Retrospective analysis of natural products provides insights for future discovery trends

Proceedings of the National Academy of Sciences of the United States of America

Volumn 114, Issue 22, 2017, Pages 5601-5606

  Pye, Cameron R ^a   Bertin, Matthew J ^b,c   Lokey, R Scott ^a   Gerwick, William H ^b,c   Linington, Roger G ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Chemical diversity; Chemoinformatics; Drug discovery; Natural products; Structural similarity

Indexed keywords

NATURAL PRODUCT; ANTIINFECTIVE AGENT; BIOLOGICAL PRODUCT;

ARTICLE; DRUG STRUCTURE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RETROSPECTIVE STUDY; TAXONOMY; CHEMISTRY; DRUG DEVELOPMENT; HUMAN; PROCEDURES; TRENDS;

ANTI-BACTERIAL AGENTS; BIOLOGICAL PRODUCTS; DRUG DISCOVERY; HUMANS; RETROSPECTIVE STUDIES;

EID: 85020047311     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1614680114     Document Type: Article

References (43)

1. Newman DJ, Cragg GM (2016) Natural products as sources of new drugs from 1981 to 2014. J Nat Prod 79:629-661.
2. Harvey AL, Edrada-Ebel R, Quinn RJ (2015) The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov 14:111-129.
3. Gwynn MN, Portnoy A, Rittenhouse SF, Payne DJ (2010) Challenges of antibacterial discovery revisited. Ann N Y Acad Sci 1213:5-19.
4. Kong D-X, Guo M-Y, Xiao Z-H, Chen L-L, Zhang H-Y (2011) Historical variation of structural novelty in a natural product library. Chem Biodivers 8:1968-1977.
5. Walsh CT (2015) A chemocentric view of the natural product inventory. Nat Chem Biol 11:620-624.
6. Ju K-S, et al. (2015) Discovery of phosphonic acid natural products by mining the genomes of 10, 000 actinomycetes. Proc Natl Acad Sci USA 112:12175-12180.
7. Jensen PR, Chavarria KL, Fenical W, Moore BS, Ziemert N (2014) Challenges and triumphs to genomics-based natural product discovery. J Ind Microbiol Biotechnol 41: 203-209.
8. Bachmann BO, Van Lanen SG, Baltz RH (2014) Microbial genome mining for accelerated natural products discovery: Is a renaissance in the making J Ind Microbiol Biotechnol 41:175-184.
9. Wright GD (2014) Something old, something new: Revisiting natural products in antibiotic drug discovery. Can J Microbiol 60:147-154.
10. Walsh CT, Wencewicz TA (2014) Prospects for new antibiotics: A molecule-centered perspective. J Antibiot (Tokyo) 67:7-22.
11. Patridge E, Gareiss P, Kinch MS, Hoyer D (2016) An analysis of FDA-approved drugs: Natural products and their derivatives. Drug Discov Today 21:204-207.
12. Debono M, et al. (1987) A21978C, a complex of new acidic peptide antibiotics: Isolation, chemistry, mass spectral structure elucidation. J Antibiot (Tokyo) 40: 761-777.
13. Theriault RJ, et al. (1987) Tiacumicins, a novel complex of 18-membered macrolide antibiotics. I. Taxonomy, fermentation and antibacterial activity. J Antibiot (Tokyo) 40:567-574.
14. Hochlowski JE, et al. (1987) Tiacumicins, a novel complex of 18-membered macrolides. II. Isolation and structure determination. J Antibiot (Tokyo) 40:575-588.
15. Koehn FE, Carter GT (2005) The evolving role of natural products in drug discovery. Nat Rev Drug Discov 4:206-220.
16. David B, Wolfender J-L, Dias DA (2014) The pharmaceutical industry and natural products: Historical status and new trends. Phytochem Rev 14:299-315.
17. Abbas S, et al. (2011) Advancement into the Arctic region for bioactive sponge secondary metabolites. Mar Drugs 9:2423-2437.
18. Rogers D, Hahn M (2010) Extended-connectivity fingerprints. J Chem Inf Model 50: 742-754.
19. Derewacz DK, et al. (2014) Structure and stereochemical determination of hypogeamicins from a cave-derived Actinomycete. J Nat Prod 77:1759-1763.
20. Andrianasolo EH, et al. (2011) Bathymodiolamides A and B, ceramide derivatives from a deep-sea hydrothermal vent invertebrate mussel, Bathymodiolus thermophilus. J Nat Prod 74:842-846.
21. Diyabalanage T, Amsler CD, McClintock JB, Baker BJ (2006) Palmerolide A, a cytotoxic macrolide from the antarctic tunicate Synoicum adareanum. J Am Chem Soc 128: 5630-5631.
22. Kusari S, Hertweck C, Spiteller M (2012) Chemical ecology of endophytic fungi: Origins of secondary metabolites. Chem Biol 19:792-798.
23. Schueffler A, Anke T (2014) Fungal natural products in research and development. Nat Prod Rep 31:1425-1448.
24. Motley JL, et al. (2016) Opportunistic sampling of roadkill as an entry point to accessing natural products assembled by bacteria associated with non-anthropoidal mammalian microbiomes. J Nat Prod 80:598-608.
25. Donia MS, et al. (2014) A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. Cell 158:1402-1414.
26. Theodore CM, et al. (2014) Genomic and metabolomic insights into the natural product biosynthetic diversity of a feral-hog-associated Brevibacillus laterosporus strain. PLoS One 9:e90124.
27. Lin Z, et al. (2013) A bacterial source for mollusk pyrone polyketides. Chem Biol 20: 73-81.
28. Calteau A, et al. (2014) Phylum-wide comparative genomics unravel the diversity of secondary metabolism in Cyanobacteria. BMC Genomics 15:977.
29. Kehr J-C, Gatte Picchi D, Dittmann E (2011) Natural product biosyntheses in cyanobacteria: A treasure trove of unique enzymes. Beilstein J Org Chem 7:1622-1635.
30. Salvador LA, et al. (2013) Potent elastase inhibitors from cyanobacteria: Structural basis and mechanisms mediating cytoprotective and anti-inflammatory effects in bronchial epithelial cells. J Med Chem 56:1276-1290.
31. Kleigrewe K, et al. (2015) Combining mass spectrometric metabolic profiling with genomic analysis: A powerful approach for discovering natural products from Cyanobacteria. J Nat Prod 78:1671-1682.
32. Rosén J, Gottfries J, Muresan S, Backlund A, Oprea TI (2009) Novel chemical space exploration via natural products. J Med Chem 52:1953-1962.
33. Pascolutti M, et al. (2015) Capturing nature's diversity. PLoS One 10:e0120942.
34. Itazaki H, et al. (1990) Isolation and structural elucidation of new cyclotetrapeptides, trapoxins A and B, having detransformation activities as antitumor agents. J Antibiot (Tokyo) 43:1524-1532.
35. Darkin-Rattray SJ, et al. (1996) Apicidin: A novel antiprotozoal agent that inhibits parasite histone deacetylase. Proc Natl Acad Sci USA 93:13143-13147.
36. Kunimoto R, Vogt M, Bajorath J (2016) Maximum common substructure-based Tversky index: An asymmetric hybrid similarity measure. J Comput Aided Mol Des 30: 523-531.
37. López-Vallejo F, Giulianotti MA, Houghten RA, Medina-Franco JL (2012) Expanding the medicinally relevant chemical space with compound libraries. Drug Discov Today 17:718-726.
38. Feher M, Schmidt JM (2003) Property distributions: Differences between drugs, natural products, molecules from combinatorial chemistry. J Chem Inf Comput Sci 43: 218-227.
39. Cimermancic P, et al. (2014) Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell 158:412-421.
40. Yamanaka K, et al. (2014) Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A. Proc Natl Acad Sci USA 111:1957-1962.
41. Rutledge PJ, Challis GL (2015) Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 13:509-523.
42. Kurita KL, Glassey E, Linington RG (2015) Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries. Proc Natl Acad Sci USA 112:11999-12004.
43. Park SR, et al. (2016) Discovery of cahuitamycins as biofilm inhibitors derived from a convergent biosynthetic pathway. Nat Commun 7:10710.