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Ushimaru R. Unusual Enzymatic C-C Bond Formation and Cleavage Reactions during Natural Product Biosynthesis. Chem Pharm Bull (Tokyo) 2024; 72:241-247. [PMID: 38432903 DOI: 10.1248/cpb.c23-00889] [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] [Indexed: 03/05/2024]
Abstract
Natural products from plants and microorganisms provide a valuable reservoir of pharmaceutical compounds. C-C bond formation and cleavage are crucial events during natural product biosynthesis, playing pivotal roles in generating diverse and intricate chemical structures that are essential for biological functions. This review summarizes our recent findings regarding biosynthetic enzymes that catalyze unconventional C-C bond formation and cleavage reactions during natural product biosynthesis.
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Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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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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Ushimaru R, Cha L, Shimo S, Li X, Paris JC, Mori T, Miyamoto K, Coffer L, Uchiyama M, Guo Y, Chang WC, Abe I. Mechanistic Analysis of Stereodivergent Nitroalkane Cyclopropanation Catalyzed by Nonheme Iron Enzymes. J Am Chem Soc 2023; 145:24210-24217. [PMID: 37874539 PMCID: PMC10725191 DOI: 10.1021/jacs.3c08413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
BelL and HrmJ are α-ketoglutarate-dependent nonheme iron enzymes that catalyze the oxidative cyclization of 6-nitronorleucine, resulting in the formation of two diastereomeric 3-(2-nitrocyclopropyl)alanine (Ncpa) products containing trans-cyclopropane rings with (1'R,2'R) and (1'S,2'S) configurations, respectively. Herein, we investigate the catalytic mechanism and stereodivergency of the cyclopropanases. The results suggest that the nitroalkane moiety of the substrate is first deprotonated to produce the nitronate form. Spectroscopic analyses and biochemical assays with substrates and analogues indicate that an iron(IV)-oxo species abstracts proS-H from C4 to initiate intramolecular C-C bond formation. A hydroxylation intermediate is unlikely to be involved in the cyclopropanation reaction. Additionally, a genome mining approach is employed to discover new homologues that perform the cyclopropanation of 6-nitronorleucine to generate cis-configured Ncpa products with (1'R,2'S) or (1'S,2'R) stereochemistries. Sequence and structure comparisons of these cyclopropanases enable us to determine the amino acid residues critical for controlling the stereoselectivity of cyclopropanation.
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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
| | - Lide Cha
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Shotaro Shimo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Xiaojun Li
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Jared C Paris
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Takahiro Mori
- 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
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Kazunori Miyamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Lindsay Coffer
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Research Initiative for Supra-Materials, Shinshu University, Nagano 380-8553, Japan
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Wei-Chen Chang
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Ikuro Abe
- 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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Ushimaru R, Abe I. Unusual Dioxygen-Dependent Reactions Catalyzed by Nonheme Iron Enzymes in Natural Product Biosynthesis. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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5
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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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Shimo S, Ushimaru R, Engelbrecht A, Harada M, Miyamoto K, Kulik A, Uchiyama M, Kaysser L, Abe I. Stereodivergent Nitrocyclopropane Formation during Biosynthesis of Belactosins and Hormaomycins. J Am Chem Soc 2021; 143:18413-18418. [PMID: 34710328 DOI: 10.1021/jacs.1c10201] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Belactosins and hormaomycins are peptide natural products containing 3-(2-aminocyclopropyl)alanine and 3-(2-nitrocyclopropyl)alanine residues, respectively, with opposite stereoconfigurations of the cyclopropane ring. Herein we demonstrate that the heme oxygenase-like enzymes BelK and HrmI catalyze the N-oxygenation of l-lysine to generate 6-nitronorleucine. The nonheme iron enzymes BelL and HrmJ then cyclize the nitroalkane moiety to the nitrocyclopropane ring with the desired stereochemistry found in the corresponding natural products. We also show that both cyclopropanases remove the 4-proS-H of 6-nitronorleucine during the cyclization, establishing the inversion and retention of the configuration at C4 during the BelL and HrmJ reactions, respectively. This study reveals the unique strategy for stereocontrolled cyclopropane synthesis in nature.
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Affiliation(s)
- Shotaro Shimo
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Richiro Ushimaru
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,ACT-X, Japan Science and Technology Agency (JST), Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Alicia Engelbrecht
- Pharmaceutical Institute, Department of Pharmaceutical Biology, University of Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Mei Harada
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Miyamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine (IMIT), University of Tübingen, 72076 Tübingen, Germany
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Research Initiative for Supra-Materials (RISM), Shinshu University, Ueda, 386-8567, Japan
| | - Leonard Kaysser
- Institute for Drug Discovery, Department of Pharmaceutical Biology, University of Leipzig, Eilenburger Str. 14, 04317 Leipzig, Germany
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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Steiningerova L, Kamenik Z, Gazak R, Kadlcik S, Bashiri G, Man P, Kuzma M, Pavlikova M, Janata J. Different Reaction Specificities of F 420H 2-Dependent Reductases Facilitate Pyrrolobenzodiazepines and Lincomycin To Fit Their Biological Targets. J Am Chem Soc 2020; 142:3440-3448. [PMID: 31944685 DOI: 10.1021/jacs.9b11234] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antitumor pyrrolobenzodiazepines (PBDs), lincosamide antibiotics, quorum-sensing molecule hormaomycin, and antimicrobial griselimycin are structurally and functionally diverse groups of actinobacterial metabolites. The common feature of these compounds is the incorporation of l-tyrosine- or l-leucine-derived 4-alkyl-l-proline derivatives (APDs) in their structures. Here, we report that the last reaction in the biosynthetic pathway of APDs, catalyzed by F420H2-dependent Apd6 reductases, contributes to the structural diversity of APD precursors. Specifically, the heterologous overproduction of six Apd6 enzymes demonstrated that Apd6 from the biosynthesis of PBDs and hormaomycin can reduce only an endocyclic imine double bond, whereas Apd6 LmbY and partially GriH from the biosyntheses of lincomycin and griselimycin, respectively, also reduce the more inert exocyclic double bond of the same 4-substituted Δ1-pyrroline-2-carboxylic acid substrate, making LmbY and GriH unusual, if not unique, among reductases. Furthermore, the differences in the reaction specificity of the Apd6 reductases determine the formation of the fully saturated APD moiety of lincomycin versus the unsaturated APD moiety of PBDs, providing molecules with optimal shapes to bind their distinct biological targets. Moreover, the Apd6 reductases establish the first F420H2-dependent enzymes from the luciferase-like hydride transferase protein superfamily in the biosynthesis of bioactive molecules. Finally, our bioinformatics analysis demonstrates that Apd6 and their homologues, widely distributed within several bacterial phyla, play a role in the formation of novel yet unknown natural products with incorporated l-proline-like precursors and likely in the microbial central metabolism.
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Affiliation(s)
- Lucie Steiningerova
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic.,Department of Genetics and Microbiology, Faculty of Science , Charles University in Prague , Vinicna 5 , 128 00 Praha 2 , Czech Republic
| | - Zdenek Kamenik
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic.,Institute of Microbiology, v.v.i., BIOCEV, Czech Academy of Sciences , 252 50 Vestec , Czech Republic
| | - Radek Gazak
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Stanislav Kadlcik
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Ghader Bashiri
- Laboratory of Structural Biology and Maurice Wilkins Center for Molecular Biodiscovery, School of Biological Sciences , University of Auckland , Auckland 1010 , New Zealand
| | - Petr Man
- Institute of Microbiology, v.v.i., BIOCEV, Czech Academy of Sciences , 252 50 Vestec , Czech Republic
| | - Marek Kuzma
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Magdalena Pavlikova
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
| | - Jiri Janata
- Institute of Microbiology, v.v.i., Czech Academy of Sciences , Videnska 1083 , 142 20 Praha 4 , Czech Republic
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Janata J, Kamenik Z, Gazak R, Kadlcik S, Najmanova L. Biosynthesis and incorporation of an alkylproline-derivative (APD) precursor into complex natural products. Nat Prod Rep 2018. [DOI: 10.1039/c7np00047b] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review covers the biosynthetic and evolutionary aspects of lincosamide antibiotics, antitumour pyrrolobenzodiazepines (PBDs) and the quorum-sensing molecule hormaomycin.
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Affiliation(s)
- J. Janata
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - Z. Kamenik
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - R. Gazak
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - S. Kadlcik
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
| | - L. Najmanova
- Institute of Microbiology
- Czech Academy of Sciences
- BIOCEV
- Vestec
- Czech Republic
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Cai X, Teta R, Kohlhaas C, Crüsemann M, Ueoka R, Mangoni A, Freeman M, Piel J. Manipulation of Regulatory Genes Reveals Complexity and Fidelity in Hormaomycin Biosynthesis. ACTA ACUST UNITED AC 2013; 20:839-46. [DOI: 10.1016/j.chembiol.2013.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 04/19/2013] [Accepted: 04/26/2013] [Indexed: 12/28/2022]
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10
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Condurso HL, Bruner SD. Structure and noncanonical chemistry of nonribosomal peptide biosynthetic machinery. Nat Prod Rep 2012; 29:1099-110. [PMID: 22729219 PMCID: PMC3442147 DOI: 10.1039/c2np20023f] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Structural biology has provided significant insights into the complex chemistry and macromolecular organization of nonribosomal peptide synthetases. In addition, novel pathways are continually described, expanding the knowledge of known biosynthetic chemistry.
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Affiliation(s)
- Heather L. Condurso
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA. Fax: 352 392 8758; Tel: 352 392 0525
| | - Steven D. Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida, 32611, USA. Fax: 352 392 8758; Tel: 352 392 0525
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Höfer I, Crüsemann M, Radzom M, Geers B, Flachshaar D, Cai X, Zeeck A, Piel J. Insights into the biosynthesis of hormaomycin, an exceptionally complex bacterial signaling metabolite. ACTA ACUST UNITED AC 2011; 18:381-91. [PMID: 21439483 DOI: 10.1016/j.chembiol.2010.12.018] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/26/2010] [Accepted: 12/02/2010] [Indexed: 11/19/2022]
Abstract
Hormaomycin produced by Streptomyces griseoflavus is a structurally highly modified depsipeptide that contains several unique building blocks with cyclopropyl, nitro, and chlorine moieties. Within the genus Streptomyces, it acts as a bacterial hormone that induces morphological differentiation and the production of bioactive secondary metabolites. In addition, hormaomycin is an extremely potent narrow-spectrum antibiotic. In this study, we shed light on hormaomycin biosynthesis by a combination of feeding studies, isolation of the biosynthetic nonribosomal peptide synthetase (NRPS) gene cluster, and in vivo and in vitro functional analysis of enzymes. In addition, several nonnatural hormaomycin congeners were generated by feeding-induced metabolic rerouting. The NRPS contains numerous highly repetitive regions that suggest an evolutionary scenario for this unusual bacterial hormone, providing new opportunities for evolution-inspired metabolic engineering of novel nonribosomal peptides.
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Affiliation(s)
- Ivonne Höfer
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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Andres N, Wolf H, Zähner H, Rössner E, Zeeck A, König WA, Sinnwell V. Stoffwechselprodukte von Mikroorganismen. 253. Mitteilung. Hormaomycin, ein neues Peptid-lacton mit morphogener Aktivität auf Streptomyceten. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19890720303] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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