1
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Ladds MJGW, van Leeuwen IMM, Drummond CJ, Chu S, Healy AR, Popova G, Fernández AP, Mollick T, Darekar S, Sedimbi SK, Nekulova M, Sachweh MCC, Campbell J, Higgins M, Tuck C, Popa M, Safont MM, Gelebart P, Fandalyuk Z, Thompson AM, Svensson R, Gustavsson AL, Johansson L, Färnegårdh K, Yngve U, Saleh A, Haraldsson M, D'Hollander ACA, Franco M, Zhao Y, Håkansson M, Walse B, Larsson K, Peat EM, Pelechano V, Lunec J, Vojtesek B, Carmena M, Earnshaw WC, McCarthy AR, Westwood NJ, Arsenian-Henriksson M, Lane DP, Bhatia R, McCormack E, Laín S. Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage. Nat Commun 2023; 14:5019. [PMID: 37596290 PMCID: PMC10439212 DOI: 10.1038/s41467-023-40764-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023] Open
Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ingeborg M M van Leeuwen
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Catherine J Drummond
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Su Chu
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Alan R Healy
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Gergana Popova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Andrés Pastor Fernández
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Tanzina Mollick
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Suhas Darekar
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Saikiran K Sedimbi
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Marta Nekulova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Marijke C C Sachweh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Johanna Campbell
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Maureen Higgins
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Chloe Tuck
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Mihaela Popa
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Mireia Mayoral Safont
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Pascal Gelebart
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Zinayida Fandalyuk
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Alastair M Thompson
- Department of Breast Surgical Oncology, MD Anderson Cancer Center, Holcombe Boulevard, Houston, TX, 77030, USA
| | - Richard Svensson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Lars Johansson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Katarina Färnegårdh
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Ulrika Yngve
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Aljona Saleh
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Martin Haraldsson
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Agathe C A D'Hollander
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marcela Franco
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Yan Zhao
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Karin Larsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Emma M Peat
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - John Lunec
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Mar Carmena
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - William C Earnshaw
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Anna R McCarthy
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ravi Bhatia
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Emmet McCormack
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
- Department of Medicine, Haematology Section, Haukeland University Hospital, Bergen, Norway
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden.
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2
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DiBello M, Healy AR, Nikolayevskiy H, Xu Z, Herzon SB. Structure Elucidation of Secondary Metabolites: Current Frontiers and Lingering Pitfalls. Acc Chem Res 2023; 56:1656-1668. [PMID: 37220079 PMCID: PMC10468810 DOI: 10.1021/acs.accounts.3c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Analytical methods allow for the structure determination of submilligram quantities of complex secondary metabolites. This has been driven in large part by advances in NMR spectroscopic capabilities, including access to high-field magnets equipped with cryogenic probes. Experimental NMR spectroscopy may now be complemented by remarkably accurate carbon-13 NMR calculations using state-of-the-art DFT software packages. Additionally, microED analysis stands to have a profound effect on structure elucidation by providing X-ray-like images of microcrystalline samples of analytes. Nonetheless, lingering pitfalls in structure elucidation remain, particularly for isolates that are unstable or highly oxidized. In this Account, we discuss three projects from our laboratory that highlight nonoverlapping challenges to the field, with implications for chemical, synthetic, and mechanism of action studies. We first discuss the lomaiviticins, complex unsaturated polyketide natural products disclosed in 2001. The original structures were derived from NMR, HRMS, UV-vis, and IR analysis. Owing to the synthetic challenges presented by their structures and the absence of X-ray crystallographic data, the structure assignments remained untested for nearly two decades. In 2021, the Nelson group at Caltech carried out microED analysis of (-)-lomaiviticin C, leading to the startling discovery that the original structure assignment of the lomaiviticins was incorrect. Acquisition of higher-field (800 MHz 1H, cold probe) NMR data as well as DFT calculations provided insights into the basis for the original misassignment and lent further support to the new structure identified by microED. Reanalysis of the 2001 data set reveals that the two structure assignments are nearly indistinguishable, underscoring the limitations of NMR-based characterization. We then discuss the structure elucidation of colibactin, a complex, nonisolable microbiome metabolite implicated in colorectal cancer. The colibactin biosynthetic gene cluster was detected in 2006, but owing to colibactin's instability and low levels of production, it could not be isolated or characterized. We used a combination of chemical synthesis, mechanism of action studies, and biosynthetic analysis to identify the substructures in colibactin. These studies, coupled with isotope labeling and tandem MS analysis of colibactin-derived DNA interstrand cross-links, ultimately led to a structure assignment for the metabolite. We then discuss the ocimicides, plant secondary metabolites that were studied as agents against drug-resistant P. falciparum. We synthesized the core structure of the ocimicides and found significant discrepancies between our experimental NMR spectroscopic data and that reported for the natural products. We determined the theoretical carbon-13 NMR shifts for 32 diastereomers of the ocimicides. These studies indicated that a revision of the connectivity of the metabolites is likely needed. We end with some thoughts on the frontiers of secondary metabolite structure determination. As modern NMR computational methods are straightforward to execute, we advocate for their systematic use in validating the assignments of novel secondary metabolites.
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Affiliation(s)
- Mikaela DiBello
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alan R Healy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Herman Nikolayevskiy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Zhi Xu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Departments of Pharmacology and Therapeutic Radiology, Yale School of Medicine, New Haven, Connecticut 06520, United States
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3
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Rahman MA, Cellnik T, Ahuja BB, Li L, Healy AR. A catalytic enantioselective stereodivergent aldol reaction. Sci Adv 2023; 9:eadg8776. [PMID: 36921040 PMCID: PMC10017038 DOI: 10.1126/sciadv.adg8776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
The aldol reaction is among the most powerful and strategically important carbon-carbon bond-forming transformations in organic chemistry. The importance of the aldol reaction in constructing chiral building blocks for complex small-molecule synthesis has spurred continuous efforts toward the development of direct catalytic variants. The realization of a general catalytic aldol reaction with control over both the relative and absolute configurations of the newly formed stereogenic centers has been a longstanding goal in the field. Here, we report a decarboxylative aldol reaction that provides access to all four possible stereoisomers of the aldol product in one step from identical reactants. The mild reaction can be carried out on a large scale in an open flask, and generates CO2 as the only by-product. The method tolerates a broad substrate scope and generates chiral β-hydroxy thioester products with substantial downstream utility.
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Affiliation(s)
- Md. Ataur Rahman
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi, United Arab Emirates (UAE)
| | - Torsten Cellnik
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi, United Arab Emirates (UAE)
| | - Brij Bhushan Ahuja
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi, United Arab Emirates (UAE)
| | - Liang Li
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi, United Arab Emirates (UAE)
- Department of Sciences and Engineering, Sorbonne University Abu Dhabi, Abu Dhabi, United Arab Emirates (UAE)
| | - Alan R. Healy
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi, United Arab Emirates (UAE)
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4
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Cellnik T, Healy AR. Sulfonyl Chlorides as Thiol Surrogates for Carbon-Sulfur Bond Formation: One-Pot Synthesis of Thioethers and Thioesters. J Org Chem 2022; 87:6454-6458. [PMID: 35388690 DOI: 10.1021/acs.joc.2c00330] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A method to synthesize thioethers and thioesters directly from readily available sulfonyl chlorides is reported. We demonstrate that a transient intermediate formed during phosphine-mediated deoxygenation of sulfonyl chlorides can be trapped in situ by activated alcohols or carboxylic acids to effect carbon-sulfur bond formation. The method is operationally simple and tolerates a broad range of functional groups. Special attention has been focused on the late-stage diversification of densely functionalized natural products and pharmaceuticals.
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Affiliation(s)
- Torsten Cellnik
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island 129188, United Arab Emirates (UAE)
| | - Alan R Healy
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island 129188, United Arab Emirates (UAE)
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5
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Healy AR, Wernke KM, Kim CS, Lees NR, Crawford JM, Herzon SB. Addendum: Synthesis and reactivity of precolibactin 886. Nat Chem 2019; 11:1167. [PMID: 31719668 DOI: 10.1038/s41557-019-0383-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Alan R Healy
- Department of Chemistry, Yale University, New Haven, CT, USA.,Chemical Biology Institute, Yale University, West Haven, CT, USA
| | - Kevin M Wernke
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Chung Sub Kim
- Department of Chemistry, Yale University, New Haven, CT, USA.,Chemical Biology Institute, Yale University, West Haven, CT, USA
| | - Nicholas R Lees
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT, USA. .,Chemical Biology Institute, Yale University, West Haven, CT, USA. .,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, CT, USA. .,Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
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6
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Xue M, Kim CS, Healy AR, Wernke KM, Wang Z, Frischling MC, Shine EE, Wang W, Herzon SB, Crawford JM. Structure elucidation of colibactin and its DNA cross-links. Science 2019; 365:science.aax2685. [PMID: 31395743 DOI: 10.1126/science.aax2685] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/24/2019] [Indexed: 12/18/2022]
Abstract
Colibactin is a complex secondary metabolite produced by some genotoxic gut Escherichia coli strains. The presence of colibactin-producing bacteria correlates with the frequency and severity of colorectal cancer in humans. However, because colibactin has not been isolated or structurally characterized, studying the physiological effects of colibactin-producing bacteria in the human gut has been difficult. We used a combination of genetics, isotope labeling, tandem mass spectrometry, and chemical synthesis to deduce the structure of colibactin. Our structural assignment accounts for all known biosynthetic and cell biology data and suggests roles for the final unaccounted enzymes in the colibactin gene cluster.
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Affiliation(s)
- Mengzhao Xue
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Chung Sub Kim
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Alan R Healy
- Department of Chemistry, Yale University, New Haven, CT 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Kevin M Wernke
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Zhixun Wang
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | | | - Emilee E Shine
- Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
| | - Weiwei Wang
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA.,W. M. Keck Biotechnology Resource Laboratory, Yale School of Medicine, New Haven, CT 06510, USA
| | - Seth B Herzon
- Department of Chemistry, Yale University, New Haven, CT 06520, USA. .,Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT 06520, USA. .,Chemical Biology Institute, Yale University, West Haven, CT 06516, USA.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, USA
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7
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Shine EE, Xue M, Patel JR, Healy AR, Surovtseva YV, Herzon SB, Crawford JM. Model Colibactins Exhibit Human Cell Genotoxicity in the Absence of Host Bacteria. ACS Chem Biol 2018; 13:3286-3293. [PMID: 30403848 DOI: 10.1021/acschembio.8b00714] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Colibactins are genotoxic secondary metabolites produced in select Enterobacteriaceae, which induce downstream DNA double-strand breaks (DSBs) in human cell lines and are thought to promote the formation of colorectal tumors. Although key structural and functional features of colibactins have been elucidated, the full molecular mechanisms regulating these phenotypes remain unknown. Here, we demonstrate that free model colibactins induce DSBs in human cell cultures and do not require delivery by host bacteria. Through domain-targeted editing, we demonstrate that a subset of native colibactins generated from observed module skipping in the nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) biosynthetic assembly line share DNA alkylation phenotypes with the model colibactins in vitro. However, module skipping eliminates the strong DNA interstrand cross-links formed by the wild-type pathway in cell culture. This product diversification during the modular NRPS-PKS biosynthesis produces a family of metabolites with varying observed mechanisms of action (DNA alkylation versus cross-linking) in cell culture. The presence of membranes separating human cells from model colibactins attenuated genotoxicity, suggesting that membrane diffusion limits colibactin activity and could account for the reported bacterium-human cell-to-cell contact phenotype. Additionally, extracellular supplementation of the colibactin resistance protein ClbS was able to intercept colibactins in an Escherichia coli-human cell transient infection model. Our studies demonstrate that free model colibactins recapitulate cellular phenotypes associated with module-skipped products in the native colibactin pathway and define specific protein domains that are required for efficient DNA interstrand cross-linking in the native pathway.
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Affiliation(s)
- Emilee E. Shine
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Mengzhao Xue
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Jaymin R. Patel
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, United States
| | - Alan R. Healy
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Yulia V. Surovtseva
- Yale Center for Molecular Discovery, West Haven, Connecticut 06516, United States
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Jason M. Crawford
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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8
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Ladds MJGW, van Leeuwen IMM, Drummond CJ, Chu S, Healy AR, Popova G, Pastor Fernández A, Mollick T, Darekar S, Sedimbi SK, Nekulova M, Sachweh MCC, Campbell J, Higgins M, Tuck C, Popa M, Safont MM, Gelebart P, Fandalyuk Z, Thompson AM, Svensson R, Gustavsson AL, Johansson L, Färnegårdh K, Yngve U, Saleh A, Haraldsson M, D'Hollander ACA, Franco M, Zhao Y, Håkansson M, Walse B, Larsson K, Peat EM, Pelechano V, Lunec J, Vojtesek B, Carmena M, Earnshaw WC, McCarthy AR, Westwood NJ, Arsenian-Henriksson M, Lane DP, Bhatia R, McCormack E, Laín S. Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage. Nat Commun 2018; 9:2071. [PMID: 29789663 PMCID: PMC5964109 DOI: 10.1038/s41467-018-04198-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ingeborg M M van Leeuwen
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Catherine J Drummond
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Su Chu
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Alan R Healy
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Gergana Popova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Andrés Pastor Fernández
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Tanzina Mollick
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Suhas Darekar
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Saikiran K Sedimbi
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Marta Nekulova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Marijke C C Sachweh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Johanna Campbell
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Maureen Higgins
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Chloe Tuck
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Mihaela Popa
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Mireia Mayoral Safont
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Pascal Gelebart
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Zinayida Fandalyuk
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Alastair M Thompson
- Department of Breast Surgical Oncology, MD Anderson Cancer Center, Holcombe Boulevard, Houston, 77030, USA
| | - Richard Svensson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Lars Johansson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Katarina Färnegårdh
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Ulrika Yngve
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Aljona Saleh
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Martin Haraldsson
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Agathe C A D'Hollander
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marcela Franco
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Yan Zhao
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Karin Larsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Emma M Peat
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - John Lunec
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Mar Carmena
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - William C Earnshaw
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Anna R McCarthy
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ravi Bhatia
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Emmet McCormack
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway.,Department of Medicine, Haematology Section, Haukeland University Hospital, Bergen, Norway
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden. .,SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden.
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9
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Ladds MJGW, van Leeuwen IMM, Drummond CJ, Chu S, Healy AR, Popova G, Pastor Fernández A, Mollick T, Darekar S, Sedimbi SK, Nekulova M, Sachweh MCC, Campbell J, Higgins M, Tuck C, Popa M, Safont MM, Gelebart P, Fandalyuk Z, Thompson AM, Svensson R, Gustavsson AL, Johansson L, Färnegårdh K, Yngve U, Saleh A, Haraldsson M, D'Hollander ACA, Franco M, Zhao Y, Håkansson M, Walse B, Larsson K, Peat EM, Pelechano V, Lunec J, Vojtesek B, Carmena M, Earnshaw WC, McCarthy AR, Westwood NJ, Arsenian-Henriksson M, Lane DP, Bhatia R, McCormack E, Laín S. A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage. Nat Commun 2018; 9:1107. [PMID: 29549331 PMCID: PMC5856786 DOI: 10.1038/s41467-018-03441-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 02/13/2018] [Indexed: 01/29/2023] Open
Abstract
The development of non-genotoxic therapies that activate wild-type p53 in tumors is of great interest since the discovery of p53 as a tumor suppressor. Here we report the identification of over 100 small-molecules activating p53 in cells. We elucidate the mechanism of action of a chiral tetrahydroindazole (HZ00), and through target deconvolution, we deduce that its active enantiomer (R)-HZ00, inhibits dihydroorotate dehydrogenase (DHODH). The chiral specificity of HZ05, a more potent analog, is revealed by the crystal structure of the (R)-HZ05/DHODH complex. Twelve other DHODH inhibitor chemotypes are detailed among the p53 activators, which identifies DHODH as a frequent target for structurally diverse compounds. We observe that HZ compounds accumulate cancer cells in S-phase, increase p53 synthesis, and synergize with an inhibitor of p53 degradation to reduce tumor growth in vivo. We, therefore, propose a strategy to promote cancer cell killing by p53 instead of its reversible cell cycle arresting effect.
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Affiliation(s)
- Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ingeborg M M van Leeuwen
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Catherine J Drummond
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Su Chu
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Alan R Healy
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Gergana Popova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Andrés Pastor Fernández
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Tanzina Mollick
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Suhas Darekar
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Saikiran K Sedimbi
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Marta Nekulova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Marijke C C Sachweh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Johanna Campbell
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Maureen Higgins
- Centre for Oncology and Molecular Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Tayside, DD1 9SY, UK
| | - Chloe Tuck
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Mihaela Popa
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Mireia Mayoral Safont
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Pascal Gelebart
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Zinayida Fandalyuk
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
| | - Alastair M Thompson
- Department of Breast Surgical Oncology, MD Anderson Cancer Center, Holcombe Boulevard, Houston, 77030, USA
| | - Richard Svensson
- Department of Pharmacy, Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Uppsala University, SE-752 37, Uppsala, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Lars Johansson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 21, Stockholm, Sweden
| | - Katarina Färnegårdh
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Ulrika Yngve
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Aljona Saleh
- Department of Medicinal Chemistry, Science for Life Laboratories, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Martin Haraldsson
- Drug Discovery and Development Platform, Science for Life Laboratory, Tomtebodavägen 23, SE-171 21, Solna, Sweden
| | - Agathe C A D'Hollander
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marcela Franco
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Yan Zhao
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Maria Håkansson
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Björn Walse
- SARomics Biostructures, Medicon Village, SE-223 81, Lund, Sweden
| | - Karin Larsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Emma M Peat
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - John Lunec
- Newcastle Cancer Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle, NE1 7RU, UK
| | - Borivoj Vojtesek
- RECAMO, Masaryk Memorial Cancer Institute, Zluty Kopec 7, 65653, Brno, Czech Republic
| | - Mar Carmena
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - William C Earnshaw
- The Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3JR, UK
| | - Anna R McCarthy
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland, KY16 9ST, UK
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden
| | - Ravi Bhatia
- Division of Hematology and Oncology, Comprehensive Cancer Center, 1720 2nd Avenue South, NP2540, Birmingham, AL, 35294-3300, USA
| | - Emmet McCormack
- Centre for Cancer Biomarkers, CCBIO, Department of Clinical Science, Hematology Section, University of Bergen, 5021, Bergen, Norway
- Department of Medicine, Haematology Section, Haukeland University Hospital, Bergen, Norway
| | - Sonia Laín
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden.
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Tomtebodavägen 23, SE-171 21, Stockholm, Sweden.
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10
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Tripathi P, Shine EE, Healy AR, Kim CS, Herzon SB, Bruner SD, Crawford JM. ClbS Is a Cyclopropane Hydrolase That Confers Colibactin Resistance. J Am Chem Soc 2017; 139:17719-17722. [PMID: 29112397 DOI: 10.1021/jacs.7b09971] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Certain commensal Escherichia coli contain the clb biosynthetic gene cluster that codes for small molecule prodrugs known as precolibactins. Precolibactins are converted to colibactins by N-deacylation; the latter are postulated to be genotoxic and to contribute to colorectal cancer formation. Though advances toward elucidating (pre)colibactin biosynthesis have been made, the functions and mechanisms of several clb gene products remain poorly understood. Here we report the 2.1 Å X-ray structure and molecular function of ClbS, a gene product that confers resistance to colibactin toxicity in host bacteria and which has been shown to be important for bacterial viability. The structure harbors a potential colibactin binding site and shares similarity to known hydrolases. In vitro studies using a synthetic colibactin analog and ClbS or an active site residue mutant reveal cyclopropane hydrolase activity that converts the electrophilic cyclopropane of the colibactins into an innocuous hydrolysis product. As the cyclopropane has been shown to be essential for genotoxic effects in vitro, this ClbS-catalyzed ring-opening provides a means for the bacteria to circumvent self-induced genotoxicity. Our study provides a molecular-level view of the first reported cyclopropane hydrolase and support for a specific mechanistic role of this enzyme in colibactin resistance.
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Affiliation(s)
- Prabhanshu Tripathi
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Emilee E Shine
- Department of Microbial Pathogenesis, Yale School of Medicine , New Haven, Connecticut 06536, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Alan R Healy
- Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Chung Sub Kim
- Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Department of Pharmacology, Yale School of Medicine , New Haven, Connecticut 06520, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida , Gainesville, Florida 32611, United States
| | - Jason M Crawford
- Department of Microbial Pathogenesis, Yale School of Medicine , New Haven, Connecticut 06536, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
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11
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Guntaka NS, Healy AR, Crawford JM, Herzon SB, Bruner SD. Structure and Functional Analysis of ClbQ, an Unusual Intermediate-Releasing Thioesterase from the Colibactin Biosynthetic Pathway. ACS Chem Biol 2017; 12:2598-2608. [PMID: 28846367 PMCID: PMC5830302 DOI: 10.1021/acschembio.7b00479] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Colibactin is a genotoxic hybrid nonribosomal peptide/polyketide secondary metabolite produced by various pathogenic and probiotic bacteria residing in the human gut. The presence of colibactin metabolites has been correlated to colorectal cancer formation in several studies. The specific function of many gene products in the colibactin gene cluster can be predicted. However, the role of ClbQ, a type II editing thioesterase, has not been established. The importance of ClbQ has been demonstrated by genetic deletions that abolish colibactin cytotoxic activity, and recent studies suggest an atypical role in releasing pathway intermediates from the assembly line. Here we report the 2.0 Å crystal structure and biochemical characterization of ClbQ. Our data reveal that ClbQ exhibits greater catalytic efficiency toward acyl-thioester substrates as compared to precolibactin intermediates and does not discriminate among carrier proteins. Cyclized pyridone-containing colibactins, which are off-pathway derivatives, are not viable substrates for ClbQ, while linear precursors are, supporting a role of ClbQ in facilitating the promiscuous off-loading of premature precolibactin metabolites and novel insights into colibactin biosynthesis.
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Affiliation(s)
- Naga Sandhya Guntaka
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Alan R. Healy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, United States
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, United States
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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12
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Abstract
A significant challenge toward studies of the human microbiota involves establishing causal links between bacterial metabolites and human health and disease states. Certain strains of commensal Escherichia coli harbor the 54-kb clb gene cluster which codes for small molecules named precolibactins and colibactins. Several studies suggest colibactins are genotoxins and support a role for clb metabolites in colorectal cancer formation. Significant advances toward elucidating the structures and biosynthesis of the precolibactins and colibactins have been made using genetic approaches, but their full structures remain unknown. In this Perspective we describe recent synthetic efforts that have leveraged biosynthetic advances and shed light on the mechanism of action of clb metabolites. These studies indicate that deletion of the colibactin peptidase ClbP, a modification introduced to promote accumulation of precolibactins, leads to the production of non-genotoxic pyridone-based isolates derived from the diversion of linear biosynthetic intermediates toward alternative cyclization pathways. Furthermore, these studies suggest the active genotoxins (colibactins) are unsaturated imines that are potent DNA damaging agents, thereby confirming an earlier mechanism of action hypothesis. Although these imines have very recently been detected in bacterial extracts, they have to date confounded isolation. As the power of "meta-omics" approaches to natural products discovery further advance, we anticipate that chemical synthetic and biosynthetic studies will become increasingly interdependent.
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Affiliation(s)
- Alan R Healy
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Department of Pharmacology, Yale School of Medicine , New Haven, Connecticut 06520, United States
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13
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Trautman EP, Healy AR, Shine EE, Herzon SB, Crawford JM. Domain-Targeted Metabolomics Delineates the Heterocycle Assembly Steps of Colibactin Biosynthesis. J Am Chem Soc 2017; 139:4195-4201. [PMID: 28240912 DOI: 10.1021/jacs.7b00659] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) comprise giant multidomain enzymes responsible for the "assembly line" biosynthesis of many genetically encoded small molecules. Site-directed mutagenesis, protein biochemical, and structural studies have focused on elucidating the catalytic mechanisms of individual multidomain proteins and protein domains within these megasynthases. However, probing their functions at the cellular level typically has invoked the complete deletion (or overexpression) of multidomain-encoding genes or combinations of genes and comparing those mutants with a control pathway. Here we describe a "domain-targeted" metabolomic strategy that combines genome editing with pathway analysis to probe the functions of individual PKS and NRPS catalytic domains at the cellular metabolic level. We apply the approach to the bacterial colibactin pathway, a genotoxic NRPS-PKS hybrid pathway found in certain Escherichia coli. The pathway produces precolibactins, which are converted to colibactins by a dedicated peptidase, ClbP. Domain-targeted metabolomics enabled the characterization of "multidomain signatures", or functional readouts of NRPS-PKS domain contributions to the pathway-dependent metabolome. These multidomain signatures provided experimental support for individual domain contributions to colibactin biosynthesis and delineated the assembly line timing events of colibactin heterocycle formation. The analysis also led to the structural characterization of two reactive precolibactin metabolites. We demonstrate the fate of these reactive intermediates in the presence and absence of ClbP, which dictates the formation of distinct product groups resulting from alternative cyclization cascades. In the presence of the peptidase, the reactive intermediates are converted to a known genotoxic scaffold, providing metabolic support of our mechanistic model for colibactin-induced genotoxicity. Domain-targeted metabolomics could be more widely used to characterize NRPS-PKS pathways with unprecedented genetic and metabolic precision.
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Affiliation(s)
- Eric P Trautman
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Alan R Healy
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Emilee E Shine
- Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Microbial Pathogenesis, Yale School of Medicine , New Haven, Connecticut 06536, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Department of Pharmacology, Yale School of Medicine , New Haven, Connecticut 06520, United States
| | - Jason M Crawford
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Microbial Pathogenesis, Yale School of Medicine , New Haven, Connecticut 06536, United States
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14
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Abstract
Precolibactins and colibactins represent a family of natural products that are encoded by the clb gene cluster and are produced by certain commensal, extraintestinal, and probiotic E. coli. clb+ E. coli induce megalocytosis and DNA double-strand breaks in eukaryotic cells, but paradoxically, this gene cluster is found in the probiotic Nissle 1917. Evidence suggests precolibactins are converted to genotoxic colibactins by colibactin peptidase (ClbP)-mediated cleavage of an N-acyl-d-Asn side chain, and all isolation efforts have employed ΔclbP strains to facilitate accumulation of precolibactins. It was hypothesized that colibactins form unsaturated imines that alkylate DNA by cyclopropane ring opening (2 → 3). However, as no colibactins have been isolated, this hypothesis has not been tested experimentally. Additionally, precolibactins A-C (7-9) contain a pyridone that cannot generate the unsaturated imines that form the basis of this hypothesis. To resolve this, we prepared 13 synthetic colibactin derivatives and evaluated their DNA binding and alkylation activity. We show that unsaturated imines, but not the corresponding pyridone derivatives, potently alkylate DNA. The imine, unsaturated lactam, and cyclopropane are essential for efficient DNA alkylation. A cationic residue enhances activity. These studies suggest that precolibactins containing a pyridone are not responsible for the genotoxicity of the clb cluster. Instead, we propose that these are off-pathway fermentation products produced by a facile double cyclodehydration route that manifests in the absence of viable ClbP. The results presented herein provide a foundation to begin to connect metabolite structure with the disparate phenotypes associated with clb+ E. coli.
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Affiliation(s)
- Alan R Healy
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States
| | - Herman Nikolayevskiy
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Jaymin R Patel
- Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Molecular, Cellular, and Developmental Biology, Yale University , New Haven, Connecticut 06520, United States
| | - Jason M Crawford
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Chemical Biology Institute, Yale University , West Haven, Connecticut 06516, United States.,Department of Microbial Pathogenesis, Yale School of Medicine , New Haven, Connecticut 06536, United States
| | - Seth B Herzon
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States.,Department of Pharmacology, Yale School of Medicine , New Haven, Connecticut 06520, United States
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15
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Healy AR, Vizcaino MI, Crawford JM, Herzon SB. Convergent and Modular Synthesis of Candidate Precolibactins. Structural Revision of Precolibactin A. J Am Chem Soc 2016; 138:5426-32. [PMID: 27025153 PMCID: PMC5049697 DOI: 10.1021/jacs.6b02276] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The colibactins are hybrid polyketide-nonribosomal peptide natural products produced by certain strains of commensal and extraintestinal pathogenic Escherichia coli. The metabolites are encoded by the clb gene cluster as prodrugs termed precolibactins. clb(+) E. coli induce DNA double-strand breaks in mammalian cells in vitro and in vivo and are found in 55-67% of colorectal cancer patients, suggesting that mature colibactins could initiate tumorigenesis. However, elucidation of their structures has been an arduous task as the metabolites are obtained in vanishingly small quantities (μg/L) from bacterial cultures and are believed to be unstable. Herein we describe a flexible and convergent synthetic route to prepare advanced precolibactins and derivatives. The synthesis proceeds by late-stage union of two complex precursors (e.g., 28 + 17 → 29a, 90%) followed by a base-induced double dehydrative cascade reaction to form two rings of the targets (e.g., 29a → 30a, 79%). The sequence has provided quantities of advanced candidate precolibactins that exceed those obtained by fermentation, and is envisioned to be readily scaled. These studies have guided a structural revision of the predicted metabolite precolibactin A (from 5a or 5b to 7) and have confirmed the structures of the isolated metabolites precolibactins B (3) and C (6). Synthetic precolibactin C (6) was converted to N-myristoyl-d-asparagine and its corresponding colibactin by colibactin peptidase ClbP. The synthetic strategy outlined herein will facilitate mechanism of action and structure-function studies of these fascinating metabolites, and is envisioned to accommodate the synthesis of additional (pre)colibactins as they are isolated.
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Affiliation(s)
- Alan R. Healy
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Maria I. Vizcaino
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Chemical Biology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06536, United States
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Pharmacology, Yale School of Medicine, New Haven, Connecticut 06520, United States
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16
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Abstract
A late stage Diels-Alder reaction is used to prepare a mixture of JBIR-22, a natural product from the Equisetin family of tetramic acids, and one of its diastereomers. This is achieved in just 8 steps from pyruvate. The success of the late stage DA approach is discussed in the context of the biosynthesis of JBIR-22 (and perhaps related natural products).
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Affiliation(s)
- A R Healy
- School of Chemistry & Biomedical Sciences Research Complex, University of St Andrews & EaStCHEM, North Haugh, St Andrews, KY16 9ST, UK.
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17
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Healy AR, Houston DR, Remnant L, Huart AS, Brychtova V, Maslon MM, Meers O, Muller P, Krejci A, Blackburn EA, Vojtesek B, Hernychova L, Walkinshaw MD, Westwood NJ, Hupp TR. Discovery of a novel ligand that modulates the protein-protein interactions of the AAA+ superfamily oncoprotein reptin. Chem Sci 2015; 6:3109-3116. [PMID: 28706685 PMCID: PMC5490336 DOI: 10.1039/c4sc03885a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/20/2015] [Indexed: 12/31/2022] Open
Abstract
Developing approaches to discover protein-protein interactions (PPIs) remains a fundamental challenge. A chemical biology platform is applied here to identify novel PPIs for the AAA+ superfamily oncoprotein reptin. An in silico screen coupled with chemical optimization provided Liddean, a nucleotide-mimetic which modulates reptin's oligomerization status, protein-binding activity and global conformation. Combinatorial peptide phage library screening of Liddean-bound reptin with next generation sequencing identified interaction motifs including a novel reptin docking site on the p53 tumor suppressor protein. Proximity ligation assays demonstrated that endogenous reptin forms a predominantly cytoplasmic complex with its paralog pontin in cancer cells and Liddean promotes a shift of this complex to the nucleus. An emerging view of PPIs in higher eukaryotes is that they occur through a striking diversity of linear peptide motifs. The discovery of a compound that alters reptin's protein interaction landscape potentially leads to novel avenues for therapeutic development.
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Affiliation(s)
- Alan R Healy
- School of Chemistry & Biomedical Sciences Research Complex , University of St Andrews & EaStCHEM , North Haugh, St Andrews , KY16 9ST , UK .
| | - Douglas R Houston
- Centre for Chemical Biology , University of Edinburgh , EH9 3JG , UK .
| | - Lucy Remnant
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Anne-Sophie Huart
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Veronika Brychtova
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | - Magda M Maslon
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Olivia Meers
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
| | - Petr Muller
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | - Adam Krejci
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | | | - Borek Vojtesek
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | - Lenka Hernychova
- RECAMO , Masaryk Memorial Cancer Institute , 656 53 Brno , Czech Republic
| | | | - Nicholas J Westwood
- School of Chemistry & Biomedical Sciences Research Complex , University of St Andrews & EaStCHEM , North Haugh, St Andrews , KY16 9ST , UK .
| | - Ted R Hupp
- Edinburgh Cancer Research Centre , Cell Signalling Unit , University of Edinburgh , EH4 2XR , UK .
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18
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Healy AR, Izumikawa M, Slawin AMZ, Shin-ya K, Westwood NJ. Stereochemical assignment of the protein-protein interaction inhibitor JBIR-22 by total synthesis. Angew Chem Int Ed Engl 2015; 54:4046-50. [PMID: 25650886 PMCID: PMC4441253 DOI: 10.1002/anie.201411141] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Indexed: 12/04/2022]
Abstract
Recent reports have highlighted the biological activity associated with a subfamily of the tetramic acid class of natural products. Despite the fact that members of this subfamily act as protein-protein interaction inhibitors that are of relevance to proteasome assembly, no synthetic work has been reported. This may be due to the fact that this subfamily contains an unnatural 4,4-disubstitued glutamic acid, the synthesis of which provides a key challenge. A highly stereoselective route to a masked form of this unnatural amino acid now enabled the synthesis of two of the possible diastereomers of JBIR-22 and allowed the assignment of its relative and absolute stereochemistry.
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Affiliation(s)
- Alan R Healy
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEMNorth Haugh, St Andrews, Fife (UK)
| | - Miho Izumikawa
- Japan Biological Informatics Consortium (JBIC) 2-4-7 Aomi, Koto-kuTokyo 135-0064 (Japan)
| | - Alexandra M Z Slawin
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEMNorth Haugh, St Andrews, Fife (UK)
| | - Kazuo Shin-ya
- National Institute of Advanced Industrial Science and Technology (AIST)2-4-7 Aomi, Koto-ku, Tokyo 135-0064 (Japan)
| | - Nicholas J Westwood
- School of Chemistry and Biomedical Sciences Research Complex, University of St Andrews and EaStCHEMNorth Haugh, St Andrews, Fife (UK)
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19
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Healy AR, Izumikawa M, Slawin AMZ, Shin‐ya K, Westwood NJ. Stereochemical Assignment of the Protein-Protein Interaction Inhibitor JBIR-22 by Total Synthesis. Angew Chem Weinheim Bergstr Ger 2015; 127:4118-4122. [PMID: 27087707 PMCID: PMC4780591 DOI: 10.1002/ange.201411141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Indexed: 11/06/2022]
Abstract
Recent reports have highlighted the biological activity associated with a subfamily of the tetramic acid class of natural products. Despite the fact that members of this subfamily act as protein-protein interaction inhibitors that are of relevance to proteasome assembly, no synthetic work has been reported. This may be due to the fact that this subfamily contains an unnatural 4,4-disubstitued glutamic acid, the synthesis of which provides a key challenge. A highly stereoselective route to a masked form of this unnatural amino acid now enabled the synthesis of two of the possible diastereomers of JBIR-22 and allowed the assignment of its relative and absolute stereochemistry.
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20
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Healy AR, Vinale F, Lorito M, Westwood NJ. Total synthesis and biological evaluation of the tetramic acid based natural product harzianic acid and its stereoisomers. Org Lett 2015; 17:692-5. [PMID: 25629709 PMCID: PMC4737532 DOI: 10.1021/ol503717r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Indexed: 12/03/2022]
Abstract
The bioactive natural product harzianic acid was prepared for the first time in just six steps (longest linear sequence) with an overall yield of 22%. The identification of conditions to telescope amide bond formation and a Lacey-Dieckmann reaction into one pot proved important. The three stereoisomers of harzianic acid were also prepared, providing material for comparison of their biological activity. While all of the isomers promoted root growth, improved antifungal activity was unexpectedly associated with isomers in the enantiomeric series opposite that of harzianic acid.
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Affiliation(s)
- Alan R. Healy
- School
of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, North Haugh, St. Andrews, Fife KY169ST, U.K.
| | - Francesco Vinale
- CNR
− Istituto per la Protezione Sostenibile delle Piante (IPSP-CNR), 80055 Portici, Italy
| | - Matteo Lorito
- CNR
− Istituto per la Protezione Sostenibile delle Piante (IPSP-CNR), 80055 Portici, Italy
- Dipartimento
di Agraria, Università degli Studi
di Napoli “Federico II”, 80138 Portici, Italy
| | - Nicholas J. Westwood
- School
of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, North Haugh, St. Andrews, Fife KY169ST, U.K.
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