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Cook MA, Pallant D, Ejim L, Sutherland AD, Wang X, Johnson JW, McCusker S, Chen X, George M, Chou S, Koteva K, Wang W, Hobson C, Hackenberger D, Waglechner N, Ejim O, Campbell T, Medina R, MacNeil LT, Wright GD. Lessons from assembling a microbial natural product and pre-fractionated extract library in an academic laboratory. J Ind Microbiol Biotechnol 2023; 50:kuad042. [PMID: 38052426 PMCID: PMC10724011 DOI: 10.1093/jimb/kuad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023]
Abstract
Microbial natural products are specialized metabolites that are sources of many bioactive compounds including antibiotics, antifungals, antiparasitics, anticancer agents, and probes of biology. The assembly of libraries of producers of natural products has traditionally been the province of the pharmaceutical industry. This sector has gathered significant historical collections of bacteria and fungi to identify new drug leads with outstanding outcomes-upwards of 60% of drug scaffolds originate from such libraries. Despite this success, the repeated rediscovery of known compounds and the resultant diminishing chemical novelty contributed to a pivot from this source of bioactive compounds toward more tractable synthetic compounds in the drug industry. The advent of advanced mass spectrometry tools, along with rapid whole genome sequencing and in silico identification of biosynthetic gene clusters that encode the machinery necessary for the synthesis of specialized metabolites, offers the opportunity to revisit microbial natural product libraries with renewed vigor. Assembling a suitable library of microbes and extracts for screening requires the investment of resources and the development of methods that have customarily been the proprietary purview of large pharmaceutical companies. Here, we report a perspective on our efforts to assemble a library of natural product-producing microbes and the establishment of methods to extract and fractionate bioactive compounds using resources available to most academic labs. We validate the library and approach through a series of screens for antimicrobial and cytotoxic agents. This work serves as a blueprint for establishing libraries of microbial natural product producers and bioactive extract fractions suitable for screens of bioactive compounds. ONE-SENTENCE SUMMARY Natural products are key to discovery of novel antimicrobial agents: Here, we describe our experience and lessons learned in constructing a microbial natural product and pre-fractionated extract library.
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Affiliation(s)
- Michael A Cook
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Daniel Pallant
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Linda Ejim
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Arlene D Sutherland
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Xiaodong Wang
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Jarrod W Johnson
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Susan McCusker
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Xuefei Chen
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Maya George
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Sommer Chou
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Kalinka Koteva
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Wenliang Wang
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Christian Hobson
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Dirk Hackenberger
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Nicholas Waglechner
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Obi Ejim
- College of Medicine, Enugu State University of Science and Technology, Agbani, Enugu State, PMB 01660, Nigeria
| | - Tracey Campbell
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Ricardo Medina
- Department of Microbiology, Chemical Bioactive Center, Central University Marta Abreu de las Villas, Santa Clara 54830, Villa Clara, Cuba
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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