1
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Gade M, Gardner JM, Jain P, Laurino P. Nucleoside-Driven Specificity of DNA Methyltransferase. Chembiochem 2023; 24:e202300094. [PMID: 37548117 DOI: 10.1002/cbic.202300094] [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: 02/05/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/08/2023]
Abstract
We have studied the adenosine binding specificities of two bacterial DNA methyltransferases, Taq methyltransferase (M.TaqI), and HhaI methyltransferase (M.HhaI). While they have similar cofactor binding pocket interactions, experimental data showed different specificity for novel S-nucleobase-l-methionine cofactors (SNMs; N=guanosyl, cytidyl, uridyl). Protein dynamics corroborate the experimental data on the cofactor specificities. For M.TaqI the specificity for S-adenosyl-l-methionine (SAM) is governed by the tight binding on the nucleoside part of the cofactor, while for M.HhaI the degree of freedom of the nucleoside chain allows the acceptance of other bases. The experimental data prove catalytically productive methylation by the M.HhaI binding pocket for all the SNMs. Our results suggest a new route for successful design of unnatural SNM analogues for methyltransferases as a tool for cofactor engineering.
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Affiliation(s)
- Madhuri Gade
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Jasmine M Gardner
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23, Uppsala, Sweden
| | - Prashant Jain
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna, Okinawa, 904-0495, Japan
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2
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Michailidou F. Engineering of Therapeutic and Detoxifying Enzymes. Angew Chem Int Ed Engl 2023; 62:e202308814. [PMID: 37433049 DOI: 10.1002/anie.202308814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 07/13/2023]
Abstract
Therapeutic enzymes present excellent opportunities for the treatment of human disease, modulation of metabolic pathways and system detoxification. However, current use of enzyme therapy in the clinic is limited as naturally occurring enzymes are seldom optimal for such applications and require substantial improvement by protein engineering. Engineering strategies such as design and directed evolution that have been successfully implemented for industrial biocatalysis can significantly advance the field of therapeutic enzymes, leading to biocatalysts with new-to-nature therapeutic activities, high selectivity, and suitability for medical applications. This minireview highlights case studies of how state-of-the-art and emerging methods in protein engineering are explored for the generation of therapeutic enzymes and discusses gaps and future opportunities in the field of enzyme therapy.
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Affiliation(s)
- Freideriki Michailidou
- Department of Health Sciences and Technology, ETH Zurich, Schmelzbergstrasse 9, 8092, Zürich, Switzerland
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3
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Hartstock K, Kueck NA, Spacek P, Ovcharenko A, Hüwel S, Cornelissen NV, Bollu A, Dieterich C, Rentmeister A. MePMe-seq: antibody-free simultaneous m 6A and m 5C mapping in mRNA by metabolic propargyl labeling and sequencing. Nat Commun 2023; 14:7154. [PMID: 37935679 PMCID: PMC10630376 DOI: 10.1038/s41467-023-42832-z] [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: 03/04/2022] [Accepted: 10/23/2023] [Indexed: 11/09/2023] Open
Abstract
Internal modifications of mRNA have emerged as widespread and versatile regulatory mechanism to control gene expression at the post-transcriptional level. Most of these modifications are methyl groups, making S-adenosyl-L-methionine (SAM) a central metabolic hub. Here we show that metabolic labeling with a clickable metabolic precursor of SAM, propargyl-selenohomocysteine (PSH), enables detection and identification of various methylation sites. Propargylated A, C, and G nucleosides form at detectable amounts via intracellular generation of the corresponding SAM analogue. Integration into next generation sequencing enables mapping of N6-methyladenosine (m6A) and 5-methylcytidine (m5C) sites in mRNA with single nucleotide precision (MePMe-seq). Analysis of the termination profiles can be used to distinguish m6A from 2'-O-methyladenosine (Am) and N1-methyladenosine (m1A) sites. MePMe-seq overcomes the problems of antibodies for enrichment and sequence-motifs for evaluation, which was limiting previous methodologies. Metabolic labeling via clickable SAM facilitates the joint evaluation of methylation sites in RNA and potentially DNA and proteins.
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Affiliation(s)
- Katja Hartstock
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nadine A Kueck
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Petr Spacek
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Sabine Hüwel
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Amarnath Bollu
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Heidelberg, Germany
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Berlin, Germany
| | - Andrea Rentmeister
- Institute of Biochemistry, Faculty of Chemistry and Pharmacy, University of Münster, Corrensstraße 36, 48149, Münster, Germany.
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4
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Bastidas Ángel AY, Campos PRO, Alberto EE. Synthetic application of chalcogenonium salts: beyond sulfonium. Org Biomol Chem 2023; 21:223-236. [PMID: 36503911 DOI: 10.1039/d2ob01822e] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The application of chalcogenonium salts in organic synthesis has grown enormously in the past decades since the discovery of the methyltransferase enzyme cofactor S-adenosyl-L-methionine (SAM), featuring a sulfonium center as the reactive functional group. Chalcogenonium salts can be employed as alkylating agents, sources of ylides and carbon-centered radicals, partners for metal-catalyzed cross-coupling reactions and organocatalysts. Herein, we will focus the discussion on heavier chalcogenonium salts (selenonium and telluronium), presenting their utility in synthetic organic transformations and, whenever possible, drawing comparisons in terms of reactivity and selectivity with the respective sulfonium analogues.
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Affiliation(s)
- Alix Y Bastidas Ángel
- Grupo de Síntese e Catálise Orgânica - GSCO, Departamento de Química, Universidade Federal de Minas Gerais - UFMG, 31.270-901, Belo Horizonte, MG, Brazil.
| | - Philipe Raphael O Campos
- Grupo de Síntese e Catálise Orgânica - GSCO, Departamento de Química, Universidade Federal de Minas Gerais - UFMG, 31.270-901, Belo Horizonte, MG, Brazil.
| | - Eduardo E Alberto
- Grupo de Síntese e Catálise Orgânica - GSCO, Departamento de Química, Universidade Federal de Minas Gerais - UFMG, 31.270-901, Belo Horizonte, MG, Brazil.
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5
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Erguven M, Cornelissen NV, Peters A, Karaca E, Rentmeister A. Enzymatic Generation of Double-Modified AdoMet Analogues and Their Application in Cascade Reactions with Different Methyltransferases. Chembiochem 2022; 23:e202200511. [PMID: 36288101 PMCID: PMC10100234 DOI: 10.1002/cbic.202200511] [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: 09/01/2022] [Revised: 10/26/2022] [Indexed: 01/25/2023]
Abstract
Methyltransferases (MTases) have become an important tool for site-specific alkylation and biomolecular labelling. In biocatalytic cascades with methionine adenosyltransferases (MATs), transfer of functional moieties has been realized starting from methionine analogues and ATP. However, the widespread use of S-adenosyl-l-methionine (AdoMet) and the abundance of MTases accepting sulfonium centre modifications limit selective modification in mixtures. AdoMet analogues with additional modifications at the nucleoside moiety bear potential for acceptance by specific MTases. Here, we explored the generation of double-modified AdoMets by an engineered Methanocaldococcus jannaschii MAT (PC-MjMAT), using 19 ATP analogues in combination with two methionine analogues. This substrate screening was extended to cascade reactions and to MTase competition assays. Our results show that MTase targeting selectivity can be improved by using bulky substituents at the N6 of adenine. The facile access to >10 new AdoMet analogues provides the groundwork for developing MAT-MTase cascades for orthogonal biomolecular labelling.
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Affiliation(s)
- Mehmet Erguven
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
- Cells in Motion Interfaculty CentreUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
| | - Nicolas V. Cornelissen
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
| | - Aileen Peters
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center35330IzmirTurkey
- Izmir International Biomedicine and Genome InstituteDokuz Eylul University, 35340 Izmir (Turkey)
| | - Andrea Rentmeister
- Department of Chemistry and PharmacyInstitute of BiochemistryUniversity of MünsterCorrensstr. 36, 48149MünsterGermany
- Cells in Motion Interfaculty CentreUniversity of MünsterWaldeyerstraße 1548149MünsterGermany
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6
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Abdelraheem E, Thair B, Varela RF, Jockmann E, Popadić D, Hailes HC, Ward JM, Iribarren AM, Lewkowicz ES, Andexer JN, Hagedoorn PL, Hanefeld U. Methyltransferases, functions and applications. Chembiochem 2022; 23:e202200212. [PMID: 35691829 PMCID: PMC9539859 DOI: 10.1002/cbic.202200212] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/10/2022] [Indexed: 11/25/2022]
Abstract
In this review the current state‐of‐the‐art of S‐adenosylmethionine (SAM)‐dependent methyltransferases and SAM are evaluated. Their structural classification and diversity is introduced and key mechanistic aspects presented which are then detailed further. Then, catalytic SAM as a target for drugs, and approaches to utilise SAM as a cofactor in synthesis are introduced with different supply and regeneration approaches evaluated. The use of SAM analogues are also described. Finally O‐, N‐, C‐ and S‐MTs, their synthetic applications and potential for compound diversification is given.
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Affiliation(s)
| | - Benjamin Thair
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - Romina Fernández Varela
- Universidad nacional di Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Emely Jockmann
- Albert-Ludwigs-Universitat Freiburg Universitatsbibliothek Freiburg, Pharmacie, GERMANY
| | | | - Helen C Hailes
- University College London Faculty of Mathematical and Physical Sciences, department of Chemistry, UNITED KINGDOM
| | - John M Ward
- University College London, Department of Biochemical Engineering, UNITED KINGDOM
| | - Adolfo M Iribarren
- Universidad Nacional de Quilmes, 3Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | - Elizabeth S Lewkowicz
- Universidad Nacional de Quilmes, Laboratorio de Biotransformaciones y Química de Ácidos Nucleicos, ARGENTINA
| | | | | | - Ulf Hanefeld
- Technische Universiteit Delft, Gebouw voor Scheikunde, Julianalaan 136, 2628 BL, Delft, NETHERLANDS
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7
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Liu D, Shu X, Xiang S, Li T, Huang C, Cheng M, Cao J, Hua Y, Liu J. N4 -allyldeoxycytidine: A New DNA Tag with Chemical Sequencing Power for Pinpointing Labelling Sites, Mapping Epigenetic Mark, and in situ Imaging. Chembiochem 2022; 23:e202200143. [PMID: 35438823 DOI: 10.1002/cbic.202200143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Indexed: 11/08/2022]
Abstract
DNA tagging with base analogs has found numerous applications. To precisely record the DNA labelling information, it will be highly beneficial to develop chemical sequencing tags that can be encoded into DNA as regular bases and decoded as mutant bases upon a mild, efficient and bioorthognal chemical treatment. Here we reported such a DNA tag, N4-allyldeoxycytidine (a4dC), to label and identify DNA by in vitro assays. The iodination of a4dC led to fast and complete formation of 3, N4-cyclized deoxycytidine, which induced base misincorporation during DNA replication and thus could be located at single base resolution. We explored the applications of a4dC in pinpointing DNA labelling sites at single base resolution, mapping epigenetic mark N4-methyldeoxycytidine, and imaging nucleic acids in situ. In addition, mammalian cellular DNA could be metabolically labelled with a4dC. Together,our study sheds light on the design of next generation DNA tags with chemical sequencing power.
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Affiliation(s)
- Donghong Liu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Xiao Shu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Siying Xiang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Tengwei Li
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Chenyang Huang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Mohan Cheng
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Jie Cao
- Zhejiang University, Life Sciences Institute; Department of Polymer Science and Engineering, CHINA
| | - Yuejin Hua
- Zhejiang University, he MOE Key Laboratory of Biosystems Homeostasis & Protection; Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, CHINA
| | - Jianzhao Liu
- Zhejiang University, Department of Polymer Science and Engineering, Zheda road 38, 310007, hangzhou, CHINA
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8
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Rudenko AY, Mariasina SS, Sergiev PV, Polshakov VI. Analogs of S-Adenosyl-L-Methionine in Studies of Methyltransferases. Mol Biol 2022; 56:229-250. [PMID: 35440827 PMCID: PMC9009987 DOI: 10.1134/s002689332202011x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/02/2023]
Abstract
Methyltransferases (MTases) play an important role in the functioning of living systems, catalyzing the methylation reactions of DNA, RNA, proteins, and small molecules, including endogenous compounds and drugs. Many human diseases are associated with disturbances in the functioning of these enzymes; therefore, the study of MTases is an urgent and important task. Most MTases use the cofactor S‑adenosyl‑L‑methionine (SAM) as a methyl group donor. SAM analogs are widely applicable in the study of MTases: they are used in studies of the catalytic activity of these enzymes, in identification of substrates of new MTases, and for modification of the substrates or substrate linking to MTases. In this review, new synthetic analogs of SAM and the problems that can be solved with their usage are discussed.
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Affiliation(s)
- A. Yu. Rudenko
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Zelinsky Institute of Organic Chemistry, 119991 Moscow, Russia
| | - S. S. Mariasina
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - V. I. Polshakov
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
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9
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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10
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Martins NS, Ángel AYB, Anghinoni JM, Lenardão EJ, Barcellos T, Alberto EE. From Stoichiometric Reagents to Catalytic Partners: Selenonium Salts as Alkylating Agents for Nucleophilic Displacement Reactions in Water. Adv Synth Catal 2022. [DOI: 10.1002/adsc.202100797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Nayara Silva Martins
- Grupo de Síntese e Catálise Orgânica – GSCO Departamento de Química Universidade Federal de Minas Gerais – UFMG 31.270-901 Belo Horizonte, MG Brazil
| | - Alix Y. Bastidas Ángel
- Grupo de Síntese e Catálise Orgânica – GSCO Departamento de Química Universidade Federal de Minas Gerais – UFMG 31.270-901 Belo Horizonte, MG Brazil
| | - João M. Anghinoni
- Laboratório de Síntese Orgânica Limpa – LASOL CCQFA Universidade Federal de Pelotas – UFPel P.O. box 354 96010-900 Pelotas, RS Brazil
| | - Eder J. Lenardão
- Laboratório de Síntese Orgânica Limpa – LASOL CCQFA Universidade Federal de Pelotas – UFPel P.O. box 354 96010-900 Pelotas, RS Brazil
| | - Thiago Barcellos
- Laboratory of Biotechnology of Natural and Synthetic Products Universidade de Caxias do Sul 95070-560 Caxias do Sul, RS Brazil
| | - Eduardo E. Alberto
- Grupo de Síntese e Catálise Orgânica – GSCO Departamento de Química Universidade Federal de Minas Gerais – UFMG 31.270-901 Belo Horizonte, MG Brazil
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11
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Gade M, Tan LL, Damry AM, Sandhu M, Brock JS, Delaney A, Villar-Briones A, Jackson CJ, Laurino P. Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. JACS AU 2021; 1:2349-2360. [PMID: 34977903 PMCID: PMC8715544 DOI: 10.1021/jacsau.1c00464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 05/14/2023]
Abstract
Protein conformational changes can facilitate the binding of noncognate substrates and underlying promiscuous activities. However, the contribution of substrate conformational dynamics to this process is comparatively poorly understood. Here, we analyze human (hMAT2A) and Escherichia coli (eMAT) methionine adenosyltransferases that have identical active sites but different substrate specificity. In the promiscuous hMAT2A, noncognate substrates bind in a stable conformation to allow catalysis. In contrast, noncognate substrates sample stable productive binding modes less frequently in eMAT owing to altered mobility in the enzyme active site. Different cellular concentrations of substrates likely drove the evolutionary divergence of substrate specificity in these orthologues. The observation of catalytic promiscuity in hMAT2A led to the detection of a new human metabolite, methyl thioguanosine, that is produced at elevated levels in a cancer cell line. This work establishes that identical active sites can result in different substrate specificity owing to the effects of substrate and enzyme dynamics.
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Affiliation(s)
- Madhuri Gade
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Li Lynn Tan
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Adam M. Damry
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Mahakaran Sandhu
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Joseph S. Brock
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | - Andie Delaney
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Alejandro Villar-Briones
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, ACT, Australia
- Australian
Research Council Centre of Excellence in Synthetic Biology, Research
School of Chemistry, Australian National
University, Canberra 2601, ACT, Australia
| | - Paola Laurino
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
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12
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Jouffroy L, Verhoeven J, Brambilla M, Verniest G, Kong H, Zhao Y, Wang W, Meerpoel L, Thuring JW, Winne JM. Regio- and Stereoselective Synthesis of C-4' Spirocyclobutyl Ribofuranose Scaffolds and Their Use as Biologically Active Nucleoside Analogues. Org Lett 2021; 23:8828-8833. [PMID: 34730365 DOI: 10.1021/acs.orglett.1c03334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Novel C-4',C-5' cyclobutane-fused spirocyclic ribonucleoside analogues were prepared. Thermal [2 + 2] cycloaddition between dichloroketene and readily derived 4'-exo-methylene furanoses afforded a first entry to the required constrained ribofuranoses, relying on a carbonyl transposition sequence. Alternatively, an unusual stereoselective ionic [2 + 2] cycloaddition using methyl propiolate promoted by methylaluminoxane gave a complementary, more direct approach to such ribofuranoses. Further conversion to the constrained adenosine analogues revealed promising structure-dependent inhibition of the protein methyltransferase PRMT5:MEP50 complex in the (sub)micromolar range.
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Affiliation(s)
- Lucile Jouffroy
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, Krijgslaan 281-S4, 9000 Gent, Belgium
| | - Jonas Verhoeven
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium.,Research Group of Organic Chemistry (ORGC), Department of Chemistry and Department of Bio-engineering Sciences, Faculty of Science and Bio-engineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Marta Brambilla
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Guido Verniest
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium.,Research Group of Organic Chemistry (ORGC), Department of Chemistry and Department of Bio-engineering Sciences, Faculty of Science and Bio-engineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Hanchu Kong
- Department of Synthetic Chemistry, Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | - Yongbin Zhao
- Department of Synthetic Chemistry, Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | - Wenbin Wang
- Department of Synthetic Chemistry, Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | - Lieven Meerpoel
- Janssen Pharmaceutica NV, Turnhoutseweg 30, 2340 Beerse, Belgium
| | | | - Johan M Winne
- Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, Krijgslaan 281-S4, 9000 Gent, Belgium
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13
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Peters A, Herrmann E, Cornelissen NV, Klöcker N, Kümmel D, Rentmeister A. Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases. Chembiochem 2021; 23:e202100437. [PMID: 34606675 PMCID: PMC9298006 DOI: 10.1002/cbic.202100437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/01/2021] [Indexed: 12/20/2022]
Abstract
Methylation and demethylation of DNA, RNA and proteins constitutes a major regulatory mechanism in epigenetic processes. Investigations would benefit from the ability to install photo‐cleavable groups at methyltransferase target sites that block interactions with reader proteins until removed by non‐damaging light in the visible spectrum. Engineered methionine adenosyltransferases (MATs) have been exploited in cascade reactions with methyltransferases (MTases) to modify biomolecules with non‐natural groups, including first evidence for accepting photo‐cleavable groups. We show that an engineered MAT from Methanocaldococcus jannaschii (PC‐MjMAT) is 308‐fold more efficient at converting ortho‐nitrobenzyl‐(ONB)‐homocysteine than the wildtype enzyme. PC‐MjMAT is active over a broad range of temperatures and compatible with MTases from mesophilic organisms. We solved the crystal structures of wildtype and PC‐MjMAT in complex with AdoONB and a red‐shifted derivative thereof. These structures reveal that aromatic stacking interactions within the ligands are key to accommodating the photocaging groups in PC‐MjMAT. The enlargement of the binding pocket eliminates steric clashes to enable AdoMet analogue binding. Importantly, PC‐MjMAT exhibits remarkable activity on methionine analogues with red‐shifted ONB‐derivatives enabling photo‐deprotection of modified DNA by visible light.
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Affiliation(s)
- Aileen Peters
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Eric Herrmann
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nils Klöcker
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
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14
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Tang Q, Pavlidis IV, Badenhorst CPS, Bornscheuer UT. From Natural Methylation to Versatile Alkylations Using Halide Methyltransferases. Chembiochem 2021; 22:2584-2590. [PMID: 33890381 PMCID: PMC8453949 DOI: 10.1002/cbic.202100153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Indexed: 11/06/2022]
Abstract
Halide methyltransferases (HMTs) enable the enzymatic synthesis of S-adenosyl-l-methionine (SAM) from S-adenosyl-l-homocysteine (SAH) and methyl iodide. Characterisation of a range of naturally occurring HMTs and subsequent protein engineering led to HMT variants capable of synthesising ethyl, propyl, and allyl analogues of SAM. Notably, HMTs do not depend on chemical synthesis of methionine analogues, as required by methionine adenosyltransferases (MATs). However, at the moment MATs have a much broader substrate scope than the HMTs. Herein we provide an overview of the discovery and engineering of promiscuous HMTs and how these strategies will pave the way towards a toolbox of HMT variants for versatile chemo- and regioselective biocatalytic alkylations.
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Affiliation(s)
- Qingyun Tang
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417489GreifswaldGermany
| | - Ioannis V. Pavlidis
- Dept. of ChemistryUniversity of CreteVoutes University Campus70013HeraklionGreece
| | | | - Uwe T. Bornscheuer
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417489GreifswaldGermany
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15
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Popadić D, Mhaindarkar D, Dang Thai MHN, Hailes HC, Mordhorst S, Andexer JN. A bicyclic S-adenosylmethionine regeneration system applicable with different nucleosides or nucleotides as cofactor building blocks. RSC Chem Biol 2021; 2:883-891. [PMID: 34179784 PMCID: PMC8190896 DOI: 10.1039/d1cb00033k] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022] Open
Abstract
The ubiquitous cofactor S-adenosyl-l-methionine (SAM) is part of numerous biochemical reactions in metabolism, epigenetics, and cancer development. As methylation usually improves physiochemical properties of compounds relevant for pharmaceutical use, the sustainable use of SAM as a methyl donor in biotechnological applications is an important goal. SAM-dependent methyltransferases are consequently an emerging biocatalytic tool for environmentally friendly and selective alkylations. However, SAM shows undesirable characteristics such as degradation under mild conditions and its stoichiometric use is economically not reasonable. Here, we report an optimised biomimetic system for the regeneration of SAM and SAM analogues consisting of effective nucleoside triphosphate formation and an additional l-methionine regeneration cycle without by-product accumulation. The bicyclic system uses seven enzymes, S-methylmethionine as methyl donor and a surplus of inorganic polyphosphate, along with catalytic amounts of l-methionine and cofactor building block reaching conversions of up to 99% (up to 200 turnovers). We also show that the cycle can be run with cofactor building blocks containing different purine and pyrimidine nucleobases, which can be fed in at the nucleoside or nucleotide stage. These alternative cofactors are in turn converted to the corresponding SAM analogues, which are considered to be a key for the development of bioorthogonal systems. In addition to purified enzymes, the bicyclic system can also be used with crude lysates highlighting its broad biocatalytic applicability.
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Affiliation(s)
- Désirée Popadić
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstr. 25 79104 Freiburg Germany
| | - Dipali Mhaindarkar
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstr. 25 79104 Freiburg Germany
| | - Mike H N Dang Thai
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstr. 25 79104 Freiburg Germany
| | - Helen C Hailes
- Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Silja Mordhorst
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstr. 25 79104 Freiburg Germany
| | - Jennifer N Andexer
- Institute of Pharmaceutical Sciences, University of Freiburg Albertstr. 25 79104 Freiburg Germany
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16
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Michailidou F, Rentmeister A. Harnessing methylation and AdoMet-utilising enzymes for selective modification in cascade reactions. Org Biomol Chem 2021; 19:3756-3762. [PMID: 33949607 DOI: 10.1039/d1ob00354b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Enzyme-mediated methylation is a very important reaction in nature, yielding a wide range of modified natural products, diversifying small molecules and fine-tuning the activity of biomacromolecules. The field has attracted much attention over the recent years and interesting applications of the dedicated enzymes in biocatalysis and biomolecular labelling have emerged. In this review article, we summarise the concepts and recent advances in developing (chemo)-enzymatic cascades for selective methylation, alkylation and photocaging as tools to study biological methylation and as biotransformations to generate site-specifically alkylated products.
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Affiliation(s)
- Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 481\49 Münster, Germany.
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 481\49 Münster, Germany.
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17
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Xiang S, Gao M, Cao J, Shu X, Cheng M, Wang F, Deng T, Liu J. Precise identification of an RNA methyltransferase's substrate modification site. Chem Commun (Camb) 2021; 57:2499-2502. [DOI: 10.1039/d0cc08260k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A simple and nonradioactive method to probe the substrate modification site and structural preference of an RNA methyltransferase.
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Affiliation(s)
- Siying Xiang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Mohan Cheng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
| | - Fengqin Wang
- College of Animal Sciences
- Key Laboratory of Animal Nutrition & Feed Sciences
- Ministry of Agriculture
- Zhejiang University
- Hangzhou
| | - Ting Deng
- State Key Laboratory of Genetic Engineering
- Collaborative Innovation Centre of Genetics and Development
- Department of Biochemistry
- Institute of Plant Biology
- School of Life Sciences
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization
- Department of Polymer Science and Engineering
- Zhejiang University
- Hangzhou
- China
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18
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Maßgeschneiderte SAM‐Synthetasen zur enzymatischen Herstellung von AdoMet‐Analoga mit Photoschutzgruppen und zur reversiblen DNA‐Modifizierung in Kaskadenreaktionen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012623] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Freideriki Michailidou
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
- Derzeitige Adresse: ETH Zürich Fachbereich Chemie und angewandte Biowissenschaften Laboratorium für Organische Chemie Vladimir-Prelog-Weg 1–5/10 8093 Zürich Schweiz
| | - Nils Klöcker
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Nicolas V. Cornelissen
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Rohit K. Singh
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Aileen Peters
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Anna Ovcharenko
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Daniel Kümmel
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Fachbereich Chemie Institut für Biochemie Universität von Münster Corrensstr. 36 48149 Münster Deutschland
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19
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Michailidou F, Klöcker N, Cornelissen NV, Singh RK, Peters A, Ovcharenko A, Kümmel D, Rentmeister A. Engineered SAM Synthetases for Enzymatic Generation of AdoMet Analogs with Photocaging Groups and Reversible DNA Modification in Cascade Reactions. Angew Chem Int Ed Engl 2020; 60:480-485. [PMID: 33017502 PMCID: PMC7839696 DOI: 10.1002/anie.202012623] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Indexed: 12/17/2022]
Abstract
Methylation and demethylation of DNA, RNA and proteins has emerged as a major regulatory mechanism. Studying the function of these modifications would benefit from tools for their site‐specific inhibition and timed removal. S‐Adenosyl‐L‐methionine (AdoMet) analogs in combination with methyltransferases (MTases) have proven useful to map or block and release MTase target sites, however their enzymatic generation has been limited to aliphatic groups at the sulfur atom. We engineered a SAM synthetase from Cryptosporidium hominis (PC‐ChMAT) for efficient generation of AdoMet analogs with photocaging groups that are not accepted by any WT MAT reported to date. The crystal structure of PC‐ChMAT at 1.87 Å revealed how the photocaged AdoMet analog is accommodated and guided engineering of a thermostable MAT from Methanocaldococcus jannaschii. PC‐MATs were compatible with DNA‐ and RNA‐MTases, enabling sequence‐specific modification (“writing”) of plasmid DNA and light‐triggered removal (“erasing”).
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Affiliation(s)
- Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany.,Current address: ETH Zürich, Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 1-5/10, 8093, Zürich, Switzerland
| | - Nils Klöcker
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Rohit K Singh
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Aileen Peters
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Anna Ovcharenko
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Daniel Kümmel
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Münster, Corrensstr. 36, 48149, Münster, Germany
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20
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21
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Mordhorst S, Andexer JN. Round, round we go - strategies for enzymatic cofactor regeneration. Nat Prod Rep 2020; 37:1316-1333. [PMID: 32582886 DOI: 10.1039/d0np00004c] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Covering: up to the beginning of 2020Enzymes depending on cofactors are essential in many biosynthetic pathways of natural products. They are often involved in key steps: catalytic conversions that are difficult to achieve purely with synthetic organic chemistry. Hence, cofactor-dependent enzymes have great potential for biocatalysis, on the condition that a corresponding cofactor regeneration system is available. For some cofactors, these regeneration systems require multiple steps; such complex enzyme cascades/multi-enzyme systems are (still) challenging for in vitro biocatalysis. Further, artificial cofactor analogues have been synthesised that are more stable, show an altered reaction range, or act as inhibitors. The development of bio-orthogonal systems that can be used for the production of modified natural products in vivo is an ongoing challenge. In light of the recent progress in this field, this review aims to provide an overview of general strategies involving enzyme cofactors, cofactor analogues, and regeneration systems; highlighting the current possibilities for application of enzymes using some of the most common cofactors.
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Affiliation(s)
- Silja Mordhorst
- Institute of Microbiology, ETH Zürich, Vladimir-Prelog-Weg 1-5/10, 8093 Zürich, Switzerland
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22
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McKean IJW, Hoskisson PA, Burley GA. Biocatalytic Alkylation Cascades: Recent Advances and Future Opportunities for Late‐Stage Functionalization. Chembiochem 2020; 21:2890-2897. [DOI: 10.1002/cbic.202000187] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/22/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Iain J. W. McKean
- Department of Pure & Applied Chemistry University of Strathclyde 295 Cathedral Street Glasgow G1 1XL United Kingdom
| | - Paul A. Hoskisson
- Strathclyde Institute of Pharmacy & Biomedical Sciences University of Strathclyde 161 Cathedral Street Glasgow G4 0RE United Kingdom
| | - Glenn A. Burley
- Department of Pure & Applied Chemistry University of Strathclyde 295 Cathedral Street Glasgow G1 1XL United Kingdom
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