Importance of microbial natural products and the need to revitalize their discovery
Tóm tắt
Microbes are the leading producers of useful natural products. Natural products from microbes and plants make excellent drugs. Significant portions of the microbial genomes are devoted to production of these useful secondary metabolites. A single microbe can make a number of secondary metabolites, as high as 50 compounds. The most useful products include antibiotics, anticancer agents, immunosuppressants, but products for many other applications, e.g., antivirals, anthelmintics, enzyme inhibitors, nutraceuticals, polymers, surfactants, bioherbicides, and vaccines have been commercialized. Unfortunately, due to the decrease in natural product discovery efforts, drug discovery has decreased in the past 20 years. The reasons include excessive costs for clinical trials, too short a window before the products become generics, difficulty in discovery of antibiotics against resistant organisms, and short treatment times by patients for products such as antibiotics. Despite these difficulties, technology to discover new drugs has advanced, e.g., combinatorial chemistry of natural product scaffolds, discoveries in biodiversity, genome mining, and systems biology. Of great help would be government extension of the time before products become generic.
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Tài liệu tham khảo
Alarcon, 2003, Production and purification of statins from Pleurotus ostreatus (Basidiomycetes) strains, Z Naturforsch, 58, 62, 10.1515/znc-2003-1-211
Alberts, 1980, Mevinolin. A highly potent competitive inhibitor of hydroxymethylglutaryl-coenzyme A reductase and a cholesterol-lowering agent, Proc Natl Acad Sci USA, 77, 3957, 10.1073/pnas.77.7.3957
Amaya, 2002, Tacrolimus and other immunosuppressive macrolides in clinical practice, Macrolide antibiotics: chemistry, biology and practice, 2, 421
Amna, 2006, Bioreactor studies on the endophytic fungus Entrophospora for the production of an anticancer alkaloid camptothecin, Can J Microbiol, 52, 189, 10.1139/w05-122
Asaduzzaman, 2009, Lantibiotics: diverse activities and unique modes of action, J Biosci Bioeng, 107, 475, 10.1016/j.jbiosc.2009.01.003
Baltz, 2007, Antimicrobials from actinomycetes: back to the future, Microbe, 2, 125
Bender, 2008, Substituents on etoposide that interact with human topoisomerase IIα in the binary enzyme-drug complex: contributions to etoposide binding and activity, Biochemistry, 46, 4501, 10.1021/bi702019z
Bentley, 2001, Bartolomeo Gosio, 1863–1944; an appreciation, Adv Appl Microbiol, 48, 229, 10.1016/S0065-2164(01)48005-1
Birkinshaw, 1952, Studies in the biochemistry of micro-organisms. 86. The molecular constitution of mycophenolic acid, a metabolic product of Penicillium brevi-compactum Dierckx. Part 3. Further observations on the structural formula for mycophenolic acid, Biochem J, 50, 630, 10.1042/bj0500630
Bode, 2002, Big effects from small changes: possible ways to explore nature’s chermical diversity, ChemBioChem, 3, 619, 10.1002/1439-7633(20020703)3:7<619::AID-CBIC619>3.0.CO;2-9
Bok, 2006, Genomic mining for Aspergillus natural products, Chem Biol, 13, 31, 10.1016/j.chembiol.2005.10.008
Brakage, 2011, Fungal secondary metabolites—strategies to activate silent genes, Fungal Genet Biol, 48, 15, 10.1016/j.fgb.2010.04.004
Breinbauer, 2002, Natural product guided compound library development, Curr Med Chem, 9, 2129, 10.2174/0929867023368773
Breinbauer, 2002, From protein domains to drug candidates—natural products as guiding principles in the design and synthesis of compound libraries, Angew Chem Int Ed, 41, 2879, 10.1002/1521-3773(20020816)41:16<2878::AID-ANIE2878>3.0.CO;2-B
Bronson, 2001, Quinolone, everninomycin, glycylcycline, carbapenem, lipopeptide and cephem antibiotics in clinical development, Curr Med Chem, 8, 1775, 10.2174/0929867013371653
Brown, 1976, Crystal and molecular structure of compactin, a new antifungal metabolite from Penicillium brevicompactum, J Chem Soc Perkins Trans, I, 1165, 10.1039/p19760001165
Bull, 2000, Search and discovery strategies for biotechnology: the paradigm shift, Microbiol Mol Biol Rev, 64, 573, 10.1128/MMBR.64.3.573-606.2000
Burrill, 2002, Personalized medicine or blockbusterology, BioPharm, 15, 46
Busti, 2006, Antibiotic-producing ability by representatives of a newly discovered lineage of actinomycetes, Microbiology, 152, 675, 10.1099/mic.0.28335-0
Campbell, 2012, History of avermectin and ivermectin, with notes on the history of other macrocyclic lactone antiparasitic agents, Curr Pharm Biotechnol, 13, 853, 10.2174/138920112800399095
Cao, 2008, A review of Judah Folkman’s remarkable achievements in biomedicine, Proc Natl Acad Sci USA, 105, 13203, 10.1073/pnas.0806582105
Cao, 2011, Rapamycin reverses cellular phenotypes and enhances mutant protein clearance in Hutchinson-Gilford progeria syndrome cells, Sci Translat Med, 3, 1, 10.1126/scitranslmed.3002346
Cardenas, 1999, The TOR signaling cascade regulates gene expression in response to nutrients, Genes Devel, 13, 3271, 10.1101/gad.13.24.3271
Carle, 2000, Ascomycins: promising agents for the treatment of inflammatory skin diseases, Expert Opin Investig Drugs, 9, 69, 10.1517/13543784.9.1.69
Chan, 2004, HMG-CoA reductase inhibitors for lowering elevated levels of C-reactive protein, Am J Health-Syst Pharm, 61, 1676, 10.1093/ajhp/61.16.1676
Choi, 2000, Intermittent maltose feeding enhances paclitaxel production in suspension culture of Taxus chinensis cells, Biotechnol Lett, 2, 1793, 10.1023/A:1005658405449
Christoffersen, 2006, Antibiotics. an investment worth making?, Nat Biotechnol, 24, 1512, 10.1038/nbt1206-1512
Connors, 2004, Pneumocandin BO production by fermentation of the fungus Glarea lozoyensis: physiological and engineering factors affecting titer and structural analogue formation, Handbook of Industrial Mycology, 515, 10.1201/9780203970553.ch19
Cragg, 2000, Antineoplastic agents from natural sources: achievements and future directions, Expert Opin Investig Drugs, 9, 2783, 10.1517/13543784.9.12.2783
Cruz, 2000, Immunosuppressive and nonimmunosuppressive cyclosporine analogs are toxic to the opportunistic fungal pathogen Cryptococcus neoformans via cyclophillin-dependent inhibition of calcineurin, Antimicrob Ag Chemother, 44, 143, 10.1128/AAC.44.1.143-149.2000
Cruz, 2001, Rapamycin and less immumosuppressive analogs are toxic to Candida albicans and Cryptococcus neoformans via FKBP12-dependent inhibition of TOR, Antimicrob Ag Chemother, 45, 3162, 10.1128/AAC.45.11.3162-3170.2001
Dejong, 2006, Genetic engineering of taxol biosynthetic genes in Saccharomyces cerevisiae, Biotechnol Bioeng, 93, 212, 10.1002/bit.20694
Demain, 2002, Prescription for an ailing pharmaceutical industry, Nat Biotechnol, 20, 331, 10.1038/nbt0402-331
Demain, 2006, From natural products discovery to commercialization: a success story, J Ind Microbiol Biotechnol, 33, 486, 10.1007/s10295-005-0076-x
Demain, 2008, Contributions of microorganisms to industrial biology, Mol Biotechnol, 38, 41, 10.1007/s12033-007-0035-z
Demain, 2005, Natural products and drug discovery, Natural products: drug discovery and therapeutic medicine, 3, 10.1007/978-1-59259-976-9_1
Deorukhkar, 2007, Back to basics: how natural products can provide the basis for new therapeutics, Expert Opin Investig Drugs, 16, 1753, 10.1517/13543784.16.11.1753
Dobson, 1999, Characterization of protein Ser/Thr phosphatases of the malaria parasite, Plasmodium falciparum: inhibition of the parasitic calcineurin by cyclophilin–cyclosporin complex, Molec Biochem Parasitol, 99, 167, 10.1016/S0166-6851(99)00010-9
Dunlap, 2007, Biomedicinals from the phytosymbionts of marine invertebrates: a molecular approach, Methods, 42, 358, 10.1016/j.ymeth.2007.03.001
Dworkin, 2007, Lingering puzzles about myxobacteria, Microbe, 2, 18
Eckstein, 2003, A new class of cyclosporin analogues for the treatment of asthma, Expert Opin Investig Drugs, 12, 647, 10.1517/13543784.12.4.647
Einhorn, 2002, Curing metastatic testicular cancer, Proc Natl Acad Sci (USA), 99, 4592, 10.1073/pnas.072067999
Endo, 2010, A historical perspective on the discovery of statins, Proc Jpn Acad Ser B, 86, 484, 10.2183/pjab.86.484
Endo, 1976, Competitive inhibition of 3-hydroxyglutaryl coenzyme A reductase by ML-236A and ML-236B fungal metabolites, having hypocholesterolemic activity, FEBS Lett, 72, 323, 10.1016/0014-5793(76)80996-9
Endo, 1980, Monocolin K, a new hypocholesterolemic agent that specifically inhibits 3-hydroxy-3-methylglutaryl coenzyme A reductase, J Antibiot, 33, 334, 10.7164/antibiotics.33.334
Engels, 2008, Cancer risk in people infected with human immunodeficiency virus in the United States, Intl J Cancer, 123, 187, 10.1002/ijc.23487
Felnagle, 2008, Nonribosomal peptide synthetases involved in the production of medically relevant natural products, Molec Pharmaceut, 5, 191, 10.1021/mp700137g
Georgopapadakou, 2001, Antifungals targeted to cell wall: focus on β-1,3-glucan synthase, Expert Opin Investig Drugs, 10, 269, 10.1517/13543784.10.2.269
Gerth, 2000, Studies on biosynthesis of epothilones: the biosynthetic origin of the carbon skeleton, J Antibiot, 53, 1373, 10.7164/antibiotics.53.1373
Gold, 2000, Neuroimmunophilin ligands: evaluation of their therapeutic potential for the treatment of neurological disorders, Expert Opin Investig Drugs, 9, 2331, 10.1517/13543784.9.10.2331
Goodin, 2008, Novel cytotoxic agents: epothilones, Am J Health Syst Pharm, 65, S10, 10.2146/ajhp080089
Guba, 2002, Rapamycin inhibits primary and metastatic tumor growth by antiangiogenesis: involvement of vascular endothelial growth factor, Nature Med, 8, 128, 10.1038/nm0202-128
Guilder, 2009, Chasing the treasures of the sea—bacterial marine natural products, Curr Opin Microbiol, 12, 252, 10.1016/j.mib.2009.05.002
Hardt, 2001, New natural epothilones from Sorangium cellulosum, Strains So ce90/B2 and So ce90/D13: isolation, structural elucidation, and SAR studies, J Nat Prods, 64, 847, 10.1021/np000629f
Hopwood, 1985, Production of hybrid antibiotics by genetic engineering, Nature, 314, 642, 10.1038/314642a0
Hranueli, 2005, Plasticity of the Streptomyces genome-evolution and engineering of new antibiotics, Curr Med Chem, 12, 1697, 10.2174/0929867054367176
Hugonnet, 2009, Meropenem-clavulanate is effective against extensively drug-resistant Mycobacterium tuberculosis, Science, 323, 1215, 10.1126/science.1167498
Jensen, 2005, Marine actinomycete diversity and natural product discovery, Ant v Leeuwenhoek, 87, 43, 10.1007/s10482-004-6540-1
Kingston, 2002, Mother nature’s combinatorial libraries; their influence on the synthesis of drugs, Curr Opin Drug Disc Devel, 5, 304
Knowles, 2003, Target selection in drug discovery, Nat Rev, 2, 63
Kumaran, 2008, Taxol from Phyllosticta citricarpa, a leaf spot fungus of the angiosperm Citrus medica, J Biosci Bioeng, 106, 103, 10.1263/jbb.106.103
Lederberg, 2000, Pathways of discovery: infectious history, Science, 288, 287, 10.1126/science.288.5464.287
Lee, 2008, Shikonin, acetylshikonin, and isobutyroylshikonin inhibit VEGF-induced angiogenesis and suppress tumor growth in Lewis lung carcinoma-bearing mice, Yakugaku Zasshi, 128, 1681, 10.1248/yakushi.128.1681
Liu, 2004, Recent progress in bioactive metabolites of marine microorganisms, Chi J Antibiot, 29, 492
Lorence, 2004, Camptothecin, over four decades of surprising findings, Phytochemistry, 65, 2735, 10.1016/j.phytochem.2004.09.001
Manzoni, 2002, Biosynthesis and biotechnological production of statins by filamentous fungi and application of these cholesterol-lowering drugs, Appl Microbiol Biotechnol, 58, 555, 10.1007/s00253-002-0932-9
Manzoni, 1999, Production of statins by filamentous fungi, Biotechnol Lett, 21, 253, 10.1023/A:1005495714248
Martinkova, 1995, Biological activity of polyketide pigments produced by the fungus Monascus, J Appl Bacteriol, 79, 609, 10.1111/j.1365-2672.1995.tb00944.x
Newman, 2003, Natural products as sources of new drugs over the period 1981–2002, J Nat Prods, 66, 1022, 10.1021/np030096l
Newman, 2008, Microbial prescreens for anticancer activity, SIM News, 58, 132
Omura, 2008, Ivermectin: 25 years old and still going strong, J Antimicrob Ag, 31, 91, 10.1016/j.ijantimicag.2007.08.023
Onyewu, 2003, Ergosterol biosynthesis inhibitors become fungicidal when combined with calcineurin inhibitors in Candida albicans, Candida glabrata, and Candida krusei, Antimicrob Ag Chemother, 47, 956, 10.1128/AAC.47.3.956-964.2003
Overbye, 2005, Antibiotics: where did we go wrong?, Drug Disc Today, 10, 45, 10.1016/S1359-6446(04)03285-4
Pandey, 2007, Prodigiosins: a novel family of immunosuppressants with anti-cancer activity, Ind J Biochem Biophys, 44, 295
Park, 2010, Genetic engineering of macrolide biosynthesis: past advances, current state and future prospects, Appl Microbiol Biotechnol, 85, 1227, 10.1007/s00253-009-2326-8
Park, 2010, Biosynthesis of rapamycin and its regulation: past achievements and recent progress, J Antibiot, 63, 434, 10.1038/ja.2010.71
Patchett, 2002, Alfred Burger award address in medicinal chemistry. Natural products and design: interrelated approaches in drug discovery, J Med Chem, 45, 5609, 10.1021/jm020424z
Paululat, 1999, Combinatorial chemistry: the impact of natural products, Chim Oggi, 17, 52
Peng, 1998, Properties of the hydroxylase in Actinomadura sp cells converting compactin to pravastatin, J Ind Microbiol Biotechnol, 20, 373, 10.1038/sj.jim.2900539
Piel, 2004, Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei, Proc Natl Acad Sci USA, 101, 16222, 10.1073/pnas.0405976101
Pinter, 2009, Diazo transfer-click reaction route to new lipophilic teicoplanin and ristocetin aglycon derivatives with high antibacterial and anti-influenza virus activity: an aggregation and receptor binding study, J Med Chem, 52, 6053, 10.1021/jm900950d
Pray, 2002, Strange bedfellows in transplant drug therapy, Scientist, 16, 36
Raskin, 2002, Plants and human health in the twentieth century, Trends Biotechnol, 20, 522, 10.1016/S0167-7799(02)02080-2
Revill, 2002, Genetically engineered analogs of ascomycin for nerve regeneration, J Pharmacol Exp Ther, 302, 1278, 10.1124/jpet.102.034264
Rohde, 2001, The TOR kinases link nutrient sensing to cell growth, J Biol Chem, 276, 9583, 10.1074/jbc.R000034200
Rokem, 2007, Systems biology of antibiotic production by microorganisms, Nat Prod Rep, 24, 1262, 10.1039/b617765b
Scheffler, 2013, Antimicrobials, drug discovery, and genome mining, Appl Microbiol Biotechnol, 97, 969, 10.1007/s00253-012-4609-8
Schiewe, 1999, Cineromycins: butyrolactones and ansamycins of the secondary metabolite pattern created by a single strain of Streptomyces, J Antibiot, 52, 635, 10.7164/antibiotics.52.635
Selitrennikoff, 2001, Antifungal proteins, Appl Environ Microbiol, 67, 2883, 10.1128/AEM.67.7.2883-2894.2001
Serizawa, 1991, A two-component-type cytochrome P-450 monoxygenase system in prokaryotes that catalyzes hydroxylation of ML-236B to pravastatin, a tissue-selective inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase, Biochim Biophys Acta, 1084, 35, 10.1016/0005-2760(91)90052-J
Smith, 2008, Therapeutic potential of type A (I) lantibiotics, a group of cationic peptide antibiotics, Curr Opin Microbiol, 11, 401, 10.1016/j.mib.2008.09.008
Song, 2008, What’s new on the antimicrobial horizon?, Intl J Antimicrob Ag, 32, S207, 10.1016/S0924-8579(09)70004-4
Stierle, 1993, Taxol and taxane production by Taxomyces andreanae, an endophytic fungus of Pacific yew, Science, 260, 214, 10.1126/science.8097061
Strobel, 2002, Rainforest endophytes and bioactive products, Crit Rev Biotechnol, 22, 315, 10.1080/07388550290789531
Strobel, 1996, Taxol from fungal endophytes and the issue of biodiversity, J Indust Microbiol, 17, 417
Strohl, 2004, Antimicrobials, Microbial diversity and bioprospecting, 336
Topliss, 2002, Natural and synthetic substances related to human health, Pure Appl Chem, 74, 1957, 10.1351/pac200274101957
Udwary, 2007, Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinospora tropica, Proc Natl Acad Sci USA, 104, 10376, 10.1073/pnas.0700962104
Vandamme, 2007, Microbial gems: microorganisms without frontiers, SIM-News, 57, 81
Vezina, 1975, Rapamycin (AY-22989), a new antifungal antibiotic. I. Taxonomy of the producing streptomycete and isolation of the active principle, J Antibiot, 28, 721, 10.7164/antibiotics.28.721
Waldemann, 2002, Nature provides the answer, Screening, 3, 46
Wall, 1996, Camptothecin and taxol: from discovery to clinic, J Ethnopharmacol, 51, 239, 10.1016/0378-8741(95)01367-9
Wang, 2000, Taxol from Tubercularia sp. strain TF5, an endophytic fungus of Taxus mairei, FEMS Microbiol Lett, 193, 249, 10.1111/j.1574-6968.2000.tb09432.x
Wilkinson, 2007, Mining and engineering natural-product biosynthetic pathways, Nature Chem Bio, 3, 379, 10.1038/nchembio.2007.7
Wong, 2012, Combinatorial biosynthesis of polyketides—a perspective, Curr Opin Chem Biol, 161, 117, 10.1016/j.cbpa.2012.01.018
Wrigley, 2004, Pharmacologically active agents of microbial origin, Microbial diversity and bioprospecting, 356
Xie, 2007, Efficient synthesis of simvastatin by use of whole-cell biocatalysis, Appl Environ Microbiol, 73, 2054, 10.1128/AEM.02820-06
Xie, 2007, Improving simvastatin bioconversion in Escherichia coli by deletion of bioH, Metab Eng, 9, 379, 10.1016/j.ymben.2007.05.006
Xue, 1999, A multi-plasmid approach to preparing large libraries of polyketides, Proc Natl Acad Sci USA, 96, 11740, 10.1073/pnas.96.21.11740
Yang, 2001, Natural product-based anti-HIV drug discovery and development facilitated by the NCI development therapeutics program, J Nat Prods, 64, 265, 10.1021/np0003995
Yoneyama, 2006, Antibiotic resistance in bacteria and its future for novel antibiotic development, Biosci Biotechnol Biochem, 70, 1060, 10.1271/bbb.70.1060
Youssef, 2002, The HMG-CoA reductase inhibitor, atorvastatin, promotes a Th2 bias and reverses paralysis in central nervous system autoimmune disease, Nature, 420, 78, 10.1038/nature01158