Bioinformatics Approaches in Natural Product Research Unraveling Nature's Chemical Diversity
Abstract
Natural products derived from plants, microbes, and marine organisms have been a rich source of bioactive compounds with diverse pharmaceutical applications. The exploration of this vast reservoir of chemical diversity has been greatly enhanced by the integration of bioinformatics approaches into natural product research. This review article provides an overview of the key bioinformatics tools and methodologies employed in deciphering, analyzing, and exploiting natural products for various therapeutic purposes.
How to cite this article:
Kaur H, Singh L. Bioinformatics Approaches in Natural Product Research: Unraveling Nature’s Chemical Diversity. Int J Adv Res Med Chem 2023; 5(2): 1-5
References
Eisner N, Law J, Christianson DW. Bioinformatics approaches for the discovery of novel microbial natural products. J Ind Microbiol Biotechnol. 2019;46(2):281- 293.
Blin K, et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 2019;47(W1):W81-W87.
Skinnider MA, Dejong CA, Rees PN, Johnston CW, Li H, Webster AL, et al. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). Nucleic Acids Res. 2015;43(20):9645-9662.
Khaldi N, Seifuddin FT, Turner G, Haft D, Nierman WC, Wolfe KH, et al. SMURF: genomic mapping of fungal secondary metabolite clusters. Fungal Genet Biol. 2010;47(9):736-741.
Bachmann BO, Van Lanen SG, Baltz RH. Microbial genome mining for accelerated natural products discovery: is a renaissance in the making? J Ind Microbiol Biotechnol. 2014;41(2):175-184.
Medema MH, Kottmann R, Yilmaz P, Cummings M, Biggins JB, Blin K, et al. Minimum information about a biosynthetic gene cluster. Nat Chem Biol. 2015;11(9):625-631.
Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43(W1):W237-W243.
Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, et al. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016;34(8):828- 837.
van Santen JA, Jacob G, Singh AL, Aniebok V, Balunas MJ, Bunsko D, et al. The Natural Products Atlas: an open access knowledge base for microbial natural products discovery. ACS Cent Sci. 2019;5(11):1824-1833.
Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072-1075.
Li DH, Chung DH, Kim KH. Antifungal activity of lignin and its degradation products against blue and green molds. Ind Crops Prod. 2019;139:111 557.
Nguyen DD, Wu CH, Moree WJ, Lamsa A, Medema MH, Zhao X, et al. MS/MS networking guided analysis of molecule and gene cluster families. Proc Natl Acad Sci U S A. 2013;110(28):E2611-E2620.
Hadjithomas M, Chen IA, Chu K, Ratner A, Palaniappan K, Szeto E, et al. IMG-ABC: a knowledge base to fuel discovery of biosynthetic gene clusters and novel secondary metabolites. MBio. 2015;6(4):e00932.
Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, et al. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell. 2014;158(2):412-421.
Harvey AL, Edrada-Ebel R, Quinn RJ. The re-emergence of natural products for drug discovery in the genomics era. Nat Rev Drug Discov. 2015;14(2):111-129.
