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Kim LJ, Ohashi M, Zhang Z, Tan D, Asay M, Cascio D, Rodriguez JA, Tang Y, Nelson HM. Prospecting for natural products by genome mining and microcrystal electron diffraction. Nat Chem Biol 2021; 17:872-877. [PMID: 34312563 DOI: 10.1038/s41589-021-00834-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/14/2021] [Indexed: 11/09/2022]
Abstract
More than 60% of pharmaceuticals are related to natural products (NPs), chemicals produced by living organisms. Despite this, the rate of NP discovery has slowed over the past few decades. In many cases the rate-limiting step in NP discovery is structural characterization. Here we report the use of microcrystal electron diffraction (MicroED), an emerging cryogenic electron microscopy (CryoEM) method, in combination with genome mining to accelerate NP discovery and structural elucidation. As proof of principle we rapidly determine the structure of a new 2-pyridone NP, Py-469, and revise the structure of fischerin, an NP isolated more than 25 years ago, with potent cytotoxicity but hitherto ambiguous structural assignment. This study serves as a powerful demonstration of the synergy of MicroED and synthetic biology in NP discovery, technologies that when taken together will ultimately accelerate the rate at which new drugs are discovered.
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Affiliation(s)
- Lee Joon Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Masao Ohashi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zhuan Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dan Tan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Matthew Asay
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Duilio Cascio
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA
| | - José A Rodriguez
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.,UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Hosea M Nelson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
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