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Qureshi M, Mokkawes T, Cao Y, de Visser SP. Mechanism of the Oxidative Ring-Closure Reaction during Gliotoxin Biosynthesis by Cytochrome P450 GliF. Int J Mol Sci 2024; 25:8567. [PMID: 39201254 PMCID: PMC11354885 DOI: 10.3390/ijms25168567] [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: 06/26/2024] [Revised: 07/30/2024] [Accepted: 08/02/2024] [Indexed: 09/02/2024] Open
Abstract
During gliotoxin biosynthesis in fungi, the cytochrome P450 GliF enzyme catalyzes an unusual C-N ring-closure step while also an aromatic ring is hydroxylated in the same reaction cycle, which may have relevance to drug synthesis reactions in biotechnology. However, as the details of the reaction mechanism are still controversial, no applications have been developed yet. To resolve the mechanism of gliotoxin biosynthesis and gain insight into the steps leading to ring-closure, we ran a combination of molecular dynamics and density functional theory calculations on the structure and reactivity of P450 GliF and tested a range of possible reaction mechanisms, pathways and models. The calculations show that, rather than hydrogen atom transfer from the substrate to Compound I, an initial proton transfer transition state is followed by a fast electron transfer en route to the radical intermediate, and hence a non-synchronous hydrogen atom abstraction takes place. The radical intermediate then reacts by OH rebound to the aromatic ring to form a biradical in the substrate that, through ring-closure between the radical centers, gives gliotoxin products. Interestingly, the structure and energetics of the reaction mechanisms appear little affected by the addition of polar groups to the model and hence we predict that the reaction can be catalyzed by other P450 isozymes that also bind the same substrate. Alternative pathways, such as a pathway starting with an electrophilic attack on the arene to form an epoxide, are high in energy and are ruled out.
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Affiliation(s)
| | | | | | - Sam P. de Visser
- Manchester Institute of Biotechnology, Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK (Y.C.)
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2
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Guo Y, Liu JZ, Limwachiranon J, Xu F, Han Y, Xu L, Xiong Z, Zhang N, Ding G, Scharf DH. Reconstitution of the Early Stage of Chetomin Biosynthesis in Aspergillus fumigatus Leads to the Production of Epipolythiodioxopiperazines. Org Lett 2024; 26:4469-4474. [PMID: 38767929 DOI: 10.1021/acs.orglett.4c01274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Using CRISPR-Cas9 technology and a microhomology-mediated end-joining repair system, we substituted genes of the gliotoxin pathway in Aspergillus fumigatus with genes responsible for chetomin biosynthesis from Chaetomium cochliodes, leading to the production of three new epipolythiodioxopiperazines (ETPs). This work represents the first successful endeavor to produce ETPs in a non-native host. Additionally, the simultaneous disruption of five genes in a single transformation marks the most extensive gene knockout event in filamentous fungi to date.
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Affiliation(s)
- Yaojie Guo
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
- The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, People's Republic of China
| | - Jian-Zi Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, People's Republic of China
| | - Jarukitt Limwachiranon
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Fan Xu
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Yi Han
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Liru Xu
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Zhenzhen Xiong
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Nan Zhang
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Gang Ding
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, People's Republic of China
| | - Daniel H Scharf
- Department of Microbiology, School of Basic Medical Sciences, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, People's Republic of China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, People's Republic of China
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3
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Pierre HC, Amrine CSM, Doyle MG, Salvi A, Raja HA, Chekan JR, Huntsman AC, Fuchs JR, Liu K, Burdette JE, Pearce CJ, Oberlies NH. Verticillins: fungal epipolythiodioxopiperazine alkaloids with chemotherapeutic potential. Nat Prod Rep 2024. [PMID: 38629495 DOI: 10.1039/d3np00068k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2024]
Abstract
Covering: 1970 through June of 2023Verticillins are epipolythiodioxopiperazine (ETP) alkaloids, many of which possess potent, nanomolar-level cytotoxicity against a variety of cancer cell lines. Over the last decade, their in vivo activity and mode of action have been explored in detail. Notably, recent studies have indicated that these compounds may be selective inhibitors of histone methyltransferases (HMTases) that alter the epigenome and modify targets that play a crucial role in apoptosis, altering immune cell recognition, and generating reactive oxygen species. Verticillin A (1) was the first of 27 analogues reported from fungal cultures since 1970. Subsequent genome sequencing identified the biosynthetic gene cluster responsible for producing verticillins, allowing a putative pathway to be proposed. Further, molecular sequencing played a pivotal role in clarifying the taxonomic characterization of verticillin-producing fungi, suggesting that most producing strains belong to the genus Clonostachys (i.e., Bionectria), Bionectriaceae. Recent studies have explored the total synthesis of these molecules and the generation of analogues via both semisynthetic and precursor-directed biosynthetic approaches. In addition, nanoparticles have been used to deliver these molecules, which, like many natural products, possess challenging solubility profiles. This review summarizes over 50 years of chemical and biological research on this class of fungal metabolites and offers insights and suggestions on future opportunities to push these compounds into pre-clinical and clinical development.
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Affiliation(s)
- Herma C Pierre
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
| | - Chiraz Soumia M Amrine
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
- Department of Physical and Earth Sciences. Arkansas Tech University, 1701 N. Boulder Ave., Russellville, Arkansas 72801, USA
| | - Michael G Doyle
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
| | - Amrita Salvi
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave (M/C 870), Chicago, Illinois 60607, USA
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
| | - Jonathan R Chekan
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
| | - Andrew C Huntsman
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, 500 W. 12th Ave., Columbus, Ohio 43210, USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, 500 W. 12th Ave., Columbus, Ohio 43210, USA
| | - Kebin Liu
- Department of Biochemistry and Molecular Biology and the Georgia Cancer Center, Medical College of Georgia, Augusta, GA 30912, USA
- Charlie Norwood Veterans Affairs Medical Center, Augusta, GA 30904, USA
| | - Joanna E Burdette
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, 900 S. Ashland Ave (M/C 870), Chicago, Illinois 60607, USA
| | | | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, P.O. Box 26170, Greensboro, North Carolina 27402, USA.
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4
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Fan J, Wei PL, Yin WB. Formation of Bridged Disulfide in Epidithiodioxopiperazines. Chembiochem 2024; 25:e202300770. [PMID: 38116907 DOI: 10.1002/cbic.202300770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 12/21/2023]
Abstract
Epidithiodioxopiperazine (ETP) alkaloids, featuring a 2,5-diketopiperazine core and transannular disulfide bridge, exhibit a broad spectrum of biological activities. However, the structural complexity has prevented efficient chemical synthesis and further clinical research. In the past few decades, many achievements have been made in the biosynthesis of ETPs. Here, we discuss the biosynthetic progress and summarize them as two comprehensible metabolic principles for better understanding the complex pathways of α, α'- and α, β'-disulfide bridged ETPs. Specifically, we systematically outline the catalytic machineries to install α, α'- and α, β'-disulfide by flavin-containing oxygenases. This concept would contribute to the medical and industrial applications of ETPs.
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Affiliation(s)
- Jie Fan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Peng-Lin Wei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, P. R. China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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5
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Alves de Castro P, Figueiredo Pinzan C, Dos Reis TF, Valero C, Van Rhijn N, Menegatti C, de Freitas Migliorini IL, Bromley M, Fleming AB, Traynor AM, Sarikaya-Bayram Ö, Bayram Ö, Malavazi I, Ebel F, Barbosa JCJ, Fill T, Pupo MT, Goldman GH. Aspergillus fumigatus mitogen-activated protein kinase MpkA is involved in gliotoxin production and self-protection. Nat Commun 2024; 15:33. [PMID: 38167253 PMCID: PMC10762094 DOI: 10.1038/s41467-023-44329-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
Aspergillus fumigatus is a saprophytic fungus that can cause a variety of human diseases known as aspergillosis. Mycotoxin gliotoxin (GT) production is important for its virulence and must be tightly regulated to avoid excess production and toxicity to the fungus. GT self-protection by GliT oxidoreductase and GtmA methyltransferase activities is related to the subcellular localization of these enzymes and how GT can be sequestered from the cytoplasm to avoid increased cell damage. Here, we show that GliT:GFP and GtmA:GFP are localized in the cytoplasm and in vacuoles during GT production. The Mitogen-Activated Protein kinase MpkA is essential for GT production and self-protection, interacts physically with GliT and GtmA and it is necessary for their regulation and subsequent presence in the vacuoles. The sensor histidine kinase SlnASln1 is important for modulation of MpkA phosphorylation. Our work emphasizes the importance of MpkA and compartmentalization of cellular events for GT production and self-defense.
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Affiliation(s)
- Patrícia Alves de Castro
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Camila Figueiredo Pinzan
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Thaila Fernanda Dos Reis
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Clara Valero
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Norman Van Rhijn
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Carla Menegatti
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | - Michael Bromley
- Manchester Fungal Infection Group, Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Alastair B Fleming
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Aimee M Traynor
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | | | - Özgür Bayram
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo, Brazil
| | - Frank Ebel
- Institut für Infektionsmedizin und Zoonosen, Medizinische Fakultät, LMU, 80539, München, Germany
| | | | - Taícia Fill
- Instituto de Química, Universidade Estadual de Campinas, Campinas, Brazil
| | - Monica Tallarico Pupo
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Gustavo H Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.
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6
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Huber EM. Epipolythiodioxopiperazine-Based Natural Products: Building Blocks, Biosynthesis and Biological Activities. Chembiochem 2022; 23:e202200341. [PMID: 35997236 PMCID: PMC10086836 DOI: 10.1002/cbic.202200341] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/19/2022] [Indexed: 01/25/2023]
Abstract
Epipolythiodioxopiperazines (ETPs) are fungal secondary metabolites that share a 2,5-diketopiperazine scaffold built from two amino acids and bridged by a sulfide moiety. Modifications of the core and the amino acid side chains, for example by methylations, acetylations, hydroxylations, prenylations, halogenations, cyclizations, and truncations create the structural diversity of ETPs and contribute to their biological activity. However, the key feature responsible for the bioactivities of ETPs is their sulfide moiety. Over the last years, combinations of genome mining, reverse genetics, metabolomics, biochemistry, and structural biology deciphered principles of ETP production. Sulfurization via glutathione and uncovering of the thiols followed by either oxidation or methylation crystallized as fundamental steps that impact expression of the biosynthesis cluster, toxicity and secretion of the metabolite as well as self-tolerance of the producer. This article showcases structure and activity of prototype ETPs such as gliotoxin and discusses the current knowledge on the biosynthesis routes of these exceptional natural products.
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Affiliation(s)
- Eva M Huber
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
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7
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Li Q, Fu A, Wei M, Xiao Y, Yin J, Huang J, Li XN, Tong Q, Chen C, Zhu H, Zhang Y. Asperemestrins A-D, Emestrin Hybrid Polymers with Bridged Skeletons from the Endophytic Fungus Aspergillus nidulans. Org Lett 2022; 24:6800-6804. [PMID: 36074729 DOI: 10.1021/acs.orglett.2c02701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Four emestrin hybrid polymers, asperemestrins A-D (1-4, respectively), were isolated from the fungus Aspergillus nidulans. Asperemestrins A-C are the first examples of emestrin-sterigmatocystin heterodimers bearing a 7/5/6/6/5/5/6/6/6 nonacyclic system with a 2,5-diazabicyclo[2.2.2]octane-3,6-dione core, while asperemestrin D features an unprecedented 2,15-dithia-17,19-diazabicyclo[14.2.2]icosa-4,8-diene-12,18,20-trione core skeleton. Their structures were determined by extensive spectroscopic data, electronic circular dichroism calculations, and single-crystal X-ray diffraction. Asperemestrin B showed moderate cytotoxicity against cancer cell lines, including SU-DHL-2, HEPG2, and HL-60.
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Affiliation(s)
- Qin Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Aimin Fu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Mengsha Wei
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Yang Xiao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Jie Yin
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Jianzheng Huang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Xiao-Nian Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, People's Republic of China
| | - Qingyi Tong
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Chunmei Chen
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Hucheng Zhu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
| | - Yonghui Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
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8
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Scharf DH, Chankhamjon P, Scherlach K, Dworschak J, Heinekamp T, Roth M, Brakhage AA, Hertweck C. N-Heterocyclization in Gliotoxin Biosynthesis is Catalyzed by a Distinct Cytochrome P450 Monooxygenase. Chembiochem 2021; 22:336-339. [PMID: 32835438 PMCID: PMC7891397 DOI: 10.1002/cbic.202000550] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 08/24/2020] [Indexed: 01/03/2023]
Abstract
Gliotoxin and related epidithiodiketopiperazines (ETP) from diverse fungi feature highly functionalized hydroindole scaffolds with an array of medicinally and ecologically relevant activities. Mutation analysis, heterologous reconstitution, and biotransformation experiments revealed that a cytochrome P450 monooxygenase (GliF) from the human-pathogenic fungus Aspergillus fumigatus plays a key role in the formation of the complex heterocycle. In vitro assays using a biosynthetic precursor from a blocked mutant showed that GliF is specific to ETPs and catalyzes an unprecedented heterocyclization reaction that cannot be emulated with current synthetic methods. In silico analyses indicate that this rare biotransformation takes place in related ETP biosynthetic pathways.
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Affiliation(s)
- Daniel H. Scharf
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
- Department of MicrobiologyZhejiang University School of MedicineYuhangtang Road 866Hangzhou310058P. R. China
- The Children's Hospital, Zhejiang University School of MedicineNational Clinical Research Center for Child HealthBinsheng Road 3333Hangzhou310052P. R. China
| | - Pranatchareeya Chankhamjon
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Kirstin Scherlach
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Jan Dworschak
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Thorsten Heinekamp
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Martin Roth
- Bio Pilot PlantLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
| | - Axel A. Brakhage
- Department of Molecular and Applied MicrobiologyLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
| | - Christian Hertweck
- Department of Biomolecular ChemistryLeibniz Institute for Natural Product Research and Infection Biology (HKI)Beutenbergstrasse 11a07745JenaGermany
- Faculty of Biological SciencesFriedrich Schiller University Jena07743JenaGermany
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9
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Wang C, Wu P, Wang Z, Wang B. The molecular mechanism of P450-catalyzed amination of the pyrrolidine derivative of lidocaine: insights from multiscale simulations. RSC Adv 2021; 11:27674-27680. [PMID: 35480638 PMCID: PMC9037892 DOI: 10.1039/d1ra04564d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/09/2021] [Indexed: 11/23/2022] Open
Abstract
Nitrogen heterocycles are key and prevalent motifs in drugs. Evolved variants of cytochrome P450BM3 (CYP102A1) from Bacillus megaterium employ high-valent oxo-iron(iv) species to catalyze the synthesis of imidazolidine-4-ones via an intramolecular C–H amination. Herein, we use multi-scale simulations, including classical molecular dynamics (MD) simulations, quantum mechanical/molecular mechanical (QM/MM) calculations and QM calculations, to reveal the molecular mechanism of the intramolecular C–H amination of the pyrrolidine derivative of lidocaine bearing cyclic amino moieties catalyzed by the variant RP/FV/EV of P450BM3, which bears five mutations compared to wild type. Our calculations show that overall catalysis includes both the enzymatic transformation in P450 and non-enzymatic transformation in water solution. The enzymatic transformation involves the exclusive hydroxylation of the C–H bond of the pyrrolidine derivative of lidocaine, leading to the hydroxylated intermediate, during which the substrate radical would be bypassed. The following dehydration and C–N coupling reactions are found to be much favored in aqueous situation compared to that in the non-polar protein environment. The present findings expand our understanding of the P450-catalyzed C(sp3)–H amination reaction. Nitrogen heterocycles are key and prevalent motifs in drugs.![]()
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Affiliation(s)
- Conger Wang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Peng Wu
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhanfeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surface, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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