Y., Moore, R. E., Paul, V. J. & Corbett, T. H. Total structure determination of apratoxin A, a potent novel cytotoxin from the marine cyanobacterium Lyngbya majuscula. J. Am. Chem. Soc. 123, 5418–5423 (2001).
    Article CAS Google Scholar
  74. Edwards, D. J. et al. Structure and biosynthesis of the jamaicamides, new mixed polyketide-peptide neurotoxins from the marine cyanobacterium Lyngbya majuscula. Chem. Biol. 11, 817–833 (2004).
    Article MathSciNet CAS Google Scholar
  75. Gerth, K., Bedorf, N., Hofle, G., Irschik, H. & Reichenbach, H. Epothilons A and B: antifungal and cytotoxic compounds from Sorangium cellulosum (Myxobacteria). Production, physico-chemical and biological properties. J. Antibiot. (Tokyo) 49, 560–563 (1996).
    Article CAS Google Scholar
  76. Sasse, F., Steinmetz, H., Heil, J., Hofle, G. & Reichenbach, H. Tubulysins, new cytostatic peptides from myxobacteria acting on microtubuli. Production, isolation, physico-chemical and biological properties. J. Antibiot. (Tokyo) 53, 879–885 (2000).
    Article CAS Google Scholar
  77. Pace, N. R. A molecular view of microbial diversity and the biosphere. Science 276, 734–740 (1997).
    Article CAS Google Scholar
  78. Kaeberlein, T., Lewis, K. & Epstein, S. S. Isolating ‘uncultivable’ microorganisms in pure culture in a simulated natural environment. Science 296, 1127–1129 (2002).
    Article ADS CAS Google Scholar
  79. Wang, G. Y. et al. Novel natural products from soil DNA libraries in a streptomycete host. Org. Lett. 2, 2401–2404 (2000).
    Article CAS Google Scholar
  80. Brady, S., Chao, C. J. & Clardy, J. New natural product families from an eDNA cluster. J. Am. Chem. Soc. 124, 9968–9969 (2002).
    Article CAS Google Scholar
  81. Zazopoulos, E. et al. A genomics-guided approach for discovering and expressing cryptic metabolic pathways. Nature Biotechnol. 21, 187–190 (2003).
    Article CAS Google Scholar
  82. Jennewein, S., Wildung, M. R., Chau, M., Walker, K. & Croteau, R. Random sequencing of an induced Taxus cell cDNA library for identification of clones involved in Taxol biosynthesis. Proc. Natl Acad. Sci. USA 101, 9149–9154 (2004).
    Article ADS CAS Google Scholar

Download references