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Ushimaru R. Three-membered ring formation catalyzed by α-ketoglutarate-dependent nonheme iron enzymes. J Nat Med 2024; 78:21-32. [PMID: 37980694 PMCID: PMC10764440 DOI: 10.1007/s11418-023-01760-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/21/2023]
Abstract
Epoxides, aziridines, and cyclopropanes are found in various medicinal natural products, including polyketides, terpenes, peptides, and alkaloids. Many classes of biosynthetic enzymes are involved in constructing these ring structures during their biosynthesis. This review summarizes our current knowledge regarding how α-ketoglutarate-dependent nonheme iron enzymes catalyze the formation of epoxides, aziridines, and cyclopropanes in nature, with a focus on enzyme mechanisms.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, 113-8657, Japan.
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2
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Lu Y, Sen K, Yong C, Gunn DSD, Purton JA, Guan J, Desmoutier A, Abdul Nasir J, Zhang X, Zhu L, Hou Q, Jackson-Masters J, Watts S, Hanson R, Thomas HN, Jayawardena O, Logsdail AJ, Woodley SM, Senn HM, Sherwood P, Catlow CRA, Sokol AA, Keal TW. Multiscale QM/MM modelling of catalytic systems with ChemShell. Phys Chem Chem Phys 2023; 25:21816-21835. [PMID: 37097706 DOI: 10.1039/d3cp00648d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.
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Affiliation(s)
- You Lu
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Kakali Sen
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Chin Yong
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - David S D Gunn
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - John A Purton
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
| | - Jingcheng Guan
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Alec Desmoutier
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Jamal Abdul Nasir
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Xingfan Zhang
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Lei Zhu
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Qing Hou
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Joe Jackson-Masters
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Sam Watts
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Rowan Hanson
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Harry N Thomas
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Omal Jayawardena
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Andrew J Logsdail
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Scott M Woodley
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Hans M Senn
- School of Chemistry, University of Glasgow, Joseph Black Building, Glasgow G12 8QQ, UK
| | - Paul Sherwood
- Department of Chemistry, Lancaster University, Lancaster, LA1 4YB, UK
| | - C Richard A Catlow
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | - Alexey A Sokol
- Kathleen Lonsdale Materials Chemistry, Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - Thomas W Keal
- STFC Scientific Computing, Daresbury Laboratory, Keckwick Lane, Daresbury, Warrington, WA4 4AD, UK.
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3
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Abstract
Ergometrine is widely used for the treatment of excessive postpartum uterine bleeding. Claviceps paspali is a common species for industrial production of ergometrine, which is often accompanied by lysergic acid α-hydroxyethylamide (LAH) and lysergic acid amide (LAA). Currently, direct evidence on the biosynthetic mechanism of LAH and LAA from lysergic acid in C. paspali is absent, except that LAH and LAA share the common precursor with ergometrine and LAA is spontaneously transformed from LAH. A comparison of the gene clusters between C. purpurea and C. paspali showed that the latter harbored the additional easO and easP genes. Thus, the knockout of easO and easP in the species should not only improve the ergometrine production but also elucidate the function. In this study, gene knockout of C. paspali by homologous recombination yielded two mutants ∆easOhetero-1 and ∆easPhetero-34 with ergometrine titers of 1559.36 mg∙L−1 and 837.57 mg∙L−1, which were four and two times higher than that of the wild-type control, respectively. While the total titer of LAH and LAA of ∆easOhetero-1 was lower than that of the wild-type control. The Aspergillus nidulans expression system was adopted to verify the function of easO and easP. Heterologous expression in A. nidulans further demonstrated that easO, but not easP, determines the formation of LAA.
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Wojdyla Z, Borowski T. Properties of the Reactants and Their Interactions within and with the Enzyme Binding Cavity Determine Reaction Selectivities. The Case of Fe(II)/2-Oxoglutarate Dependent Enzymes. Chemistry 2022; 28:e202104106. [PMID: 34986268 DOI: 10.1002/chem.202104106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 12/12/2022]
Abstract
Fe(II)/2-oxoglutarate dependent dioxygenases (ODDs) share a double stranded beta helix (DSBH) fold and utilise a common reactive intermediate, ferryl species, to catalyse oxidative transformations of substrates. Despite the structural similarities, ODDs accept a variety of substrates and facilitate a wide range of reactions, that is hydroxylations, desaturations, (oxa)cyclisations and ring rearrangements. In this review we present and discuss the factors contributing to the observed (regio)selectivities of ODDs. They span from inherent properties of the reactants, that is, substrate molecule and iron cofactor, to the interactions between the substrate and the enzyme's binding cavity; the latter can counterbalance the effect of the former. Based on results of both experimental and computational studies dedicated to ODDs, we also line out the properties of the reactants which promote reaction outcomes other than the "default" hydroxylation. It turns out that the reaction selectivity depends on a delicate balance of interactions between the components of the investigated system.
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Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Kraków, Niezapominajek 8, 30239 Krakow, Poland
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Ma S, Mandalapu D, Wang S, Zhang Q. Biosynthesis of cyclopropane in natural products. Nat Prod Rep 2021; 39:926-945. [PMID: 34860231 DOI: 10.1039/d1np00065a] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Covering: 2012 to 2021Cyclopropane attracts wide interests in the fields of synthetic and pharmaceutical chemistry, and chemical biology because of its unique structural and chemical properties. This structural motif is widespread in natural products, and is usually essential for biological activities. Nature has evolved diverse strategies to access this structural motif, and increasing knowledge of the enzymes forming cyclopropane (i.e., cyclopropanases) has been revealed over the last two decades. Here, the scientific literature from the last two decades relating to cyclopropane biosynthesis is summarized, and the enzymatic cyclopropanations, according to reaction mechanism, which can be grouped into two major pathways according to whether the reaction involves an exogenous C1 unit from S-adenosylmethionine (SAM) or not, is discussed. The reactions can further be classified based on the key intermediates required prior to cyclopropane formation, which can be carbocations, carbanions, or carbon radicals. Besides the general biosynthetic pathways of the cyclopropane-containing natural products, particular emphasis is placed on the mechanism and engineering of the enzymes required for forming this unique structure motif.
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Affiliation(s)
- Suze Ma
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | | | - Shu Wang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
| | - Qi Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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Wu L, Li Z, Zhao F, Zhao B, Phillip FO, Feng J, Liu H, Yu K. Increased Organic Fertilizer and Reduced Chemical Fertilizer Increased Fungal Diversity and the Abundance of Beneficial Fungi on the Grape Berry Surface in Arid Areas. Front Microbiol 2021; 12:628503. [PMID: 34025598 PMCID: PMC8139630 DOI: 10.3389/fmicb.2021.628503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/12/2021] [Indexed: 01/23/2023] Open
Abstract
Fertilizer practices can significantly impact the fruit quality and microbial diversity of the orchards. The fungi on the surface of fruits are essential for fruit storability and safety. However, it is not clear whether fertilization affects the fungal diversity and community structure on the surface of grape berries. Here, grape quality and the fungal diversity on the surface of grapes harvested from three fertilizer treatments were analyzed shortly after grape picking (T0) and following 8 days of storage (T1). The study involved three treatments: (1) common chemical fertilizer for 2 years (CH); (2) increased organic fertilizer and reduced chemical fertilizer for 1 year (A.O); and (3) increased organic fertilizer and reduced chemical fertilizer for 2 years (B.O). The application of increased organic fertilizer and reduced chemical fertilizer increased the soluble solids content (SSC) of the grape berries and decreased the pH of the grape juice. A total of 827,947 high-quality fungal sequences were recovered and assigned to 527 operational taxonomic units. Members of the Ascomycota phylum were dominant in all samples and accounted for 94.41% of the total number of detected sequences, followed by the Basidiomycota (5.05%), and unidentified fungi (0.54%). Alpha and beta diversity analyses revealed significantly different fungal populations in the three fertilizer treatments over the two time periods. The fungal diversity and richness on the grape berry surface in the B.O and A.O treatments were higher than those in the CH treatment. Among the detected fungi, the B.O treatments were mainly Pichia, Aureobasidium, and Candida genera, while the CH treatments were Botrytis, Aspergillus, and Penicillium. Moreover, significant differences were revealed between the two assessment times (T0 and T1). The samples from the T0 timepoint had higher fungal richness and diversity than the samples from T1 timepoint. Increasing organic fertilizer usage in grape management could improve grape quality and went on to increase the fungal diversity, as well as the relative abundance (RA) of beneficial fungi on grape berry surfaces. The correlation analysis suggested that the pH of the grape juice was significantly negatively correlated with fungal diversity parameters.
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Affiliation(s)
- Linnan Wu
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Zhiqiang Li
- Shihezi Academy of Agricultural Sciences, Shihezi, China
| | - Fengyun Zhao
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Benzhou Zhao
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Fesobi Olumide Phillip
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Jianrong Feng
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Huaifeng Liu
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
| | - Kun Yu
- Department of Horticulture, College of Agriculture, The Key Laboratory of Characteristics of Fruit and Vegetable Cultivation and Utilization of Germoplasm Resources of the Xinjiang Production and Construction Crops, Shihezi University, Shihezi, China
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Waheed SO, Chaturvedi SS, Karabencheva-Christova TG, Christov CZ. Catalytic Mechanism of Human Ten-Eleven Translocation-2 (TET2) Enzyme: Effects of Conformational Changes, Electric Field, and Mutations. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05034] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sodiq O. Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shobhit S. Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | | | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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8
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Biosynthesis, total synthesis, and biological profiles of Ergot alkaloids. THE ALKALOIDS: CHEMISTRY AND BIOLOGY 2021; 85:1-112. [DOI: 10.1016/bs.alkal.2020.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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9
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Wojdyla Z, Borowski T. Enzyme Multifunctionality by Control of Substrate Positioning Within the Catalytic Cycle—A QM/MM Study of Clavaminic Acid Synthase. Chemistry 2020; 27:2196-2211. [DOI: 10.1002/chem.202004426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Zuzanna Wojdyla
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8 30239 Krakow Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of Sciences Niezapominajek 8 30239 Krakow Poland
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10
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Sheng X, Kazemi M, Planas F, Himo F. Modeling Enzymatic Enantioselectivity using Quantum Chemical Methodology. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00983] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xiang Sheng
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Masoud Kazemi
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Ferran Planas
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm SE-106 91, Sweden
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11
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Jakubczyk D, Dussart F. Selected Fungal Natural Products with Antimicrobial Properties. Molecules 2020; 25:E911. [PMID: 32085562 PMCID: PMC7070998 DOI: 10.3390/molecules25040911] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 01/14/2023] Open
Abstract
Fungal natural products and their effects have been known to humankind for hundreds of years. For example, toxic ergot alkaloids produced by filamentous fungi growing on rye poisoned thousands of people and livestock throughout the Middle Ages. However, their later medicinal applications, followed by the discovery of the first class of antibiotics, penicillins and other drugs of fungal origin, such as peptidic natural products, terpenoids or polyketides, have altered the historically negative reputation of fungal "toxins". The development of new antimicrobial drugs is currently a major global challenge, mainly due to antimicrobial resistance phenomena. Therefore, the structures, biosynthesis and antimicrobial activity of selected fungal natural products are described here.
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Affiliation(s)
- Dorota Jakubczyk
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Francois Dussart
- Department of Agriculture, Horticulture and Engineering Science, Scotland’s Rural College (SRUC), Edinburgh EH9 3JG, UK;
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Ren X, Chandgude AL, Fasan R. Highly Stereoselective Synthesis of Fused Cyclopropane-γ-Lactams via Biocatalytic Iron-Catalyzed Intramolecular Cyclopropanation. ACS Catal 2020; 10:2308-2313. [PMID: 32257580 PMCID: PMC7111458 DOI: 10.1021/acscatal.9b05383] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report the development of an iron-based biocatalytic strategy for the asymmetric synthesis of fused cyclopropane-γ-lactams, which are key structural motifs found in synthetic drugs and bioactive natural products. Using a combination of mutational landscape and iterative site-saturation mutagenesis, sperm whale myoglobin was evolved into a biocatalyst capable of promoting the cyclization of a diverse range of allyl diazoacetamide substrates into the corresponding bicyclic lactams in high yields and with high enantioselectivity (up to 99% ee). These biocatalytic transformations can be performed in whole cells and could be leveraged to enable the efficient (chemo)enzymatic construction of chiral cyclopropane-γ-lactams as well as β-cyclopropyl amines and cyclopropane-fused pyrrolidines, as valuable building blocks and synthons for medicinal chemistry and natural product synthesis.
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Affiliation(s)
| | | | - Rudi Fasan
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, NY 14627, United States
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