1
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Li YH, Chen JH, Yang Z. Exo-Selective Diels-Alder Reactions. Chemistry 2024; 30:e202304371. [PMID: 38412422 DOI: 10.1002/chem.202304371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Indexed: 02/29/2024]
Abstract
The Diels-Alder reaction stands as one of the most pivotal transformations in organic chemistry. Its efficiency, marked by the formation of two carbon-carbon bonds and up to four new stereocenters in a single step, underscores its versatility and indispensability in synthesizing natural products and pharmaceuticals. The most significant stereoselectivity feature is the "endo rule". While this rule underpins the predictability of the stereochemical outcomes, it also underscores the challenges in achieving the opposite diastereoselectivity, making the exo-Diels-Alder reactions often considered outliers. This review delves into recent examples of exo-Diels-Alder reactions, shedding light on the factors inverting the intrinsic tendency. We explore the roles of steric, electrostatic, and orbital interactions, as well as thermodynamic equilibriums in influencing exo/endo selectivity. Furthermore, we illustrate strategies to manipulate these factors, employing approaches such as bulky substituents, s-cis conformations, transient structural constraints, and innovative control physics. Through these analyses, our aim is to provide a comprehensive understanding of how to predict and design exo-Diels-Alder reactions, paving the way for new diastereoselective catalyst systems and expanding the chemical scope of Diels-Alder reactions.
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Affiliation(s)
- Yuan-He Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Jia-Hua Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Zhen Yang
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education and Beijing National Laboratory for Molecular Science (BNLMS), and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, 518055
- Shenzhen Bay Laboratory, Shenzhen, 518067, China
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2
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Enzymatic control of endo- and exo-stereoselective Diels–Alder reactions with broad substrate scope. Nat Catal 2021. [DOI: 10.1038/s41929-021-00717-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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3
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Nájera C, Sansano JM, Yus M. Diels-Alder reactions of 1-amino-1,3-dienes and related systems. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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Hickey DP, Godman NP, Schmidtke DW, Glatzhofer DT. Chloroferrocene-mediated laccase bioelectrocatalyst for the rapid reduction of O2. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5
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Sato M, Kishimoto S, Yokoyama M, Jamieson CS, Narita K, Maeda N, Hara K, Hashimoto H, Tsunematsu Y, Houk KN, Tang Y, Watanabe K. Catalytic mechanism and endo-to-exo selectivity reversion of an octalin-forming natural Diels–Alderase. Nat Catal 2021; 4:223-232. [DOI: 10.1038/s41929-021-00577-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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6
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Zou Y, Yang S, Sanders JN, Li W, Yu P, Wang H, Tang Z, Liu W, Houk KN. Computational Investigation of the Mechanism of Diels-Alderase PyrI4. J Am Chem Soc 2020; 142:20232-20239. [PMID: 33190496 DOI: 10.1021/jacs.0c10813] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We studied the mechanisms of activation and stereoselectivity of a monofunctional Diels-Alderase (PyrI4)-catalyzed intramolecular Diels-Alder reaction that leads to formation of the key spiro-tetramate moiety in the biosynthesis of the pyrroindomycin family of natural products. Key activation effects of PyrI4 include acid catalysis and an induced-fit mechanism that cooperate with the unique "lid" feature of PyrI4 to stabilize the Diels-Alder transition state. PyrI4 enhances the intrinsic Diels-Alder stereoselectivity of the substrate and leads to stereospecific formation of the product.
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Affiliation(s)
- Yike Zou
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Song Yang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Wei Li
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Peiyuan Yu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Hongbo Wang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Zhijun Tang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
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7
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Ghattas W, Mahy JP, Réglier M, Simaan AJ. Artificial Enzymes for Diels-Alder Reactions. Chembiochem 2020; 22:443-459. [PMID: 32852088 DOI: 10.1002/cbic.202000316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/17/2020] [Indexed: 12/13/2022]
Abstract
The Diels-Alder (DA) reaction is a cycloaddition of a conjugated diene and an alkene (dienophile) leading to the formation of a cyclohexene derivative through a concerted mechanism. As DA reactions generally proceed with a high degree of regio- and stereoselectivity, they are widely used in synthetic organic chemistry. Considering eco-conscious public and governmental movements, efforts are now directed towards the development of synthetic processes that meet environmental concerns. Artificial enzymes, which can be developed to catalyze abiotic reactions, appear to be important synthetic tools in the synthetic biology field. This review describes the different strategies used to develop protein-based artificial enzymes for DA reactions, including for in cellulo approaches.
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Affiliation(s)
- Wadih Ghattas
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Université Paris Sud, Université Paris-Saclay, Orsay, 91405 Cedex 8, France
| | - Jean-Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS, Université Paris Sud, Université Paris-Saclay, Orsay, 91405 Cedex 8, France
| | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Avenue Escadrille Normandie Niemen, Service 342, Marseille, 13397, France
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Avenue Escadrille Normandie Niemen, Service 342, Marseille, 13397, France
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8
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Chowdhury R, Maranas CD. From directed evolution to computational enzyme engineering—A review. AIChE J 2019. [DOI: 10.1002/aic.16847] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ratul Chowdhury
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania
| | - Costas D. Maranas
- Department of Chemical Engineering The Pennsylvania State University University Park Pennsylvania
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9
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Ghattas W, Dubosclard V, Tachon S, Beaumet M, Guillot R, Réglier M, Simaan AJ, Mahy J. Cu
II
‐Containing 1‐Aminocyclopropane Carboxylic Acid Oxidase Is an Efficient Stereospecific Diels–Alderase. Angew Chem Int Ed Engl 2019; 58:14605-14609. [DOI: 10.1002/anie.201909407] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Wadih Ghattas
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
| | - Virginie Dubosclard
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
| | - Sybille Tachon
- Institut des Sciences Moléculaires de Marseille (iSm2), UMR 7313 CNRS – Aix Marseille Univ Centrale Marseille Marseille 13013 Cedex France
| | - Morane Beaumet
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
| | - Marius Réglier
- Institut des Sciences Moléculaires de Marseille (iSm2), UMR 7313 CNRS – Aix Marseille Univ Centrale Marseille Marseille 13013 Cedex France
| | - A. Jalila Simaan
- Institut des Sciences Moléculaires de Marseille (iSm2), UMR 7313 CNRS – Aix Marseille Univ Centrale Marseille Marseille 13013 Cedex France
| | - Jean‐Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
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10
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Ghattas W, Dubosclard V, Tachon S, Beaumet M, Guillot R, Réglier M, Simaan AJ, Mahy J. Cu
II
‐Containing 1‐Aminocyclopropane Carboxylic Acid Oxidase Is an Efficient Stereospecific Diels–Alderase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Wadih Ghattas
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
| | - Virginie Dubosclard
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
| | - Sybille Tachon
- Institut des Sciences Moléculaires de Marseille (iSm2), UMR 7313 CNRS – Aix Marseille Univ Centrale Marseille Marseille 13013 Cedex France
| | - Morane Beaumet
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
| | - Marius Réglier
- Institut des Sciences Moléculaires de Marseille (iSm2), UMR 7313 CNRS – Aix Marseille Univ Centrale Marseille Marseille 13013 Cedex France
| | - A. Jalila Simaan
- Institut des Sciences Moléculaires de Marseille (iSm2), UMR 7313 CNRS – Aix Marseille Univ Centrale Marseille Marseille 13013 Cedex France
| | - Jean‐Pierre Mahy
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182 CNRS – Univ Paris Sud Université Paris-Saclay Orsay 91405 Cedex France
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11
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Rohling R, Tranca IC, Hensen EJM, Pidko EA. Mechanistic Insight into the [4 + 2] Diels-Alder Cycloaddition over First Row d-Block Cation-Exchanged Faujasites. ACS Catal 2019; 9:376-391. [PMID: 30775064 PMCID: PMC6369662 DOI: 10.1021/acscatal.8b03482] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/18/2018] [Indexed: 01/07/2023]
Abstract
The Diels-Alder cycloaddition (DAC) is a powerful tool to construct C-C bonds. The DAC reaction can be accelerated in several ways, one of which is reactant confinement as observed in supramolecular complexes and Diels-Alderases. Another method is altering the frontier molecular orbitals (FMOs) of the reactants by using homogeneous transition-metal complexes whose active sites exhibit d-orbitals suitable for net-bonding orbital interactions with the substrates. Both features can be combined in first row d-block (TM) exchanged faujasite catalysts where the zeolite framework acts as a stabilizing ligand for the active site while confining the reactants. Herein, we report on a mechanistic and periodic DFT study on TM-(Cu(I), Cu(II), Zn(II), Ni(II), Cr(III), Sc(III), V(V))exchanged faujasites to elucidate the effect of d-shell filling on the DAC reaction between 2,5-dimethylfuran and ethylene. Two pathways were found: one being the concerted one-step and the other being the stepwise two-step pathway. A decrease in d-shell filling results in a concomitant increase in reactant activation as evidenced by increasingly narrow energy gaps and lower activation barriers. For models holding relatively small d-block cations, the zeolite framework was found to bias the DAC reaction toward an asynchronous one-step pathway instead of the two-step pathway. This work is an example of how the active site properties and the surrounding chemical environment influence the reaction mechanism of chemical transformations.
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Affiliation(s)
- Roderigh
Y. Rohling
- Inorganic
Materials Chemistry group, Department of Chemical Engineering, and Energy Technology,
Department of Mechanical Engineering, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Ionut C. Tranca
- Inorganic
Materials Chemistry group, Department of Chemical Engineering, and Energy Technology,
Department of Mechanical Engineering, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Emiel J. M. Hensen
- Inorganic
Materials Chemistry group, Department of Chemical Engineering, and Energy Technology,
Department of Mechanical Engineering, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Evgeny A. Pidko
- Inorganic
Materials Chemistry group, Department of Chemical Engineering, and Energy Technology,
Department of Mechanical Engineering, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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12
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Huang CJ, Li EY. Molecular design principles towards exo-exclusive Diels–Alder reactions. RSC Adv 2019; 9:7246-7250. [PMID: 35519943 PMCID: PMC9061082 DOI: 10.1039/c8ra10438g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/24/2019] [Indexed: 11/21/2022] Open
Abstract
The exo selective Diels–Alder reactions, reported as special cases, usually involve catalytic reaction conditions and specific cyclic structural motifs on the diene and/or the dienophile. Here we report a systematic computational investigation on the substituent effect for simple, linear dienes and dienophiles towards exo control in Diels–Alder reactions under thermal conditions. Through detailed characterization of reaction pathways for Diels–Alder cycloadditions between linear dienes and dienophiles with various substituents, we summarize a set of design principles aiming for an optimal and nearly-exclusive exo selectivity. These results shall lead to valuable guidelines and more versatile strategies in organic synthesis that are in accordance with the principles of green chemistry. Exo-exclusive stereoselectivity for simple, terminal-substituted dienes and dienophiles may be achieved under thermal conditions through a delicate control of substituent identities.![]()
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Affiliation(s)
- Ci-Jhang Huang
- Department of Chemistry
- National Taiwan Normal University
- Taipei
- Taiwan
| | - Elise Y. Li
- Department of Chemistry
- National Taiwan Normal University
- Taipei
- Taiwan
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13
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Rohling R, Tranca IC, Hensen EJM, Pidko EA. Electronic Structure Analysis of the Diels-Alder Cycloaddition Catalyzed by Alkali-Exchanged Faujasites. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2018; 122:14733-14743. [PMID: 30018699 PMCID: PMC6038092 DOI: 10.1021/acs.jpcc.8b04409] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 06/07/2018] [Indexed: 05/22/2023]
Abstract
The Diels-Alder cycloaddition (DAC) reaction is a commonly employed reaction for the formation of C-C bonds. DAC catalysis can be achieved by using Lewis acids and via reactant confinement in aqueous nanocages. Low-silica alkali-exchanged faujasite catalysts combine these two factors in one material. They can be used in the tandem DAC/dehydration reaction of biomass-derived 2,5-dimethylfuran (DMF) with ethylene toward p-xylene, in which the DAC reaction step initiates the overall reaction cycle. In this work, we performed periodic density functional theory (DFT) calculations on the DAC reaction between DMF and C2H4 in low-silica alkali(M)-exchanged faujasites (MY; Si/Al = 2.4; M = Li+, Na+, K+, Rb+, Cs+). The aim was to investigate how confinement of reactants in MY catalysts changed their electronic structure and the DAC-reactivity trend among the evaluated MY zeolites. The conventional high-silica alkali-exchanged isolated site model (MFAU; Si/Al = 47) served as a reference. The results show that confinement leads to initial-state (IS) destabilization and transition-state (TS) stabilization. Among the tested MY, most significant IS destabilization is found in RbY. Only antibonding orbital interactions between the reactants/reactive complex and cations were found, indicating that TS stabilization arises from ionic interactions. Additionally, in RbY the geometry of the transition state is geometrically most similar to that of the initial and final state. RbY also exhibits an optimal combination of the confinement-effects, resulting in having the lowest computed DAC-activation energy. The overall effect is a DAC-reactivity trend inversion in MY as compared to the trend found in MFAU where the activation energy correlates with the Lewis acidity of the exchangeable cations.
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Affiliation(s)
- Roderigh
Y. Rohling
- Inorganic
Materials Chemistry group, Department of Chemical Engineering, and Energy Technology,
Department of Mechanical Engineering, Eindhoven
University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Ionut C. Tranca
- Inorganic
Materials Chemistry group, Department of Chemical Engineering, and Energy Technology,
Department of Mechanical Engineering, Eindhoven
University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Emiel J. M. Hensen
- Inorganic
Materials Chemistry group, Department of Chemical Engineering, and Energy Technology,
Department of Mechanical Engineering, Eindhoven
University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Evgeny A. Pidko
- Inorganic
Materials Chemistry group, Department of Chemical Engineering, and Energy Technology,
Department of Mechanical Engineering, Eindhoven
University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
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14
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Zuo Y, Su Z, Wang J, Hu C. Theoretical study on the mechanism and selectivity of asymmetric cycloaddition reactions of 3-vinylindole catalyzed by chiral N,N'-dioxide-Ni(II) complex. Catal Today 2017. [DOI: 10.1016/j.cattod.2017.05.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Liu L, Cotelle Y, Bornhof AB, Besnard C, Sakai N, Matile S. Anion-π Catalysis of Diels-Alder Reactions. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707730] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Le Liu
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Yoann Cotelle
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Anna-Bea Bornhof
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Céline Besnard
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Stefan Matile
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
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16
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Liu L, Cotelle Y, Bornhof AB, Besnard C, Sakai N, Matile S. Anion-π Catalysis of Diels-Alder Reactions. Angew Chem Int Ed Engl 2017; 56:13066-13069. [DOI: 10.1002/anie.201707730] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Le Liu
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Yoann Cotelle
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Anna-Bea Bornhof
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Céline Besnard
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
| | - Stefan Matile
- Department of Organic Chemistry; University of Geneva; Geneva Switzerland
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17
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Liu Z, Lin X, Yang N, Su Z, Hu C, Xiao P, He Y, Song Z. Unique Steric Effect of Geminal Bis(silane) To Control the High Exo-selectivity in Intermolecular Diels–Alder Reaction. J Am Chem Soc 2016; 138:1877-83. [PMID: 26799581 DOI: 10.1021/jacs.5b09689] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Zengjin Liu
- Key Laboratory of Drug Targeting and Drug
Delivery System,
Ministry of Education, Department of Medicinal Chemistry, West China
School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
| | - Xinglong Lin
- Key Laboratory of Drug Targeting and Drug
Delivery System,
Ministry of Education, Department of Medicinal Chemistry, West China
School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
| | - Na Yang
- Key
Laboratory of Green Chemistry and Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Zhishan Su
- Key
Laboratory of Green Chemistry and Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Changwei Hu
- Key
Laboratory of Green Chemistry and Technology, Ministry of Education,
College of Chemistry, Sichuan University, Chengdu 610064, P. R. China
| | - Peihong Xiao
- Key Laboratory of Drug Targeting and Drug
Delivery System,
Ministry of Education, Department of Medicinal Chemistry, West China
School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
| | - Yanyang He
- Key Laboratory of Drug Targeting and Drug
Delivery System,
Ministry of Education, Department of Medicinal Chemistry, West China
School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
| | - Zhenlei Song
- Key Laboratory of Drug Targeting and Drug
Delivery System,
Ministry of Education, Department of Medicinal Chemistry, West China
School of Pharmacy, Sichuan University, Chengdu 610041, P. R. China
- State
Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
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18
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Świderek K, Tuñón I, Moliner V, Bertran J. Computational strategies for the design of new enzymatic functions. Arch Biochem Biophys 2015; 582:68-79. [PMID: 25797438 PMCID: PMC4554825 DOI: 10.1016/j.abb.2015.03.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/09/2015] [Accepted: 03/13/2015] [Indexed: 11/28/2022]
Abstract
In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels-Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful design strategies.
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Affiliation(s)
- K Świderek
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain; Institute of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - I Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjasot, Spain
| | - V Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castellón, Spain
| | - J Bertran
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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19
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Sprague D, Nugent BM, Yoder RA, Vara BA, Johnston JN. Adaptation of a small-molecule hydrogen-bond donor catalyst to an enantioselective hetero-Diels-Alder reaction hypothesized for brevianamide biosynthesis. Org Lett 2015; 17:880-3. [PMID: 25697748 PMCID: PMC4339957 DOI: 10.1021/ol503626w] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Indexed: 12/22/2022]
Abstract
Chiral diamine-derived hydrogen-bond donors were evaluated for their ability to effect stereocontrol in an intramolecular hetero-Diels-Alder (HDA) reaction hypothesized in the biosynthesis of brevianamides A and B. Collectively, these results provide proof of principle that small-molecule hydrogen-bond catalysis, if even based on a hypothetical biosynthesis construct, holds significant potential within enantioselective natural product synthesis.
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Affiliation(s)
- Daniel
J. Sprague
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Benjamin M. Nugent
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ryan A. Yoder
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Brandon A. Vara
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Jeffrey N. Johnston
- Department of Chemistry and
Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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20
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Matsuo T, Hirota S. Artificial enzymes with protein scaffolds: Structural design and modification. Bioorg Med Chem 2014; 22:5638-56. [DOI: 10.1016/j.bmc.2014.06.021] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 01/04/2023]
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21
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Sista P, Ghosh K, Martinez JS, Rocha RC. Metallo-Biopolymers: Conjugation Strategies and Applications. POLYM REV 2014. [DOI: 10.1080/15583724.2014.913063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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Juríček M, Strutt NL, Barnes JC, Butterfield AM, Dale EJ, Baldridge KK, Stoddart JF, Siegel JS. Induced-fit catalysis of corannulene bowl-to-bowl inversion. Nat Chem 2014; 6:222-8. [PMID: 24557137 DOI: 10.1038/nchem.1842] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 12/09/2013] [Indexed: 01/07/2023]
Abstract
Stereoelectronic complementarity between the active site of an enzyme and the transition state of a reaction is one of the tenets of enzyme catalysis. This report illustrates the principles of enzyme catalysis (first proposed by Pauling and Jencks) through a well-defined model system that has been fully characterized crystallographically, computationally and kinetically. Catalysis of the bowl-to-bowl inversion processes that pertain to corannulene is achieved by combining ground-state destabilization and transition-state stabilization within the cavity of an extended tetracationic cyclophane. This synthetic receptor fulfils a role reminiscent of a catalytic antibody by stabilizing the planar transition state for the bowl-to-bowl inversion of (ethyl)corannulene (which accelerates this process by a factor of ten at room temperature) by an induced-fit mechanism first formulated by Koshland.
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Affiliation(s)
- Michal Juríček
- Center for the Chemistry of Integrated Systems, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Nathan L Strutt
- Center for the Chemistry of Integrated Systems, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Jonathan C Barnes
- Center for the Chemistry of Integrated Systems, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Anna M Butterfield
- Organic Chemistry Institute (OCI), University of Zürich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland
| | - Edward J Dale
- Center for the Chemistry of Integrated Systems, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Kim K Baldridge
- 1] Organic Chemistry Institute (OCI), University of Zürich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland [2] School of Pharmaceutical Science and Technology, Tianjin University (A210/Building 24), 92 Weijin Road, Nankai District, Tianjin, 300072 PRC, China
| | - J Fraser Stoddart
- Center for the Chemistry of Integrated Systems, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
| | - Jay S Siegel
- 1] Organic Chemistry Institute (OCI), University of Zürich, Winterthurerstrasse 190, Zürich, CH-8057, Switzerland [2] School of Pharmaceutical Science and Technology, Tianjin University (A210/Building 24), 92 Weijin Road, Nankai District, Tianjin, 300072 PRC, China
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23
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Ponomarenko N, Chatziefthimiou SD, Kurkova I, Mokrushina Y, Mokrushina Y, Stepanova A, Smirnov I, Avakyan M, Bobik T, Mamedov A, Mitkevich V, Belogurov A, Fedorova OS, Dubina M, Golovin A, Lamzin V, Friboulet A, Makarov AA, Wilmanns M, Gabibov A. Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:708-19. [PMID: 24598740 PMCID: PMC3949517 DOI: 10.1107/s1399004713032446] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022]
Abstract
The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was found that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the VL and VH domains. These VL/VH domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.
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Affiliation(s)
- Natalia Ponomarenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Spyros D. Chatziefthimiou
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Inna Kurkova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Yuliana Mokrushina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Yuliana Mokrushina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Anastasiya Stepanova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Ivan Smirnov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Marat Avakyan
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Tatyana Bobik
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Azad Mamedov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Alexey Belogurov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
- Institute of Gene Biology, Moscow 117334, Russian Federation
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Michael Dubina
- St Petersburg Academic University, St Petersburg 194021, Russian Federation
| | - Andrey Golovin
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Victor Lamzin
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alain Friboulet
- Université de Technologie de Compiègne, Unité Mixte de Recherche 6022, Centre National de la Recherche Scientifique, 60205 Compiègne, France
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alexander Gabibov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
- Institute of Gene Biology, Moscow 117334, Russian Federation
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
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24
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Plażuk D, Zakrzewski J, Salmain M, Błauż A, Rychlik B, Strzelczyk P, Bujacz A, Bujacz G. Ferrocene–Biotin Conjugates Targeting Cancer Cells: Synthesis, Interaction with Avidin, Cytotoxic Properties and the Crystal Structure of the Complex of Avidin with a Biotin–Linker–Ferrocene Conjugate. Organometallics 2013. [DOI: 10.1021/om4003126] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Damian Plażuk
- Department of Organic Chemistry, Faculty of Chemistry, University of Łódź, Tamka 12, 91-403
Łódź, Poland
| | - Janusz Zakrzewski
- Department of Organic Chemistry, Faculty of Chemistry, University of Łódź, Tamka 12, 91-403
Łódź, Poland
| | - Michèle Salmain
- Chimie ParisTech, Laboratoire Charles
Friedel, and CNRS, UMR 7223, 11 rue Pierre et Marie Curie, F-75005
Paris, France
| | - Andrzej Błauż
- Cytometry Laboratory, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Street, 90-237
Łódź, Poland
| | - Błażej Rychlik
- Cytometry Laboratory, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Street, 90-237
Łódź, Poland
| | - Paweł Strzelczyk
- Institute of Technical Biochemistry, Łódź University of Technology, Stefanowskiego 4/10, 90-924 Łódź, Poland
| | - Anna Bujacz
- Institute of Technical Biochemistry, Łódź University of Technology, Stefanowskiego 4/10, 90-924 Łódź, Poland
| | - Grzegorz Bujacz
- Institute of Technical Biochemistry, Łódź University of Technology, Stefanowskiego 4/10, 90-924 Łódź, Poland
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25
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Hottin A, Wright DW, Steenackers A, Delannoy P, Dubar F, Biot C, Davies GJ, Behr JB. α-L-Fucosidase Inhibition by Pyrrolidine-Ferrocene Hybrids: Rationalization of Ligand-Binding Properties by Structural Studies. Chemistry 2013; 19:9526-33. [DOI: 10.1002/chem.201301001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Indexed: 12/22/2022]
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26
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computational enzyme design. Angew Chem Int Ed Engl 2013; 52:5700-25. [PMID: 23526810 DOI: 10.1002/anie.201204077] [Citation(s) in RCA: 370] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Indexed: 11/07/2022]
Abstract
Recent developments in computational chemistry and biology have come together in the "inside-out" approach to enzyme engineering. Proteins have been designed to catalyze reactions not previously accelerated in nature. Some of these proteins fold and act as catalysts, but the success rate is still low. The achievements and limitations of the current technology are highlighted and contrasted to other protein engineering techniques. On its own, computational "inside-out" design can lead to the production of catalytically active and selective proteins, but their kinetic performances fall short of natural enzymes. When combined with directed evolution, molecular dynamics simulations, and crowd-sourced structure-prediction approaches, however, computational designs can be significantly improved in terms of binding, turnover, and thermal stability.
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Affiliation(s)
- Gert Kiss
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Dr. East, Los Angeles, CA 90095, USA
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27
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Kiss G, Çelebi-Ölçüm N, Moretti R, Baker D, Houk KN. Computerbasiertes Enzymdesign. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201204077] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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28
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Martić S, Gabriel M, Turowec JP, Litchfield DW, Kraatz HB. Versatile Strategy for Biochemical, Electrochemical and Immunoarray Detection of Protein Phosphorylations. J Am Chem Soc 2012; 134:17036-45. [DOI: 10.1021/ja302586q] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sanela Martić
- Department of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Michelle Gabriel
- Department of Biochemistry,
Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Jacob P. Turowec
- Department of Biochemistry,
Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - David W. Litchfield
- Department of Biochemistry,
Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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29
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Reetz MT. Artificial Metalloenzymes as Catalysts in Stereoselective Diels-Alder Reactions. CHEM REC 2012; 12:391-406. [DOI: 10.1002/tcr.201100043] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Indexed: 11/05/2022]
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30
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Salmon AJ, Williams ML, Hofmann A, Poulsen SA. Protein crystal structures with ferrocene and ruthenocene-based enzyme inhibitors. Chem Commun (Camb) 2012; 48:2328-30. [DOI: 10.1039/c2cc15625c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Bernardi L, Fochi M, Comes Franchini M, Ricci A. Bioinspired organocatalytic asymmetric reactions. Org Biomol Chem 2012; 10:2911-22. [DOI: 10.1039/c2ob07037e] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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32
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MPV reduction using AlIII–calix[4]arene Lewis acid catalysts: Molecular-level insight into effect of ketone binding. J Catal 2011. [DOI: 10.1016/j.jcat.2011.08.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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33
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Kraut S, Bebenroth D, Nierth A, Kobitski AY, Nienhaus GU, Jäschke A. Three critical hydrogen bonds determine the catalytic activity of the Diels-Alderase ribozyme. Nucleic Acids Res 2011; 40:1318-30. [PMID: 21976731 PMCID: PMC3273808 DOI: 10.1093/nar/gkr812] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Compared to protein enzymes, our knowledge about how RNA accelerates chemical reactions is rather limited. The crystal structures of a ribozyme that catalyzes Diels-Alder reactions suggest a rich tertiary architecture responsible for catalysis. In this study, we systematically probe the relevance of crystallographically observed ground-state interactions for catalytic function using atomic mutagenesis in combination with various analytical techniques. The largest energetic contribution apparently arises from the precise shape complementarity between transition state and catalytic pocket: A single point mutant that folds correctly into the tertiary structure but lacks one H-bond that normally stabilizes the pocket is completely inactive. In the rate-limiting chemical step, the dienophile is furthermore activated by two weak H-bonds that contribute ∼7-8 kJ/mol to transition state stabilization, as indicated by the 25-fold slower reaction rates of deletion mutants. These H-bonds are also responsible for the tight binding of the Diels-Alder product by the ribozyme that causes product inhibition. For high catalytic activity, the ribozyme requires a fine-tuned balance between rigidity and flexibility that is determined by the combined action of one inter-strand H-bond and one magnesium ion. A sharp 360° turn reminiscent of the T-loop motif observed in tRNA is found to be important for catalytic function.
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Affiliation(s)
- Stefanie Kraut
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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34
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Agopcan S, Çelebi-Ölçüm N, Üçışık MN, Sanyal A, Aviyente V. Origins of the diastereoselectivity in hydrogen bonding directed Diels–Alder reactions of chiral dienes with achiral dienophiles: a computational study. Org Biomol Chem 2011; 9:8079-88. [DOI: 10.1039/c1ob06285a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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35
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Affiliation(s)
- Jose M. Palomo
- Departamento de Biocatálisis, Instituto de Catálisis (CSIC), c/ Marie Curie 2, Cantoblanco Campus UAM, 28049 Madrid, Spain, Fax: +34‐91‐585‐4760
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36
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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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37
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38
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Abstract
The Diels-Alder reaction has both enabled and shaped the art and science of total synthesis over the last few decades to an extent which, arguably, has yet to be eclipsed by any other transformation in the current synthetic repertoire. With myriad applications of this magnificent pericyclic reaction, often as a crucial element in elegant and programmed cascade sequences facilitating complex molecule construction, the Diels-Alder cycloaddition has afforded numerous and unparalleled solutions to a diverse range of synthetic puzzles provided by nature in the form of natural products. In celebration of the 100th anniversary of Alder's birth, selected examples of the awesome power of the reaction he helped to discover are discussed in this review in the context of total synthesis to illustrate its overall versatility and underscore its vast potential which has yet to be fully realized.
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Affiliation(s)
- K C Nicolaou
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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39
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Gagnon KT, Ju SY, Goshe MB, Maxwell ES, Franzen S. A role for hydrophobicity in a Diels-Alder reaction catalyzed by pyridyl-modified RNA. Nucleic Acids Res 2009; 37:3074-82. [PMID: 19304744 PMCID: PMC2685102 DOI: 10.1093/nar/gkp177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
New classes of RNA enzymes or ribozymes have been obtained by in vitro evolution and selection of RNA molecules. Incorporation of modified nucleotides into the RNA sequence has been proposed to enhance function. DA22 is a modified RNA containing 5-(4-pyridylmethyl) carboxamide uridines, which has been selected for its ability to promote a Diels–Alder cycloaddition reaction. Here, we show that DA_TR96, the most active member of the DA22 RNA sequence family, which was selected with pyridyl-modified nucleotides, accelerates a cycloaddition reaction between anthracene and maleimide derivatives with high turnover. These widely used reactants were not used in the original selection for DA22 and yet here they provide the first demonstration of DA_TR96 as a true multiple-turnover catalyst. In addition, the absence of a structural or essential kinetic role for Cu2+, as initially postulated, and nonsequence-specific hydrophobic interactions with the anthracene substrate have led to a reevaluation of the pyridine modification's role. These findings broaden the catalytic repertoire of the DA22 family of pyridyl-modified RNAs and suggest a key role for the hydrophobic effect in the catalytic mechanism.
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Affiliation(s)
- Keith T Gagnon
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
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40
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Lam YH, Cheong PHY, Blasco Mata JM, Stanway SJ, Gouverneur V, Houk KN. Diels-Alder exo selectivity in terminal-substituted dienes and dienophiles: experimental discoveries and computational explanations. J Am Chem Soc 2009; 131:1947-57. [PMID: 19154113 PMCID: PMC2635921 DOI: 10.1021/ja8079548] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Diels-Alder reactions of a series of silyloxydienes and silylated dienes with acyclic alpha,beta-unsaturated ketones and N-acyloxazolidinones have been investigated. The endo/exo stereochemical outcome is strongly influenced by the substitution pattern of the reactants. High exo selectivity was observed when the termini of the diene and the dienophile involved in the shorter of the forming bonds were both substituted, while the normal endo preference was found otherwise. The exo-selective asymmetric Diels-Alder reactions using Evans' oxazolidinone chiral auxiliary furnished a high level of pi-facial selectivity in the same sense as their well-documented endo-selective counterparts. Computational results for these Diels-Alder reactions were consistent with the experimental endo/exo selectivity in most cases. A twist-asynchronous model accounts for the geometries and energies of the computed transition structures.
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Affiliation(s)
- Yu-hong Lam
- Chemistry Research Laboratory, University of Oxford, UK
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41
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Kirin SI, Schatzschneider U, Köster SD, Siebler D, Metzler-Nolte N. A systematic evaluation of different hydrogen bonding patterns in unsymmetrical 1,n′-disubstituted ferrocenoyl peptides. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.01.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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42
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Tsumoto K, Yokota A, Tanaka Y, Ui M, Tsumuraya T, Fujii I, Kumagai I, Nagumo Y, Oguri H, Inoue M, Hirama M. Critical contribution of aromatic rings to specific recognition of polyether rings. The case of ciguatoxin CTX3C-ABC and its specific antibody 1C49. J Biol Chem 2008; 283:12259-66. [PMID: 18326040 DOI: 10.1074/jbc.m710553200] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To address how proteins recognize polyether toxin compounds, we focused on the interaction between the ABC ring compound of ciguatoxin 3C and its specific antibody, 1C49. Surface plasmon resonance analyses indicated that Escherichia coli-expressed variable domain fragments (Fv) of 1C49 had the high affinity constants and slow dissociation constants typical of antigen-antibody interactions. Linear van't Hoff analyses suggested that the interaction is enthalpy-driven. We resolved the crystal structure of 1C49 Fv bound to ABC ring compound of ciguatoxin 3C at a resolution of 1.7A. The binding pocket of the antibody had many aromatic rings and bound the antigen by shape complementarity typical of hapten-antibody interactions. Three hydrogen bonds and many van der Waals interactions were present. We mutated several residues of the antibody to Ala, and we used surface plasmon resonance to analyze the interactions between the mutated antibodies and the antigen. This analysis identified Tyr-91 and Trp-96 in the light chain as hot spots for the interaction, and other residues made incremental contributions by conferring enthalpic advantages and reducing the dissociation rate constant. Systematic mutation of Tyr-91 indicated that CH-pi and pi-pi interactions between the aromatic ring at this site and the antigen made substantial contributions to the association, and van der Waals interactions inhibited dissociation, suggesting that aromaticity and bulkiness are critical for the specific recognition of polyether compounds by proteins.
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Affiliation(s)
- Kouhei Tsumoto
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan.
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Fischer B, Fukuzawa K, Wenzel W. Receptor-specific scoring functions derived from quantum chemical models improve affinity estimates for in-silico drug discovery. Proteins 2008; 70:1264-73. [PMID: 17876816 DOI: 10.1002/prot.21607] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The adaptation of forcefield-based scoring function to specific receptors remains an important challenge for in-silico drug discovery. Here we compare binding energies of forcefield-based scoring functions with models that are reparameterized on the basis of large-scale quantum calculations of the receptor. We compute binding energies of eleven ligands to the human estrogen receptor subtype alpha (ERalpha) and four ligands to the human retinoic acid receptor of isotype gamma (RARgamma). Using the FlexScreen all-atom receptor-ligand docking approach, we compare docking simulations parameterized by quantum-mechanical calculation of a large protein fragment with purely forcefield-based models. The use of receptor flexibility in the FlexScreen permits the treatment of all ligands in the same receptor model. We find a high correlation between the classical binding energy obtained in the docking simulation and quantum mechanical binding energies and a good correlation with experimental affinities R=0.81 for ERalpha and R=0.95 for RARgamma using the quantum derived scoring functions. A significant part of this improvement is retained, when only the receptor is treated with quantum-based parameters, while the ligands are parameterized with a purely classical model.
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Affiliation(s)
- Bernhard Fischer
- Forschungszentrum Karlsruhe, Institut für Nanotechnologie, Postfach 3640, D-76021 Karlsruhe, Germany
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Ranieri DI, Corgliano DM, Franco EJ, Hofstetter H, Hofstetter O. Investigation of the stereoselectivity of an anti-amino acid antibody using molecular modeling and ligand docking. Chirality 2008; 20:559-70. [DOI: 10.1002/chir.20522] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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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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Abstract
Hydrogen bonding is responsible for the structure of much of the world around us. The unusual and complex properties of bulk water, the ability of proteins to fold into stable three-dimensional structures, the fidelity of DNA base pairing, and the binding of ligands to receptors are among the manifestations of this ubiquitous noncovalent interaction. In addition to its primacy as a structural determinant, hydrogen bonding plays a crucial functional role in catalysis. Hydrogen bonding to an electrophile serves to decrease the electron density of this species, activating it toward nucleophilic attack. This principle is employed frequently by Nature's catalysts, enzymes, for the acceleration of a wide range of chemical processes. Recently, organic chemists have begun to appreciate the tremendous potential offered by hydrogen bonding as a mechanism for electrophile activation in small-molecule, synthetic catalyst systems. In particular, chiral hydrogen-bond donors have emerged as a broadly applicable class of catalysts for enantioselective synthesis. This review documents these advances, emphasizing the structural and mechanistic features that contribute to high enantioselectivity in hydrogen-bond-mediated catalytic processes.
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Affiliation(s)
- Mark S Taylor
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, MA 02138, USA
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Fischer B, Basili S, Merlitz H, Wenzel W. Accuracy of binding mode prediction with a cascadic stochastic tunneling method. Proteins 2007; 68:195-204. [PMID: 17427957 DOI: 10.1002/prot.21382] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We investigate the accuracy of the binding modes predicted for 83 complexes of the high-resolution subset of the ASTEX/CCDC receptor-ligand database using the atomistic FlexScreen approach with a simple forcefield-based scoring function. The median RMS deviation between experimental and predicted binding mode was just 0.83 A. Over 80% of the ligands dock within 2 A of the experimental binding mode, for 60 complexes the docking protocol locates the correct binding mode in all of ten independent simulations. Most docking failures arise because (a) the experimental structure clashed in our forcefield and is thus unattainable in the docking process or (b) because the ligand is stabilized by crystal water.
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Affiliation(s)
- Bernhard Fischer
- Forschungszentrum Karlsruhe, Institut für Nanotechnologie, Postfach 3640, D-76021 Karlsruhe, Germany
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Heinze K, Wild U, Beckmann M. Solid-Phase Synthesis of Chiral Modular Ferrocene-Based Peptides. Eur J Inorg Chem 2007. [DOI: 10.1002/ejic.200600857] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Barisić L, Cakić M, Mahmoud KA, Liu YN, Kraatz HB, Pritzkow H, Kirin SI, Metzler-Nolte N, Rapić V. Helically Chiral Ferrocene Peptides Containing 1′-Aminoferrocene-1-Carboxylic Acid Subunits as Turn Inducers. Chemistry 2006; 12:4965-80. [PMID: 16721886 DOI: 10.1002/chem.200600156] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We present a detailed structural study of peptide derivatives of 1'-aminoferrocene-1-carboxylic acid (ferrocene amino acid, Fca), one of the simplest organometallic amino acids. Fca was incorporated into di- to pentapeptides with D- and L-alanine residues attached to either the carboxy or amino group, or to both. Crystallographic and spectroscopic studies (circular dicroism (CD), IR, and NMR) of about two dozen compounds were used to gain a detailed insight into their structures in the solid state as well as in solution. Four derivatives were characterized by single-crystal X-ray analysis, namely Boc-Fca-Ala-OMe (16), Boc-Fca-D-Ala-OMe (17), Boc-Fca-beta-Ala-OMe (18), and Boc-Ala-Fca-Ala-Ala-OMe (21) (Boc=tert-butyloxycarbamyl). CD spectroscopy is an extremely useful tool to elucidate the helical chirality of the metallocene core. Unlike in all other known ferrocene peptides, the helical chirality of the ferrocene is governed solely by the chirality of the amino acid attached to the N terminus of Fca. Depending on the degree of substitution of both cyclopentadiene (Cp) rings, different hydrogen-bonding patterns are realized. (1)H NMR and IR spectroscopy, together with the results from X-ray crystallography, give detailed information regarding not only the hydrogen-bonding patterns of the compounds, but also the equilibria between different conformers in solution. Differences in chemical shifts of NH protons in dimethyl sulfoxide ([D(6)]DMSO) and CDCl(3), that is, the variation ratio (vr), is used for the first time as a measure of the hydrogen-bonding strength of individual COHN bonds in ferrocenoyl peptides. In dipeptides with one intramolecular hydrogen bond between the pendant chains, for example, in dipeptide 16, an equilibrium between hydrogen-bonded and open forms is observed, as testified by a vr value of around 0.5. Higher peptides, such as tetrapeptide 21, are able to form two intramolecular hydrogen bonds stabilizing one single conformation in CDCl(3) solution (vr approximately 0). Due to the low barrier of Cp-ring rotation, new and unnatural hydrogen-bonding patterns are emerging. The systematic work described herein lays a solid foundation for the rational design of metallocene peptides with unusual structures and properties.
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Affiliation(s)
- Lidija Barisić
- Faculty of Food Technology and Biotechnology, Pierottijeva 6, HR-10000 Zagreb, Croatia.
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50
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Reetz MT, Jiao N. Copper–Phthalocyanine Conjugates of Serum Albumins as Enantioselective Catalysts in Diels–Alder Reactions. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200504561] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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