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Prospecting for natural products by genome mining and microcrystal electron diffraction

Kim, Lee Joon and Ohashi, Masao and Zhang, Zhuan and Tan, Dan and Asay, Matthew and Cascio, Duilio and Rodriguez, José A. and Tang, Yi and Nelson, Hosea M. (2021) Prospecting for natural products by genome mining and microcrystal electron diffraction. Nature Chemical Biology, 17 (8). pp. 872-877. ISSN 1552-4450. doi:10.1038/s41589-021-00834-2. https://resolver.caltech.edu/CaltechAUTHORS:20210802-213700110

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[img] Crystallographic Info File (CIF) (Crystallographic data containing structure factors for Py-469) - Supplemental Material
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[img] Crystallographic Info File (CIF) (Crystallographic data containing structure factors for fischerin) - Supplemental Material
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[img] Crystallographic Info File (CIF) (Crystallographic data containing structure factors for austinol) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 1: Biosynthetic gene clusters that are homologous to those of fischerin (2) and N-hydroxyapiosporamide (7); and multiple sequence alignment of SAM-binding motif of cis-MT domain in PKS-NRPSs) - Supplemental Material
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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.


Item Type:Article
Related URLs:
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https://doi.org/10.1038/s41589-021-00834-2DOIArticle
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https://pubs.acs.org/doi/10.1021/cen-09928-scicon4Featured InC&EN -- Science Concentrates
ORCID:
AuthorORCID
Kim, Lee Joon0000-0002-0786-7614
Cascio, Duilio0000-0001-8285-754X
Rodriguez, José A.0000-0001-8471-2504
Nelson, Hosea M.0000-0002-4666-2793
Alternate Title:Structural Determination of an Orphan Natural Product Using Microcrystal Electron Diffraction and Genome Mining
Additional Information:© 2021 Nature Publishing Group. Received 11 March 2021; Accepted 14 June 2021; Published 26 July 2021. The authors thank M. R. Sawaya (UCLA-DOE Institute) for assistance in crystallography in data processing and refinement. This research used resources at the X-ray Crystallography Core Facility of the UCLA-DOE Institute, which is supported by the US Department of Energy (DE-FC02-02ER63421). J.A.R. acknowledges support from STROBE, an NSF Science and Technology Center through Grant DMR-1548924, DOE Grant DE-FC02-02ER63421 and NIH-NIGMS Grant R35 GM128867. J.A.R. is supported as a Pew Scholar and a Beckman Young Investigator. Y.T. acknowledges support from the NIH (1R01AI141481). The authors also thank the David and Lucile Packard Foundation (Fellowships to H.M.N., J.A.R. and Y.T.) and Bristol Myers Squibb (Unrestricted Grant in Synthetic Organic Chemistry to H.M.N.) for generous support. Data availability: Crystallographic information files (CIFs) for compounds 2, 3 and 8 containing atomic coordinates and structure factors have been deposited at the Cambridge Crystallographic Data Center (deposition numbers 2020516, 2038723 and 2020510, respectively). Copies of the data can be obtained free of charge at https://www.ccdc.cam.ac.uk/structures/. Source data for Extended Data Fig. 5 has been provided in Supplementary Table 6. Author Contributions: H.M.N. and Y.T. supervised the project. M.O., Z.Z. and D.T. performed in vivo experiments, as well as compound isolation and characterization. L.J.K. performed crystallization experiments, collected and processed the MicroED data, and solved the structures. L.J.K. and M.A. refined the structures. D.C. assisted in structure refinement. L.J.K. and D.C. performed the atom substitution test. J.A.R. assisted in designing MicroED experiments and helped with MicroED data analysis. L.J.K. and M.O. prepared the figures. H.M.N., Y.T., L.J.K. and M.O. wrote the manuscript. The authors declare no competing interests.
Funders:
Funding AgencyGrant Number
Department of Energy (DOE)DE-FC02-02ER63421
NSFDMR-1548924
Department of Energy (DOE)DE-FC02-02ER63421
NIHR35 GM128867
Pew Charitable TrustUNSPECIFIED
Arnold and Mabel Beckman FoundationUNSPECIFIED
NIH1R01AI141481
David and Lucile Packard FoundationUNSPECIFIED
Bristol Myers SquibbUNSPECIFIED
Subject Keywords:Biosynthesis; Natural products; Structure determination
Issue or Number:8
DOI:10.1038/s41589-021-00834-2
Record Number:CaltechAUTHORS:20210802-213700110
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210802-213700110
Official Citation:Kim, L.J., Ohashi, M., Zhang, Z. et al. Prospecting for natural products by genome mining and microcrystal electron diffraction. Nat Chem Biol 17, 872–877 (2021). https://doi.org/10.1038/s41589-021-00834-2
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:110117
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:02 Aug 2021 21:53
Last Modified:26 Aug 2021 18:46

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