1
|
Maschio L, Back CR, Alnawah J, Bowen JI, Johns ST, Mbatha SZ, Han LC, Lees NR, Zorn K, Stach JEM, Hayes MA, van der Kamp MW, Pudney CR, Burston SG, Willis CL, Race PR. Delineation of the complete reaction cycle of a natural Diels-Alderase. Chem Sci 2024; 15:11572-11583. [PMID: 39055018 PMCID: PMC11268479 DOI: 10.1039/d4sc02908a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/19/2024] [Indexed: 07/27/2024] Open
Abstract
The Diels-Alder reaction is one of the most effective methods for the synthesis of substituted cyclohexenes. The development of protein catalysts for this reaction remains a major priority, affording new sustainable routes to high value target molecules. Whilst a small number of natural enzymes have been shown capable of catalysing [4 + 2] cycloadditions, there is a need for significant mechanistic understanding of how these prospective Diels-Alderases promote catalysis to underpin their development as biocatalysts for use in synthesis. Here we present a molecular description of the complete reaction cycle of the bona fide natural Diels-Alderase AbyU, which catalyses formation of the spirotetronate skeleton of the antibiotic abyssomicin C. This description is derived from X-ray crystallographic studies of AbyU in complex with a non-transformable synthetic substrate analogue, together with transient kinetic analyses of the AbyU catalysed reaction and computational reaction simulations. These studies reveal the mechanistic intricacies of this enzyme system and establish a foundation for the informed reengineering of AbyU and related biocatalysts.
Collapse
Affiliation(s)
- Laurence Maschio
- School of Biochemistry, University Walk, University of Bristol BS8 1TD UK
| | - Catherine R Back
- School of Biochemistry, University Walk, University of Bristol BS8 1TD UK
| | - Jawaher Alnawah
- School of Chemistry, University of Bristol Cantock's Close BS8 1TS UK
- Department of Chemistry, King Faisal University, College of Science Al-Ahsa 31982 Saudi Arabia
| | - James I Bowen
- School of Chemistry, University of Bristol Cantock's Close BS8 1TS UK
| | - Samuel T Johns
- School of Biochemistry, University Walk, University of Bristol BS8 1TD UK
| | | | - Li-Chen Han
- School of Chemistry, University of Bristol Cantock's Close BS8 1TS UK
| | - Nicholas R Lees
- School of Chemistry, University of Bristol Cantock's Close BS8 1TS UK
| | - Katja Zorn
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca Pepparedsleden 1 431 83 Mölndal Sweden
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University NE1 7RU UK
| | - Martin A Hayes
- Discovery Sciences, Biopharmaceuticals R&D, AstraZeneca Pepparedsleden 1 431 83 Mölndal Sweden
| | | | - Christopher R Pudney
- Department of Biology and Biochemistry, University of Bath Claverton Down BA2 7AY UK
| | - Steven G Burston
- School of Biochemistry, University Walk, University of Bristol BS8 1TD UK
| | | | - Paul R Race
- School of Natural and Environmental Sciences, Newcastle University NE1 7RU UK
| |
Collapse
|
2
|
Komogortsev AN, Lichitskii BV, Melekhina VG. 1,1'-Carbonyldiimidazole-mediated transformation of allomaltol containing hydrazides into substituted 3-acetyltetronic acids. Org Biomol Chem 2023; 21:7224-7230. [PMID: 37642509 DOI: 10.1039/d3ob01136d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
For the first time, the reaction of allomaltol containing hydrazides with 1,1'-carbonyldiimidazole (CDI) was studied. It was shown that under the considered conditions, 3-hydroxy-4-pyranone derivatives were transformed into 3-acetyltetronic acids bearing a pyrrolidin-2-one moiety. We have found that the key intermediates of the investigated process are substituted 6-oxa-1-azaspiro[4.5]dec-7-ene-2,9-diones. The structures of one final product and one intermediate were confirmed by X-ray analysis. The disclosed reaction was tested using a wide range of substituted allomaltols with various carboxamide units. It was demonstrated that in the case of hetaryl containing hydrazides and hydroxamic acids, the direction of the process is completely changed and cyclization into substituted pyrano[3,2-b]pyrans occurs.
Collapse
Affiliation(s)
- Andrey N Komogortsev
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky Pr., 47, Moscow 119991, Russian Federation.
| | - Boris V Lichitskii
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky Pr., 47, Moscow 119991, Russian Federation.
| | - Valeriya G Melekhina
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky Pr., 47, Moscow 119991, Russian Federation.
| |
Collapse
|
3
|
Devine AJ, Parnell AE, Back CR, Lees NR, Johns ST, Zulkepli AZ, Barringer R, Zorn K, Stach JEM, Crump MP, Hayes MA, van der Kamp MW, Race PR, Willis CL. The Role of Cytochrome P450 AbyV in the Final Stages of Abyssomicin C Biosynthesis. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202213053. [PMID: 38516347 PMCID: PMC10952897 DOI: 10.1002/ange.202213053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 03/23/2024]
Abstract
Abyssomicin C and its atropisomer are potent inhibitors of bacterial folate metabolism. They possess complex polycyclic structures, and their biosynthesis has been shown to involve several unusual enzymatic transformations. Using a combination of synthesis and in vitro assays we reveal that AbyV, a cytochrome P450 enzyme from the aby gene cluster, catalyses a key late-stage epoxidation required for the installation of the characteristic ether-bridged core of abyssomicin C. The X-ray crystal structure of AbyV has been determined, which in combination with molecular dynamics simulations provides a structural framework for our functional data. This work demonstrates the power of combining selective carbon-13 labelling with NMR spectroscopy as a sensitive tool to interrogate enzyme-catalysed reactions in vitro with no need for purification.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Rob Barringer
- School of BiochemistryUniversity of BristolBS81TDBristolUK
| | - Katja Zorn
- BioPharmaceuticals R&DAstraZenecaPepparedsleden 143183MölndalSweden
| | - James E. M. Stach
- School of Natural and Environmental SciencesNewcastle UniversityNE17RUNewcastle-upon-TyneUK
| | | | - Martin A. Hayes
- BioPharmaceuticals R&DAstraZenecaPepparedsleden 143183MölndalSweden
| | | | - Paul R. Race
- School of BiochemistryUniversity of BristolBS81TDBristolUK
| | | |
Collapse
|
4
|
Devine AJ, Parnell AE, Back CR, Lees NR, Johns ST, Zulkepli AZ, Barringer R, Zorn K, Stach JEM, Crump MP, Hayes MA, van der Kamp MW, Race PR, Willis CL. The Role of Cytochrome P450 AbyV in the Final Stages of Abyssomicin C Biosynthesis. Angew Chem Int Ed Engl 2023; 62:e202213053. [PMID: 36314667 PMCID: PMC10107801 DOI: 10.1002/anie.202213053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/16/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
Abyssomicin C and its atropisomer are potent inhibitors of bacterial folate metabolism. They possess complex polycyclic structures, and their biosynthesis has been shown to involve several unusual enzymatic transformations. Using a combination of synthesis and in vitro assays we reveal that AbyV, a cytochrome P450 enzyme from the aby gene cluster, catalyses a key late-stage epoxidation required for the installation of the characteristic ether-bridged core of abyssomicin C. The X-ray crystal structure of AbyV has been determined, which in combination with molecular dynamics simulations provides a structural framework for our functional data. This work demonstrates the power of combining selective carbon-13 labelling with NMR spectroscopy as a sensitive tool to interrogate enzyme-catalysed reactions in vitro with no need for purification.
Collapse
Affiliation(s)
- Andrew J Devine
- School of Chemistry, University of Bristol, BS81TS, Bristol, UK
| | - Alice E Parnell
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Catherine R Back
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Nicholas R Lees
- School of Chemistry, University of Bristol, BS81TS, Bristol, UK
| | - Samuel T Johns
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Ainul Z Zulkepli
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Rob Barringer
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | - Katja Zorn
- BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | - James E M Stach
- School of Natural and Environmental Sciences, Newcastle University, NE17RU, Newcastle-upon-Tyne, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, BS81TS, Bristol, UK
| | - Martin A Hayes
- BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183, Mölndal, Sweden
| | | | - Paul R Race
- School of Biochemistry, University of Bristol, BS81TD, Bristol, UK
| | | |
Collapse
|
5
|
Kan J, Chen Z, Qiu Z, Lv L, Li C, Li CJ. Umpolung carbonyls enable direct allylation and olefination of carbohydrates. SCIENCE ADVANCES 2022; 8:eabm6840. [PMID: 35263121 PMCID: PMC8906572 DOI: 10.1126/sciadv.abm6840] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Mother Nature has its own arts to build a vast number of carbohydrates; however, there is still a lack of tools for selective functionalization of native carbohydrates through C─C bond formation. Such a long-standing challenge for the synthetic community lies into the intrinsic problems related to the innate properties of carbohydrates, e.g., the ease to oligomerization or polymerization, the difficulty of chemoselectivity control in the presence of multiple hydroxyl groups, the great challenge to retain the multiple chiral centers during the transformation, etc. Here, by applying an umpolung strategy of carbohydrate carbonyls, we report a direct deoxygenative allylation and olefination of carbohydrates to tackle the abovementioned issues. The reaction is compatible with a wide range of natural carbohydrates, providing a direct synthetic method to use carbohydrates as multiple C-centered chiral synthons to achieve C─C bond cross-coupling reactions. Furthermore, the synthetic applicability is demonstrated by late-stage modifications of natural products and pharmaceutical derivatives.
Collapse
Affiliation(s)
- Jian Kan
- Department of Chemistry and FRQNT Center for Green Chemistry and Catalysis, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002, P. R. China
| | - Zhangpei Chen
- Department of Chemistry and FRQNT Center for Green Chemistry and Catalysis, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
- Center for Molecular Science and Engineering, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Zihang Qiu
- Department of Chemistry and FRQNT Center for Green Chemistry and Catalysis, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Leiyang Lv
- Department of Chemistry and FRQNT Center for Green Chemistry and Catalysis, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Chenchen Li
- Department of Chemistry and FRQNT Center for Green Chemistry and Catalysis, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Chao-Jun Li
- Department of Chemistry and FRQNT Center for Green Chemistry and Catalysis, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| |
Collapse
|
6
|
Princiotto S, Jayasinghe L, Dallavalle S. Recent advances in the synthesis of naturally occurring tetronic acids. Bioorg Chem 2021; 119:105552. [PMID: 34929518 DOI: 10.1016/j.bioorg.2021.105552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/08/2021] [Indexed: 11/18/2022]
Abstract
During the last decades the interest towards natural products containing the tetronic acid moiety augmented significantly, due to their challenging structures and to the wide range of biological activities they display. This increasing enthusiasm has led to noteworthy advances in the development of innovative methodologies for the construction of the butenolide nucleus. This review provides an overview of the progress in the synthesis of tetronic acid as a structural key motif of natural compounds, covering the last 15 years. Herein, the most representative synthetic pathways towards structurally diverse natural tetronic acids are grouped according to the strategy followed. The first part describes the functionalization of a preformed tetronic acid core by intermolecular reactions (cross-coupling reactions, nucleophilic substitution, multicomponent reactions) whereas the second part deals with intramolecular approaches (Dieckmann, cycloaddition or ring expansion reactions) to construct the heterocyclic core. This rational subcategorization allowed us to make some considerations about the best approaches for the synthesis of specific substrates, including modern intriguing methodologies such as microwave irradiation, solid phase anchoring, bio-transformations and continuous flow processes.
Collapse
Affiliation(s)
- Salvatore Princiotto
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy
| | | | - Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milan, Italy; National Institute of Fundamental Studies, Kandy 20000, Sri Lanka.
| |
Collapse
|
7
|
Little RF, Hertweck C. Chain release mechanisms in polyketide and non-ribosomal peptide biosynthesis. Nat Prod Rep 2021; 39:163-205. [PMID: 34622896 DOI: 10.1039/d1np00035g] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Review covering up to mid-2021The structure of polyketide and non-ribosomal peptide natural products is strongly influenced by how they are released from their biosynthetic enzymes. As such, Nature has evolved a diverse range of release mechanisms, leading to the formation of bioactive chemical scaffolds such as lactones, lactams, diketopiperazines, and tetronates. Here, we review the enzymes and mechanisms used for chain release in polyketide and non-ribosomal peptide biosynthesis, how these mechanisms affect natural product structure, and how they could be utilised to introduce structural diversity into the products of engineered biosynthetic pathways.
Collapse
Affiliation(s)
- Rory F Little
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology, HKI, Germany.
| |
Collapse
|
8
|
Clinger JA, Wang X, Cai W, Zhu Y, Miller MD, Zhan CG, Van Lanen SG, Thorson JS, Phillips GN. The crystal structure of AbsH3: A putative flavin adenine dinucleotide-dependent reductase in the abyssomicin biosynthesis pathway. Proteins 2020; 89:132-137. [PMID: 32852843 DOI: 10.1002/prot.25994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/01/2020] [Accepted: 07/26/2020] [Indexed: 11/06/2022]
Abstract
Natural products and natural product-derived compounds have been widely used for pharmaceuticals for many years, and the search for new natural products that may have interesting activity is ongoing. Abyssomicins are natural product molecules that have antibiotic activity via inhibition of the folate synthesis pathway in microbiota. These compounds also appear to undergo a required [4 + 2] cycloaddition in their biosynthetic pathway. Here we report the structure of an flavin adenine dinucleotide-dependent reductase, AbsH3, from the biosynthetic gene cluster of novel abyssomicins found in Streptomyces sp. LC-6-2.
Collapse
Affiliation(s)
| | - Xiachang Wang
- Jiangsu Key Laboratory for Functional Substance of Chinese Medicine, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Wenlong Cai
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Yanyan Zhu
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | | | - Chang-Guo Zhan
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Steven G Van Lanen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - Jon S Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA.,Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
| |
Collapse
|
9
|
Vidali VP, Canko A, Peroulias AD, Georgas ET, Bouzas E, Herniman JM, Couladouros EA. An Improved Biomimetic Formal Synthesis of Abyssomicin C and atrop
-Abyssomicin C. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Veroniki P. Vidali
- NCSR "Demokritos"; Institute of Nanoscience & Nanotechnology; Patr. Grigoriou & Neapoleos 25 153 41 Athens Greece
| | - Aleksander Canko
- NCSR "Demokritos"; Institute of Nanoscience & Nanotechnology; Patr. Grigoriou & Neapoleos 25 153 41 Athens Greece
- Department of Food Science and Human Nutrition; Agricultural University of Athens; Athens Greece
| | - Angelos D. Peroulias
- School of Chemistry; University of Southampton; 17 1BJ Southampton SO United Kingdom
| | - Evangelos T. Georgas
- NCSR "Demokritos"; Institute of Nanoscience & Nanotechnology; Patr. Grigoriou & Neapoleos 25 153 41 Athens Greece
- Department of Chemistry; University of Athens; Athens Greece
| | - Emmanuel Bouzas
- Department of Food Science and Human Nutrition; Agricultural University of Athens; Athens Greece
| | - Julie M. Herniman
- School of Chemistry; University of Southampton; 17 1BJ Southampton SO United Kingdom
| | - Elias A. Couladouros
- Department of Food Science and Human Nutrition; Agricultural University of Athens; Athens Greece
| |
Collapse
|
10
|
IUPAC 2019 Distinguished Women in Chemistry or Chemical Engineering. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
11
|
IUPAC 2019 Distinguished Women in Chemistry or Chemical Engineering. Angew Chem Int Ed Engl 2019; 58:6485-6486. [DOI: 10.1002/anie.201903940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
12
|
Hill RA, Sutherland A. Hot off the Press. Nat Prod Rep 2019. [DOI: 10.1039/c9np90010a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as preuisolactone A from Preussia isomera.
Collapse
|