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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Gao CY, Yang GY, Ding XW, Xu JH, Cheng X, Zheng GW, Chen Q. Engineering of Halide Methyltransferase BxHMT through Dynamic Cross-Correlation Network Analysis. Angew Chem Int Ed Engl 2024; 63:e202401235. [PMID: 38623716 DOI: 10.1002/anie.202401235] [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: 01/18/2024] [Revised: 03/18/2024] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
Halide methyltransferases (HMTs) provide an effective way to regenerate S-adenosyl methionine (SAM) from S-adenosyl homocysteine and reactive electrophiles, such as methyl iodide (MeI) and methyl toluene sulfonate (MeOTs). As compared with MeI, the cost-effective unnatural substrate MeOTs can be accessed directly from cheap and abundant alcohols, but shows only limited reactivity in SAM production. In this study, we developed a dynamic cross-correlation network analysis (DCCNA) strategy for quickly identifying hot spots influencing the catalytic efficiency of the enzyme, and applied it to the evolution of HMT from Paraburkholderia xenovorans. Finally, the optimal mutant, M4 (V55T/C125S/L127T/L129P), exhibited remarkable improvement, with a specific activity of 4.08 U/mg towards MeOTs, representing an 82-fold increase as compared to the wild-type (WT) enzyme. Notably, M4 also demonstrated a positive impact on the catalytic ability with other methyl donors. The structural mechanism behind the enhanced enzyme activity was uncovered by molecular dynamics simulations. Our work not only contributes a promising biocatalyst for the regeneration of SAM, but also offers a strategy for efficient enzyme engineering.
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Affiliation(s)
- Chun-Yu Gao
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Gui-Ying Yang
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Xu-Wei Ding
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, OH 43210, United States
| | - Gao-Wei Zheng
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
| | - Qi Chen
- State Key Laboratory of Bioreactor Engineering and Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, China
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3
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Schülke KH, Fröse JS, Klein A, Garcia-Borràs M, Hammer SC. Efficient Transferase Engineering for SAM Analog Synthesis from Iodoalkanes. Chembiochem 2024; 25:e202400079. [PMID: 38477872 DOI: 10.1002/cbic.202400079] [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: 01/29/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/14/2024]
Abstract
S-Adenosyl-l-methionine (SAM) is an important cosubstrate in various biochemical processes, including selective methyl transfer reactions. Simple methods for the (re)generation of SAM analogs could expand the chemistry accessible with SAM-dependent transferases and go beyond methylation reactions. Here we present an efficient enzyme engineering strategy to synthesize different SAM analogs from "off-the-shelf" iodoalkanes through enzymatic alkylation of S-adenosyl-l-homocysteine (SAH). This was achieved by mutating multiple hydrophobic and structurally dynamic amino acids simultaneously. Combinatorial mutagenesis was guided by the natural amino acid diversity and generated a highly functional mutant library. This approach increased the speed as well as the scale of enzyme engineering by providing a panel of optimized enzymes with orders of magnitude higher activities for multiple substrates in just one round of enzyme engineering. The optimized enzymes exhibit catalytic efficiencies up to 31 M-1 s-1, convert various iodoalkanes, including substrates bearing cyclopropyl or aromatic moieties, and catalyze S-alkylation of SAH with very high stereoselectivities (>99 % de). We further report a high throughput chromatographic screening system for reliable and rapid SAM analog analysis. We believe that the methods and enzymes described herein will further advance the field of selective biocatalytic alkylation chemistry by enabling SAM analog regeneration with "off-the-shelf" reagents.
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Affiliation(s)
- Kai H Schülke
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Jana S Fröse
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Alina Klein
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Marc Garcia-Borràs
- Department Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, 17003, Girona, Catalonia, Spain
| | - Stephan C Hammer
- Organic Chemistry and Biocatalysis, Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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4
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Yang E, Dalton DM. N1-Selective Methylation of Pyrazoles via α-Halomethylsilanes as Masked Methylating Reagents. J Org Chem 2024; 89:4221-4224. [PMID: 38422621 DOI: 10.1021/acs.joc.3c02841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
The development of a highly selective N-methylation of pyrazole heterocycles using commercially available, bench-stable α-halomethylsilanes as masked methylating reagents is described. Sterically bulky α-halomethylsilanes significantly improve the selectivity of N-alkylation over traditional methylating reagents and readily undergo protodesilylation in the presence of a fluoride source and water to give N-methyl pyrazoles. Selectivities of 92:8 to >99:1 N1/N2 regioisomeric ratios were achieved with a range of pyrazole substrates in good yields.
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Affiliation(s)
- Emma Yang
- Department of Small Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Derek M Dalton
- Department of Small Molecule Process Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
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5
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Ju S, Kuzelka KP, Guo R, Krohn-Hansen B, Wu J, Nair SK, Yang Y. A biocatalytic platform for asymmetric alkylation of α-keto acids by mining and engineering of methyltransferases. Nat Commun 2023; 14:5704. [PMID: 37709735 PMCID: PMC10502145 DOI: 10.1038/s41467-023-40980-w] [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: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023] Open
Abstract
Catalytic asymmetric α-alkylation of carbonyl compounds represents a long-standing challenge in synthetic organic chemistry. Herein, we advance a dual biocatalytic platform for the efficient asymmetric alkylation of α-keto acids. First, guided by our recently obtained crystal structures, we develop SgvMVAV as a general biocatalyst for the enantioselective methylation, ethylation, allylation and propargylation of a range of α-keto acids with total turnover numbers (TTNs) up to 4,600. Second, we mine a family of bacterial HMTs from Pseudomonas species sharing less than 50% sequence identities with known HMTs and evaluated their activities in SAM regeneration. Our best performing HMT from P. aeruginosa, PaHMT, displays the highest SAM regeneration efficiencies (TTN up to 7,700) among HMTs characterized to date. Together, the synergistic use of SgvMVAV and PaHMT affords a fully biocatalytic protocol for asymmetric methylation featuring a record turnover efficiency, providing a solution to the notorious problem of asymmetric alkylation.
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Affiliation(s)
- Shuyun Ju
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Kaylee P Kuzelka
- Department of Biochemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rui Guo
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Benjamin Krohn-Hansen
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Jianping Wu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA
| | - Satish K Nair
- Department of Biochemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA, USA.
- Biomolecular Science and Engineering (BMSE) Program, University of California, Santa Barbara, CA, USA.
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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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Ospina F, Schülke KH, Soler J, Klein A, Prosenc B, Garcia‐Borràs M, Hammer SC. Selective Biocatalytic N-Methylation of Unsaturated Heterocycles. Angew Chem Int Ed Engl 2022; 61:e202213056. [PMID: 36202763 PMCID: PMC9827881 DOI: 10.1002/anie.202213056] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Indexed: 11/19/2022]
Abstract
Methods for regioselective N-methylation and -alkylation of unsaturated heterocycles with "off the shelf" reagents are highly sought-after. This reaction could drastically simplify synthesis of privileged bioactive molecules. Here we report engineered and natural methyltransferases for challenging N-(m)ethylation of heterocycles, including benzimidazoles, benzotriazoles, imidazoles and indazoles. The reactions are performed through a cyclic enzyme cascade that consists of two methyltransferases using only iodoalkanes or methyl tosylate as simple reagents. This method enables the selective synthesis of important molecules that are otherwise difficult to access, proceeds with high regioselectivity (r.r. up to >99 %), yield (up to 99 %), on a preparative scale, and with nearly equimolar concentrations of simple starting materials.
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Affiliation(s)
- Felipe Ospina
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Kai H. Schülke
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Jordi Soler
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 69Girona17003CataloniaSpain
| | - Alina Klein
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Benjamin Prosenc
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
| | - Marc Garcia‐Borràs
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaCarrer Maria Aurèlia Capmany 69Girona17003CataloniaSpain
| | - Stephan C. Hammer
- Faculty of ChemistryOrganic Chemistry and BiocatalysisBielefeld UniversityUniversitätsstraße 2533615BielefeldGermany
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8
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Amariei DA, Pozhydaieva N, David B, Schneider P, Classen T, Gohlke H, Weiergräber OH, Pietruszka J. Enzymatic C3-Methylation of Indoles Using Methyltransferase PsmD─Crystal Structure, Catalytic Mechanism, and Preparative Applications. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Diana A. Amariei
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
| | - Nadiia Pozhydaieva
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
| | - Benoit David
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich 52426, Germany
| | - Pascal Schneider
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
| | - Thomas Classen
- Institute of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy Science Center (BioSC) Forschungszentrum Jülich, Jülich 52426, Germany
| | - Holger Gohlke
- Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich 52426, Germany
- Institute for Pharmaceutical and Medicinal Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf 40225, Germany
| | - Oliver H. Weiergräber
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich 52425, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry & Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf in Forschungszentrum Jülich, Jülich 52426, Germany
- Institute of Bio- and Geosciences (IBG-1: Bioorganic Chemistry) & Bioeconomy Science Center (BioSC) Forschungszentrum Jülich, Jülich 52426, Germany
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9
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Wen X, Leisinger F, Leopold V, Seebeck FP. Synthetic Reagents for Enzyme‐Catalyzed Methylation. Angew Chem Int Ed Engl 2022; 61:e202208746. [DOI: 10.1002/anie.202208746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaojin Wen
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| | - Florian Leisinger
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| | - Viviane Leopold
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
| | - Florian P. Seebeck
- Department of Chemistry University of Basel Mattenstrasse 24a 4002 Basel Switzerland
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10
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Leveson‐Gower RB, Roelfes G. Biocatalytic Friedel-Crafts Reactions. ChemCatChem 2022; 14:e202200636. [PMID: 36606067 PMCID: PMC9804301 DOI: 10.1002/cctc.202200636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/10/2022] [Indexed: 01/07/2023]
Abstract
Friedel-Crafts alkylation and acylation reactions are important methodologies in synthetic and industrial chemistry for the construction of aryl-alkyl and aryl-acyl linkages that are ubiquitous in bioactive molecules. Nature also exploits these reactions in many biosynthetic processes. Much work has been done to expand the synthetic application of these enzymes to unnatural substrates through directed evolution. The promise of such biocatalysts is their potential to supersede inefficient and toxic chemical approaches to these reactions, with mild operating conditions - the hallmark of enzymes. Complementary work has created many bio-hybrid Friedel-Crafts catalysts consisting of chemical catalysts anchored into biomolecular scaffolds, which display many of the same desirable characteristics. In this Review, we summarise these efforts, focussing on both mechanistic aspects and synthetic considerations, concluding with an overview of the frontiers of this field and routes towards more efficient and benign Friedel-Crafts reactions for the future of humankind.
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Affiliation(s)
| | - Gerard Roelfes
- Stratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
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11
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Wen X, Leisinger F, Leopold V, Seebeck FP. Synthetic reagents for enzyme‐catalyzed methylation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xiaojin Wen
- University of Basel: Universitat Basel Department of Chemistry SWITZERLAND
| | - Florian Leisinger
- University of Basel: Universitat Basel Department of Chemistry SWITZERLAND
| | - Viviane Leopold
- University of Basel: Universitat Basel Department of Chemistry SWITZERLAND
| | - Florian P. Seebeck
- University of Basel Department of Chemistry St. Johanns-Ring 19 4056 Basel SWITZERLAND
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12
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Fessner ND, Badenhorst CPS, Bornscheuer UT. Enzyme Kits to Facilitate the Integration of Biocatalysis into Organic Chemistry – First Aid for Synthetic Chemists. ChemCatChem 2022. [DOI: 10.1002/cctc.202200156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Nico D. Fessner
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Christoffel P. S. Badenhorst
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Uwe T. Bornscheuer
- Dept. of Biotechnology & Enzyme Catalysis Institute of Biochemistry University of Greifswald Felix-Hausdorff-Str. 4 17487 Greifswald Germany
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13
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Lankau T, Ken HC, Chang HM, Yu CH. A Computational Study of the Promiscuity of the SAM-Dependent Methyltransferase AtHTMT1. ACS OMEGA 2022; 7:12753-12764. [PMID: 35474790 PMCID: PMC9026064 DOI: 10.1021/acsomega.1c07327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
A two-pronged computational approach was taken to study the promiscuity of the SAM+-dependent methyl transferase AtHTMT1 from thale cress with several nucleophiles (Cl-, Br-, I-, NCO-, NCS-). First, enzyme-free methyl transfer reactions were studied with M05/6-311+G(2d,p) DFT calculations and electrostatic continuum models (PCM/SMD) for various chemical environments. Second, QM/MM MD simulations with semiempirical Hamiltonians (PM7, PM6-D3, AM1, PM6-D3H4) and the AMBER 14SB force field were used to study the enzyme catalyzed reaction in silico. The combination of the DFT and MD results shows that reactant desolvation generally accelerates the reaction, but it cannot explain the selectivity of the enzyme. The critical position of H2O molecules at the reactive site favors the reaction of NCS- over Cl- and Br- in agreement with experiments, but not observed in the quantum calculations for the cytosol. The addition of selected H2O molecules to the N terminus of NCS- greatly increases its reactivity, while H2O molecules attached to Cl- slow the reaction. The partial solvation of the nucleophiles in the reactive pouch holds the key to understanding the reactivity of AtHTMT1.
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Affiliation(s)
| | | | | | - Chin Hui Yu
- . Phone: +886 (0)3 5162080. Fax: +886 (0)3 5721534
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14
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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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15
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Schülke KH, Ospina F, Hörnschemeyer K, Gergel S, Hammer SC. Substrate profiling of anion methyltransferases for promiscuous synthesis of S-adenosylmethionine analogs from haloalkanes. Chembiochem 2021; 23:e202100632. [PMID: 34927779 PMCID: PMC9303522 DOI: 10.1002/cbic.202100632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/18/2021] [Indexed: 11/06/2022]
Abstract
Biocatalytic alkylation reactions can be performed with high chemo-, regio- and stereoselectivity using S -adenosyl-l-methionine (SAM)-dependent methyltransferases (MTs) and SAM analogs. Currently, however, this methodology is limited in application due to the rather laborious protocols to access SAM analogs. It has recently been shown that halide methyltransferases (HMTs) enable synthesis and recycling of SAM analogs with readily available haloalkanes as starting material. Here we expand this work by using substrate profiling of the anion MT enzyme family to explore promiscuous SAM analog synthesis. Our study shows that anion MTs are in general very promiscuous with respect to the alkyl chain as well as the halide leaving group. Substrate profiling further suggests that promiscuous anion MTs cluster in sequence space. Next to iodoalkanes, cheaper, less toxic and more available bromoalkanes have been converted and several haloalkanes bearing short alkyl groups, alkyl rings, and functional groups such as alkene, alkyne and aromatic moieties are accepted as substrates. Further, we applied the SAM analogs as electrophiles in enzyme-catalyzed regioselective pyrazole allylation with 3-bromopropene as starting material.
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Affiliation(s)
- Kai H Schülke
- Universität Bielefeld: Universitat Bielefeld, Fakultät für Chemie, GERMANY
| | - Felipe Ospina
- Universität Bielefeld: Universitat Bielefeld, Fakultät für Chemie, GERMANY
| | | | - Sebastian Gergel
- Universität Bielefeld: Universitat Bielefeld, Fakultät für Chemie, GERMANY
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Ospina F, Schülke KH, Hammer SC. Biocatalytic Alkylation Chemistry: Building Molecular Complexity with High Selectivity. Chempluschem 2021; 87:e202100454. [PMID: 34821073 DOI: 10.1002/cplu.202100454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/05/2021] [Indexed: 12/28/2022]
Abstract
Biocatalysis has traditionally been viewed as a field that primarily enables access to chiral centers. This includes the synthesis of chiral alcohols, amines and carbonyl compounds, often through functional group interconversion via hydrolytic or oxidation-reduction reactions. This limitation is partly being overcome by the design and evolution of new enzymes. Here, we provide an overview of a recently thriving research field that we summarize as biocatalytic alkylation chemistry. In the past 3-4 years, numerous new enzymes have been developed that catalyze sp3 C-C/N/O/S bond formations. These enzymes utilize different mechanisms to generate molecular complexity by coupling simple fragments with high activity and selectivity. In many cases, the engineered enzymes perform reactions that are difficult or impossible to achieve with current small-molecule catalysts such as organocatalysts and transition-metal complexes. This review further highlights that the design of new enzyme function is particularly successful when off-the-shelf synthetic reagents are utilized to access non-natural reactive intermediates. This underscores how biocatalysis is gradually moving to a field that build molecules through selective bond forming reactions.
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Affiliation(s)
- Felipe Ospina
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Kai H Schülke
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Stephan C Hammer
- Faculty of Chemistry, Bielefeld University, Universitätsstraße 25, 33615, Bielefeld, Germany
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