1
|
Tu J, Svatunek D, Parvez S, Eckvahl HJ, Xu M, Peterson RT, Houk KN, Franzini RM. Isonitrile-responsive and bioorthogonally removable tetrazine protecting groups. Chem Sci 2019; 11:169-179. [PMID: 32110368 PMCID: PMC7012038 DOI: 10.1039/c9sc04649f] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 11/05/2019] [Indexed: 11/21/2022] Open
Abstract
Tetrazylmethyl groups are reported here as bioorthogonal protecting groups that are readily removed by isonitriles, establishing a valuable addition to the dissociative bioorthogonal chemistry and synthetic methodology toolboxes.
In vivo compatible reactions have a broad range of possible applications in chemical biology and the pharmaceutical sciences. Here we report tetrazines that can be removed by exposure to isonitriles under very mild conditions. Tetrazylmethyl derivatives are easily accessible protecting groups for amines and phenols. The isonitrile-induced removal is rapid and near-quantitative. Intriguingly, the deprotection is especially effective with (trimethylsilyl)methyl isocyanide, and serum albumin can catalyze the elimination under physiological conditions. NMR and computational studies revealed that an imine-tautomerization step is often rate limiting, and the unexpected cleavage of the Si–C bond accelerates this step in the case with (trimethylsilyl)methyl isocyanide. Tetrazylmethyl-removal is compatible with use on biomacromolecules, in cellular environments, and in living organisms as demonstrated by cytotoxicity experiments and fluorophore-release studies on proteins and in zebrafish embryos. By combining tetrazylmethyl derivatives with previously reported tetrazine-responsive 3-isocyanopropyl groups, it was possible to liberate two fluorophores in vertebrates from a single bioorthogonal reaction. This chemistry will open new opportunities towards applications involving multiplexed release schemes and is a valuable asset to the growing toolbox of bioorthogonal dissociative reactions.
Collapse
Affiliation(s)
- Julian Tu
- Department of Medicinal Chemistry , College of Pharmacy , University of Utah , Salt Lake City , 84112 , USA .
| | - Dennis Svatunek
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA
| | - Saba Parvez
- Department of Pharmacology and Toxicology , College of Pharmacy , University of Utah , Salt Lake City , 84112 , USA
| | - Hannah J Eckvahl
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA
| | - Minghao Xu
- Department of Medicinal Chemistry , College of Pharmacy , University of Utah , Salt Lake City , 84112 , USA .
| | - Randall T Peterson
- Department of Pharmacology and Toxicology , College of Pharmacy , University of Utah , Salt Lake City , 84112 , USA
| | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , USA
| | - Raphael M Franzini
- Department of Medicinal Chemistry , College of Pharmacy , University of Utah , Salt Lake City , 84112 , USA .
| |
Collapse
|
2
|
Zadlo A, Koszelewski D, Borys F, Ostaszewski R. Evaluation of Pseudoenantiomeric Mixed Carbonates as Efficient Fluorogenic Probes for Enantioselectivity Screening. Chembiochem 2015; 17:71-6. [DOI: 10.1002/cbic.201500509] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Anna Zadlo
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Dominik Koszelewski
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Filip Borys
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| | - Ryszard Ostaszewski
- Institute of Organic Chemistry; Polish Academy of Sciences; Kasprzaka 44/52 01-224 Warsaw Poland
| |
Collapse
|
3
|
Zadlo A, Koszelewski D, Borys F, Ostaszewski R. Mixed Carbonates as Useful Substrates for a Fluorogenic Assay for Lipases and Esterases. Chembiochem 2015; 16:677-82. [DOI: 10.1002/cbic.201402528] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 11/10/2022]
|
4
|
Liebl W, Angelov A, Juergensen J, Chow J, Loeschcke A, Drepper T, Classen T, Pietruszka J, Ehrenreich A, Streit WR, Jaeger KE. Alternative hosts for functional (meta)genome analysis. Appl Microbiol Biotechnol 2014; 98:8099-109. [PMID: 25091044 DOI: 10.1007/s00253-014-5961-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/25/2022]
Abstract
Microorganisms are ubiquitous on earth, often forming complex microbial communities in numerous different habitats. Most of these organisms cannot be readily cultivated in the laboratory using standard media and growth conditions. However, it is possible to gain access to the vast genetic, enzymatic, and metabolic diversity present in these microbial communities using cultivation-independent approaches such as sequence- or function-based metagenomics. Function-based analysis is dependent on heterologous expression of metagenomic libraries in a genetically amenable cloning and expression host. To date, Escherichia coli is used in most cases; however, this has the drawback that many genes from heterologous genomes and complex metagenomes are expressed in E. coli either at very low levels or not at all. This review emphasizes the importance of establishing alternative microbial expression systems consisting of different genera and species as well as customized strains and vectors optimized for heterologous expression of membrane proteins, multigene clusters encoding protein complexes or entire metabolic pathways. The use of alternative host-vector systems will complement current metagenomic screening efforts and expand the yield of novel biocatalysts, metabolic pathways, and useful metabolites to be identified from environmental samples.
Collapse
Affiliation(s)
- Wolfgang Liebl
- Lehrstuhl für Mikrobiologie, Technische Universität München, Emil-Ramann-Str. 4, 85654, Freising, Germany,
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Guillemer S, Persillon C, Masson JM, Ravot G. Cell-free protein-based enzyme discovery and protein-ligand interaction study. Methods Mol Biol 2014; 1118:131-47. [PMID: 24395413 DOI: 10.1007/978-1-62703-782-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Cell-free expression-based screening is sometimes more suitable than cell-based assays for enzyme discovery. The advantage of cell-free systems for expression of toxic, poorly expressed, or insoluble proteins has already been well documented. Cell-free methods can advantageously replace cell-based ones when screening has to be performed on cell lysates prepared from harvested cells, for instance, when dealing with protein-ligand interactions particularly when the latter is hydrophobic. From our experience, cell-free extracts efficient in both transcription and translation can be prepared from potentially any microorganism. Here we present a general method for preparation of cell-free extracts from prokaryotic and eukaryotic cells, selection of the best systems, and optimized conditions for specific protein expression. The method allows to select proteins for their ability to bind a selected target, to identify the inhibitors of such binding, or to identify novel enzymatic activities.
Collapse
|
6
|
Reymond JL, Darbre T. Peptide and glycopeptide dendrimer apple trees as enzyme models and for biomedical applications. Org Biomol Chem 2012; 10:1483-92. [PMID: 22274649 DOI: 10.1039/c2ob06938e] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Solid phase peptide synthesis (SPPS) provides peptides with a dendritic topology when diamino acids are introduced in the sequences. Peptide dendrimers with one to three amino acids between branches can be prepared with up to 38 amino acids (MW ~ 5,000 Da). Larger peptide dendrimers (MW ~ 30,000) were obtained by a multivalent chloroacetyl cysteine (ClAc) ligation. Structural studies of peptide dendrimers by CD, FT-IR, NMR and molecular dynamics reveal molten globule states containing up to 50% of α-helix. Esterase and aldolase peptide dendrimers displaying dendritic effects and enzyme kinetics (k(cat)/k(uncat) ~ 10(5)) were designed or discovered by screening large combinatorial libraries. Strong ligands for Pseudomonas aeruginosa lectins LecA and LecB able to inhibit biofilm formation were obtained with glycopeptide dendrimers. Efficient ligands for cobalamin, cytotoxic colchicine conjugates and antimicrobial peptide dendrimers were also developed showing the versatility of dendritic peptides. Complementing the multivalency, the amino acid composition of the dendrimers strongly influenced the catalytic or biological activity obtained demonstrating the importance of the "apple tree" configuration for protein-like function in peptide dendrimers.
Collapse
Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Berne, Switzerland.
| | | |
Collapse
|
7
|
Leslie AK, Li D, Koide K. Amine-Promoted β-Elimination of a β-Aryloxy Aldehyde for Fluorogenic Chemodosimeters. J Org Chem 2011; 76:6860-5. [DOI: 10.1021/jo200947e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amanda K. Leslie
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Dandan Li
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
8
|
Charmantray F, Légeret B, Hélaine V, Hecquet L. Fluorogenic substrates for the screening assay of transketolase through beta-elimination of umbelliferone—Development, scope and limitations. J Biotechnol 2010; 145:359-66. [DOI: 10.1016/j.jbiotec.2009.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Revised: 11/23/2009] [Accepted: 12/31/2009] [Indexed: 10/20/2022]
|
9
|
Avital-Shmilovici M, Shabat D. Enzymatic activation of hydrophobic self-immolative dendrimers: The effect of reporters with ionizable functional groups. Bioorg Med Chem Lett 2009; 19:3959-62. [DOI: 10.1016/j.bmcl.2009.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Revised: 03/01/2009] [Accepted: 03/03/2009] [Indexed: 10/21/2022]
|
10
|
Bedia C, Camacho L, Casas J, Abad JL, Delgado A, Van Veldhoven PP, Fabriàs G. Synthesis of a Fluorogenic Analogue of Sphingosine-1-Phosphate and Its Use to Determine Sphingosine-1-Phosphate Lyase Activity. Chembiochem 2009; 10:820-2. [DOI: 10.1002/cbic.200800809] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
11
|
Guo HM, Tanaka F. A fluorogenic aldehyde bearing a 1,2,3-triazole moiety for monitoring the progress of aldol reactions. J Org Chem 2009; 74:2417-24. [PMID: 19222210 PMCID: PMC2663967 DOI: 10.1021/jo900013w] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a new type of fluorogenic aldehyde bearing a 1,2,3-triazole moiety that is useful for monitoring the progress of aldol reactions through an increase in fluorescence. Whereas 6-methoxy-2-naphthaldehyde was highly fluorescent, the fluorogenic aldehyde, 4-formylbenzene connected to the 6-methoxy-2-naphthyl group through a 1,2,3-triazole moiety, was essentially nonfluorescent in aqueous solutions. We suggest that the 4-formylphenyl group acts as a quencher to suppress the fluorescence of the 6-methoxy-2-naphthyltriazole moiety. The product of the aldol reaction of this aldehyde does not have a quenching moiety and showed more than 800-fold higher fluorescence than the aldehyde. Assay systems using the fluorogenic aldehyde were validated by screening of aldol catalysts, ranking of the activities of the catalysts, and evaluation of reaction conditions.
Collapse
Affiliation(s)
- Hai-Ming Guo
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Fujie Tanaka
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| |
Collapse
|
12
|
Abstract
Enzyme assays are analytical tools to visualize enzyme activities. In recent years a large variety of enzyme assays have been developed to assist the discovery and optimization of industrial enzymes, in particular for "white biotechnology" where selective enzymes are used with great success for economically viable, mild and environmentally benign production processes. The present article highlights the aspects of fluorogenic and chromogenic substrates, sensors, and enzyme fingerprinting, which are our particular areas of interest.
Collapse
Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, Berne, 3012, Switzerland.
| | | | | |
Collapse
|
13
|
Charmantray F, Hélaine V, Làsikovà A, Legeret B, Hecquet L. Chemoenzymatic synthesis of l-tyrosine derivative for a transketolase assay. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2008.03.099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
14
|
Reymond JL. Substrate Arrays for Fluorescence-Based Enzyme Fingerprinting and High-Throughput Screening. Ann N Y Acad Sci 2008; 1130:12-20. [DOI: 10.1196/annals.1430.000] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
15
|
Danieli E, Shabat D. Molecular probe for enzymatic activity with dual output. Bioorg Med Chem 2007; 15:7318-24. [PMID: 17869526 DOI: 10.1016/j.bmc.2007.08.046] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 08/07/2007] [Accepted: 08/17/2007] [Indexed: 10/22/2022]
Abstract
A novel molecular probe for enzymatic activity with a dual output detection-mode has been developed. The probe effectively detected the presence of the bacterial protease penicillin-G-amidase; a single cleavage by the enzyme initiated the fragmentation of a self immolative dendritic platform to release two reporter units. The signals of the free reporters were detected by two different spectroscopic techniques, fluorescence and UV-vis. This is the first reported molecular probe with two different chromogenic reporter units activated by a specific stimulus.
Collapse
Affiliation(s)
- Eyal Danieli
- Department of Organic Chemistry, School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | | |
Collapse
|
16
|
Reymond JL, Babiak P. Screening systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 105:31-58. [PMID: 17408081 DOI: 10.1007/10_2006_032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Enzyme screening technology has undergone massive developments in recent years, particularly in the area of high-throughput screening and microarray methods. Screening consists of testing each sample of a sample library individually for the targeted reaction. This requires enzyme assays that accurately test relevant parameters of the reaction, such as catalytic turnover with a given substrate and selectivity parameters such as enantio- and regioselectivity. Enzyme assays also play an important role outside of enzyme screening, in particular for drug screening, medical diagnostics, and in the area of cellular and tissue imaging. In the 1990s, methods for high-throughput screening of enzyme activities were perceived as a critical bottleneck. As illustrated partly in this chapter, a large repertoire of efficient screening strategies are available today that allow testing of almost any reaction with high-throughput.
Collapse
Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry & Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland.
| | | |
Collapse
|
17
|
Shamis M, Barbas CF, Shabat D. A new visual screening assay for catalytic antibodies with retro-aldol retro-Michael activity. Bioorg Med Chem Lett 2006; 17:1172-5. [PMID: 17234408 DOI: 10.1016/j.bmcl.2006.12.057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Revised: 12/07/2006] [Accepted: 12/08/2006] [Indexed: 11/22/2022]
Abstract
Fast and convenient methods are required for the detection of novel catalysts. We have developed a new assay to allow direct visualization of retro-aldol retro-Michael catalytic activity and have demonstrated it with catalytic antibody 38C2. The assay is based on a catalytic cleavage of a physiologically stable substrate to release 3,4-cyclohexeneoesculetin. The latter then reacts with iron(III) to generate a non-soluble complex that precipitates in the form of a black dye. This assay may be used for screening new catalysts for retro-aldol retro-Michael activity with improved efficiency for specific prodrug activation.
Collapse
Affiliation(s)
- Marina Shamis
- Department of Organic Chemistry, School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978, Israel
| | | | | |
Collapse
|
18
|
Kofoed J, Darbre T, Reymond JL. Artificial aldolases from peptide dendrimer combinatorial libraries. Org Biomol Chem 2006; 4:3268-81. [PMID: 17036115 DOI: 10.1039/b607342e] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide dendrimers were investigated as synthetic models for aldolase enzymes. Combinatorial libraries were prepared with aldolase active residues such as lysine and proline placed at the dendrimer core or near the surface. On-bead selection for aldolase activity was carried out using the dye-labelled 1,3-diketone 1a, suitable for covalent trapping of enamine-reactive side-chains, and the fluorogenic enolization probe 6. Aldolase dendrimers catalyzed the aldol reaction of acetone, dihydroxyacetone and cyclohexanone with nitrobenzaldehyde. Much like enzymes, the dendrimers exhibited strong aldolase activity in aqueous medium, but were also active in organic solvent. Dendrimer-catalyzed aldol reactions reached complete conversion in 3 h at 25 degrees C with 1 mol% catalyst and gave aldol products with up to 65% ee. A positive dendritic effect in catalysis was observed with both lysine and proline based aldolase dendrimer catalysts.
Collapse
Affiliation(s)
- Jacob Kofoed
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012, Berne, Switzerland
| | | | | |
Collapse
|
19
|
Sevestre A, Charmantray F, Hélaine V, Lásiková A, Hecquet L. Synthesis of stereochemical probes for new fluorogenic assays for yeast transketolase variants. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.02.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
20
|
Chen Y, Xie N. Fluorescence detection of conversion of phenolic Schiff bases to benzoxazoles. J Photochem Photobiol A Chem 2006. [DOI: 10.1016/j.jphotochem.2005.08.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
21
|
Tanaka F. Development of protein, peptide, and small molecule catalysts using catalysis-based selection strategies. CHEM REC 2006; 5:276-85. [PMID: 16211623 DOI: 10.1002/tcr.20051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have developed peptide catalysts and antibody catalysts that catalyze aldol, retro-aldol, and Michael reactions via an enamine mechanism using reaction-based selections with 1,3-diketone derivatives. Nucleophilic amino groups of the catalysts were covalently trapped during the selections. We have also developed fluorogenic substrates that are useful for real-time monitoring of the progress of bond-forming reactions, such as aldol reactions, by an increase in fluorescence. These fluorogenic substrates have been used to monitor peptide-catalyzed, antibody-catalyzed, enzyme-catalyzed, and small molecule-catalyzed reactions. Catalysis-based screening using fluorogenic substrates will accelerate rapid identification of superior catalysts and reaction conditions.
Collapse
Affiliation(s)
- Fujie Tanaka
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
| |
Collapse
|
22
|
Kofoed J, Darbre T, Reymond JL. Dual mechanism of zinc-proline catalyzed aldol reactions in water. Chem Commun (Camb) 2006:1482-4. [PMID: 16575434 DOI: 10.1039/b600703a] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The aldol reaction of acetone with aldehydes in aqueous medium under catalysis by zinc-proline (Zn(L-Pro)2) and secondary amines such as proline, (2S,4R)-4-hydroxyproline (Hyp) and (S)-(+)-1-(2-pyrrolidinomethyl)pyrrolidine (PMP) is shown to proceed by an enamine mechanism, as evidenced by reductive trapping of the iminium intermediate, while the aldol reaction of dihydroxyacetone (DHA) under catalysis by zinc-proline and by general bases such as N-methylmorpholine (NMM) is shown to occur under rate-limiting deprotonation of the alpha-carbon and formation of an enolate intermediate.
Collapse
Affiliation(s)
- Jacob Kofoed
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, CH-3012 Berne, Switzerland
| | | | | |
Collapse
|
23
|
Sicard R, Chen L, Marsaioli A, Reymond JL. A Fluorescence-Based Assay for Baeyer-Villiger Monooxygenases, Hydroxylases and Lactonases. Adv Synth Catal 2005. [DOI: 10.1002/adsc.200505040] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
24
|
|
25
|
Abstract
Enzyme assays for high-throughput screening and enzyme engineering, which are often based on derivatives of coumarin, nitrophenol, fluorescein, nitrobenzofurazane or rhodamine dyes, can be divided into two categories: those that depend on labelled substrates, and those that depend on sensing the reactions of unmodified substrates. Labelled substrates include, for example, fluorogenic and chromogenic substrates that generate a reporter molecule by beta-elimination, fluorescence resonance energy transfer (FRET) substrates and isotopic labels for enantioselectivity screening. By contrast, endpoint sensing can be done using amine reagents, fluorescent affinity labels for phosphorylated proteins, or synthetic multifunctional pores. Sensing assays can also be done in real time by using, for example, aldehyde trapping to follow vinyl ester acylation in organic solvent or calcein-copper fluorescence for sensing amino acids. The current trend is to assemble many such assays in parallel for enzyme profiling and enzyme fingerprinting.
Collapse
Affiliation(s)
- Jean-Philippe Goddard
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | | |
Collapse
|
26
|
Greenberg WA, Varvak A, Hanson SR, Wong K, Huang H, Chen P, Burk MJ. Development of an efficient, scalable, aldolase-catalyzed process for enantioselective synthesis of statin intermediates. Proc Natl Acad Sci U S A 2004; 101:5788-93. [PMID: 15069189 PMCID: PMC395986 DOI: 10.1073/pnas.0307563101] [Citation(s) in RCA: 174] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A process is reported for efficient, enantioselective production of key intermediates for the common chiral side chain of statin-type cholesterol-lowering drugs such as Lipitor (atorvastatin) and Crestor (rosuvastatin). The process features a one-pot tandem aldol reaction catalyzed by a deoxyribose-5-phosphate aldolase (DERA) to form a 6-carbon intermediate with installation of two stereogenic centers from 2-carbon starting materials. An improvement of almost 400-fold in volumetric productivity relative to the published enzymatic reaction conditions has been achieved, resulting in a commercially attractive process that has been run on up to a 100-g scale in a single batch at a rate of 30.6 g/liter per h. Catalyst load has been improved by 10-fold as well, from 20 to 2.0 wt % DERA. These improvements were achieved by a combination of discovery from environmental DNA of DERAs with improved activity and reaction optimization to overcome substrate inhibition. The two stereogenic centers are set by DERA with enantiomeric excess at >99.9% and diastereomeric excess at 96.6%. In addition, down-stream chemical steps have been developed to convert the enzymatic product efficiently to versatile intermediates applicable to preparation of atorvastatin and rosuvastatin.
Collapse
|
27
|
|
28
|
Kofoed J, Nielsen J, Reymond JL. Discovery of new peptide-based catalysts for the direct asymmetric aldol reaction. Bioorg Med Chem Lett 2003; 13:2445-7. [PMID: 12852940 DOI: 10.1016/s0960-894x(03)00498-0] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A series of oligo-peptide based catalysts were prepared using Fmoc solid-phase peptide synthesis. It was found that peptides with N-terminal proline residues catalyzed an aldol reaction yielding enantiomeric enriched product. Peptide H-Pro-Glu-Leu-Phe-OH catalyzed the reaction with good activity and moderate enantioselectivity (66% ee). Furthermore, it was shown that an acidic side chain and/or C-termini are essential to catalysis.
Collapse
Affiliation(s)
- Jacob Kofoed
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Bern, Switzerland
| | | | | |
Collapse
|
29
|
Tanaka F, Thayumanavan R, Barbas CF. Fluorescent detection of carbon-carbon bond formation. J Am Chem Soc 2003; 125:8523-8. [PMID: 12848558 DOI: 10.1021/ja034069t] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have developed a new spectroscopic system for detecting carbon-carbon bond formation by fluorescence to enhance high-throughput catalyst screening and rapid characterization of catalysts on a small scale. Fluorogenic substrates composed of a fluorophore possessing an amino group are readily prepared as amides of alpha,beta-unsaturated carbonyl compounds and generally exhibit low fluorescence, while Michael or Diels-Alder reactions of these fluorogenic substrates provide products of significantly increased fluorescence. The product's fluorescence is approximately 20- to 100-fold higher than that of the substrate. The assay system was validated by screening potential catalysts of the Michael reaction and in solvent optimization experiments. The covalent combination of fluorophores possessing an amino group with alpha,beta-unsaturated carbonyl compounds should provide a diverse range of fluorogenic substrates that may be used to rapidly screen catalysts and to optimize reaction conditions.
Collapse
Affiliation(s)
- Fujie Tanaka
- The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
| | | | | |
Collapse
|
30
|
Gutiérrez MC, Sleegers A, Simpson HD, Alphand V, Furstoss R. The first fluorogenic assay for detecting a Baeyer–Villigerase activity in microbial cells. Org Biomol Chem 2003; 1:3500-6. [PMID: 14599010 DOI: 10.1039/b306687h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first fluorogenic assay allowing for detection of microbial enzymes able to perform Baeyer-Villiger oxidation is described. This is based on the use of 4-oxopentyl umbelliferyl ether 1 as a fluorogenic substrate. When Baeyer-Villigerases active against this test ketone are present in the selected whole cells, 1 is transformed into 3-hydroxypropyl umbelliferyl ether 3, which, in a subsequent step, releases the fluorescent product umbelliferone. Different microorganisms, known to be endowed with Baeyer-Villigerase activity, were assayed.
Collapse
Affiliation(s)
- María C Gutiérrez
- Groupe Biocatalyse et Chimie Fine UMR-CNRS 6111, Université de la Mediterranée, Faculté des Sciences de Luminy, case 901, 163 Avenue de Luminy, 13288 Marseille, Cedex 9, France
| | | | | | | | | |
Collapse
|
31
|
Dias S, Jovic F, Renard PY, Taran F, Créminon C, Mioskowski C, Grassi J. Immunologically driven chemical engineering of antibodies for catalytic activity. J Immunol Methods 2002; 269:81-98. [PMID: 12379354 DOI: 10.1016/s0022-1759(02)00226-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
We describe a new strategy for the preparation of catalytic antibodies based on a two-step procedure. Firstly, monoclonal antibodies are selected only if displaying the following binding features: binding both the substrate and a reactive group in such a way that the two groups are in a reactive position towards each other. Secondly, the selected monoclonal antibodies (mAbs) are chemically engineered by covalently binding the reactive group into the binding pocket of the antibody. Using previously isolated monoclonal antibodies, we have focused our studies on the control of this second step.
Collapse
Affiliation(s)
- Sonia Dias
- Service de Pharmacologie et d'Immunologie, DRM/DSV CEA Saclay, 91191 Gif sur Yvette cedex, France
| | | | | | | | | | | | | |
Collapse
|
32
|
Traverse JF, Snapper ML. High-throughput methods for the development of new catalytic asymmetric reactions. Drug Discov Today 2002; 7:1002-12. [PMID: 12546918 DOI: 10.1016/s1359-6446(02)02436-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chiral, single enantiomer pharmaceuticals have become increasingly more important. Therefore, research aimed at providing new methods for their selective preparation has taken on an even greater importance. One of the most efficient strategies for the synthesis of non-racemic, chiral molecules is asymmetric catalysis. There are many variables involved in the discovery of a new catalytic asymmetric transformation; hence, methods for the rapid screening of large numbers of catalysts have been developed. Herein, these techniques and strategies for the rapid discovery of novel asymmetric catalysts are reviewed.
Collapse
Affiliation(s)
- John F Traverse
- Department of Chemistry, Boston College, Eugene F. Merkert Chemistry Center, Room 125, 2609 Beacon Street, Chesnut Hill, MA 02467, USA
| | | |
Collapse
|
33
|
Wahler D, Reymond JL. Methylamine adenine dinucleotide (MAD): a co-factor to turn alcohol dehydrogenases into aldolases. CAN J CHEM 2002. [DOI: 10.1139/v02-074] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Methylamine adenine dinucleotide (MAD) was prepared in seven steps and 15.3% overall yield from 1-acetoxy-2,3,5-tri-O-benzoyl-D-ribose by chemoenzymatic synthesis. The key step was the phosphatephosphate coupling between adenosine monophosphate and 2,5-anhydro-1-deoxy-1-phenylacetamide-6-phosphate-D-allitol (3) mediated by carbonyl diimidazole (CDI), followed by the removal of the phenylacetamido group by penicillin G acylase. The MAD co-factor provided a primary amine functionality that was suitably positioned to promote the enamine aldolization of 2-oxopropionamide with aldehydes within the active site of alcohol dehydrogenases, which should lead to the transformation of these stereoselective enzymes into aldolases. Preliminary investigations did not reveal any activity with horse liver alcohol dehydrogenase or yeast alcohol dehydrogenase.Key words: aldolases, alcohol dehydrogenases, co-factor enginering, nucleosides, acylases.
Collapse
|
34
|
|
35
|
Abstract
Recent progress in high-throughput enzyme assays includes new examples of fluorogenic and chromogenic substrates, fluorescence resonance energy transfer substrates, and applications of the pH and pM indicator methods. Recent developments of Horeau's pseudo-enantiomer derivatisation method to screen enantioselectivities in high-throughput have also been reported.
Collapse
Affiliation(s)
- D Wahler
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | | |
Collapse
|
36
|
Fessner WD, Helaine V. Biocatalytic synthesis of hydroxylated natural products using aldolases and related enzymes. Curr Opin Biotechnol 2001; 12:574-86. [PMID: 11849940 DOI: 10.1016/s0958-1669(01)00265-8] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Synthetic building blocks bearing hydroxylated chiral centers are important targets for biocatalysis. Many C-C bond forming enzymes have recently been investigated for new applications and new strategies towards the synthesis of natural products and related oxygenated compounds. Several old catalysts have been studied to increase our functional knowledge of natural aldolase-type enzymes, and new mutated catalysts or catalytic antibodies have been tested for their synthetic utility.
Collapse
Affiliation(s)
- W D Fessner
- Department of Organic Chemistry, Darmstadt University of Technology, Petersenstrasse 22, D-64287 Darmstadt, Germany
| | | |
Collapse
|
37
|
Abstract
There have been a number of recent advances in catalysis assays applicable for screening biocatalyst libraries in high-throughput format. These include instrumental assays such as high-performance liquid chromatography, mass spectrometry, capillary electrophoresis and IR-thermography, reagent-based assays producing spectroscopic signals (UV/VIS or fluorescence) in response to reaction progress, and assays based on fluorogenic or chromogenic substrates. These fluorogenic substrates enable the assaying of a variety of enzymes in enantioselective and stereoselective manner, including alcohol dehydrogenases, aldolases, lipases, amidases, epoxide hydrolases and phosphatases.
Collapse
Affiliation(s)
- D Wahler
- Departement für Chemie und Biochemie, Universität Bern, Switzerland
| | | |
Collapse
|