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Niwa T, Nishibashi K, Sato H, Ujiie K, Yamashita K, Egami H, Hamashima Y. Structure Dependence in Asymmetric Deprotonative Fluorination and Fluorocyclization Reactions of Allylamine Derivatives with Linked Binaphthyl Dicarboxylate Phase-Transfer Catalyst. J Am Chem Soc 2021; 143:16599-16609. [PMID: 34590843 DOI: 10.1021/jacs.1c06783] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The asymmetric fluorofunctionalization of γ,γ-disubstituted allylamine derivatives (e.g., 3, 7, and 8) was investigated using our dianionic phase-transfer catalyst. Depending on the substituents on the alkene moiety, the reaction afforded chiral allylic fluorides and fluorinated dihydrooxazines in a highly enantioselective manner (up to 99% ee). The absolute stereochemistry of these products was found to be opposite to that in our previously reported fluorocyclization of γ-monosubstituted allylic amides (e.g., 13 and 14). To probe this interesting phenomenon, we investigated the influence of the substitution pattern of the alkene moiety on the reaction by means of NMR experiments and kinetic studies. The rate laws of the deprotonative fluorination and the fluorocyclization of γ,γ-disubstituted substrates were v = k[cat]0.6, while that of the fluorocyclization of γ-monosubstituted substrates was v = k[substrate][cat]0.4. An exponent of less than 1 suggests the involvement of an aggregated state of the catalyst ion pair in the catalytic cycle. Interestingly, a positive nonlinear effect was observed in the reactions of the γ,γ-disubstituted substrates, while a negative nonlinear effect was observed in the case of the γ-monosubstituted substrates. Thus, the reaction pathway depends on the presence or absence of an alkyl substituent at the γ position of the substrates, and on the basis of our mechanistic studies we propose that the active catalytic species for γ,γ-disubstituted substrates is a catalyst ion pair aggregate, whereas that for γ-monosubstituted substrates is the more active monomeric catalyst ion pair species, even though its concentration would be low.
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Affiliation(s)
- Tomoki Niwa
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kousuke Nishibashi
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hitomi Sato
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kiyoshi Ujiie
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Kenji Yamashita
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Hiromichi Egami
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
| | - Yoshitaka Hamashima
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan
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Angelastro A, Ruiz-Pernía JJ, Tuñón I, Moliner V, Luk LYP, Allemann RK. Loss of Hyperconjugative Effects Drives Hydride Transfer during Dihydrofolate Reductase Catalysis. ACS Catal 2019; 9:10343-10349. [PMID: 32051770 PMCID: PMC7007191 DOI: 10.1021/acscatal.9b02839] [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: 07/12/2019] [Revised: 09/20/2019] [Indexed: 02/06/2023]
Abstract
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Hydride transfer
is widespread in nature and has an essential role
in applied research. However, the mechanisms of how this transformation
occurs in living organisms remain a matter of vigorous debate. Here,
we examined dihydrofolate reductase (DHFR), an enzyme that catalyzes
hydride from C4′ of NADPH to C6 of 7,8-dihydrofolate (H2F). Despite many investigations of the mechanism of this reaction,
the contribution of polarization of the π-bond of H2F in driving hydride transfer remains unclear. H2F was
stereospecifically labeled with deuterium β to the reacting
center, and β-deuterium kinetic isotope effects were measured.
Our experimental results combined with analysis derived from QM/MM
simulations reveal that hydride transfer is triggered by polarization
at the C6 of H2F. The σ Cβ–H
bonds contribute to the buildup of the cationic character during the
chemical transformation, and hyperconjugation influences the formation
of the transition state. Our findings provide key insights into the
hydride transfer mechanism of the DHFR-catalyzed reaction, which is
a target for antiproliferative drugs and a paradigmatic model in mechanistic
enzymology.
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Affiliation(s)
- Antonio Angelastro
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | | | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Louis Y. P. Luk
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Rudolf K. Allemann
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
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3
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Mansoorabadi SO, Thibodeaux CJ, Liu HW. The diverse roles of flavin coenzymes--nature's most versatile thespians. J Org Chem 2007; 72:6329-42. [PMID: 17580897 PMCID: PMC2519020 DOI: 10.1021/jo0703092] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Flavin coenzymes play a variety of roles in biological systems. This Perspective highlights the chemical versatility of flavins by reviewing research on five flavoenzymes that have been studied in our laboratory. Each of the enzymes discussed in this review [the acyl-CoA dehydrogenases (ACDs), CDP-6-deoxy-l-threo-d-glycero-4-hexulose-3-dehydrase reductase (E3), CDP-4-aceto-3,6-dideoxygalactose synthase (YerE), UDP-galactopyranose mutase (UGM), and type II isopentenyl diphosphate:dimethylallyl diphosphate isomerase (IDI-2)] utilizes flavin in a distinct role. In particular, the catalytic mechanisms of two of these enzymes, UGM and IDI-2, may involve novel flavin chemistry.
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Affiliation(s)
- Steven O. Mansoorabadi
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
| | - Christopher J. Thibodeaux
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
| | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA
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4
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Pongdee R, Liu HW. Elucidation of enzyme mechanisms using fluorinated substrate analogues. Bioorg Chem 2004; 32:393-437. [PMID: 15381404 DOI: 10.1016/j.bioorg.2004.06.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2004] [Indexed: 11/24/2022]
Abstract
A great variety of biological reactions that are physiologically important are catalyzed by enzymes. Understanding the reaction course of these enzyme-catalyzed transformations are of significant importance since the insights gained from these experiments may facilitate the design of methods to control or mimic their actions. A common strategy to study enzyme catalyses is to use fluorinated substrate analogues as mechanistic probes, since fluorine is an effective hydroxyl group mimic and can also be used to replace a hydrogen atom. Using fluorinated substrate probes have enabled researchers to obtain crucial information regarding the catalytic mechanism of enzymatic reactions. Many of these compounds are good enzyme inhibitors and have been developed into clinically useful chemotherapeutic agents. This review will discuss some examples of the use of fluorine containing compounds as mechanistic probes/enzyme inhibitors, many of which are selected from our own work.
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Affiliation(s)
- Rongson Pongdee
- Division of Medicinal Chemistry, Department of Chemistry and Biochemistry, College of Pharmacy, University of Texas, Austin, TX 78712, USA
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5
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Ahn HJ, Yoon HJ, Lee B, Suh SW. Crystal structure of chorismate synthase: a novel FMN-binding protein fold and functional insights. J Mol Biol 2004; 336:903-15. [PMID: 15095868 DOI: 10.1016/j.jmb.2003.12.072] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chorismate synthase catalyzes the conversion of 5-enolpyruvylshikimate 3-phosphate to chorismate in the shikimate pathway, which represents an attractive target for discovering antimicrobial agents and herbicides. Chorismate serves as a common precursor for the synthesis of aromatic amino acids and many aromatic compounds in microorganisms and plants. Chorismate synthase requires reduced FMN as a cofactor but the catalyzed reaction involves no net redox change. Here, we have determined the crystal structure of chorismate synthase from Helicobacter pylori in both FMN-bound and FMN-free forms. It is a tetrameric enzyme, with each monomer possessing a novel "beta-alpha-beta sandwich fold". Highly conserved regions, including several flexible loops, cluster together around the bound FMN to form the active site. The unique FMN-binding site is formed largely by a single subunit, with a small contribution from a neighboring subunit. The isoalloxazine ring of the bound FMN is significantly non-planar. Our structure illuminates the essential functional roles played by the cofactor.
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Affiliation(s)
- Hyung Jun Ahn
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-0742, South Korea
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Kitzing K, Auweter S, Amrhein N, Macheroux P. Mechanism of chorismate synthase. Role of the two invariant histidine residues in the active site. J Biol Chem 2003; 279:9451-61. [PMID: 14668332 DOI: 10.1074/jbc.m312471200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chorismate synthase catalyzes the last step in the common shikimate pathway leading to aromatic compounds such as the aromatic amino acids. The reaction consists of the 1,4-anti-elimination of the 3-phosphate group and the C-(6proR) hydrogen from 5-enolpyruvylshikimate 3-phosphate to yield chorismate. Although this reaction does not involve a net redox change, the enzyme has an absolute requirement for reduced flavin mononucleotide, which is not consumed during the reaction. Two invariant histidine residues are found in the active site of the enzyme: His(17) and His(106). Using site-directed mutagenesis, both histidines were replaced by alanine, reducing the activity 10- and 20-fold in the H106A and H17A mutant protein, respectively. Based on the characterization of the two single mutant proteins, it is proposed that His(106) serves to protonate the monoanionic reduced FMN, whereas His(17) protonates the leaving phosphate group of the substrate. An enzymatic reaction mechanism in keeping with the experimental results is presented.
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Affiliation(s)
- Karina Kitzing
- Swiss Federal Institute of Technology Zürich, Department of Agricultural and Food Sciences, Universitätstrasse 2, CH-8092 Zürich, Switzerland
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Abstract
Density functional calculations (B3LYP/6-31+G(d,p)) were carried out to investigate the mechanism of the anti-1,4-elimination of phosphate from 5-enolpyruvylshikimate-3-phosphate 1 that is catalyzed by chorismate synthase. Of particular interest was the functional role of the reduced flavin cofactor. [reaction: see text]
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Affiliation(s)
- O Dmitrenko
- Department of Chemistry and Chemical Biology, Brown Laboratory, University of Delaware, Newark, DE 19716, USA
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Bickelhaupt FM. Base-induced 1,4-elimination: insights from theory and mass spectrometry. MASS SPECTROMETRY REVIEWS 2001; 20:347-361. [PMID: 11997943 DOI: 10.1002/mas.10007] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Experimental and theoretical studies on gas-phase base-induced 1,4-elimination reactions are summarized and discussed. The emphasis is on the synergy that is achieved by combining the complementary data from mass spectrometry and theoretical chemistry. The scope and applications of 1,4-eliminations are discussed and compared with other elementary reactions; e.g., 1,2-elimination and aliphatic (S(N)2) and allylic (S(N)2') nucleophilic substitution. Furthermore, the syn versus anti stereochemistry of 1,4-elimination reactions and the effect of E versus Z stereochemistry of the substrate are examined. Particular attention is paid to the mechanistic nature of 1,4-elimination, i.e., E2 or E1cb, as well as special features such as the single-well E2 and E1cb mechanism. Also, new results from density functional theory computations (BP86/TZ2P) are presented.
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Affiliation(s)
- F M Bickelhaupt
- Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands.
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Osborne A, Thorneley RN, Abell C, Bornemann S. Studies with substrate and cofactor analogues provide evidence for a radical mechanism in the chorismate synthase reaction. J Biol Chem 2000; 275:35825-30. [PMID: 10956653 DOI: 10.1074/jbc.m005796200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chorismate synthase catalyzes the conversion of 5-enolpyruvylshikimate 3-phosphate (EPSP) to chorismate. The strict requirement for a reduced FMN cofactor and a trans-1,4-elimination are unusual. (6R)-6-Fluoro-EPSP was shown to be converted to chorismate stoichiometrically with enzyme-active sites in the presence of dithionite. This conversion was associated with the oxidation of FMN to give a stable flavin semiquinone. The IC(50) of the fluorinated substrate analogue was 0.5 and 250 microm with the Escherichia coli enzyme, depending on whether it was preincubated with the enzyme or not. The lack of dissociation of the flavin semiquinone and chorismate from the enzyme appears to be the basis of the essentially irreversible inhibition by this analogue. A dithionite-dependent transient formation of flavin semiquinone during turnover of (6S)-6-fluoro-EPSP has been observed. These reactions are best rationalized by radical chemistry that is strongly supportive of a radical mechanism occurring during normal turnover. The lack of activity with 5-deaza-FMN provides additional evidence for the role of flavin in catalysis by the E. coli enzyme.
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Affiliation(s)
- A Osborne
- Biological Chemistry Department, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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