1
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Rudenko AY, Mariasina SS, Bolikhova AK, Nikulin MV, Ozhiganov RM, Vasil'ev VG, Ikhalaynen YA, Khandazhinskaya AL, Khomutov MA, Sergiev PV, Khomutov AR, Polshakov VI. Organophosphorus S-adenosyl- L-methionine mimetics: synthesis, stability, and substrate properties. Front Chem 2024; 12:1448747. [PMID: 39148665 PMCID: PMC11325224 DOI: 10.3389/fchem.2024.1448747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 07/11/2024] [Indexed: 08/17/2024] Open
Abstract
S-Adenosyl-l-methionine (SAM)-mediated methylation of biomolecules controls their function and regulates numerous vital intracellular processes. Analogs of SAM with a reporter group in place of the S-methyl group are widely used to study these processes. However, many of these analogs are chemically unstable that largely limits their practical application. We have developed a new compound, SAM-P H , which contains an H-phosphinic group (-P(O)(H)OH) instead of the SAM carboxylic group. SAM-P H is significantly more stable than SAM, retains functional activity in catechol-O-methyltransferase and methyltransferase WBSCR27 reactions. The last is associated with Williams-Beuren syndrome. Rac-SAM-P H was synthesized chemically, while (R,S)-SAM-P H and its analogs were prepared enzymatically either from H-phosphinic analogs of methionine (Met-PH) or H-phosphinic analog of S-adenosyl-l-homocysteine (SAH-P H ) using methionine adenosyltransferase 2A or halide methyltransferases, respectively. SAH-P H undergoes glycoside bond cleavage in the presence of methylthioadenosine nucleosidase like natural SAH. Thus, SAM-P H and its analogs are promising new tools for investigating methyltransferases and incorporating reporter groups into their substrates.
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Affiliation(s)
- Alexander Yu Rudenko
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
- Faculty of Fundamental Medicine, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Sofia S Mariasina
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
- Faculty of Fundamental Medicine, M. V. Lomonosov Moscow State University, Moscow, Russia
- Chemistry Department, M. V. Lomonosov Moscow State University, Moscow, Russia
- Research and Educational Resource Center "Pharmacy", RUDN University, Moscow, Russia
| | - Anastasiia K Bolikhova
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
- Chemistry Department, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Maxim V Nikulin
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Ratislav M Ozhiganov
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
- Higher Chemical College RAS, Mendeleev University of Chemical Technology, Moscow, Russia
| | - Vasiliy G Vasil'ev
- Research and Educational Resource Center "Pharmacy", RUDN University, Moscow, Russia
| | - Yuri A Ikhalaynen
- Chemistry Department, M. V. Lomonosov Moscow State University, Moscow, Russia
| | | | - Maxim A Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Peter V Sergiev
- Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
- Chemistry Department, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Alex R Khomutov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, M. V. Lomonosov Moscow State University, Moscow, Russia
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2
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Ditzel A, Zhao F, Gao X, Phillips GN. Utilizing a cell-free protein synthesis platform for the biosynthesis of a natural product, caffeine. Synth Biol (Oxf) 2023; 8:ysad017. [PMID: 38149044 PMCID: PMC10750991 DOI: 10.1093/synbio/ysad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 12/28/2023] Open
Abstract
Natural products are a valuable source of pharmaceuticals, providing a majority of the small-molecule drugs in use today. However, their production through organic synthesis or in heterologous hosts can be difficult and time-consuming. Therefore, to allow for easier screening and production of natural products, we demonstrated the use of a cell-free protein synthesis system to partially assemble natural products in vitro using S-Adenosyl Methionine (SAM)-dependent methyltransferase enzyme reactions. The tea caffeine synthase, TCS1, was utilized to synthesize caffeine within a cell-free protein synthesis system. Cell-free systems also provide the benefit of allowing the use of substrates that would normally be toxic in a cellular environment to synthesize novel products. However, TCS1 is unable to utilize a compound like S-adenosyl ethionine as a cofactor to create ethylated caffeine analogs. The automation and reduced metabolic engineering requirements of cell-free protein synthesis systems, in combination with other synthesis methods, may enable the more efficient generation of new compounds. Graphical Abstract.
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Affiliation(s)
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
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3
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Alexander AK, Elshahawi SI. Promiscuous Enzymes for Residue-Specific Peptide and Protein Late-Stage Functionalization. Chembiochem 2023; 24:e202300372. [PMID: 37338668 PMCID: PMC10496146 DOI: 10.1002/cbic.202300372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 06/21/2023]
Abstract
The late-stage functionalization of peptides and proteins holds significant promise for drug discovery and facilitates bioorthogonal chemistry. This selective functionalization leads to innovative advances in in vitro and in vivo biological research. However, it is a challenging endeavor to selectively target a certain amino acid or position in the presence of other residues containing reactive groups. Biocatalysis has emerged as a powerful tool for selective, efficient, and economical modifications of molecules. Enzymes that have the ability to modify multiple complex substrates or selectively install nonnative handles have wide applications. Herein, we highlight enzymes with broad substrate tolerance that have been demonstrated to modify a specific amino acid residue in simple or complex peptides and/or proteins at late-stage. The different substrates accepted by these enzymes are mentioned together with the reported downstream bioorthogonal reactions that have benefited from the enzymatic selective modifications.
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Affiliation(s)
- Ashley K Alexander
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
| | - Sherif I Elshahawi
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Rinker Health Science Campus, Irvine, CA 92618, USA
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4
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Ding W, Zhou M, Li H, Li M, Qiu Y, Yin Y, Pan L, Yang W, Du Y, Zhang X, Tang Z, Liu W. Biocatalytic Fluoroalkylation Using Fluorinated S-Adenosyl-l-methionine Cofactors. Org Lett 2023; 25:5650-5655. [PMID: 37490590 DOI: 10.1021/acs.orglett.3c02028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Modification of organic molecules with fluorine functionalities offers a critical approach to develop new pharmaceuticals. Here, we report a multienzyme strategy for biocatalytic fluoroalkylation using S-adenosyl-l-methionine (SAM)-dependent methyltransferases (MTs) and fluorinated SAM cofactors prepared from ATP and fluorinated l-methionine analogues by an engineered human methionine adenosyltransferase hMAT2AI322A. This work introduces the first example of biocatalytic 3,3-difluoroallylation. Importantly, this strategy can be applied to late-stage site-selective fluoroalkylation of complex molecule vancomycin with conversions up to 99%.
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Affiliation(s)
- Wenping Ding
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Minqi Zhou
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Huayu Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Miao Li
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yanping Qiu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Yu Yin
- School of Pharmacy, Shanghai Jiaotong University, Shanghai 200240, China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wenchao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Yanan Du
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xingang Zhang
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, China
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
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5
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Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
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6
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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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7
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Li W, Bilal M, Singh AK, Sher F, Ashraf SS, Franco M, Américo-Pinheiro JHP, Iqbal HMN. Broadening the Scope of Biocatalysis Engineering by Tailoring Enzyme Microenvironment: A Review. Catal Letters 2022. [DOI: 10.1007/s10562-022-04065-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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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: 35] [Impact Index Per Article: 17.5] [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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9
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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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10
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DNA Labeling Using DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:535-562. [DOI: 10.1007/978-3-031-11454-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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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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12
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Weiss N, Seneviranthe C, Jiang M, Wang K, Luo M. Profiling and Validation of Live-Cell Protein Methylation with Engineered Enzymes and Methionine Analogues. Curr Protoc 2021; 1:e213. [PMID: 34370893 DOI: 10.1002/cpz1.213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Protein methyltransferases (PMTs) regulate many aspects of normal and disease processes through substrate methylation, with S-adenosyl-L-methionine (SAM) as a cofactor. It has been challenging to elucidate cellular protein lysine and arginine methylation because these modifications barely alter physical properties of target proteins and often are context dependent, transient, and substoichiometric. To reveal bona fide methylation events associated with specific PMT activities in native contexts, we developed the live-cell Bioorthogonal Profiling of Protein Methylation (lcBPPM) technology, in which the substrates of specific PMTs are labeled by engineered PMTs inside living cells, with in situ-synthesized SAM analogues as cofactors. The biorthogonality of this technology is achieved because these SAM analogue cofactors can only be processed by the engineered PMTs-and not native PMTs-to modify the substrates with distinct chemical groups. Here, we describe the latest lcBPPM protocol and its application to reveal proteome-wide methylation and validate specific methylation events. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Live-cell labeling of substrates of protein methyltransferases GLP1 and PRMT1 with lcBPPM-feasible enzymes and SAM analogue precursors Support Protocol: Gram-scale synthesis of Hey-Met Basic Protocol 2: Click labeling of lcBPPM cell lysates with a biotin-azide probe Alternate Protocol: Click labeling of small-scale lcBPPM cell lysates with a TAMRA-azide dye for in-gel fluorescence visualization Basic Protocol 3: Enrichment of biotinylated lcBPPM proteome with streptavidin beads Basic Protocol 4: Proteome-wide identification of lcBPPM targets with mass spectrometry Basic Protocol 5: Validation of individual lcBPPM targets by western blot.
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Affiliation(s)
- Nicole Weiss
- BCMB Allied Program, Weill Cornell Medical College, Cornell University, New York, New York
| | - Chamara Seneviranthe
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ming Jiang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York
| | - Ke Wang
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, New York
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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 PMCID: PMC7611180 DOI: 10.1039/d1ob00354b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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14
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Jalali E, Thorson JS. Enzyme-mediated bioorthogonal technologies: catalysts, chemoselective reactions and recent methyltransferase applications. Curr Opin Biotechnol 2021; 69:290-298. [PMID: 33901763 DOI: 10.1016/j.copbio.2021.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/28/2022]
Abstract
Transferases have emerged as among the best catalysts for enzyme-mediated bioorthogonal functional group installation to advance innovative in vitro, cell-based and in vivo chemical biology applications. This review introduces the key considerations for selecting enzyme catalysts and chemoselective reactions most amenable to bioorthogonal platform development and highlights relevant key technology development and applications for one ubiquitous transferase subclass - methyltransferases (MTs). Within this context, recent advances in MT-enabled bioorthogonal labeling/conjugation relevant to DNA, RNA, protein, and natural products (i.e. complex small molecule metabolites) are highlighted.
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Affiliation(s)
- Elnaz Jalali
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY 40536, United States
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY 40536, United States; Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, Lexington, KY 40536, United States.
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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: 23] [Impact Index Per Article: 7.7] [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, 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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17
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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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18
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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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