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Ouyang Y, O'Hagan MP, Willner I. Functional catalytic nanoparticles (nanozymes) for sensing. Biosens Bioelectron 2022; 218:114768. [DOI: 10.1016/j.bios.2022.114768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/29/2022]
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2
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Vynios DH. MICROSCALE DETERMINATIONS USING SOLID PHASE ASSAYS: APPLICATIONS TO BIOCHEMICAL, CLINICAL AND BIOTECHNOLOGICAL SECTORS. A REVIEW. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-100102044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Demitrios H. Vynios
- a Laboratory of Biochemistry, Section of Organic Chemistry, Biochemistry, and Natural Products, Department of Chemistry , University of Patras , Patras , 261 10 , Greece
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3
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Adler M, Adler S, Boche G. Tetrahedral intermediates in reactions of carboxylic acid derivatives with nucleophiles. J PHYS ORG CHEM 2005. [DOI: 10.1002/poc.807] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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4
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Design and synthesis of a Mn(III)-porphyrin steroid conjugate used as a new cleavable affinity label: on the road to semi-synthetic catalytic antibodies. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.07.057] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Cannizzaro CE, Ashley JA, Janda KD, Houk KN. Experimental determination of the absolute enantioselectivity of an antibody-catalyzed Diels-Alder reaction and theoretical explorations of the origins of stereoselectivity. J Am Chem Soc 2003; 125:2489-506. [PMID: 12603137 DOI: 10.1021/ja020879d] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The exo and endo Diels-Alder adducts of p-methoxycarbonylbenzyl trans-1,3-butadiene-1-carbamate and N,N-dimethylacrylamide have been synthesized, and the absolute configurations of resolved enantiomers have been determined. On the basis of this information, the absolute enantioselectivities of the Diels-Alder reaction catalyzed by antibodies 13G5 and 4D5 as well as other catalytic antibodies elicited in the same immunizations have been established. The effects of different arrangements of catalytic residues on the structure and energetics of the possible Diels-Alder transition states were modeled quantum mechanically at the B3LYP/6-311++G**//B3LYP/6-31+G** level of theory. Flexible docking of these enantiomeric transition states in the antibody active site followed by molecular dynamics on the resulting complexes provided a prediction of the transition-state binding modes and an explanation of the origin of the observed enantioselectivity of antibody 13G5.
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Affiliation(s)
- Carina E Cannizzaro
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1569, USA
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6
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Abstract
Antibody 38C2 efficiently catalyzes deuterium-exchange reactions at the alpha position of a variety of ketones and aldehydes, including substrates that have a variety of sensitive functional groups. In addition to the regio- and chemoselectivity of these reactions, the catalytic rates (kcat) and rate-enhancement values (kcat/kun) are among the highest values ever observed with catalytic antibodies. Comparison of the substrate range of the catalytic antibody with highly evolved aldolase enzymes, such as rabbit-muscle aldolase, highlights the much broader practical scope of the antibody, which accepts a wide range of substrates. The hydrogen-exchange reaction was used for calibration and mapping of the antibody active site. Isotope-exchange experiments with cycloheptanone reveal that the formation of the Schiff base species (as concluded from the 16O/18O exchange rate at the carbonyl oxygen) is much faster than the formation of the enamine intermediate (as concluded from the H/D exchange rate), and both steps are faster than the antibody-catalyzed aldol addition reaction.
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Affiliation(s)
- Avidor Shulman
- Department of Chemistry and Institute of Catalysis Science and Technology, Technion-Israel Institute of Technology Technion City, Haifa
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7
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Sinha SC, Sun J, Miller GP, Wartmann M, Lerner RA. Catalytic Antibody Route to the Naturally Occurring Epothilones: Total Synthesis of Epothilones A-F. Chemistry 2001; 7:1691-702. [PMID: 11349910 DOI: 10.1002/1521-3765(20010417)7:8<1691::aid-chem16910>3.0.co;2-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Naturally occurring epothilones have been synthesized starting from enantiomerically pure aldol compounds 9-11, which were obtained by antibody catalysis. Aldolase antibody 38C2 catalyzed the resolution of (+/-)-9 by enantioselective retro-aldol reaction to afford 9 in 90% ee at 50 % conversion. Compounds 10 and 11 were obtained in more than 99% ee at 50% conversion by resolution of their racemic mixtures using newly developed aldolase antibodies 84G3, 85H6 or 93F3. Compounds 9, 10 and 11 were resolved in multigram quantities and then converted to the epothilones by metathesis processes, which were catalyzed by Grubbs' catalysts.
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Affiliation(s)
- S C Sinha
- Department of Molecular Biology and the Skaggs Institute for Chemical Biology, the Scripps Research Institute, La Jolla, California 92037, USA.
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8
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Abstract
A series of fluorogenic polypropionate fragments has been prepared. These undergo retroaldolization to an intermediate aldehyde that liberates the fluorescent product umbelliferone by a secondary beta-elimination reaction. leading to a >20-fold increase in fluorescence (lambda(em) = 460 +/- 20 nm, lambdaex = 360 +/- 20 nm). By applying the principle of microscopic reversibility to the reversible aldol reaction, we can use these substrates to detect stereoselective aldolases. Test substrates are available to probe the classical cases of syn- and anti-selective aldolization (11a-d), Cram/ anti-Cram-selective aldolization (10a-d), and double stereoselective aldolization (3a-h). The selectivity of aldolase antibody 38C2 for these substrates is demonstrated as an example. The assay is suitable for high-throughput screening for catalysis in microtiter plates, and therefore provides a convenient tool for the isolation of new stereoselective aldolases from catalyst libraries.
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Affiliation(s)
- R Pérez Carlón
- Departement für Chemie und Biochemie, Universität Bern, Switzerland
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9
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Shulman H, Makarov C, Ogawa AK, Romesberg F, Keinan E. Chemically Reactive Immunogens Lead to Functional Convergence of the Immune Response. J Am Chem Soc 2000. [DOI: 10.1021/ja000616o] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hagit Shulman
- Contribution from the Department of Chemistry and Institute of Catalysis Science and Technology, TechnionIsrael Institute of Technology, Technion City, Haifa 32000, Israel, and Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Carina Makarov
- Contribution from the Department of Chemistry and Institute of Catalysis Science and Technology, TechnionIsrael Institute of Technology, Technion City, Haifa 32000, Israel, and Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Anthony K. Ogawa
- Contribution from the Department of Chemistry and Institute of Catalysis Science and Technology, TechnionIsrael Institute of Technology, Technion City, Haifa 32000, Israel, and Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Floyd Romesberg
- Contribution from the Department of Chemistry and Institute of Catalysis Science and Technology, TechnionIsrael Institute of Technology, Technion City, Haifa 32000, Israel, and Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Ehud Keinan
- Contribution from the Department of Chemistry and Institute of Catalysis Science and Technology, TechnionIsrael Institute of Technology, Technion City, Haifa 32000, Israel, and Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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10
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Shulman H, Eberhard A, Eberhard C, Ulitzur S, Keinan E. Highly sensitive and rapid detection of antibody catalysis by luminescent bacteria. Bioorg Med Chem Lett 2000; 10:2353-6. [PMID: 11055354 DOI: 10.1016/s0960-894x(00)00455-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A highly sensitive, inexpensive, and facile bioluminescent assay for the detection of catalytic antibodies has been developed. This assay may be used for the early detection of antibody catalysis. The efficiency of this technique was exemplified by the use of the luminescent bacterium VhM42 for monitoring an antibody-catalyzed retroaldol fragmentation reaction with aldolase antibodies 38C2 and 24H6.
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Affiliation(s)
- H Shulman
- Department of Chemistry and Institute of Catalysis Science and Technology, Technion-Israel Institute of Technology, Technion City, Haifa, Israel
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11
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12
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Sinha SC, Sun J, Miller G, Barbas CF, Lerner RA. Sets of aldolase antibodies with antipodal reactivities. Formal synthesis of epothilone E by large-scale antibody-catalyzed resolution of thiazole aldol. Org Lett 1999; 1:1623-6. [PMID: 10836025 DOI: 10.1021/ol990261h] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[formula: see text] Three monoclonal aldolase antibodies, generated against a beta-diketone hapten by reactive immunization, catalyzed rapid and highly enantioselective retro-aldol reactions of ent-8a-k, providing optically pure 8a-k by kinetic resolution. Compounds (+/-)-8a, (+/-)-8g, and (+/-)-8k have been resolved in multigram quantities using 0.003, 0.005, and 0.0004 mol% antibody catalysts, respectively. Resolved compounds 8a-k are useful synthons for the construction of epothilones A-E (2-6) and their analogues. Here, a formal synthesis of epothilone E, 6 has been achieved starting from compound 8g.
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Affiliation(s)
- S C Sinha
- Department of Molecular Biology, Skaggs Institute for Chemical Biology, Scripps Research Institute, La Jolla, California 92037, USA.
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13
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Nimri S, Keinan E. Antibody−Metalloporphyrin Catalytic Assembly Mimics Natural Oxidation Enzymes. J Am Chem Soc 1999. [DOI: 10.1021/ja990314q] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shai Nimri
- Contribution from the Department of Chemistry and Institute of Catalysis Science and Technology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel, and Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Ehud Keinan
- Contribution from the Department of Chemistry and Institute of Catalysis Science and Technology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel, and Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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14
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Sinha SC, Barbas CF, Lerner RA. The antibody catalysis route to the total synthesis of epothilones. Proc Natl Acad Sci U S A 1998; 95:14603-8. [PMID: 9843936 PMCID: PMC24496 DOI: 10.1073/pnas.95.25.14603] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An efficient monoclonal aldolase antibody that proceeds by an enamine mechanism was generated by reactive immunization. Here, this catalyst has been used in the total synthesis of epothilones A (1) and C (3). The starting materials for the synthesis of these molecules have been obtained by using antibody-catalyzed aldol and retro-aldol reactions. These precursors were then converted to epothilones A (1) and C (3) to complete the total synthesis.
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Affiliation(s)
- S C Sinha
- The Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. or
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15
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Taylor MJ, Hoffman TZ, Yli-Kauhaluoma JT, Lerner RA, Janda KD. A Light-Activated Antibody Catalyst. J Am Chem Soc 1998. [DOI: 10.1021/ja982711r] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew J. Taylor
- Contribution from the The Scripps Research Institute, Department of Chemistry and The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California, 92037
| | - Timothy Z. Hoffman
- Contribution from the The Scripps Research Institute, Department of Chemistry and The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California, 92037
| | - Jari T. Yli-Kauhaluoma
- Contribution from the The Scripps Research Institute, Department of Chemistry and The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California, 92037
| | - Richard A. Lerner
- Contribution from the The Scripps Research Institute, Department of Chemistry and The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California, 92037
| | - Kim D. Janda
- Contribution from the The Scripps Research Institute, Department of Chemistry and The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California, 92037
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16
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Heine A, Stura EA, Yli-Kauhaluoma JT, Gao C, Deng Q, Beno BR, Houk KN, Janda KD, Wilson IA. An antibody exo Diels-Alderase inhibitor complex at 1.95 angstrom resolution. Science 1998; 279:1934-40. [PMID: 9506943 DOI: 10.1126/science.279.5358.1934] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A highly specific Diels-Alder protein catalyst was made by manipulating the antibody repertoire of the immune system. The catalytic antibody 13G5 catalyzes a disfavored exo Diels-Alder transformation in a reaction for which there is no natural enzyme counterpart and that yields a single regioisomer in high enantiomeric excess. The crystal structure of the antibody Fab in complex with a ferrocenyl inhibitor containing the essential haptenic core that elicited 13G5 was determined at 1.95 angstrom resolution. Three key antibody residues appear to be responsible for the observed catalysis and product control. Tyrosine-L36 acts as a Lewis acid activating the dienophile for nucleophilic attack, and asparagine-L91 and aspartic acid-H50 form hydrogen bonds to the carboxylate side chain that substitutes for the carbamate diene substrate. This hydrogen-bonding scheme leads to rate acceleration and also pronounced stereoselectivity. Docking experiments with the four possible ortho transition states of the reaction explain the specific exo effect and suggest that the (3R,4R)-exo stereoisomer is the preferred product.
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Affiliation(s)
- A Heine
- The Skaggs Institute of Chemical Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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18
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Abstract
One of the fascinations of catalytic antibodies is the possibility of harnessing the mechanisms available to enzymes for chemical transformation and applying them to the broad realm of chemistry encountered in organic synthesis. Recently, the catalytic repertoire of antibodies has been extended to include mechanistically more complex bimolecular reactions and the immunological response to the hapten can be more thoroughly examined as a result of the advent of new screening technology using bacterial phages or auxotrophic cell lines.
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Affiliation(s)
- D B Smithrud
- Department of Chemistry, Pennsylvania State University, University Park 16802, USA.
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