101
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Wuellner U, Gavrilyuk J, Barbas C. Expanding the Concept of Chemically Programmable Antibodies to RNA Aptamers: Chemically Programmed Biotherapeutics. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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102
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Strategies for development of dengue virus inhibitors. Antiviral Res 2010; 85:450-62. [DOI: 10.1016/j.antiviral.2009.12.011] [Citation(s) in RCA: 211] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Revised: 12/16/2009] [Accepted: 12/30/2009] [Indexed: 01/03/2023]
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103
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Origins of catalysis by computationally designed retroaldolase enzymes. Proc Natl Acad Sci U S A 2010; 107:4937-42. [PMID: 20194782 DOI: 10.1073/pnas.0913638107] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have investigated recently reported computationally designed retroaldolase enzymes with the goal of understanding the extent and the origins of their catalytic power. Direct comparison of the designed enzymes to primary amine catalysts in solution revealed a rate acceleration of 10(5)-fold for the most active of the designed retroaldolases. Through pH-rate studies of the designed retroaldolases and evaluation of a Brønsted correlation for a series of amine catalysts, we found that lysine pK(a) values are shifted by 3-4 units in the enzymes but that the catalytic contributions from the shifted pK(a) values are estimated to be modest, about 10-fold. For the most active of the reported enzymes, we evaluated the catalytic contribution of two other design components: a motif intended to stabilize a bound water molecule and hydrophobic substrate binding interactions. Mutational analysis suggested that the bound water motif does not contribute to the rate acceleration. Comparison of the rate acceleration of the designed substrate relative to a minimal substrate suggested that hydrophobic substrate binding interactions contribute around 10(3)-fold to the enzymatic rate acceleration. Altogether, these results suggest that substrate binding interactions and shifting the pK(a) of the catalytic lysine can account for much of the enzyme's rate acceleration. Additional observations suggest that these interactions are limited in the specificity of placement of substrate and active site catalytic groups. Thus, future design efforts may benefit from a focus on achieving precision in binding interactions and placement of catalytic groups.
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104
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Acevedo O. Role of water in the multifaceted catalytic antibody 4B2 for allylic isomerization and Kemp elimination reactions. J Phys Chem B 2010; 113:15372-81. [PMID: 19860435 DOI: 10.1021/jp9069114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Specificity toward a single reaction is a well-known characteristic of catalytic antibodies. However, contrary to convention, catalytic antibody 4B2 possesses the ability to efficiently catalyze two unrelated reactions: a Kemp elimination and an allylic isomerization of a beta,gamma-unsaturated ketone. To elucidate how this multifaceted antibody operates, mixed quantum and molecular mechanics calculations coupled to Monte Carlo simulations were carried out. The antibody was determined to derive its adaptability for the mechanistically different reactions through the rearrangement of water molecules in the active site into advantageous geometric orientations for enhanced electrostatic stabilization. In the case of the Kemp elimination, a general base, Glu L34, carried out the proton abstraction from the isoxazole ring of 5-nitro-benzisoxazole while water molecules delivered specific stabilization at the transition state. The role of water was found to be more pronounced in the allylic isomerization because the solvent actively participated in the stepwise mechanism. A rate-limiting abstraction of the alpha-proton from the beta,gamma-unsaturated ketone via Glu L34 led to the formation of a neutral dienol intermediate, which was rapidly reprotonated at the gamma-position via a solvent hydronium ion. Preferential channeling of H(3)O(+) in the active site ensured a stereoselective proton exchange from the alpha- to the gamma-position, in good agreement with deuterium exchange NMR and HPLC experiments. Ideas for improved water-mediated catalytic antibody designs are presented. In a technical advancement, improvements to a recent polynomial fitting and integration technique utilizing free energy perturbation theory delivered greater accuracy and speed gains.
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Affiliation(s)
- Orlando Acevedo
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
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105
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Chen XH, Yu J, Gong LZ. The role of double hydrogen bonds in asymmetric direct aldol reactions catalyzed by amino amide derivatives. Chem Commun (Camb) 2010; 46:6437-48. [PMID: 20694218 DOI: 10.1039/c0cc00754d] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Xiao-Hua Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry, University of Science and Technology of China, Hefei, 230026, China
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106
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Mase N, Barbas, III CF. In water, on water, and by water: mimicking nature's aldolases with organocatalysis and water. Org Biomol Chem 2010; 8:4043-50. [DOI: 10.1039/c004970k] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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107
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Zhu X, Tanaka F, Lerner RA, Barbas CF, Wilson IA. Direct observation of an enamine intermediate in amine catalysis. J Am Chem Soc 2009; 131:18206-7. [PMID: 19968282 PMCID: PMC3227542 DOI: 10.1021/ja907271a] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An enamine intermediate is believed to be the central feature of biological catalysts, such as aldolases and small molecule amine organocatalysts. Despite decades of investigation of naturally occurring aldolase enzymes and recent studies on designed aldolase antibodies and organocatalysts, direct structural observation of an enamine intermediate has proven to be rare. Herein, we report the observation of a stable enamine intermediate in the crystal structure of an aldolase antibody 33F12 in complex with a 1,3-diketone derivative. This enamine complex structure provides strong evidence that fewer residues are essential for amine catalysis within the hydrophobic environments of this catalytic antibody than speculated for natural aldolase enzymes and should serve to guide future studies aimed at the rational design of these types of catalysts, as well as organocatalysts. Indeed, enamine catalysis in proteins might be more simplistic than previously imagined.
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Affiliation(s)
- Xueyong Zhu
- Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fujie Tanaka
- Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Richard A. Lerner
- Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Carlos F. Barbas
- Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- Departments of Chemistry and Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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108
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Itoh S, Kitamura M, Yamada Y, Aoki S. Chiral catalysts dually functionalized with amino acid and Zn2+ complex components for enantioselective direct aldol reactions inspired by natural aldolases: design, synthesis, complexation properties, catalytic activities, and mechanistic study. Chemistry 2009; 15:10570-84. [PMID: 19746465 DOI: 10.1002/chem.200900733] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Aldolases are enzymes that catalyze stereospecific aldol reactions in a reversible manner. Naturally occurring aldolases include class I aldolases, which catalyze aldol reactions via enamine intermediates, and class II aldolases, in which Zn(2+) enolates of substrates react with acceptor aldehydes. In this work, Zn(2+) complexes of L-prolyl-pendant[15]aneN(5) (ZnL(3)), L-prolyl-pendant[12]aneN(4) (ZnL(4)), and L-valyl-pendant[12]aneN(4) (ZnL(5)) were designed and synthesized for use as chiral catalysts for enantioselective aldol reactions. The complexation constants for L(3) to L(5) with Zn(2+) [logK(s)(ZnL)] were determined to be 14.1 (for ZnL(3)), 7.6 (for ZnL(4)), and 9.6 (for ZnL(5)), indicating that ZnL(3) is more stable than ZnL(4) and ZnL(5). The deprotonation constants of Zn(2+)-bound water [pK(a)(ZnL) values] for ZnL(3), ZnL(4), and ZnL(5) were calculated to be 9.2 (for ZnL(3)), 8.2 (for ZnL(4)), and 8.6 (for ZnL(5)), suggesting that the Zn(2+) ions in ZnL(3) is a less acidic Lewis acid than in ZnL(4) and ZnL(5). These values also indicated that the amino groups on the side chains weakly coordinate to Zn(2+). We carried out aldol reactions between acetone and 2-chlorobenzaldehyde and other aldehydes in the presence of catalytic amounts of the chiral Zn(2+) complexes in acetone/H(2)O at 25 and 37 degrees C. Whereas ZnL(3) yielded the aldol product in 43% yield and 1% ee (R), ZnL(4) and ZnL(5) afforded good chemical yields and high enantioselectivities of up to 89% ee (R). UV titrations of proline and ZnL(4) with acetylacetone (acac) in DMSO/H(2)O (1:2) indicate that ZnL(4) facilitates the formation of the ZnL(4)(acac)(-) complex (K(app)=2.1x10(2) M(-1)), whereas L-proline forms a Schiff base with acac with a very small equilibrium constant. These results suggest that the amino acid components and the Zn(2+) ions in ZnL(4) and ZnL(5) function in a cooperative manner to generate the Zn(2+)-enolate of acetone, thus permitting efficient enantioselective C-C bond formation with aldehydes.
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Affiliation(s)
- Susumu Itoh
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan
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109
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Fu A, Li H, Chu T, Zou H, Feng P, Yuan S, Duan Y. Theoretical studies of stereoselectivities in the direct anti-Mannich and syn-aldol reactions catalyzed by axially chiral amino sulfonamide. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.molcata.2009.08.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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110
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Zotova N, Moran A, Armstrong A, Blackmond D. A Coherent Mechanistic Rationale for Additive Effects and Autoinductive Behaviour in Proline-Mediated Reactions. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200900665] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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111
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Holm L, Moody P, Howarth M. Electrophilic affibodies forming covalent bonds to protein targets. J Biol Chem 2009; 284:32906-13. [PMID: 19759009 DOI: 10.1074/jbc.m109.034322] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antibody affinity limits sensitivity of detection in many areas of biology and medicine. High affinity usually depends on achieving the optimal combination of the natural 20 amino acids in the antibody binding site. Here, we investigate the effect on recognition of protein targets of placing an unnatural electrophile adjacent to the target binding site. We positioned a weak electrophile, acrylamide, near the binding site between an affibody, a non-immunoglobulin binding scaffold, and its protein target. The proximity between cysteine, lysine, or histidine on the target protein drove covalent bond formation to the electrophile on the affibody. Covalent bonds did not form to a non-interacting point mutant of the target, and there was minimal cross-reactivity with serum, cell lysate, or when imaging at the cell surface. Electrophilic affibodies showed more stable protein imaging at the surface of mammalian cells, and the sensitivity of protein detection in an immunoassay improved by two orders of magnitude. Thus electrophilic affibodies combined good specificity with improved detection of protein targets.
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Affiliation(s)
- Lotta Holm
- Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
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112
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Abstract
As the focus of synthesis increasingly shifts from its historical emphasis on molecular structure to function, improved strategies are clearly required for the generation of molecules with defined physical, chemical, and biological properties. In contrast, living organisms are remarkably adept at producing molecules and molecular assemblies with an impressive array of functions - from enzymes and antibodies to the photosynthetic center. Thus, the marriage of Nature's synthetic strategies, molecules, and biosynthetic machinery with more traditional synthetic approaches might enable the generation of molecules with properties difficult to achieve by chemical strategies alone. Here we illustrate the potential of this approach and overview some opportunities and challenges in the coming years.
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Affiliation(s)
- Xu Wu
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, California 92121, USA
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113
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Goswami RK, Huang ZZ, Forsyth JS, Felding-Habermann B, Sinha SC. Multiple catalytic aldolase antibodies suitable for chemical programming. Bioorg Med Chem Lett 2009; 19:3821-4. [PMID: 19428247 PMCID: PMC2923540 DOI: 10.1016/j.bmcl.2009.04.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Revised: 04/04/2009] [Accepted: 04/07/2009] [Indexed: 10/20/2022]
Abstract
Chemical programming of nine murine antibodies with catalytic aldolase activity was examined using compounds, equipped with diketone or pro-vinyl ketone linkers that inhibit integrin adhesion receptor functions. The results showed that most Abs were programmed using the diketone compounds in a manner similar to previously reported catalytic antibody 38C2. On the other hand, only those antibodies, which catalyzed the retro aldol reaction of the pro-vinyl ketone linkers efficiently, were programmed. Conjugated to integrin targeting compounds, at least three new antibodies, including 84G3, 85H6, and 90G8, exhibited high specific binding to human tumor cells expressing integrin alpha(v)beta(3.).
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Affiliation(s)
- Rajib Kumar Goswami
- The Skaggs Institute for Chemical Biology, Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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114
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Ho MC, Ménétret JF, Tsuruta H, Allen KN. The origin of the electrostatic perturbation in acetoacetate decarboxylase. Nature 2009; 459:393-7. [PMID: 19458715 DOI: 10.1038/nature07938] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 02/25/2009] [Indexed: 11/10/2022]
Abstract
Acetoacetate decarboxylase (AADase) has long been cited as the prototypical example of the marked shifts in the pK(a) values of ionizable groups that can occur in an enzyme active site. In 1966, it was hypothesized that in AADase the origin of the large pK(a) perturbation (-4.5 log units) observed in the nucleophilic Lys 115 results from the proximity of Lys 116, marking the first proposal of microenvironment effects in enzymology. The electrostatic perturbation hypothesis has been demonstrated in a number of enzymes, but never for the enzyme that inspired its conception, owing to the lack of a three-dimensional structure. Here we present the X-ray crystal structures of AADase and of the enamine adduct with the substrate analogue 2,4-pentanedione. Surprisingly, the shift of the pK(a) of Lys 115 is not due to the proximity of Lys 116, the side chain of which is oriented away from the active site. Instead, Lys 116 participates in the structural anchoring of Lys 115 in a long, hydrophobic funnel provided by the novel fold of the enzyme. Thus, AADase perturbs the pK(a) of the nucleophile by means of a desolvation effect by placement of the side chain into the protein core while enforcing the proximity of polar residues, which facilitate decarboxylation through electrostatic and steric effects.
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Affiliation(s)
- Meng-Chiao Ho
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02118-2394, USA
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115
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Gavrilyuk JI, Wuellner U, Salahuddin S, Goswami RK, Sinha SC, Barbas CF. An efficient chemical approach to bispecific antibodies and antibodies of high valency. Bioorg Med Chem Lett 2009; 19:3716-20. [PMID: 19497743 DOI: 10.1016/j.bmcl.2009.05.047] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 05/12/2009] [Accepted: 05/13/2009] [Indexed: 11/25/2022]
Abstract
Irreversible chemical programming of monoclonal aldolase antibody (mAb) 38C2 has been accomplished with beta-lactam equipped mono- and bifunctional targeting modules, including a cyclic-RGD peptide linked to either the peptide (D-Lys(6))-LHRH or another cyclic RGD unit and a small-molecule integrin inhibitor SCS-873 conjugated to (D-Lys(6))LHRH. We also prepared monofunctional targeting modules containing either cyclic RGD or (D-Lys(6))-LHRH peptides. Binding of the chemically programmed antibodies to integrin receptors alpha(v)beta(3) and alpha(v)beta(5) and to the luteinizing hormone releasing hormone receptor were evaluated. The bifunctional and bivalent c-RGD/LHRH and SCS-783/LHRH, the monofunctional and tetravalent c-RGD/c-RGD, and the monofunctional bivalent c-RGD chemically programmed antibodies bound specifically to the isolated integrin receptor proteins as well as to integrins expressed on human melanoma M-21 cells. c-RGD/LHRH, SCS-783/LHRH, and LHRH chemically programmed antibodies bound specifically to the LHRH receptors expressed on human ovarian cancer cells. This approach provides an efficient, versatile, and economically viable route to high-valency therapeutic antibodies that target defined combinations of specific receptors. Additionally, this approach should be applicable to chemically programmed vaccines.
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Affiliation(s)
- Julia I Gavrilyuk
- The Skaggs Institute for Chemical Biology, Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
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116
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de Graaf AJ, Kooijman M, Hennink WE, Mastrobattista E. Nonnatural Amino Acids for Site-Specific Protein Conjugation. Bioconjug Chem 2009; 20:1281-95. [DOI: 10.1021/bc800294a] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Albert J. de Graaf
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80.082, 3508 TB Utrecht, The Netherlands
| | - Marlous Kooijman
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80.082, 3508 TB Utrecht, The Netherlands
| | - Wim E. Hennink
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80.082, 3508 TB Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Faculty of Science, Utrecht University, P.O. Box 80.082, 3508 TB Utrecht, The Netherlands
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117
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Gavrilyuk JI, Wuellner U, Barbas CF. Beta-lactam-based approach for the chemical programming of aldolase antibody 38C2. Bioorg Med Chem Lett 2009; 19:1421-4. [PMID: 19181522 DOI: 10.1016/j.bmcl.2009.01.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 01/07/2009] [Accepted: 01/12/2009] [Indexed: 10/21/2022]
Abstract
Irreversible chemical programming of monoclonal aldolase antibody (mAb) 38C2 has been accomplished with beta-lactam-equipped targeting modules. A model study was first performed with beta-lactam conjugated to biotin. This conjugate efficiently and selectively modified the catalytic site lysine (LysH93) of mAb 38C2. We then conjugated a beta-lactam to a cyclic-RGD peptide to chemically program mAb 38C2 to target integrin receptors alpha(v)beta(3) and alpha(v)beta(5). The chemically programmed antibody bound specifically to the isolated integrin receptor proteins as well as the integrins expressed on human melanoma cells. This approach provides an efficient and versatile solution to irreversible chemical programming of aldolase antibodies.
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Affiliation(s)
- Julia I Gavrilyuk
- The Skaggs Institute for Chemical Biology and the Departments of Molecular Biology and Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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118
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Ishikawa F, Tsumuraya T, Fujii I. A Single Antibody Catalyzes Multiple Chemical Transformations upon Replacement of the Functionalized Small Nonprotein Components. J Am Chem Soc 2008; 131:456-7. [DOI: 10.1021/ja808792x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fumihiro Ishikawa
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8570, Japan
| | - Takeshi Tsumuraya
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8570, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-2 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8570, Japan
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119
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de Geus DC, van Roon AMM, Thomassen EAJ, Hokke CH, Deelder AM, Abrahams JP. Characterization of a diagnostic Fab fragment binding trimeric Lewis X. Proteins 2008; 76:439-47. [DOI: 10.1002/prot.22356] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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120
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Protonated (S)-prolinamide derivatives—water compatible organocatalysts for direct asymmetric aldol reaction. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.09.020] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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121
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Melchiorre P, Marigo M, Carlone A, Bartoli G. Asymmetric aminocatalysis--gold rush in organic chemistry. Angew Chem Int Ed Engl 2008; 47:6138-71. [PMID: 18666089 DOI: 10.1002/anie.200705523] [Citation(s) in RCA: 1111] [Impact Index Per Article: 69.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Catalysis with chiral secondary amines (asymmetric aminocatalysis) has become a well-established and powerful synthetic tool for the chemo- and enantioselective functionalization of carbonyl compounds. In the last eight years alone, this field has grown at such an extraordinary pace that it is now recognized as an independent area of synthetic chemistry, where the goal is the preparation of any chiral molecule in an efficient, rapid, and stereoselective manner. This has been made possible by the impressive level of scientific competition and high quality research generated in this area. This Review describes this "Asymmetric Aminocatalysis Gold Rush" and charts the milestones in its development. As in all areas of science, progress depends on human effort.
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Affiliation(s)
- Paolo Melchiorre
- Department of Organic Chemistry A. Mangini, Alma Mater Studiorum-Università di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.
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122
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Melchiorre P, Marigo M, Carlone A, Bartoli G. Die asymmetrische Aminokatalyse - Goldrausch in der organischen Chemie. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705523] [Citation(s) in RCA: 446] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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123
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Theoretical studies of stereoselectivities in the direct anti- and syn-aldol reactions catalyzed by different amino acid derivatives. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.tetasy.2008.05.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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124
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125
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Angelici G, Falgiani A, Luppi G, Kaptein B, Broxterman QB, Tomasini C. Atom Economic and Highly Syn‐selective Prolinamide‐Catalyzed Cross‐aldol Addition of Hydroxyacetone to Aromatic Aldehydes. SYNTHETIC COMMUN 2008. [DOI: 10.1080/00397910701863715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Gaetano Angelici
- a Chemistry Department “G. Ciamician,” , Alma Mater Studiorum University of Bologna , Bologna, Italy
| | - Annamaria Falgiani
- a Chemistry Department “G. Ciamician,” , Alma Mater Studiorum University of Bologna , Bologna, Italy
| | - Gianluigi Luppi
- a Chemistry Department “G. Ciamician,” , Alma Mater Studiorum University of Bologna , Bologna, Italy
| | - Bernard Kaptein
- b DSM Research, Pharmaceutical Products , Advanced Synthesis and Catalysis , Geleen, The Netherlands
| | - Quirinus B. Broxterman
- b DSM Research, Pharmaceutical Products , Advanced Synthesis and Catalysis , Geleen, The Netherlands
| | - Claudia Tomasini
- a Chemistry Department “G. Ciamician,” , Alma Mater Studiorum University of Bologna , Bologna, Italy
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126
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Affiliation(s)
- Santanu Mukherjee
- Max-Planck-Institut für Kohlenforschung, D-45470 Mülheim an der Ruhr, Germany
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127
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Barbas C. Organocatalysis Lost: Modern Chemistry, Ancient Chemistry, and an Unseen Biosynthetic Apparatus. Angew Chem Int Ed Engl 2008; 47:42-7. [DOI: 10.1002/anie.200702210] [Citation(s) in RCA: 474] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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128
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Barbas C. Die verlorene Organokatalyse: moderne Chemie, klassische Chemie und ein unbemerkter Biosynthesemechanismus. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200702210] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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129
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Font D, Sayalero S, Bastero A, Jimeno C, Pericàs MA. Toward an Artificial Aldolase. Org Lett 2007; 10:337-40. [PMID: 18095700 DOI: 10.1021/ol702901z] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daniel Font
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans, 16, E-43007 Tarragona, Spain, and Departament de Química Orgànica, Universitat de Barcelona (UB), E-08028 Barcelona, Spain
| | - Sonia Sayalero
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans, 16, E-43007 Tarragona, Spain, and Departament de Química Orgànica, Universitat de Barcelona (UB), E-08028 Barcelona, Spain
| | - Amaia Bastero
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans, 16, E-43007 Tarragona, Spain, and Departament de Química Orgànica, Universitat de Barcelona (UB), E-08028 Barcelona, Spain
| | - Ciril Jimeno
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans, 16, E-43007 Tarragona, Spain, and Departament de Química Orgànica, Universitat de Barcelona (UB), E-08028 Barcelona, Spain
| | - Miquel A. Pericàs
- Institute of Chemical Research of Catalonia (ICIQ), Av. Països Catalans, 16, E-43007 Tarragona, Spain, and Departament de Química Orgànica, Universitat de Barcelona (UB), E-08028 Barcelona, Spain
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130
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Wang YW, Peng Y. (S)-2-(Iodo-meth-yl)-1-tosyl-pyrrolidine. Acta Crystallogr Sect E Struct Rep Online 2007; 64:o56. [PMID: 21200932 PMCID: PMC2915014 DOI: 10.1107/s1600536807059223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 11/14/2007] [Indexed: 11/11/2022]
Abstract
In the title mol-ecule, C(12)H(16)INO(2)S, the pyrrolidine ring is in an envelope conformation. The dihedral angle between the four essentially coplanar atoms of the pyrrolidine ring and the benzene ring is 75.5 (4)°.
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Affiliation(s)
- Ya-Wen Wang
- Department of Chemistry, State Key Laboratory of Applied Organic Chemstry, College of Chemical Engineering, Lanzhou University, Lanzhou 730000, People's Republic of China
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131
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132
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Crist RM, Vasileiou C, Rabago-Smith M, Geiger JH, Borhan B. Engineering a rhodopsin protein mimic. J Am Chem Soc 2007; 128:4522-3. [PMID: 16594659 DOI: 10.1021/ja058591m] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to the difficulties in handling and manipulating membrane-bound proteins, such as rhodopsin, and the lack of crystallographic information on the cone opsins, we have opted to engineer a protein mimic of the transmembrane G-protein coupled receptor. Human cellular retinoic acid binding protein (CRABPII), a well studied and characterized protein, has been reengineered into a protein that now will bind retinal as a protonated Schiff base with high binding affinity (Kd = 2 nM) mimicking that of rhodopsin.
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Affiliation(s)
- Rachael M Crist
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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133
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Xu XY, Wang YZ, Gong LZ. Design of Organocatalysts for Asymmetric Direct Syn-Aldol Reactions. Org Lett 2007; 9:4247-9. [PMID: 17914888 DOI: 10.1021/ol701798x] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Two new organocatalysts 3a and 3b, derived from L-leucine and (S)-beta-amino alcohols that were prepared from L-valine, were designed and afforded the direct syn-aldol reactions of a wide scope of aldehydes with various ketones with an excellent diastereomeric ratio of up to >20/1 and enantioselectivities of up to 99% ee.
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Affiliation(s)
- Xiao-Ying Xu
- Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu 610041, China
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134
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Patil MP, Sunoj RB. Insights on co-catalyst-promoted enamine formation between dimethylamine and propanal through ab initio and density functional theory study. J Org Chem 2007; 72:8202-15. [PMID: 17900139 DOI: 10.1021/jo071004q] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The mechanistic details on enamine formation between dimethylamine and propanal are unraveled using the ab initio and density functional theory methods. The addition of secondary amine to the electrophile and simultaneous proton transfer results in a carbinolamine intermediate, which subsequently undergoes dehydration to form enamine. The direct addition of amine as well as the dehydration of the resulting carbinolamine intermediate is predicted to possess fairly high activation barrier implying that a unimolecular process is unlikely to be responsible for enamine formation. Different models are therefore proposed which could explain the relative ease of enamine formation under neat condition as well as under the influence of methanol as the co-catalyst. The explicit inclusion of either the reagent or the co-catalyst is considered in the transition states as stabilizing agents. The participation of the reagent or the co-catalyst as a monofunctional ancillary species is found to stabilize the transition states relative to the unassisted or the direct addition/dehydration pathways. The reduction in enthalpy of activation is found to be much more dramatic when two co-catalysts participate in an active bifunctional mode in the rate-determining dehydration step. The transition structures exhibited characteristic features of a relay proton transfer mechanism. The free energy of activation associated with the two methanol-assisted pathway is found to be 16.7 kcal/mol lower than that of the unassisted pathway. The results are found to be in concurrence with the available reports on the rate acceleration by co-catalysts in the Michael reaction between enamine and methyl vinyl ketone under neat conditions.
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Affiliation(s)
- Mahendra P Patil
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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135
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Gao G, Prasad R, Lodwig SN, Unkefer CJ, Beard WA, Wilson SH, London RE. Determination of lysine pK values using [5-13C]lysine: application to the lyase domain of DNA Pol beta. J Am Chem Soc 2007; 128:8104-5. [PMID: 16787052 PMCID: PMC2846763 DOI: 10.1021/ja061473u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Determination of the protonation state of titratable protein residues is of critical importance for the interpretation of active site chemistry, as well as for understanding the role of electrostatic interactions in protein folding and stability. However, protein titration studies are limited by the fact that, at extreme pH values, increasing fractions of unfolded or partially unfolded structures may be present. This problem is particularly acute for lysine residues which have high pK values. In the present study, we point out that the use of the 13C resonance of lysine C-5 as a reporter for titration of the epsilon-amino group is preferable to the use of C-6 due to the 5-fold greater titration shift, so that reasonable results can be obtained using a two parameter fit of data obtained over a more limited pH range. A new synthetic procedure for [5-13C]lysine is described, and the pK value for Lys72 in the lyase domain of DNA polymerase beta has been determined using the [5-13C]lysine-labeled enzyme. The results agree well with recent studies of the Pol lambda lyase domain, demonstrating that the pK value for this residue is not optimized for Schiff base chemistry (Gao et al., Biochemistry 2006, 45, 1785-1794). We also have re-evaluated data for the pK of Lys73 in the TEM-1 beta-lactamase.
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136
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Austria C, Zhang J, Valle H, Zhang Q, Chew E, Nguyen DT, Gu JY, Feng P, Bu X. Amine-controlled assembly of metal-sulfite architecture from 1D chains to 3D framework. Inorg Chem 2007; 46:6283-90. [PMID: 17622134 PMCID: PMC5713879 DOI: 10.1021/ic070325h] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Whereas open-framework materials have been made in a variety of chemical compositions, few are known in which 3-connected SO3(2)- anions serve as basic building units. Here, we report four new metal-sulfite polymeric structures, (ZnSO3)Py (1, py = pyridine), (ZnSO3)2(2,2'-bipy)H2O (2, 2,2'-bipy = 2,2'-bipyridine), (ZnSO3)2(TMDPy) (3, TMDPy = 4,4'-trimethylenedipyridine), and (MnSO3)2en (4, en = ethylenediamine) that have been synthesized hydrothermally and structurally characterized. In these compounds, low-dimensional 1D and 2D inorganic subunits are assembled into higher 2D or 3D covalent frameworks by organic ligands. In addition to the structure-directing effect of organic ligands, the flexible coordination chemistry of Zn2+ and SO3(2)- also contributes to the observed structural diversity. In compounds 1-3, Zn2+ sites alternate with trigonal pyramidal SO3(2)- anions to form three types of [ZnSO3]n chains, whereas in compound 4, a 2D-corrugated [MnSO3]n layer is present. Compound 1 features a rail-like chain with pendant pyridine rings. The pi-pi interaction between 2,2'-bipy ligands is found between adjacent chains in compound 2, resulting in 2D sheets that are further stacked through interlayer hydrogen bonds. Compound 3 exhibits a very interesting inorganic [(ZnSO3)2]n chain constructed from two chairlike subunits, and such chains are bridged by TMDPy ligands into a 2D sheet. In compound 4, side-by-side helical chains permeate through 2D-corrugated [MnSO3]n layers, which are pillared by neutral ethylenediamine molecules into a 3D framework that can be topologically represented as a (3,6)-connected net. The results presented here illustrate the rich structural chemistry of metal-sulfites and the potential of sulfite anions as a unique structural building block for the construction of novel open-framework materials, in particular, those containing polymeric inorganic subunits that may have interesting physical properties such as low-dimensional magnetism or electronic properties.
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Affiliation(s)
- Cristina Austria
- Department of Chemistry and Biochemistry, California State University Long Beach, Long Beach, CA 90840, USA
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137
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Novel enantiocontrol system with aminoacyl derivatives of glucoside as enamine-based organocatalysts for aldol reaction in aqueous media. Tetrahedron Lett 2007. [DOI: 10.1016/j.tetlet.2007.05.139] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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138
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Sagi A, Rishpon J, Shabat D. Amperometric assay for aldolase activity: antibody-catalyzed ferrocenylamine formation. Anal Chem 2007; 78:1459-61. [PMID: 16503594 DOI: 10.1021/ac0517141] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Screening of new catalysts for aldolase activity is a major task in bioorganic chemistry. For this purpose, fast and convenient methods are required for the detection of the catalysts. We have developed the first amperometric assay for aldol or retro-aldol catalytic activity. A new ferrocene-aldol derivative was synthesized with redox activity significantly different from that of ferrocenylamine. It was shown that the reaction between aldolase antibody 38C2 and a ferrocene-aldol substrate generated free ferrocenylamine, which could be detected and quantified by simple electrochemical measurement. The amperometric assay was applied to perform a Michaelis-Menten analysis of catalytic antibody 38C2 in order to determine the enzymatic kinetic parameters.
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Affiliation(s)
- Amit Sagi
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel Aviv 69978 Israel
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139
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Debler EW, Kaufmann GF, Kirchdoerfer RN, Mee JM, Janda KD, Wilson IA. Crystal structures of a quorum-quenching antibody. J Mol Biol 2007; 368:1392-402. [PMID: 17400249 PMCID: PMC1994716 DOI: 10.1016/j.jmb.2007.02.081] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2006] [Revised: 02/17/2007] [Accepted: 02/27/2007] [Indexed: 01/28/2023]
Abstract
A large number of Gram-negative bacteria employ N-acyl homoserine lactones (AHLs) as signaling molecules in quorum sensing, which is a population density-dependent mechanism to coordinate gene expression. Antibody RS2-1G9 was elicited against a lactam mimetic of the N-acyl homoserine lactone and represents the only reported monoclonal antibody that recognizes the naturally-occuring N-acyl homoserine lactone with high affinity. Due to its high cross-reactivity, RS2-1G9 showed remarkable inhibition of quorum sensing signaling in Pseudomonas aeruginosa, a common opportunistic pathogen in humans. The crystal structure of Fab RS2-1G9 in complex with a lactam analog revealed complete encapsulation of the polar lactam moiety in the antibody-combining site. This mode of recognition provides an elegant immunological solution for tight binding to an aliphatic, lipid-like ligand with a small head group lacking typical haptenic features, such as aromaticity or charge, which are often incorporated into hapten design to generate high-affinity antibodies. The ability of RS2-1G9 to discriminate between closely related AHLs is conferred by six hydrogen bonds to the ligand. Conversely, cross-reactivity of RS2-1G9 towards the lactone is likely to originate from conservation of these hydrogen bonds as well as an additional hydrogen bond to the oxygen of the lactone ring. A short, narrow tunnel exiting at the protein surface harbors a portion of the acyl chain and would not allow entry of the head group. The crystal structure of the antibody without its cognate lactam or lactone ligands revealed a considerably altered antibody-combining site with a closed binding pocket. Curiously, a completely buried ethylene glycol molecule mimics the lactam ring and, thus, serves as a surrogate ligand. The detailed structural delineation of this quorum-quenching antibody will aid further development of an antibody-based therapy against bacterial pathogens by interference with quorum sensing.
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Affiliation(s)
- Erik W. Debler
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Gunnar F. Kaufmann
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Robert N. Kirchdoerfer
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Jenny M. Mee
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Kim D. Janda
- Departments of Chemistry and Immunology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
- The Worm Institute for Research and Medicine (WIRM), The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
| | - Ian A. Wilson
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037
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140
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Zhou L, Wang L. Chiral Ionic Liquid Containing L-Proline Unit as a Highly Efficient and Recyclable Asymmetric Organocatalyst for Aldol Reaction. CHEM LETT 2007. [DOI: 10.1246/cl.2007.628] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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141
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Woycechowsky KJ, Vamvaca K, Hilvert D. Novel enzymes through design and evolution. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2007; 75:241-94, xiii. [PMID: 17124869 DOI: 10.1002/9780471224464.ch4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The generation of enzymes with new catalytic activities remains a major challenge. So far, several different strategies have been developed to tackle this problem, including site-directed mutagenesis, random mutagenesis (directed evolution), antibody catalysis, computational redesign, and de novo methods. Using these techniques, a broad array of novel enzymes has been created (aldolases, decarboxylases, dehydratases, isomerases, oxidases, reductases, and others), although their low efficiencies (10 to 100 M(-1) s(-l)) compared to those of the best natural enzymes (10(6) to 10(8) M(-1) s(-1)) remains a significant concern. Whereas rational design might be the most promising and versatile approach to generating new activities, directed evolution seems to be the best way to optimize the catalytic properties of novel enzymes. Indeed, impressive successes in enzyme engineering have resulted from a combination of rational and random design.
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142
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Wu X, Jiang Z, Shen HM, Lu Y. Highly Efficient Threonine-Derived Organocatalysts for Direct Asymmetric Aldol Reactions in Water. Adv Synth Catal 2007. [DOI: 10.1002/adsc.200600564] [Citation(s) in RCA: 198] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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143
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Chen XH, Luo SW, Tang Z, Cun LF, Mi AQ, Jiang YZ, Gong LZ. Organocatalyzed highly enantioselective direct aldol reactions of aldehydes with hydroxyacetone and fluoroacetone in aqueous media: the use of water to control regioselectivity. Chemistry 2007; 13:689-701. [PMID: 17013967 DOI: 10.1002/chem.200600801] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An organocatalyst prepared from (2R,3R)-diethyl 2-amino-3-hydroxysuccinate and L-proline exhibited high regio- and enantioselectivities for the direct aldol reactions of hydroxyacetone and fluoroacetone with aldehydes in aqueous media. It was found that water could be used to control the regioselectivity. The presence of 20-30 mol% of the catalyst afforded the direct aldol reactions of a wide range of aldehydes with hydroxyacetone to give the otherwise disfavored products with excellent enantioselectivities, ranging from 91 to 99% ee, and high regioselectivities. Aldolizations of fluoroacetone with aldehydes mediated by 30 mol% of the organocatalyst in aqueous media preferentially occurred at the methyl group, yielding products with high enantioselectivities (up to 91% ee); however, these additions took place dominantly at the fluoromethyl group in THF. Optically active 3,5-disubstituted tetrahydrofurans and (2S,4R)-dihydroxy-4-biphenylbutyric acid were prepared by starting from the aldol reaction of hydroxyacetone. Theoretical studies on the role of water in controlling the regioselectivity revealed that the hydrogen bonds formed between the amide oxygen of proline amide, the hydroxy of hydroxyacetone, and water are responsible for the regioselectivity by microsolvation with explicit one water molecule as a hydrogen-bond donor and/or an acceptor.
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Affiliation(s)
- Xiao-Hua Chen
- Key Laboratory for Asymmetric Synthesis and Chirotechnology of Sichuan Province, Chengdu Institute of Organic Chemistry, Chinese Academy of Sciences, Chengdu, 610041, China
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144
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Téllez-Sanz R, Yassin Z, Bernier-Villamor V, Ortiz-Salmerón E, Musso-Buendia JA, Barón C, Ruíz-Pérez LM, González-Pacanowska D, García-Fuentes L. Effect of an Asp80Ala substitution on the binding of dUTP and dUMP to Trypanosoma cruzi dUTPase. Biochimie 2007; 89:972-80. [PMID: 17459559 DOI: 10.1016/j.biochi.2007.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2006] [Accepted: 03/09/2007] [Indexed: 10/23/2022]
Abstract
dUTPase (deoxyuridine 5'-triphosphate nucleotide hydrolase) is an enzyme responsible for maintaining low levels of intracellular dUTP and thus prevents uracil incorporation into DNA by DNA polymerases during replication and repair processes. The thermodynamics of binding for both dUTP and dUMP (deoxyuridine 5'-monophosphate) to the D80A mutant form of Trypanosoma cruzi dUTPase have been investigated by fluorescence spectroscopy and high-sensitivity isothermal titration calorimetry. In the presence of magnesium, approximately a 30-fold decrease in the value of the k(cat) and a 15-fold increase in the K(m) for dUTP hydrolysis was calculated while a 5-fold decrease was observed in the affinity for dUMP. In the absence of magnesium, the affinity for dUTP binding was similar for both enzymes while that for dUMP was lowered 3-fold as a consequence of the mutation. Calorimetric titrations in several buffers with different ionization heats rendered similar proton exchanges during the binding of dUMP. Thus, apparently the side chain of Asp 80 does not seem to vary its protonation state during the binding process. The enthalpy change values for the D80A mutant hardly change with temperature and, in addition, were Mg(2+) independent. We conclude that the D80A mutation induces only a slight conformational change in the active site yet results in a significant alteration of nucleotide binding and modifies the ability of the enzyme to discriminate between dUTP and dUMP when magnesium is present.
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Affiliation(s)
- Ramiro Téllez-Sanz
- Departamento de Química Física, Bioquímica y Química Inorgánica, Facultad de Ciencias Experimentales, Universidad de Almería, La Cañada de San Urbano, 04120 Almería, Spain
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145
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Lerner RA. Manufacturing immunity to disease in a test tube: the magic bullet realized. Angew Chem Int Ed Engl 2007; 45:8106-25. [PMID: 17120282 DOI: 10.1002/anie.200603381] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although it took over one hundred years, Ehrlich's concept of the magic bullet is now a reality. Today, therapeutic antibodies are, arguably, the most important class of new drugs for the treatment of illnesses ranging from Alzheimer's disease to cancer. The emergence of therapeutic antibodies had to wait for advances in immunochemistry that allowed construction of antibodies in vitro. The centerpiece of the new technology is the combinatorial antibody library, which essentially allows one to synthesize an artificial immune system with a diversity that exceeds that of the natural repertoire. The construction of such libraries was perceived to be difficult because, if the natural immune system was to be used as the starting material, construction of the libraries would entail protocols that are the opposite of usual cloning. In gene cloning one starts with complexity and reduces it to a singularity. In the generation of diversity by construction of combinatorial antibody libraries, one starts with a collection of clones, randomly expands their complexity, and then returns them to recoverable singularities. The methods developed to accomplish this seemingly formidable task now allow construction of antibodies in a test tube to any antigen. These synthetic antibodies may be qualitatively and quantitatively superior to those of nature.
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Affiliation(s)
- Richard A Lerner
- Department of Chemistry, The Scripps Research Institute and The Skaggs Institute of Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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146
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147
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Xu XY, Wang YZ, Cun LF, Gong LZ. l-Proline amides catalyze direct asymmetric aldol reactions of aldehydes with methylthioacetone and fluoroacetone. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.tetasy.2007.01.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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148
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Sulzer-Mossé S, Alexakis A. Chiral amines as organocatalysts for asymmetric conjugate addition to nitroolefins and vinyl sulfones via enamine activation. Chem Commun (Camb) 2007:3123-35. [PMID: 17653365 DOI: 10.1039/b701216k] [Citation(s) in RCA: 445] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over the last decade the potential of organocatalysis has successfully been demonstrated. In particular, chiral amines such as pyrrolidine analogues have emerged as a broadly applicable class of organocatalyst for asymmetric conjugate addition via enamine activation. This Feature Article documents the development of these catalysts, emphasizing the design and mechanistic features that supply high selectivity in asymmetric Michael reactions.
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Affiliation(s)
- Sarah Sulzer-Mossé
- Department of Organic Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Geneva, Switzerland
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149
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150
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Nguyen DT, Chew E, Zhang Q, Choi A, Bu X. Metal−Organic Frameworks from Zinc Sulfite Clusters, Chains, and Sheets: 4-Connected, (3,4)-Connected 3-D Frameworks and 2-D Arrays of Catenane-Like Interlocking Rings. Inorg Chem 2006; 45:10722-7. [PMID: 17173428 DOI: 10.1021/ic061677b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Even though open-framework solids have been made in a variety of compositions such as silicates, phosphates, germanates, borates, and phosphites, few are known that are based on trigonal-pyramidal sulfite anions. We report here the first synthetic and structural studies of metal-organic framework materials in the zinc sulfite composition. It is demonstrated here that Zn2+ and SO32- can form various neutral inorganic subunits that can be 0-D clusters, 1-D chains, or 2-D sheets. These inorganic subunits of different dimensionality can subsequently be connected into extended frameworks of higher dimensionality through bifunctional ligands. In (ZnSO3)2en, infinite corrugated ZnSO3 layers are pillared by ethylenediamine (en) molecules into a 3-D network that can be classified as a (3,4)-connected net based on tetrahedral Zn nodes and trigonal-pyramidal S nodes. In (ZnSO3)pip, infinite ZnSO3 chains are cross-linked with piperazine molecules into a 3-D framework that can be classified as 4-connected net based on tetrahedral Zn nodes only. In (ZnSO3)2(TMDPy)2, (ZnSO3)2 dimers are doubly bridged by trimethylenedipyridine molecules into an infinite chain with a string of circles. Each circle along the chain is interlocked with another circle from a chain in the perpendicular direction, creating a 2-D pattern with an infinite-square array of catenane-like units.
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Affiliation(s)
- Dan-Tam Nguyen
- Department of Chemistry and Biochemistry, California State University-Long Beach, 1250 Bellflower Boulevard, Long Beach, CA 90840, USA
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