1
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Zhao X, Li W, Zhou L, Zhao X, Zhang Y, Li B, Li R, Zhu L. Cu(II)-Catalyzed Hydroboration Reactions of 1,1-Disubstituted α,β-Unsaturated Ketones, Esters, and Amides in Pure Water. J Org Chem 2024. [PMID: 38860473 DOI: 10.1021/acs.joc.3c02942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Here, a Cu2(OH)2CO3-catalyzed hydroboration reaction of 1,1-disubstituted α,β-unsaturated compounds has been developed. The reaction was carried out using water as a solvent at room temperature except for N-monosubstituted α,β-unsaturated amides. This method is applicable to diverse 1,1-disubstituted α,β-unsaturated ketones, esters, and amides, showing excellent reactivity (up to 98% yield). Gram-scale experiments and functional group transformations further demonstrated the practicality of this method.
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Affiliation(s)
- Xue Zhao
- School of Chemistry and Materials Science, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Xiaogan 432000, China
| | - Weishuang Li
- School of Chemistry and Materials Science, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Xiaogan 432000, China
| | - Lijie Zhou
- School of Chemistry and Materials Science, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Xiaogan 432000, China
| | - Xuhong Zhao
- School of Chemistry and Materials Science, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Xiaogan 432000, China
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
| | - Yaoyao Zhang
- School of Chemistry and Materials Science, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Xiaogan 432000, China
| | - Bojie Li
- School of Chemistry and Materials Science, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Xiaogan 432000, China
| | - Rong Li
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
| | - Lei Zhu
- School of Chemistry and Materials Science, Hubei Key Laboratory of Quality Control of Characteristic Fruits and Vegetables, Hubei Engineering University, Xiaogan 432000, China
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, School of Materials Science & Engineering, Hubei University, Wuhan 430062, China
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2
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Suzuki K, Maeda S. Multistructural microiteration combined with QM/MM-ONIOM electrostatic embedding. Phys Chem Chem Phys 2022; 24:16762-16773. [PMID: 35775395 DOI: 10.1039/d2cp02270b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multistructural microiteration (MSM) is a method to take account of contributions of multiple surrounding structures in a geometrical optimization or reaction path calculation using the quantum mechanics/molecular mechanics (QM/MM) ONIOM method. In this study, we combined MSM with the electrostatic embedding (EE) scheme of the QM/MM-ONIOM method by extending its original formulation for mechanical embedding (ME). MSM-EE takes account of the polarization in the QM region induced by point charges assigned to atoms in the multiple surrounding structures, where the point charges are scaled by the weight factor of each surrounding structure determined through MSM. The performance of MSM-EE was compared with that of the other methods, i.e., ONIOM-ME, ONIOM-EE, and MSM-ME, by applying them to three chemical processes: (1) chorismate-to-prephenate transformation in aqueous solution, (2) the same transformation as (1) in an enzyme, and (3) hydroxylation in p-hydroxybenzoate hydroxylase. These numerical tests of MSM-EE yielded barriers and reaction energies close to experimental values with computational costs comparable to those of the other three methods.
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Affiliation(s)
- Kimichi Suzuki
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan. .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan. .,Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.,JST, ERATO Maeda Artificial Intelligence for Chemical Reaction Design and Discovery Project, Sapporo 060-0810, Japan.,Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
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3
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Hubrich F, Müller M, Andexer JN. Chorismate- and isochorismate converting enzymes: versatile catalysts acting on an important metabolic node. Chem Commun (Camb) 2021; 57:2441-2463. [PMID: 33605953 DOI: 10.1039/d0cc08078k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chorismate and isochorismate represent an important branching point connecting primary and secondary metabolism in bacteria, fungi, archaea and plants. Chorismate- and isochorismate-converting enzymes are potential targets for new bioactive compounds, as well as valuable biocatalysts for the in vivo and in vitro synthesis of fine chemicals. The diversity of the products of chorismate- and isochorismate-converting enzymes is reflected in the enzymatic three-dimensional structures and molecular mechanisms. Due to the high reactivity of chorismate and its derivatives, these enzymes have evolved to be accurately tailored to their respective reaction; at the same time, many of them exhibit a fascinating flexibility regarding side reactions and acceptance of alternative substrates. Here, we give an overview of the different (sub)families of chorismate- and isochorismate-converting enzymes, their molecular mechanisms, and three-dimensional structures. In addition, we highlight important results of mutagenetic approaches that generate a broader understanding of the influence of distinct active site residues for product formation and the conversion of one subfamily into another. Based on this, we discuss to what extent the recent advances in the field might influence the general mechanistic understanding of chorismate- and isochorismate-converting enzymes. Recent discoveries of new chorismate-derived products and pathways, as well as biocatalytic conversions of non-physiological substrates, highlight how this vast field is expected to continue developing in the future.
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Affiliation(s)
- Florian Hubrich
- ETH Zurich, Institute of Microbiology, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland.
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4
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Unke OT, Koner D, Patra S, Käser S, Meuwly M. High-dimensional potential energy surfaces for molecular simulations: from empiricism to machine learning. MACHINE LEARNING-SCIENCE AND TECHNOLOGY 2020. [DOI: 10.1088/2632-2153/ab5922] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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5
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Ledovskaya MS, Voronin VV, Rodygin KS, Ananikov VP. Efficient labeling of organic molecules using 13C elemental carbon: universal access to 13C2-labeled synthetic building blocks, polymers and pharmaceuticals. Org Chem Front 2020. [DOI: 10.1039/c9qo01357a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Synthetic methodology enabled by 13C-elemental carbon is reported. Calcium carbide Ca13C2 was applied to introduce a universal 13C2 unit in the synthesis of labeled alkynes, O,S,N-vinyl derivatives, labeled polymers and 13C2-pyridazine drug core.
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Affiliation(s)
| | | | - Konstantin S. Rodygin
- Institute of Chemistry
- Saint Petersburg State University
- Peterhof
- Russia
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences
| | - Valentine P. Ananikov
- Institute of Chemistry
- Saint Petersburg State University
- Peterhof
- Russia
- N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences
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6
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Mahanta N, Hicks KA, Naseem S, Zhang Y, Fedoseyenko D, Ealick SE, Begley TP. Menaquinone Biosynthesis: Biochemical and Structural Studies of Chorismate Dehydratase. Biochemistry 2019; 58:1837-1840. [DOI: 10.1021/acs.biochem.9b00105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Nilkamal Mahanta
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Katherine A. Hicks
- Department of Chemistry, The State University of New York Cortland, Cortland, New York 13045, United States
| | - Saad Naseem
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Zhang
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Dmytro Fedoseyenko
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven E. Ealick
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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7
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Brickel S, Meuwly M. Molecular Determinants for Rate Acceleration in the Claisen Rearrangement Reaction. J Phys Chem B 2018; 123:448-456. [DOI: 10.1021/acs.jpcb.8b11059] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH-4056, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, Basel CH-4056, Switzerland
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8
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Zhang XK, Liu F, Fiers WD, Sun WM, Guo J, Liu Z, Aldrich CC. Synthesis of Transition-State Inhibitors of Chorismate Utilizing Enzymes from Bromobenzene cis-1,2-Dihydrodiol. J Org Chem 2017; 82:3432-3440. [PMID: 28282140 DOI: 10.1021/acs.joc.6b02801] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to survive in a mammalian host, Mycobacterium tuberculosis (Mtb) produces aryl-capped siderophores known as the mycobactins for iron acquisition. Salicylic acid is a key building block of the mycobactin core and is synthesized by the bifunctional enzyme MbtI, which converts chorismate into isochorismate via a SN2″ reaction followed by further transformation into salicylate through a [3,3]-sigmatropic rearrangement. MbtI belongs to a family of chorismate-utilizing enzymes (CUEs) that have conserved topology and active site residues. The transition-state inhibitor 1 described by Bartlett, Kozlowski, and co-workers is the most potent reported inhibitor to date of CUEs. Herein, we disclose a concise asymmetric synthesis and the accompanying biochemical characterization of 1 along with three closely related analogues beginning from bromobenzene cis-1S,2S-dihydrodiol produced through microbial oxidation that features a series of regio- and stereoselective transformations for introduction of the C-4 hydroxy and C-6 amino substituents. The flexible synthesis enables late-stage introduction of the carboxy group and other bioisosteres at the C-1 position as well as installation of the enol-pyruvate side chain at the C-5 position.
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Affiliation(s)
- Xiao-Kang Zhang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Feng Liu
- Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street Southeast, 8-174 WDH, Minneapolis, Minnesota 55455, United States
| | - William D Fiers
- Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street Southeast, 8-174 WDH, Minneapolis, Minnesota 55455, United States
| | - Wen-Mei Sun
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Jun Guo
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Zheng Liu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University , 152 Luoyu Road, Wuhan, Hubei 430079, People's Republic of China
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota , 308 Harvard Street Southeast, 8-174 WDH, Minneapolis, Minnesota 55455, United States
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9
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Targeting intracellular p-aminobenzoic acid production potentiates the anti-tubercular action of antifolates. Sci Rep 2016; 6:38083. [PMID: 27905500 PMCID: PMC5131483 DOI: 10.1038/srep38083] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/03/2016] [Indexed: 12/18/2022] Open
Abstract
The ability to revitalize and re-purpose existing drugs offers a powerful approach for novel treatment options against Mycobacterium tuberculosis and other infectious agents. Antifolates are an underutilized drug class in tuberculosis (TB) therapy, capable of disrupting the biosynthesis of tetrahydrofolate, an essential cellular cofactor. Based on the observation that exogenously supplied p-aminobenzoic acid (PABA) can antagonize the action of antifolates that interact with dihydropteroate synthase (DHPS), such as sulfonamides and p-aminosalicylic acid (PAS), we hypothesized that bacterial PABA biosynthesis contributes to intrinsic antifolate resistance. Herein, we demonstrate that disruption of PABA biosynthesis potentiates the anti-tubercular action of DHPS inhibitors and PAS by up to 1000 fold. Disruption of PABA biosynthesis is also demonstrated to lead to loss of viability over time. Further, we demonstrate that this strategy restores the wild type level of PAS susceptibility in a previously characterized PAS resistant strain of M. tuberculosis. Finally, we demonstrate selective inhibition of PABA biosynthesis in M. tuberculosis using the small molecule MAC173979. This study reveals that the M. tuberculosis PABA biosynthetic pathway is responsible for intrinsic resistance to various antifolates and this pathway is a chemically vulnerable target whose disruption could potentiate the tuberculocidal activity of an underutilized class of antimicrobial agents.
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10
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Darwish TA, Yepuri NR, Holden PJ, James M. Quantitative analysis of deuterium using the isotopic effect on quaternary 13C NMR chemical shifts. Anal Chim Acta 2016; 927:89-98. [DOI: 10.1016/j.aca.2016.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/29/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
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11
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Klas K, Tsukamoto S, Sherman DH, Williams RM. Natural Diels-Alderases: Elusive and Irresistable. J Org Chem 2016; 80:11672-85. [PMID: 26495876 DOI: 10.1021/acs.joc.5b01951] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Eight examples of biosynthetic pathways wherein a natural enzyme has been identified and claimed to function as a catalyst for the [4 + 2] cycloaddition reaction, namely, Diels-Alderases, are briefly reviewed. These are discussed in the context of the mechanistic challenges associated with the technical difficulty of proving that the net formal [4 + 2] cycloaddition under study indeed proceeds through a synchronous mechanism and that the putative biosynthetic enzyme deploys the pericyclic transition state required for a Diels-Alder cycloaddition reaction.
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Affiliation(s)
- Kimberly Klas
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80524, United States
| | - Sachiko Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University , 5-1 Oe-honmachi, Kumamoto 862-0973, Japan
| | - David H Sherman
- Life Sciences Institute and Departments of Medicinal Chemistry, Microbiology & Immunology, and Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Robert M Williams
- Department of Chemistry, Colorado State University , Fort Collins, Colorado 80524, United States.,University of Colorado Cancer Center , Aurora, Colorado 80045, United States
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12
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Hubrich F, Juneja P, Müller M, Diederichs K, Welte W, Andexer JN. Chorismatase Mechanisms Reveal Fundamentally Different Types of Reaction in a Single Conserved Protein Fold. J Am Chem Soc 2015; 137:11032-7. [DOI: 10.1021/jacs.5b05559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florian Hubrich
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstr.
25, 79104 Freiburg, Germany
| | - Puneet Juneja
- Department
of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Michael Müller
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstr.
25, 79104 Freiburg, Germany
| | - Kay Diederichs
- Department
of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Wolfram Welte
- Department
of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Jennifer N. Andexer
- Institute
of Pharmaceutical Sciences, University of Freiburg, Albertstr.
25, 79104 Freiburg, Germany
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13
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Liu Z, Liu F, Aldrich CC. Stereocontrolled Synthesis of a Potential Transition-State Inhibitor of the Salicylate Synthase MbtI from Mycobacterium tuberculosis. J Org Chem 2015; 80:6545-52. [PMID: 26035083 DOI: 10.1021/acs.joc.5b00455] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mycobactins are small-molecule iron chelators (siderophores) produced by Mycobacterium tuberculosis (Mtb) for iron mobilization. The bifunctional salicylate synthase MbtI catalyzes the first step of mycobactin biosynthesis through the conversion of the primary metabolite chorismate into salicylic acid via isochorismate. We report the design, synthesis, and biochemical evaluation of an inhibitor based on the putative transition state (TS) for the isochorismatase partial reaction of MbtI. The inhibitor mimics the hypothesized charge buildup at C-4 of chorismate in the TS as well as C-O bond formation at C-6. Another important design element of the inhibitor is replacement of the labile pyruvate side chain in chorismate with a stable C-linked propionate isostere. We developed a stereocontrolled synthesis of the highly functionalized cyclohexene inhibitor that features an asymmetric aldol reaction using a titanium enolate, diastereoselective Grignard addition to a tert-butanesulfinyl aldimine, and ring closing olefin metathesis as key steps.
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Affiliation(s)
- Zheng Liu
- †Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Feng Liu
- †Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- †Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street Southeast, Minneapolis, Minnesota 55455, United States
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14
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In vitro production and purification of isochorismate using a two-enzyme cascade. J Biotechnol 2014; 191:93-8. [DOI: 10.1016/j.jbiotec.2014.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/26/2014] [Accepted: 06/03/2014] [Indexed: 11/24/2022]
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15
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Meneely KM, Luo Q, Lamb AL. Redesign of MST enzymes to target lyase activity instead promotes mutase and dehydratase activities. Arch Biochem Biophys 2013; 539:70-80. [PMID: 24055536 DOI: 10.1016/j.abb.2013.09.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 11/20/2022]
Abstract
The isochorismate and salicylate synthases are members of the MST family of enzymes. The isochorismate synthases establish an equilibrium for the conversion chorismate to isochorismate and the reverse reaction. The salicylate synthases convert chorismate to salicylate with an isochorismate intermediate; therefore, the salicylate synthases perform isochorismate synthase and isochorismate-pyruvate lyase activities sequentially. While the active site residues are highly conserved, there are two sites that show trends for lyase-activity and lyase-deficiency. Using steady state kinetics and HPLC progress curves, we tested the "interchange" hypothesis that interconversion of the amino acids at these sites would promote lyase activity in the isochorismate synthases and remove lyase activity from the salicylate synthases. An alternative, "permute" hypothesis, that chorismate-utilizing enzymes are designed to permute the substrate into a variety of products and tampering with the active site may lead to identification of adventitious activities, is tested by more sensitive NMR time course experiments. The latter hypothesis held true. The variant enzymes predominantly catalyzed chorismate mutase-prephenate dehydratase activities, sequentially generating prephenate and phenylpyruvate, augmenting previously debated (mutase) or undocumented (dehydratase) adventitious activities.
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Affiliation(s)
- Kathleen M Meneely
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, United States
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16
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Lou M, Gilpin ME, Burger SK, Malik AM, Gawuga V, Popović V, Capretta A, Berti PJ. Transition state analysis of acid-catalyzed hydrolysis of an enol ether, enolpyruvylshikimate 3-phosphate (EPSP). J Am Chem Soc 2012; 134:12947-57. [PMID: 22765168 DOI: 10.1021/ja3043382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton transfer to carbon represents a significant catalytic challenge because of the large intrinsic energetic barrier and the frequently unfavorable thermodynamics. Multiple kinetic isotope effects (KIEs) were measured for acid-catalyzed hydrolysis of the enol ether functionality of enolpyruvylshikimate 3-phosphate (EPSP) as a nonenzymatic analog of the EPSP synthase (AroA) reaction. The large solvent deuterium KIE demonstrated that protonating C3 was the rate-limiting step, and the lack of solvent hydron exchange into EPSP demonstrated that protonation was irreversible. The reaction mechanism was stepwise, with C3, the methylene carbon, being protonated to form a discrete oxacarbenium ion intermediate before water attack at the cationic center, that is, an AH(‡)*AN (or AH(‡) + AN) mechanism. The calculated 3-(14)C and 3,3-(2)H2 KIEs varied as a function of the extent of proton transfer at the transition state, as reflected in the C3-H(+) bond order, nC3-H+. The calculated 3-(14)C KIE was a function primarily of C3 coupling with the movement of the transferring proton, as reflected in the reaction coordinate contribution ((light)ν(‡)/(heavy)ν(‡)), rather than of changes in bonding. Coupling was strongest in early and late transition states, where the reaction coordinate frequency was lower. The other calculated (14)C and (18)O KIEs were more sensitive to interactions with counterions and solvation in the model structures than nC3-H+. The KIEs revealed a moderately late transition state with significant oxacarbenium ion character and with a C3-H(+) bond order ≈0.6.
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Affiliation(s)
- Meiyan Lou
- Department of Chemistry & Chemical Biology, and †Department of Biochemistry & Biomedical Sciences, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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17
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Ferrer S, Martí S, Moliner V, Tuñón I, Bertrán J. Understanding the different activities of highly promiscuous MbtI by computational methods. Phys Chem Chem Phys 2012; 14:3482-9. [DOI: 10.1039/c2cp23149b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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18
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Luo Q, Meneely KM, Lamb AL. Entropic and enthalpic components of catalysis in the mutase and lyase activities of Pseudomonas aeruginosa PchB. J Am Chem Soc 2011; 133:7229-33. [PMID: 21504201 DOI: 10.1021/ja202091a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The isochorismate-pyruvate lyase from Pseudomonas aeruginosa (PchB) catalyzes two pericyclic reactions, demonstrating the eponymous activity and also chorismate mutase activity. The thermodynamic parameters for these enzyme-catalyzed activities, as well as the uncatalyzed isochorismate decomposition, are reported from temperature dependence of k(cat) and k(uncat) data. The entropic effects do not contribute to enzyme catalysis as expected from previously reported chorismate mutase data. Indeed, an entropic penalty for the enzyme-catalyzed mutase reaction (ΔS(++) = -12.1 ± 0.6 cal/(mol K)) is comparable to that of the previously reported uncatalyzed reaction, whereas that of the enzyme-catalyzed lyase reaction (ΔS(++) = -24.3 ± 0.2 cal/(mol K)) is larger than that of the uncatalyzed lyase reaction (-15.77 ± 0.02 cal/(mol K)) documented here. With the assumption that chemistry is rate-limiting, we propose that a reactive substrate conformation is formed upon loop closure of the active site and that ordering of the loop contributes to the entropic penalty for converting the enzyme substrate complex to the transition state.
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Affiliation(s)
- Qianyi Luo
- Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, USA
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19
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Vasan M, Neres J, Williams J, Wilson DJ, Teitelbaum AM, Remmel RP, Aldrich CC. Inhibitors of the salicylate synthase (MbtI) from Mycobacterium tuberculosis discovered by high-throughput screening. ChemMedChem 2011; 5:2079-87. [PMID: 21053346 DOI: 10.1002/cmdc.201000275] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A simple steady-state kinetic high-throughput assay was developed for the salicylate synthase MbtI from Mycobacterium tuberculosis, which catalyzes the first committed step of mycobactin biosynthesis. The mycobactins are small-molecule iron chelators produced by M. tuberculosis, and their biosynthesis has been identified as a promising target for the development of new antitubercular agents. The assay was miniaturized to a 384-well plate format and high-throughput screening was performed at the National Screening Laboratory for the Regional Centers of Excellence in Biodefense and Emerging Infectious Diseases (NSRB). Three classes of compounds were identified comprising the benzisothiazolones (class I), diarylsulfones (class II), and benzimidazole-2-thiones (class III). Each of these compound series was further pursued to investigate their biochemical mechanism and structure-activity relationships. Benzimidazole-2-thione 4 emerged as the most promising inhibitor owing to its potent reversible inhibition.
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Affiliation(s)
- Mahalakshmi Vasan
- Center for Drug Design, University of Minnesota, Minneapolis, 55455, USA
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Kerbarh O, Ciulli A, Chirgadze DY, Blundell TL, Abell C. Nucleophile Selectivity of Chorismate-Utilizing Enzymes. Chembiochem 2007; 8:622-4. [PMID: 17335098 DOI: 10.1002/cbic.200700019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Olivier Kerbarh
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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Claeyssens F, Harvey JN, Manby FR, Mata RA, Mulholland AJ, Ranaghan KE, Schütz M, Thiel S, Thiel W, Werner HJ. High-accuracy computation of reaction barriers in enzymes. Angew Chem Int Ed Engl 2007; 45:6856-9. [PMID: 16991165 DOI: 10.1002/anie.200602711] [Citation(s) in RCA: 211] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Frederik Claeyssens
- School of Chemistry, University of Bristol, Cantocks Close, Bristol, BS8 1TS, UK
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Claeyssens F, Harvey JN, Manby FR, Mata RA, Mulholland AJ, Ranaghan KE, Schütz M, Thiel S, Thiel W, Werner HJ. High-Accuracy Computation of Reaction Barriers in Enzymes. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200602711] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Giraldo J, Roche D, Rovira X, Serra J. The catalytic power of enzymes: Conformational selection or transition state stabilization? FEBS Lett 2006; 580:2170-7. [PMID: 16616138 DOI: 10.1016/j.febslet.2006.03.060] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Revised: 03/19/2006] [Accepted: 03/20/2006] [Indexed: 11/19/2022]
Abstract
The mechanism by which enzymes produce enormous rate enhancements in the reactions they catalyze remains unknown. Two viewpoints, selection of ground state conformations and stabilization of the transition state, are present in the literature in apparent opposition. To provide more insight into current discussion about enzyme efficiency, a two-state model of enzyme catalysis was developed. The model was designed to include both the pre-chemical (ground state conformations) and the chemical (transition state) components of the process for the substrate both in water and in the enzyme. Although the model is of general applicability, the chorismate to prephenate reaction catalyzed by chorismate mutase was chosen for illustrative purposes. The resulting kinetic equations show that the catalytic power of enzymes, quantified as the k(cat)/k(uncat) ratio, is the product of two terms: one including the equilibrium constants for the substrate conformational states and the other including the rate constants for the uncatalyzed and catalyzed chemical reactions. The model shows that these components are not mutually exclusive and can be simultaneously present in an enzymic system, being their relative contribution a property of the enzyme. The developed mathematical expressions reveal that the conformational and reaction components of the process perform differently for the translation of molecular efficiency (changes in energy levels) into observed enzymic efficiency (changes in k(cat)), being, in general, more productive the component involving the transition state.
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Affiliation(s)
- Jesús Giraldo
- Grup Biomatemàtic de Recerca, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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Okvist M, Dey R, Sasso S, Grahn E, Kast P, Krengel U. 1.6 A crystal structure of the secreted chorismate mutase from Mycobacterium tuberculosis: novel fold topology revealed. J Mol Biol 2006; 357:1483-99. [PMID: 16499927 DOI: 10.1016/j.jmb.2006.01.069] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 01/17/2006] [Accepted: 01/18/2006] [Indexed: 10/25/2022]
Abstract
The presence of exported chorismate mutases produced by certain organisms such as Mycobacterium tuberculosis has been shown to correlate with their pathogenicity. As such, these proteins comprise a new group of promising selective drug targets. Here, we report the high-resolution crystal structure of the secreted dimeric chorismate mutase from M. tuberculosis (*MtCM; encoded by Rv1885c), which represents the first 3D-structure of a member of this chorismate mutase family, termed the AroQ(gamma) subclass. Structures are presented both for the unliganded enzyme and for a complex with a transition state analog. The protomer fold resembles the structurally characterized (dimeric) Escherichia coli chorismate mutase domain, but exhibits a new topology, with helix H4 of *MtCM carrying the catalytic site residue missing in the shortened helix H1. Furthermore, the structure of each *MtCM protomer is significantly more compact and only harbors one active site pocket, which is formed entirely by one polypeptide chain. Apart from the structural model, we present evidence as to how the substrate may enter the active site.
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Affiliation(s)
- Mats Okvist
- Department of Chemistry and Bioscience, Chalmers University of Technology, P.O. Box 462, SE-40530 Göteborg, Sweden
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Zhang X, Bruice TC. The proficiency of a thermophilic chorismate mutase enzyme is solely through an entropic advantage in the enzyme reaction. Proc Natl Acad Sci U S A 2005; 102:18356-60. [PMID: 16344484 PMCID: PMC1317962 DOI: 10.1073/pnas.0509234102] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A study of the Thermus thermophilus chorismate mutase (TtCM) is described by using quantum mechanics (self-consistent-charge density-functional tight binding)/molecular mechanics, umbrella sampling, and the weighted histogram analysis method. The computed free energies of activation for the reactions in water and TtCM are comparable to the experimental values. The free energies for formation of near attack conformer have been determined to be 8.06 and 0.05 kcal/mol in water and TtCM, respectively. The near attack conformer stabilization contributes approximately 90% to the proficiency of the enzymatic reaction compared with the reaction in water. The transition state (TS) structures and partial atom charges are much the same in the enzymatic and water reactions. The difference in the electrostatic interactions of Arg-89 with O13 in the enzyme-substrate complex and enzyme-TS complex provides the latter with but 0.55 kcal/mol of 1.92 kcal/mol total TS stabilization. Differences in electrostatic interactions between components at the active site in the enzyme-substrate complex and enzyme-TS complex are barely significant, such that TS stabilization is of minor importance and the enzymatic catalysis is through an entropic advantage.
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Affiliation(s)
- Xiaohua Zhang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, USA
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