High-Throughput Mining of Novel Compounds from Known Microbes: A Boost to Natural Product Screening

• Published in: Molecules (Basel, Switzerland) Vol. 29; no. 13; p. 3237
• Main Authors: Meena, Surya Nandan, Wajs-Bonikowska, Anna, Girawale, Savita, Imran, Md, Poduwal, Preethi, Kodam, Kisan M
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 08.07.2024
• Subjects: antiSMASH; Artificial intelligence; Bacteria - genetics; Bacteria - metabolism; Bioinformatics; Biological activity; Biological Products - chemistry; biosynthetic gene clusters (BGCs); Computational Biology - methods; Data Mining; Drug Discovery - methods; Drugs; Genes; genome mining; Genomes; Genomics; High-Throughput Screening Assays - methods; HiTES; Metabolites; microbes; Microorganisms; Multigene Family; natural product; Natural products; NMR; Nuclear magnetic resonance; Peptides; R&D; Research & development; Researchers; microbes; HiTES; natural product; biosynthetic gene clusters (BGCs); dereplication; antiSMASH; genome mining; LAESI-IMS
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules29133237

Advanced techniques can accelerate the pace of natural product discovery from microbes, which has been lagging behind the drug discovery era. Therefore, the present review article discusses the various interdisciplinary and cutting-edge techniques to present a concrete strategy that enables the high-throughput screening of novel natural compounds (NCs) from known microbes. Recent bioinformatics methods revealed that the microbial genome contains a huge untapped reservoir of silent biosynthetic gene clusters (BGC). This article describes several methods to identify the microbial strains with hidden mines of silent BGCs. Moreover, antiSMASH 5.0 is a free, accurate, and highly reliable bioinformatics tool discussed in detail to identify silent BGCs in the microbial genome. Further, the latest microbial culture technique, HiTES (high-throughput elicitor screening), has been detailed for the expression of silent BGCs using 500-1000 different growth conditions at a time. Following the expression of silent BGCs, the latest mass spectrometry methods are highlighted to identify the NCs. The recently emerged LAESI-IMS (laser ablation electrospray ionization-imaging mass spectrometry) technique, which enables the rapid identification of novel NCs directly from microtiter plates, is presented in detail. Finally, various trending 'dereplication' strategies are emphasized to increase the effectiveness of NC screening.