1
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Chen X, Johnson RM, Li B. A Permissive Amide N-Methyltransferase for Dithiolopyrrolones. ACS Catal 2023; 13:1899-1905. [PMID: 38106463 PMCID: PMC10720983 DOI: 10.1021/acscatal.2c05439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Amide N-methylation is important for the activity and permeability of bioactive compounds but can be challenging to perform selectively. The broad-spectrum antimicrobial natural products thiolutin and holomycin differ only by an N-methyl group at the endocyclic amide of thiolutin, but only thiolutin exhibits antifungal activity. The enzyme responsible for amide N--methylation in thiolutin biosynthesis has remained elusive. Here, we identified and characterized the amide N-methyltransferase DtpM that is encoded >400 kb outside of the thiolutin gene cluster. DtpM catalyzes efficient conversion of holomycin to thiolutin, exhibits broad substrate scope toward dithiolopyrrolones, and has high thermal stability. In addition, sequence similarity network analysis suggests DtpM is more closely related to phenol O-methyltransferases than some amide methyltransferases. This study expands the limited examples of amide N-methyltransferases and may facilitate chemoenzymatic synthesis of diverse dithiolopyrrolone compounds as potential therapeutics.
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Affiliation(s)
- Xiaoyan Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Rachel M Johnson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Bo Li
- Department of Chemistry, and Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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2
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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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3
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Skrzypczak N, Przybylski P. Structural diversity and biological relevance of benzenoid and atypical ansamycins and their congeners. Nat Prod Rep 2022; 39:1678-1704. [PMID: 35262153 DOI: 10.1039/d2np00004k] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Covering: 2011 to 2021The structural division of ansamycins, including those of atypical cores and different lengths of the ansa chains, is presented. Recently discovered benzenoid and atypical ansamycin scaffolds are presented in relation to their natural source and biosynthetic routes realized in bacteria as well as their muta and semisynthetic modifications influencing biological properties. To better understand the structure-activity relationships among benzenoid ansamycins structural aspects together with mechanisms of action regarding different targets in cells, are discussed. The most promising directions for structural optimizations of benzenoid ansamycins, characterized by predominant anticancer properties, were discussed in view of their potential medical and pharmaceutical applications. The bibliography of the review covers mainly years from 2011 to 2021.
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Affiliation(s)
- Natalia Skrzypczak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland.
| | - Piotr Przybylski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznanskiego 8, 61-614 Poznan, Poland.
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4
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Enzymatic methylation of the amide bond. Curr Opin Struct Biol 2020; 65:79-88. [DOI: 10.1016/j.sbi.2020.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 05/13/2020] [Accepted: 06/04/2020] [Indexed: 11/23/2022]
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5
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Li X, Wu X, Shen Y. Identification of the Bacterial Maytansinoid Gene Cluster asc Provides Insights into the Post-PKS Modifications of Ansacarbamitocin Biosynthesis. Org Lett 2019; 21:5823-5826. [PMID: 31299158 DOI: 10.1021/acs.orglett.9b01891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new biosynthetic gene cluster for the bacterial maytansinoids, ansacarbamitocins (ASCs), was identified in Amycolatopsis alba DSM 44262. The post-PKS modifications of ASCs were elucidated on the basis of bioinformatics analysis. Specific gene disruption and heterologous expression led to the isolation of seven new bacterial maytansinoids. The 3'-O-methyltransferase and 3-O-carbamyltransferase involved in bacterial maytansinoid biosynthesis were identified for the first time. The new bacterial maytansinoids 7 and 13 showed strong antitumor activities against four human cancer cell lines.
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Affiliation(s)
- Xiaoman Li
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , No. 44 West Wenhua Road , Jinan , Shandong 250012 , P. R. China
| | - Xingkang Wu
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , No. 44 West Wenhua Road , Jinan , Shandong 250012 , P. R. China
| | - Yuemao Shen
- Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences , Shandong University , No. 44 West Wenhua Road , Jinan , Shandong 250012 , P. R. China
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6
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Song H, van der Velden NS, Shiran SL, Bleiziffer P, Zach C, Sieber R, Imani AS, Krausbeck F, Aebi M, Freeman MF, Riniker S, Künzler M, Naismith JH. A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds. SCIENCE ADVANCES 2018; 4:eaat2720. [PMID: 30151425 PMCID: PMC6108569 DOI: 10.1126/sciadv.aat2720] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 07/17/2018] [Indexed: 05/04/2023]
Abstract
The peptide bond, the defining feature of proteins, governs peptide chemistry by abolishing nucleophilicity of the nitrogen. This and the planarity of the peptide bond arise from the delocalization of the lone pair of electrons on the nitrogen atom into the adjacent carbonyl. While chemical methylation of an amide bond uses a strong base to generate the imidate, OphA, the precursor protein of the fungal peptide macrocycle omphalotin A, self-hypermethylates amides at pH 7 using S-adenosyl methionine (SAM) as cofactor. The structure of OphA reveals a complex catenane-like arrangement in which the peptide substrate is clamped with its amide nitrogen aligned for nucleophilic attack on the methyl group of SAM. Biochemical data and computational modeling suggest a base-catalyzed reaction with the protein stabilizing the reaction intermediate. Backbone N-methylation of peptides enhances their protease resistance and membrane permeability, a property that holds promise for applications to medicinal chemistry.
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Affiliation(s)
- Haigang Song
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife KY16 9ST, UK
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Niels S. van der Velden
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Sally L. Shiran
- Biomedical Sciences Research Complex, North Haugh, University of St. Andrews, Fife KY16 9ST, UK
| | - Patrick Bleiziffer
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Christina Zach
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Ramon Sieber
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Aman S. Imani
- Department of Biochemistry, Molecular Biology, and Biophysics, and BioTechnology Institute, University of Minnesota–Twin Cities, St. Paul, MN 55108, USA
| | - Florian Krausbeck
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Michael F. Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics, and BioTechnology Institute, University of Minnesota–Twin Cities, St. Paul, MN 55108, USA
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Corresponding author. (S.R.); (M.K.); (J.H.N.)
| | - Markus Künzler
- Institute of Microbiology, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
- Corresponding author. (S.R.); (M.K.); (J.H.N.)
| | - James H. Naismith
- Division of Structural Biology, Wellcome Trust Centre of Human Genomics, Roosevelt Drive, Oxford OX3 7BN, UK
- State Key Laboratory of Biotherapy, Sichuan University, Chengdu, China
- Research Complex at Harwell, Rutherford Laboratory, Didcot, Oxfordshire OX11 0FA, UK
- Corresponding author. (S.R.); (M.K.); (J.H.N.)
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7
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Ning X, Wang X, Wu Y, Kang Q, Bai L. Identification and Engineering of Post-PKS Modification Bottlenecks for Ansamitocin P-3 Titer Improvement inActinosynnema pretiosumsubsp. pretiosumATCC 31280. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700484] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/21/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Xinjuan Ning
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Xinran Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Yuanting Wu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Qianjin Kang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology; Shanghai Jiao Tong University; Shanghai 200240 China
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8
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Ding L, Franke J, Hertweck C. Divergolide congeners illuminate alternative reaction channels for ansamycin diversification. Org Biomol Chem 2015; 13:1618-23. [DOI: 10.1039/c4ob02244k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Isolation and structure elucidation of six new divergolides reveal unusual ansamycin diversification reactions including formation of the unusual isobutenyl side chain from a branched polyketide synthase extender unit, azepinone ring closure, macrolide ring contraction and formation of a seco variant by a neighboring group-assisted decarboxylation.
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Affiliation(s)
- Ling Ding
- Leibniz Institute for Natural Product Research and Infection Biology
- HKI
- Department of Biomolecular Chemistry
- 07745 Jena
- Germany
| | - Jakob Franke
- Leibniz Institute for Natural Product Research and Infection Biology
- HKI
- Department of Biomolecular Chemistry
- 07745 Jena
- Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology
- HKI
- Department of Biomolecular Chemistry
- 07745 Jena
- Germany
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9
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Hillwig ML, Fuhrman HA, Ittiamornkul K, Sevco TJ, Kwak DH, Liu X. Identification and characterization of a welwitindolinone alkaloid biosynthetic gene cluster in the stigonematalean Cyanobacterium Hapalosiphon welwitschii. Chembiochem 2014; 15:665-9. [PMID: 24677572 DOI: 10.1002/cbic.201300794] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Indexed: 11/05/2022]
Abstract
The identification of a 36 kb welwitindolinone (wel) biosynthetic gene cluster in Hapalosiphon welwitschii UTEX B1830 is reported. Characterization of the enzymes responsible for assembling the early biosynthetic intermediates geranyl pyrophosphate and 3-((Z)-2′-isocyanoethenyl)indole as well as a dedicated N-methyltransferase in the maturation of N-methylwelwitindolinone C isothiocyanate solidified the link between the wel pathway and welwitindolinone biosynthesis. Comparative analysis of the ambiguine and welwitindolinone biosynthetic pathways in two different organisms provided insights into the origins of diverse structures within hapalindole-type molecules.
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10
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Fan Y, Gao Y, Zhou J, Wei L, Chen J, Hua Q. Process optimization with alternative carbon sources and modulation of secondary metabolism for enhanced ansamitocin P-3 production in Actinosynnema pretiosum. J Biotechnol 2014; 192 Pt A:1-10. [DOI: 10.1016/j.jbiotec.2014.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/10/2014] [Accepted: 10/13/2014] [Indexed: 12/19/2022]
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11
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Scharf DH, Habel A, Heinekamp T, Brakhage AA, Hertweck C. Opposed effects of enzymatic gliotoxin N- and S-methylations. J Am Chem Soc 2014; 136:11674-9. [PMID: 25062268 DOI: 10.1021/ja5033106] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gliotoxin (1), a virulence factor of the human pathogenic fungus Aspergillus fumigatus, is the prototype of epipoly(thiodioxopiperazine) (ETP) toxins. Here we report the discovery and functional analysis of two methyl transferases (MTs) that play crucial roles for ETP toxicity. Genome comparisons, knockouts, and in vitro enzyme studies identified a new S-adenosyl-l-methionine-dependent S-MT (TmtA) that is, surprisingly, encoded outside the gli gene cluster. We found that TmtA irreversibly inactivates ETP by S-alkylation and that this detoxification strategy appears to be not only limited to ETP producers. Furthermore, we unveiled that GliN functions as a freestanding amide N-MT. GliN-mediated amide methylation confers stability to ETP, damping the spontaneous formation of tri- and tetrasulfides. In addition, enzymatic N-alkylation constitutes the last step in gliotoxin biosynthesis and is a prerequisite for the cytotoxicity of the molecule. Thus, these specialized alkylating enzymes have dramatic and fully opposed effects: complete activation or inactivation of the toxin.
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Affiliation(s)
- Daniel H Scharf
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute , Beutenbergstrasse 11a, 07745 Jena, Germany
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12
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Pan W, Kang Q, Wang L, Bai L, Deng Z. Asm8, a specific LAL-type activator of 3-amino-5-hydroxybenzoate biosynthesis in ansamitocin production. SCIENCE CHINA-LIFE SCIENCES 2013; 56:601-8. [PMID: 23832249 DOI: 10.1007/s11427-013-4502-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 05/28/2013] [Indexed: 11/25/2022]
Abstract
The highly potent antitumor agent ansamitocin P3 is a macrolactam isolated from Actinosynnema pretiosum ATCC 31565. A 120-kb DNA fragment was previously identified as the ansamitocin biosynthetic gene cluster, and contains genes for polyketide assembly, precursor synthesis, post-polyketide synthesis modification, and regulation. Within the biosynthetic gene cluster, asm8 encodes an 1117-amino-acid protein with a high degree of similarity to the large ATP-binding LuxR family-type regulators. In the current study, we determined that inactivation of asm8 by gene replacement in ATCC 31565 resulted in the complete loss of ansamitocin production, and that complementation with a cloned asm8 gene restored ansamitocin biosynthesis. Interestingly, the disruption of asm8 decreased the transcription of genes responsible for 3-amino-5-hydroxybenzoate (AHBA) formation, the starter unit required for ansamitocin biosynthesis. Subsequently, feeding of exogenous AHBA to the asm8 mutant restored ansamitocin biosynthesis, which showed that Asm8 is a specific positive regulator in AHBA biosynthesis. In addition, investigation of asm8 homologs identified two new ansamitocin producers, and inactivation of the asm8 homolog in A. pretiosum ATCC 31280 abolished ansamitocin production in this strain. Characterization of the positive regulator Asm8 and discovery of the two new ansamitocin producers paves the way for further improving production of this important antitumor agent.
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Affiliation(s)
- Wenqin Pan
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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13
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Kitson RRA, Moody CJ. Learning from nature: advances in geldanamycin- and radicicol-based inhibitors of Hsp90. J Org Chem 2013; 78:5117-41. [PMID: 23496136 DOI: 10.1021/jo4002849] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural products have been fundamental in the development of new therapeutic agents predicated on the inhibition of heat shock protein 90 (Hsp90). This Perspective describes the influential role of the benzoquinone ansamycin geldanamycin and the resorcylic acid macrolactone radicicol not only in driving forward drug discovery programs but also in inspiring organic chemists to develop innovative methodology for the synthesis of natural products and analogues with improved properties.
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Affiliation(s)
- Russell R A Kitson
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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14
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Struck AW, Thompson ML, Wong LS, Micklefield J. S-Adenosyl-Methionine-Dependent Methyltransferases: Highly Versatile Enzymes in Biocatalysis, Biosynthesis and Other Biotechnological Applications. Chembiochem 2012. [DOI: 10.1002/cbic.201200556] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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16
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Dual Carbamoylations on the Polyketide and Glycosyl Moiety by Asm21 Result in Extended Ansamitocin Biosynthesis. ACTA ACUST UNITED AC 2011; 18:1571-80. [DOI: 10.1016/j.chembiol.2011.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 10/29/2011] [Accepted: 11/07/2011] [Indexed: 11/23/2022]
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