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Zakary O, Body M, Charpentier T, Sarou-Kanian V, Legein C. Structural Modeling of O/F Correlated Disorder in TaOF 3 and NbOF 3-x(OH) x by Coupling Solid-State NMR and DFT Calculations. Inorg Chem 2023; 62:16627-16640. [PMID: 37747836 DOI: 10.1021/acs.inorgchem.3c02844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The structure of MOF3 (M = Nb, Ta) compounds was precisely modeled by combining powder X-ray diffraction, solid-state NMR spectroscopy, and semiempirical dispersion-corrected DFT calculations. It consists of stacked ∞(MOF3) layers along the c⃗ direction formed by heteroleptic corner-connected MX6 (X = O, F) octahedra. 19F NMR resonance assignments and occupancy rates of the anionic crystallographic sites have been revised. The bridging site is shared equally by the anions, and the terminal site is occupied by F only. An O/F correlated disorder is expected since cis-MO2F4 octahedra are favored, resulting in one-dimensional -F-M-O-M- strings along the <100> and <010> directions. Ten different 2 × 2 × 1 supercells per compound, fulfilling these characteristics, were built. Using DFT calculations and the GIPAW approach, the supercells were relaxed and the 19F isotropic chemical shift values were determined. The agreement between the experimental and calculated 19F spectra is excellent for TaOF3. The 1H and 19F experimental NMR spectra revealed that some of the bridging F atoms are substituted by OH groups, especially in NbOF3. New supercells involving OH groups were generated. Remarkably, the best agreement is obtained for the supercells with the composition closest to that estimated from the 19F NMR spectra, i.e., NbOF2.85(OH)0.15.
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Affiliation(s)
- Ouail Zakary
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRSLe Mans Université, 72805 Le Mans Cedex 9, France
| | - Monique Body
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRSLe Mans Université, 72805 Le Mans Cedex 9, France
| | | | | | - Christophe Legein
- Institut des Molécules et Matériaux du Mans (IMMM) - UMR 6283 CNRSLe Mans Université, 72805 Le Mans Cedex 9, France
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2
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Synthesis of Trifluoromethylated Monoterpene Amino Alcohols. Molecules 2022; 27:molecules27207068. [PMID: 36296661 PMCID: PMC9607099 DOI: 10.3390/molecules27207068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
For the first time, monoterpene trifluoromethylated β-hydroxy-benzyl-O-oximes were synthesized in 81–95% yields by nucleophilic addition of the Ruppert–Prakash reagent (TMSCF3) to the corresponding β-keto-benzyl-O-oximes based on (+)-nopinone, (−)-verbanone and (+)-camphoroquinone. Trifluoromethylation has been determined to entirely proceed chemo- and stereoselective at the C=O rather than C=N bond. Trifluoromethylated benzyl-O-oximes were reduced to the corresponding α-trifluoromethyl-β-amino alcohols in 82–88% yields. The structure and configuration of the compounds obtained have been established.
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3
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Urner LM, Lee GY, Treacy JW, Turlik A, Khan SI, Houk KN, Jung ME. Intramolecular N-H⋅⋅⋅F Hydrogen Bonding Interaction in a Series of 4-Anilino-5-Fluoroquinazolines: Experimental and Theoretical Characterization of Electronic and Conformational Effects. Chemistry 2022; 28:e202103135. [PMID: 34767667 PMCID: PMC9482468 DOI: 10.1002/chem.202103135] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Indexed: 01/12/2023]
Abstract
The 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline scaffold is presented as a novel model system for the characterization of the weak NH⋅⋅⋅F hydrogen bonding (HB) interaction. In this scaffold, the aniline NH proton is forced into close proximity with the nearby fluorine (dH,F ∼2.0 Å, ∠∼138°), and a through-space interaction is observed by NMR spectroscopy with couplings (1h JNH,F ) of 19±1 Hz. A combination of experimental (NMR spectroscopy and X-ray crystallography) and theoretical methods (DFT calculations) were used for the characterization of this weak interaction. In particular, the effects of conformational rigidity and steric compression on coupling were investigated. This scaffold was used for the direct comparison of fluoride with methoxy as HB acceptors, and the susceptibility of the NH⋅⋅⋅F interaction to changes in electron distribution and resonance was probed by preparing a series of molecules with different electron-donating or -withdrawing groups in the positions para to the NH and F. The results support the idea that fluorine can act as a weak HB acceptor, and the HB strength can be modulated through additive and linear electronic substituent effects.
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Affiliation(s)
- Lorenz M. Urner
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Ga Young Lee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Joseph W. Treacy
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Aneta Turlik
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Saeed I. Khan
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
| | - Michael E. Jung
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 (USA)
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4
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Prinz C, Starke L, Ramspoth TF, Kerkering J, Martos Riaño V, Paul J, Neuenschwander M, Oder A, Radetzki S, Adelhoefer S, Ramos Delgado P, Aravina M, Millward JM, Fillmer A, Paul F, Siffrin V, von Kries JP, Niendorf T, Nazaré M, Waiczies S. Pentafluorosulfanyl (SF 5) as a Superior 19F Magnetic Resonance Reporter Group: Signal Detection and Biological Activity of Teriflunomide Derivatives. ACS Sens 2021; 6:3948-3956. [PMID: 34666481 PMCID: PMC8630787 DOI: 10.1021/acssensors.1c01024] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022]
Abstract
Fluorine (19F) magnetic resonance imaging (MRI) is severely limited by a low signal-to noise ratio (SNR), and tapping it for 19F drug detection in vivo still poses a significant challenge. However, it bears the potential for label-free theranostic imaging. Recently, we detected the fluorinated dihydroorotate dehydrogenase (DHODH) inhibitor teriflunomide (TF) noninvasively in an animal model of multiple sclerosis (MS) using 19F MR spectroscopy (MRS). In the present study, we probed distinct modifications to the CF3 group of TF to improve its SNR. This revealed SF5 as a superior alternative to the CF3 group. The value of the SF5 bioisostere as a 19F MRI reporter group within a biological or pharmacological context is by far underexplored. Here, we compared the biological and pharmacological activities of different TF derivatives and their 19F MR properties (chemical shift and relaxation times). The 19F MR SNR efficiency of three MRI methods revealed that SF5-substituted TF has the highest 19F MR SNR efficiency in combination with an ultrashort echo-time (UTE) MRI method. Chemical modifications did not reduce pharmacological or biological activity as shown in the in vitro dihydroorotate dehydrogenase enzyme and T cell proliferation assays. Instead, SF5-substituted TF showed an improved capacity to inhibit T cell proliferation, indicating better anti-inflammatory activity and its suitability as a viable bioisostere in this context. This study proposes SF5 as a novel superior 19F MR reporter group for the MS drug teriflunomide.
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Affiliation(s)
- Christian Prinz
- Berlin
Ultrahigh Field Facility (B.U.F.F.), Max
Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße
10, 13125 Berlin, Germany
- Experimental
and Clinical Research Center, a joint cooperation between the Charité
- Universitätsmedizin Berlin and the Max Delbrück Center
for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Ludger Starke
- Berlin
Ultrahigh Field Facility (B.U.F.F.), Max
Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße
10, 13125 Berlin, Germany
| | - Tizian-Frank Ramspoth
- Medicinal
Chemistry, Leibniz-Institut für Molekulare
Pharmakologie (FMP), Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Janis Kerkering
- Experimental
and Clinical Research Center, a joint cooperation between the Charité
- Universitätsmedizin Berlin and the Max Delbrück Center
for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Vera Martos Riaño
- Medicinal
Chemistry, Leibniz-Institut für Molekulare
Pharmakologie (FMP), Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Jérôme Paul
- Medicinal
Chemistry, Leibniz-Institut für Molekulare
Pharmakologie (FMP), Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Martin Neuenschwander
- Screening
Unit, Leibniz-Institut für Molekulare
Pharmakologie (FMP), Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Andreas Oder
- Screening
Unit, Leibniz-Institut für Molekulare
Pharmakologie (FMP), Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Silke Radetzki
- Screening
Unit, Leibniz-Institut für Molekulare
Pharmakologie (FMP), Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Siegfried Adelhoefer
- Berlin
Ultrahigh Field Facility (B.U.F.F.), Max
Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße
10, 13125 Berlin, Germany
| | - Paula Ramos Delgado
- Berlin
Ultrahigh Field Facility (B.U.F.F.), Max
Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße
10, 13125 Berlin, Germany
- Experimental
and Clinical Research Center, a joint cooperation between the Charité
- Universitätsmedizin Berlin and the Max Delbrück Center
for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Mariya Aravina
- Berlin
Ultrahigh Field Facility (B.U.F.F.), Max
Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße
10, 13125 Berlin, Germany
| | - Jason M. Millward
- Berlin
Ultrahigh Field Facility (B.U.F.F.), Max
Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße
10, 13125 Berlin, Germany
- Experimental
and Clinical Research Center, a joint cooperation between the Charité
- Universitätsmedizin Berlin and the Max Delbrück Center
for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Ariane Fillmer
- Physikalisch-Technische
Bundesanstalt (PTB), Abbestraße 2-12, 10587 Berlin, Germany
| | - Friedemann Paul
- Experimental
and Clinical Research Center, a joint cooperation between the Charité
- Universitätsmedizin Berlin and the Max Delbrück Center
for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße 10, 13125 Berlin, Germany
- Charité
− Universitätsmedizin Berlin, corporate member of Freie
Universität Berlin, Humboldt-Universität zu Berlin,
and Berlin Institute of Health (BIH), Charitéplatz 1, 10117 Berlin, Germany
| | - Volker Siffrin
- Experimental
and Clinical Research Center, a joint cooperation between the Charité
- Universitätsmedizin Berlin and the Max Delbrück Center
for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Jens-Peter von Kries
- Screening
Unit, Leibniz-Institut für Molekulare
Pharmakologie (FMP), Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Thoralf Niendorf
- Berlin
Ultrahigh Field Facility (B.U.F.F.), Max
Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße
10, 13125 Berlin, Germany
- Experimental
and Clinical Research Center, a joint cooperation between the Charité
- Universitätsmedizin Berlin and the Max Delbrück Center
for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Marc Nazaré
- Medicinal
Chemistry, Leibniz-Institut für Molekulare
Pharmakologie (FMP), Robert Rössle Straße 10, 13125 Berlin, Germany
| | - Sonia Waiczies
- Berlin
Ultrahigh Field Facility (B.U.F.F.), Max
Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße
10, 13125 Berlin, Germany
- Experimental
and Clinical Research Center, a joint cooperation between the Charité
- Universitätsmedizin Berlin and the Max Delbrück Center
for Molecular Medicine in the Helmholtz Association, Robert Rössle Straße 10, 13125 Berlin, Germany
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5
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Berrino E, Michelet B, Martin‐Mingot A, Carta F, Supuran CT, Thibaudeau S. Modulating the Efficacy of Carbonic Anhydrase Inhibitors through Fluorine Substitution. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Emanuela Berrino
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Bastien Michelet
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
| | - Agnès Martin‐Mingot
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
| | - Fabrizio Carta
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Claudiu T. Supuran
- University of Florence NEUROFARBA Dept. Sezione di Scienze Farmaceutiche e Nutraceutiche Via Ugo Schiff 6 50019 Sesto Fiorentino Florence Italy
| | - Sébastien Thibaudeau
- Superacid Group in “Organic Synthesis” Team Université de Poitiers CNRS UMR 7285 IC2MP Bât. B28, 4 rue Michel Brunet, TSA 51106 86073 Poitiers Cedex 09 France
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6
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Buchholz CR, Pomerantz WCK. 19F NMR viewed through two different lenses: ligand-observed and protein-observed 19F NMR applications for fragment-based drug discovery. RSC Chem Biol 2021; 2:1312-1330. [PMID: 34704040 PMCID: PMC8496043 DOI: 10.1039/d1cb00085c] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
19F NMR has emerged as a powerful tool in drug discovery, particularly in fragment-based screens. The favorable magnetic resonance properties of the fluorine-19 nucleus, the general absence of fluorine in biological settings, and its ready incorporation into both small molecules and biopolymers, has enabled multiple applications of 19F NMR using labeled small molecules and proteins in biophysical, biochemical, and cellular experiments. This review will cover developments in ligand-observed and protein-observed 19F NMR experiments tailored towards drug discovery with a focus on fragment screening. We also cover the key advances that have furthered the field in recent years, including quantitative, structural, and in-cell methodologies. Several case studies are described for each application to highlight areas for innovation and to further catalyze new NMR developments for using this versatile nucleus.
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Affiliation(s)
- Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
| | - William C K Pomerantz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
- Department of Chemistry, University of Minnesota 207 Pleasant St. SE Minneapolis Minnesota 55455 USA
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7
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Organocatalytic Asymmetric Michael Addition in Aqueous Media by a Hydrogen-Bonding Catalyst and Application for Inhibitors of GABAB Receptor. Catalysts 2021. [DOI: 10.3390/catal11091134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Catalysts based on (R, R)-1,2-diphenylethylenediamine are, as chiral organic catalysts, applied to the asymmetric Michael addition to α, β-unsaturated nitroalkenes under neutral conditions. The role of an aqueous medium for organic catalytic activity can be reversed concerning hydrophilic-hydrophobic function depending on the reaction conditions. In this study, to provide an environmentally friendly system, the thiourea-based catalyst substituted with 3,5-(CF3)2-Ph was used in water solvents. The hydrophobic effect of the substituent provided fast reaction, high chemical yield, and mirror-image selectivity. This reaction allowed the preparation of GABAB agonists in an optically pure manner. Additionally, GABA (γ-aminobutyric acid) analogs such as baclofen and phenibut were synthesized as R-type S-type with high optical purity.
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8
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Vulpetti A, Dalvit C. Hydrogen Bond Acceptor Propensity of Different Fluorine Atom Types: An Analysis of Experimentally and Computationally Derived Parameters. Chemistry 2021; 27:8764-8773. [PMID: 33949737 DOI: 10.1002/chem.202100301] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/29/2022]
Abstract
The propensity of organic fluorine acting as a weak hydrogen bond acceptor (HBA) in intermolecular and intramolecular interactions has been the subject of many experimental and theoretical studies often reaching different conclusions. Over the last few years, new and stronger evidences have emerged for the direct involvement of fluorine in weak hydrogen bond (HB) formation. However, not all the fluorine atom types can act as weak HBA. In this work, the differential HBA propensity of various types of fluorine atoms was analyzed with a particular emphasis for the different types of alkyl fluorides. This was carried out by evaluating ab initio computed parameters, experimental 19 F NMR chemical shifts and small molecule crystallographic structures (extracted from the CSD database). According to this analysis, shielded (with reference to the 19 F NMR chemical shift) alkyl mono-fluorinated motifs display the highest HBA propensity in agreement with solution studies. Although much weaker than other well-characterized HB complexes, the fragile HBs formed by these fluorinated motifs have important implications for the chemical-physical and structural properties of the molecules, chemical reactions, and protein-ligand recognition.
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Affiliation(s)
- Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
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9
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Berrino E, Michelet B, Martin-Mingot A, Carta F, Supuran CT, Thibaudeau S. Modulating the Efficacy of Carbonic Anhydrase Inhibitors through Fluorine Substitution. Angew Chem Int Ed Engl 2021; 60:23068-23082. [PMID: 34028153 DOI: 10.1002/anie.202103211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/19/2021] [Indexed: 12/19/2022]
Abstract
The insertion of fluorine atoms and/or fluoroalkyl groups can lead to many beneficial effects in biologically active molecules, such as enhanced metabolic stability, bioavailability, lipophilicity, and membrane permeability, as well as a strengthening of protein-ligand binding interactions. However, this "magic effect" of fluorine atom(s) insertion can often be meaningless. Taking advantage of the wide range of data coming from the quest for carbonic anhydrase (CA) fluorinated inhibitors, this Minireview attempts to give "general guidelines" on how to wisely insert fluorine atom(s) within an inhibitor moiety to precisely enhance or disrupt ligand-protein interactions, depending on the target location of the fluorine substitution in the ligand. Multiple approaches such as ITC, kinetic and inhibition studies, X-ray crystallography, and NMR spectroscopy are useful in dissecting single binding contributions to the overall observed effect. The exploitation of innovative directions made in the field of protein and ligand-based fluorine NMR screening is also discussed to avoid misconduct and finely tune the exploitation of selective fluorine atom insertion in the future.
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Affiliation(s)
- Emanuela Berrino
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Bastien Michelet
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
| | - Agnès Martin-Mingot
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
| | - Fabrizio Carta
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Claudiu T Supuran
- University of Florence, NEUROFARBA Dept., Sezione di Scienze Farmaceutiche e Nutraceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Sébastien Thibaudeau
- Superacid Group in "Organic Synthesis" Team, Université de Poitiers, CNRS UMR 7285 IC2MP, Bât. B28, 4 rue Michel Brunet, TSA 51106, 86073, Poitiers Cedex 09, France
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10
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Elek M, Djokovic N, Frank A, Oljacic S, Zivkovic A, Nikolic K, Stark H. Synthesis, in silico, and in vitro studies of novel dopamine D 2 and D 3 receptor ligands. Arch Pharm (Weinheim) 2021; 354:e2000486. [PMID: 33615541 DOI: 10.1002/ardp.202000486] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/30/2022]
Abstract
Dopamine is an important neurotransmitter in the human brain and its altered concentrations can lead to various neurological diseases. We studied the binding of novel compounds at the dopamine D2 (D2 R) and D3 (D3 R) receptor subtypes, which belong to the D2 -like receptor family. The synthesis, in silico, and in vitro characterization of 10 dopamine receptor ligands were performed. Novel ligands were docked into the D2 R and D3 R crystal structures to examine the precise binding mode. A quantum mechanics/molecular mechanics study was performed to gain insights into the nature of the intermolecular interactions between the newly introduced pentafluorosulfanyl (SF5 ) moiety and D2 R and D3 R. A radioligand displacement assay determined that all of the ligands showed moderate-to-low nanomolar affinities at D2 R and D3 R, with a slight preference for D3 R, which was confirmed in the in silico studies. N-{4-[4-(2-Methoxyphenyl)piperazin-1-yl]butyl}-4-(pentafluoro-λ6-sulfanyl)benzamide (7i) showed the highest D3 R affinity and selectivity (pKi values of 7.14 [D2 R] and 8.42 [D3 R]).
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Affiliation(s)
- Milica Elek
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, Duesseldorf, NRW, Germany
| | - Nemanja Djokovic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Annika Frank
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, Duesseldorf, NRW, Germany
| | - Slavica Oljacic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Zivkovic
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, Duesseldorf, NRW, Germany
| | - Katarina Nikolic
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Holger Stark
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitaetsstr. 1, Duesseldorf, NRW, Germany
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11
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Fuente-Gómez GJ, Kellum CL, Miranda AC, Duff MR, Howell EE. Differentiation of the binding of two ligands to a tetrameric protein with a single symmetric active site by 19 F NMR. Protein Sci 2020; 30:477-484. [PMID: 33269489 PMCID: PMC7784773 DOI: 10.1002/pro.4007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/20/2020] [Accepted: 11/26/2020] [Indexed: 01/31/2023]
Abstract
R67 dihydrofolate reductase (R67 DHFR) is a plasmid‐encoded enzyme that confers resistance to the antibacterial drug trimethoprim. R67 DHFR is a tetramer with a single active site that is unusual as both cofactor and substrate are recognized by symmetry‐related residues. Such promiscuity has limited our previous efforts to differentiate ligand binding by NMR. To address this problem, we incorporated fluorine at positions 4, 5, 6, or 7 of the indole rings of tryptophans 38 and 45 and characterized the spectra to determine which probe was optimal for studying ligand binding. Two resonances were observed for all apo proteins. Unexpectedly, the W45 resonance appeared broad, and truncation of the disordered N‐termini resulted in the appearance of one sharp W45 resonance. These results are consistent with interaction of the N‐terminus with W45. Binding of the cofactor broadened W38 for all fluorine probes, whereas substrate, dihydrofolate, binding resulted in the appearance of three new resonances for 4‐ and 5‐fluoroindole labeled protein and severe line broadening for 6‐ and 7‐fluoroindole R67 DHFR. W45 became slightly broader upon ligand binding. With only two peaks in the 19F NMR spectra, our data were able to differentiate cofactor and substrate binding to the single, symmetric active site of R67 DHFR and yield binding affinities.
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Affiliation(s)
- Gabriel J Fuente-Gómez
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Creighton L Kellum
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Alexis C Miranda
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Michael R Duff
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
| | - Elizabeth E Howell
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee-Knoxville, Knoxville, Tennessee, USA
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12
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Comprehensive and High-Throughput Exploration of Chemical Space Using Broadband 19 F NMR-Based Screening. Angew Chem Int Ed Engl 2020; 59:14809-14817. [PMID: 32363632 DOI: 10.1002/anie.202002463] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/27/2020] [Indexed: 12/20/2022]
Abstract
Fragment-based lead discovery has become a fundamental approach to identify ligands that efficiently interact with disease-relevant targets. Among the numerous screening techniques, fluorine-detected NMR has gained popularity owing to its high sensitivity, robustness, and ease of use. To effectively explore chemical space, a universal NMR experiment, a rationally designed fragment library, and a sample composition optimized for a maximal number of compounds and minimal measurement time are required. Here, we introduce a comprehensive method that enabled the efficient assembly of a high-quality and diverse library containing nearly 4000 fragments and screening for target-specific binders within days. At the core of the approach is a novel broadband relaxation-edited NMR experiment that covers the entire chemical shift range of drug-like 19 F motifs in a single measurement. Our approach facilitates the identification of diverse binders and the fast ligandability assessment of new targets.
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Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA.,Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Regis Denay
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
| | - Christelle Henry
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Alvar D Gossert
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 - Magnetic Resonance, Karlsruhe Institute of Technology (KIT), 76131, Karlsruhe, Germany
| | - Andreas O Frank
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, 5300 Chiron Way, Emeryville, CA, 94608, USA
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13
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Lingel A, Vulpetti A, Reinsperger T, Proudfoot A, Denay R, Frommlet A, Henry C, Hommel U, Gossert AD, Luy B, Frank AO. Comprehensive and High‐Throughput Exploration of Chemical Space Using Broadband
19
F NMR‐Based Screening. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andreas Lingel
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Anna Vulpetti
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Tony Reinsperger
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andrew Proudfoot
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Regis Denay
- Global Discovery Chemistry Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alexandra Frommlet
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
| | - Christelle Henry
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Ulrich Hommel
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Alvar D. Gossert
- Chemical Biology and Therapeutics Novartis Institutes for BioMedical Research Novartis Campus 4056 Basel Switzerland
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance Karlsruhe Institute of Technology (KIT) 76131 Karlsruhe Germany
| | - Andreas O. Frank
- Global Discovery Chemistry Novartis Institutes for BioMedical Research 5300 Chiron Way Emeryville CA 94608 USA
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14
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Rosenberg RE, Chapman BK, Ferrill RN, Jung ES, Samaan CA. Approximating the Strength of the Intramolecular Hydrogen Bond in 2-Fluorophenol and Related Compounds: A New Application of a Classic Technique. J Phys Chem A 2020; 124:3851-3858. [PMID: 32312049 DOI: 10.1021/acs.jpca.0c01641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fluorinated organic compounds are ubiquitous in the pharmaceutical and agricultural industries. To better discern the mode of action of these compounds, it is critical to understand the strengths of hydrogen bonds involving fluorine. While established techniques can determine these strengths for intermolecular complexes, there is no analogous scheme for intramolecular hydrogen bonds. This work uses 1H nuclear magnetic resonance spectroscopy to measure the strength of intramolecular hydrogen bonds in ortho-substituted phenols. Titration of each phenol with DMSO in CCl4 yields a free energy of binding (ΔG). Subtraction of this value from the ΔG of binding of the standard, 4-fluorophenol, is shown to give the difference in ΔG for the cis and trans isomers of the ortho-substituted phenols. This difference is conventionally taken to be approximately equal to the ΔG of the intramolecular hydrogen bond. These data complement theoretical methods, which yield slightly larger ΔGs. Both theory and experiment point to a weak intramolecular hydrogen bond in 2-fluorophenol. The other 2-X-phenols have stronger hydrogen bonds, following the order F < Cl ≈ Br < OCH3. The methodology developed here can be readily applied to other systems with intramolecular hydrogen bonds.
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Affiliation(s)
- Robert E Rosenberg
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Bradley K Chapman
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Rachel N Ferrill
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Eiu Suk Jung
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
| | - Chris A Samaan
- Department of Chemistry, Transylvania University,300 North Broadway, Lexington, Kentucky 40508, United States
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15
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Jeyaram RA, Radha CA, Gromiha MM, Veluraja K. Design of fluorinated sialic acid analog inhibitor to H5 hemagglutinin of H5N1 influenza virus through molecular dynamics simulation study. J Biomol Struct Dyn 2019; 38:3504-3513. [PMID: 31594458 DOI: 10.1080/07391102.2019.1677500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Influenza epidemics and pandemics are caused by influenza A virus. The cell surface protein of hemagglutinin and neuraminidase is responsible for viral infection and release of progeny virus on the host cell membrane. Now 18 hemagglutinin and 11 neuraminidase subtypes are identified. The avian influenza virus of H5N1 is an emergent threat to public health issues. To control the influenza viral infection it is necessary to develop antiviral inhibitors and vaccination. In the present investigation we carried out 50 ns Molecular Dynamics simulation on H5 hemagglutinin of Influenza A virus H5N1 complexed with fluorinated sialic acid by substituting fluorine atoms at any two hydroxyls of sialic acid by considering combinatorial combination. The binding affinity between the protein-ligand complex system is investigated by calculating pair interaction energy and MM-PBSA binding free energy. All the complex structures are stabilized by hydrogen bonding interactions between the H5 protein and the ligand fluorinated sialic acid. It is concluded from all the analyses that the fluorinated complexes enhance the inhibiting potency against H5 hemagglutinin and the order of inhibiting potency is SIA-F9 ≫ SIA-F2 ≈ SIA-F7 ≈ SIA-F2F4 ≈ SIA-F2F9 ≈ SIA-F7F9 > SIA-F7F8 ≈ SIA-F2F8 ≈ SIA-F8F9 > SIA-F4 ≈ SIA-F4F7 ≈ SIA-F4F8 ≈ SIA-F8 ≈ SIA-F2F7 ≈ SIA > SIA-F4F9. This study suggests that one can design the inhibitor by using the mono fluorinated models SIA-F9, SIA-F2 and SIA-F7 and difluorinated models SIA-F2F4, SIA-F2F9 and SIA-F7F9 to inhibit H5 of H5N1 to avoid Influenza A viral infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- R A Jeyaram
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, Tamil Nadu, India
| | - K Veluraja
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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16
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Di Pietrantonio C, Pandey A, Gould J, Hasabnis A, Prosser RS. Understanding Protein Function Through an Ensemble Description: Characterization of Functional States by 19F NMR. Methods Enzymol 2019; 615:103-130. [DOI: 10.1016/bs.mie.2018.09.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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17
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Robalo JR, Vila Verde A. Unexpected trends in the hydrophobicity of fluorinated amino acids reflect competing changes in polarity and conformation. Phys Chem Chem Phys 2019; 21:2029-2038. [DOI: 10.1039/c8cp07025c] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hydration free energy of fluorinated amino acids is calculated with molecular simulations and explained with an analytical model.
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Affiliation(s)
- João R. Robalo
- Max Planck Institute for Colloids and Interfaces
- Department of Theory & Bio-systems
- Science Park
- Potsdam 14424
- Germany
| | - Ana Vila Verde
- Max Planck Institute for Colloids and Interfaces
- Department of Theory & Bio-systems
- Science Park
- Potsdam 14424
- Germany
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18
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A Chiron approach towards the stereoselective synthesis of polyfluorinated carbohydrates. Nat Commun 2018; 9:4721. [PMID: 30413697 PMCID: PMC6226540 DOI: 10.1038/s41467-018-06901-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 09/26/2018] [Indexed: 12/04/2022] Open
Abstract
The replacement of hydroxyl groups by fluorine atoms on hexopyranose scaffolds may allow access to the discovery of new chemical entities possessing unique physical, chemical and ultimately even biological properties. The prospect of significant effects generated by such multiple and controlled substitutions encouraged us to develop diverse synthetic routes towards the stereoselective synthesis of polyfluorinated hexopyranoses, six of which are unprecedented. Hence, we report the synthesis of heavily fluorinated galactose, glucose, mannose, talose, allose, fucose, and galacturonic acid methyl ester using a Chiron approach from inexpensive levoglucosan. Structural analysis of single-crystal X-ray diffractions and NMR studies confirm the conservation of favored 4C1 conformation for fluorinated carbohydrate analogs, while a slightly distorted conformation due to repulsive 1,3-diaxial F···F interaction is observed for the trifluorinated talose derivative. Finally, the relative stereochemistry of multi-vicinal fluorine atoms has a strong effect on the lipophilicities (logP). Polyfluorinated hexopyranoses display unique physical, chemical and biological properties, however their stereoselective synthesis is highly challenging. Here, the authors report a synthetic approach based on the chemical manipulation of inexpensive levoglucosan to obtain heavily fluorinated monosaccharides stereoselectively.
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19
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Dalvit C, Vulpetti A. Ligand-Based Fluorine NMR Screening: Principles and Applications in Drug Discovery Projects. J Med Chem 2018; 62:2218-2244. [DOI: 10.1021/acs.jmedchem.8b01210] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
| | - Anna Vulpetti
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
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20
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Xi N, Sun X, Li M, Sun M, Xi MA, Zhan Z, Yao J, Bai X, Wu Y, Liao M. Noncovalent Interactions of Fluorine with Amide and CH 2 Groups in N-Phenyl γ-Lactams: Covalently Identical Fluorine Atoms in Nonequivalent Chemical Environments. J Org Chem 2018; 83:11586-11594. [PMID: 30180581 DOI: 10.1021/acs.joc.8b01562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We designed and synthesized N-phenyl γ-lactam derivatives possessing two covalently identical ortho-F nuclei on the N-phenyl group. The F nuclei sited in different chemical environments where they were spatially adjacent to amide and alkyl groups due to hindered rotation around the central N-Ar bond. 19F NMR spectroscopic and X-ray crystallographic methods were used to distinguish the axially prochiral F nuclei and provide structural insights for through-space interactions between F and amide/CH2 groups. Direct spectroscopic evidence for multipolar interactions in F···amide and F···CH2 pairs were provided.
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Affiliation(s)
- Ning Xi
- The School of Pharmaceutical Sciences , Jilin University , 1266 Fujin Road , Changchun , Jilin 130021 , China.,Sunshine Lake Pharmaceutical Co., Ltd , Dongyangguang Hi-tech Park, Dongguan , Guangdong 523871 , China.,Calitor Sciences LLC , PO Box 19185, Newbury Park , California 91319-9185 , United States
| | - Xiaohua Sun
- The School of Pharmaceutical Sciences , Jilin University , 1266 Fujin Road , Changchun , Jilin 130021 , China
| | - Minxiong Li
- Sunshine Lake Pharmaceutical Co., Ltd , Dongyangguang Hi-tech Park, Dongguan , Guangdong 523871 , China
| | - Mingming Sun
- Sunshine Lake Pharmaceutical Co., Ltd , Dongyangguang Hi-tech Park, Dongguan , Guangdong 523871 , China
| | - Michael A Xi
- Calitor Sciences LLC , PO Box 19185, Newbury Park , California 91319-9185 , United States
| | - Zeping Zhan
- Sunshine Lake Pharmaceutical Co., Ltd , Dongyangguang Hi-tech Park, Dongguan , Guangdong 523871 , China
| | - Jia Yao
- Sunshine Lake Pharmaceutical Co., Ltd , Dongyangguang Hi-tech Park, Dongguan , Guangdong 523871 , China
| | - Xu Bai
- The School of Pharmaceutical Sciences , Jilin University , 1266 Fujin Road , Changchun , Jilin 130021 , China
| | - Yanjun Wu
- Sunshine Lake Pharmaceutical Co., Ltd , Dongyangguang Hi-tech Park, Dongguan , Guangdong 523871 , China
| | - Min Liao
- Sunshine Lake Pharmaceutical Co., Ltd , Dongyangguang Hi-tech Park, Dongguan , Guangdong 523871 , China
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21
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Chaubey B, Pal S. Binding Interaction of Organofluorine–Serum Albumin: A Comparative Ligand-Detected 19F NMR Analysis. J Phys Chem B 2018; 122:9409-9418. [DOI: 10.1021/acs.jpcb.8b06583] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Bhawna Chaubey
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Samanwita Pal
- Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342037, India
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22
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Ichiishi N, Caldwell JP, Lin M, Zhong W, Zhu X, Streckfuss E, Kim HY, Parish CA, Krska SW. Protecting group free radical C-H trifluoromethylation of peptides. Chem Sci 2018; 9:4168-4175. [PMID: 29780547 PMCID: PMC5941281 DOI: 10.1039/c8sc00368h] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 04/02/2018] [Indexed: 12/22/2022] Open
Abstract
Two radical-based approaches have been developed to effect the trifluoromethylation of aryl C-H bonds in native peptides either using stoichiometric oxidant or visible light photoredox catalysis. The reported methods are able to derivatize tyrosine and tryptophan sidechains under biocompatible conditions, and a number of examples are reported involving fully unprotected peptides with up to 51 amino acids. The development of this chemistry adds to the growing array of chemical methods for selectively modifying amino acid residues in the context of complex peptides. The direct incorporation of trifluoromethyl groups into biopolymers enables the study of a range of biological and biochemical systems, and preliminary results indicate this method can be extended to the incorporation of other fluoroalkyl groups for bioconjugation applications.
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Affiliation(s)
- Naoko Ichiishi
- Chemistry Capabilities and Screening , Merck Sharp & Dohme Corp. , Kenilworth , New Jersey 07033 , USA .
| | - John P Caldwell
- Kenilworth Discovery Chemistry , Merck Sharp & Dohme Corp. , Kenilworth , New Jersey 07033 , USA
| | - Melissa Lin
- Analytical Research & Development , Merck Sharp & Dohme Corp. , Rahway , NJ , USA
| | - Wendy Zhong
- Analytical Research & Development , Merck Sharp & Dohme Corp. , Rahway , NJ , USA
| | - Xiaohong Zhu
- Kenilworth Discovery Chemistry , Merck Sharp & Dohme Corp. , Kenilworth , New Jersey 07033 , USA
| | - Eric Streckfuss
- West Point Discovery Chemistry , Merck Sharp & Dohme Corp. , West Point , Pennsylvania 19486 , USA
| | - Hai-Young Kim
- Analytical Research & Development , Merck Sharp & Dohme Corp. , Rahway , NJ , USA
| | - Craig A Parish
- Discovery Chemistry Modalities , Merck Sharp & Dohme Corp. , Kenilworth , New Jersey 07033 , USA .
| | - Shane W Krska
- Chemistry Capabilities and Screening , Merck Sharp & Dohme Corp. , Kenilworth , New Jersey 07033 , USA .
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23
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Rosenberg RE. The Strength of Hydrogen Bonds between Fluoro-Organics and Alcohols, a Theoretical Study. J Phys Chem A 2018; 122:4521-4529. [DOI: 10.1021/acs.jpca.8b01148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Robert E. Rosenberg
- Department of Chemistry, Transylvania University, 300 North Broadway, Lexington, Kentucky 40508, United States
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24
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Dissecting the Structure-Activity Relationship of Galectin-Ligand Interactions. Int J Mol Sci 2018; 19:ijms19020392. [PMID: 29382172 PMCID: PMC5855614 DOI: 10.3390/ijms19020392] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 01/18/2018] [Accepted: 01/24/2018] [Indexed: 02/08/2023] Open
Abstract
Galectins are β-galactoside-binding proteins. As carbohydrate-binding proteins, they participate in intracellular trafficking, cell adhesion, and cell-cell signaling. Accumulating evidence indicates that they play a pivotal role in numerous physiological and pathological activities, such as the regulation on cancer progression, inflammation, immune response, and bacterial and viral infections. Galectins have drawn much attention as targets for therapeutic interventions. Several molecules have been developed as galectin inhibitors. In particular, TD139, a thiodigalactoside derivative, is currently examined in clinical trials for the treatment of idiopathic pulmonary fibrosis. Herein, we provide an in-depth review on the development of galectin inhibitors, aiming at the dissection of the structure-activity relationship to demonstrate how inhibitors interact with galectin(s). We especially integrate the structural information established by X-ray crystallography with several biophysical methods to offer, not only in-depth understanding at the molecular level, but also insights to tackle the existing challenges.
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25
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Alapour S, de la Torre BG, Ramjugernath D, Koorbanally NA, Albericio F. Application of Decafluorobiphenyl (DFBP) Moiety as a Linker in Bioconjugation. Bioconjug Chem 2018; 29:225-233. [DOI: 10.1021/acs.bioconjchem.7b00800] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Saba Alapour
- School
of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Beatriz G. de la Torre
- KRISP, College of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4001, South Africa
| | - Deresh Ramjugernath
- School
of Chemical Engineering, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Neil A. Koorbanally
- School
of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Fernando Albericio
- School
of Chemistry and Physics, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
- CIBER-BBN,
Networking Centre on Bioengineering, Biomaterials and Nanomedicine,
and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona, Spain
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26
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Jia Q, Li Q, Luo M, Li HB. Understanding the effects of vicinal carbon substituents and configuration on organofluorine hydrogen-bonding interaction. RSC Adv 2018; 8:38980-38986. [PMID: 35558337 PMCID: PMC9090643 DOI: 10.1039/c8ra08122k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 11/15/2018] [Indexed: 11/21/2022] Open
Abstract
An investigation of C–F⋯H–O hydrogen bonds in the complexes CHnXCHnF⋯H2O (n = 0, 1, 2; X = H, F, Cl, Br) was performed at the MP2/aug-cc-pVTZ level. We found that the electron-withdrawing halogen substituents on the vicinal carbon cause the fluorine atom, participating in the hydrogen bond formation, to be less negatively charged. Thus, the halogen groups weaken the strength of organofluorine hydrogen bond by inductive effect. The position of the substituents on the vicinal carbon affects the strength of the C–F⋯H–O interaction. Compared with that in other isomers, the electron withdrawing substituent in 1-fluoro-ethane with stagger conformation as well as in 1-fluoro-ethene with trans configuration much weakens the interaction of C–F⋯H–O due to the hyperconjugative interaction between σ(C–F) and . By analogy, the electron-donating ones could largely strengthen it. We found that there is a good linear relationship between electron density at the BCP of F⋯H and Wiberg bond indexes (WBI) as well as between natural bond-bond polarizability (NBBP) and WBI, which indicates that the magnitude of NBBP and WBI could be a good indicator of the hydrogen bond strength. The vicinal substituents, with gauche/stagger isomer in CH2XCH2F and cis/trans isomer in CHXCHF, affect the interaction of C(spn)–F⋯H–O organofluorine hydrogen bonds differently.![]()
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Affiliation(s)
- Qingqing Jia
- School of Ocean
- Shandong University
- Weihai 264209
- People's Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Mo Luo
- School of Ocean
- Shandong University
- Weihai 264209
- People's Republic of China
| | - Hai-Bei Li
- School of Ocean
- Shandong University
- Weihai 264209
- People's Republic of China
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27
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Fluorine NMR spectroscopy and computational calculations for assessing intramolecular hydrogen bond involving fluorine and for characterizing the dynamic of a fluorinated molecule. J Fluor Chem 2017. [DOI: 10.1016/j.jfluchem.2017.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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28
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Ferreira de Freitas R, Schapira M. A systematic analysis of atomic protein-ligand interactions in the PDB. MEDCHEMCOMM 2017; 8:1970-1981. [PMID: 29308120 PMCID: PMC5708362 DOI: 10.1039/c7md00381a] [Citation(s) in RCA: 232] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 09/15/2017] [Indexed: 12/20/2022]
Abstract
As the protein databank (PDB) recently passed the cap of 123 456 structures, it stands more than ever as an important resource not only to analyze structural features of specific biological systems, but also to study the prevalence of structural patterns observed in a large body of unrelated structures, that may reflect rules governing protein folding or molecular recognition. Here, we compiled a list of 11 016 unique structures of small-molecule ligands bound to proteins - 6444 of which have experimental binding affinity - representing 750 873 protein-ligand atomic interactions, and analyzed the frequency, geometry and impact of each interaction type. We find that hydrophobic interactions are generally enriched in high-efficiency ligands, but polar interactions are over-represented in fragment inhibitors. While most observations extracted from the PDB will be familiar to seasoned medicinal chemists, less expected findings, such as the high number of C-H···O hydrogen bonds or the relatively frequent amide-π stacking between the backbone amide of proteins and aromatic rings of ligands, uncover underused ligand design strategies.
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Affiliation(s)
| | - Matthieu Schapira
- Structural Genomics Consortium , University of Toronto , Toronto , ON M5G 1L7 , Canada .
- Department of Pharmacology and Toxicology , University of Toronto , Toronto , ON M5S 1A8 , Canada
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29
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Sundhoro M, Park J, Jayawardana KW, Chen X, Jayawardena HSN, Yan M. Poly(HEMA-co-HEMA-PFPA): Synthesis and preparation of stable micelles encapsulating imaging nanoparticles. J Colloid Interface Sci 2017; 500:1-8. [PMID: 28395159 DOI: 10.1016/j.jcis.2017.03.099] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 11/28/2022]
Abstract
We report the preparation of stable micelles from random copolymers of 2-hydroxyethyl methacrylate (HEMA) and perfluorophenyl azide (PFPA)-derivatized HEMA (HEMA-PFPA). The copolymers were synthesized by RAFT polymerization at room temperature under mild conditions without affecting the azide functionality. Upon addition of water to the copolymer solution in DMSO, the random copolymers self-assembled into micelles even at the percentage of HEMA-PFPA as low as 4.5%. The size of the micelles can be controlled by the molecular weight and the concentration of the copolymer, and the percentage of HEMA-PFPA in the copolymer. In addition, iron oxide nanoparticles and quantum dots were successfully encapsulated into the micelles with high encapsulation efficiency (∼80%). These nanoparticles, which were hydrophobic and formed agglomerates in water, became fully dispersed after encapsulating into the micelles. The micelles were stable and the size remained unchanged for at least 6months.
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Affiliation(s)
- Madanodaya Sundhoro
- Department of Chemistry, University of Massachusetts Lowell, 1 University Ave, Lowell, MA 01854, United States
| | - Jaehyeung Park
- Department of Chemistry, University of Massachusetts Lowell, 1 University Ave, Lowell, MA 01854, United States
| | - Kalana W Jayawardana
- Department of Chemistry, University of Massachusetts Lowell, 1 University Ave, Lowell, MA 01854, United States
| | - Xuan Chen
- Department of Chemistry, University of Massachusetts Lowell, 1 University Ave, Lowell, MA 01854, United States
| | - H Surangi N Jayawardena
- Department of Chemistry, University of Massachusetts Lowell, 1 University Ave, Lowell, MA 01854, United States
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, 1 University Ave, Lowell, MA 01854, United States; Department of Chemistry, KTH - Royal Institute of Technology, Teknikringen, 30, S-100 44 Stockholm, Sweden.
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30
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Novakov IA, Yablokov AS, Navrotskii MB, Mkrtchyan AS, Vernigora AA, Babushkin AS, Kachala VV, Ruchko EA. Synthesis of 3-oxoesters and functional derivatives of pyrimidin-4(3Н)-one based on 1-(2,6-dihalophenyl)cyclopropan-1-carboxylic acids. RUSS J GEN CHEM+ 2017. [DOI: 10.1134/s1070363217020128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Graton J, Compain G, Besseau F, Bogdan E, Watts JM, Mtashobya L, Wang Z, Weymouth-Wilson A, Galland N, Le Questel JY, Linclau B. Influence of Alcohol β-Fluorination on Hydrogen-Bond Acidity of Conformationally Flexible Substrates. Chemistry 2016; 23:2811-2819. [DOI: 10.1002/chem.201604940] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Jerome Graton
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Guillaume Compain
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Francois Besseau
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Elena Bogdan
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Joseph M. Watts
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Lewis Mtashobya
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Zhong Wang
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Alex Weymouth-Wilson
- Dextra Laboratories Ltd; The Science and Technology Centre; Earley Gate, Whiteknights Road Reading RG6 6BZ UK
| | - Nicolas Galland
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Bruno Linclau
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
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32
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Affiliation(s)
- Robert E. Rosenberg
- Department of Chemistry, Transylvania University, 300 North Broadway, Lexington, Kentucky 40508, United States
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33
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Abstract
As methods to incorporate noncanonical amino acid residues into proteins have become more powerful, interest in their use to modify the physical and biological properties of proteins and enzymes has increased. This chapter discusses the use of highly fluorinated analogs of hydrophobic amino acids, for example, hexafluoroleucine, in protein design. In particular, fluorinated residues have proven to be generally effective in increasing the thermodynamic stability of proteins. The chapter provides an overview of the different fluorinated amino acids that have been used in protein design and the various methods available for producing fluorinated proteins. It discusses model proteins systems into which highly fluorinated amino acids have been introduced and the reasons why fluorinated residues are generally stabilizing, with particular reference to thermodynamic and structural studies from our laboratory. Lastly, details of the methodology we have developed to measure the thermodynamic stability of oligomeric fluorinated proteins are presented, as this may be generally applicable to many proteins.
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Affiliation(s)
- E N G Marsh
- University of Michigan, Ann Arbor, MI, United States.
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34
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Dalvit C, Vulpetti A. Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening. Chemistry 2016; 22:7592-601. [DOI: 10.1002/chem.201600446] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Claudio Dalvit
- Faculty of Science University of Neuchâtel 2000 Neuchâtel Switzerland
- Sanofi, LG-CR/SDI/SBB 94403 Vitry-sur-Seine France
| | - Anna Vulpetti
- Novartis Institutes for Biomedical Research, Global Discovery Chemistry, CADD 4002 Basel Switzerland
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35
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Arntson KE, Pomerantz WCK. Protein-Observed Fluorine NMR: A Bioorthogonal Approach for Small Molecule Discovery. J Med Chem 2015; 59:5158-71. [PMID: 26599421 DOI: 10.1021/acs.jmedchem.5b01447] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The (19)F isotope is 100% naturally abundant and is the second most sensitive and stable NMR-active nucleus. Unlike the ubiquitous hydrogen atom, fluorine is nearly absent in biological systems, making it a unique bioorthogonal atom for probing molecular interactions in biology. Over 73 fluorinated proteins have been studied by (19)F NMR since the seminal studies of Hull and Sykes in 1974. With advances in cryoprobe production and fluorinated amino acid incorporation strategies, protein-based (19)F NMR offers opportunities to the medicinal chemist for characterizing and ultimately discovering new small molecule protein ligands. This review will highlight new advances using (19)F NMR for characterizing small molecule interactions with both small and large proteins as well as detailing NMR resonance assignment challenges and amino acid incorporation approaches.
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Affiliation(s)
- Keith E Arntson
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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36
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Linclau B, Peron F, Bogdan E, Wells N, Wang Z, Compain G, Fontenelle CQ, Galland N, Le Questel JY, Graton J. Intramolecular OH⋅⋅⋅Fluorine Hydrogen Bonding in Saturated, Acyclic Fluorohydrins: The γ-Fluoropropanol Motif. Chemistry 2015; 21:17808-16. [PMID: 26494542 PMCID: PMC4676915 DOI: 10.1002/chem.201503253] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Indexed: 11/23/2022]
Abstract
Fluorination is commonly exercised in compound property optimization. However, the influence of fluorination on hydrogen-bond (HB) properties of adjacent functional groups, as well as the HB-accepting capacity of fluorine itself, is still not completely understood. Although the formation of OH⋅⋅⋅F intramolecular HBs (IMHBs) has been established for conformationally restricted fluorohydrins, such interaction in flexible compounds remained questionable. Herein is demonstrated for the first time-and in contrast to earlier reports-the occurrence of OH⋅⋅⋅F IMHBs in acyclic saturated γ-fluorohydrins, even for the parent 3-fluoropropan-1-ol. The relative stereochemistry is shown to have a crucial influence on the corresponding (h1) JOH⋅⋅⋅F values, as illustrated by syn- and anti-4-fluoropentan-2-ol (6.6 and 1.9 Hz). The magnitude of OH⋅⋅⋅F IMHBs and their strong dependence on the overall molecular conformational profile, fluorination motif, and alkyl substitution level, is rationalized by quantum chemical calculations. For a given alkyl chain, the "rule of shielding" applies to OH⋅⋅⋅F IMHB energies. Surprisingly, the predicted OH⋅⋅⋅F IMHB energies are only moderately weaker than these of the corresponding OH⋅⋅⋅OMe. These results provide new insights of the impact of fluorination of aliphatic alcohols, with attractive perspectives for rational drug design.
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Affiliation(s)
- Bruno Linclau
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK), Fax: (+44) 23-8059-6805.
| | - Florent Peron
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK), Fax: (+44) 23-8059-6805
| | - Elena Bogdan
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2, rue de la Houssinière - BP 92208, 44322 NANTES Cedex 3 (France), Fax: (+3) 2-51-12-54-02
| | - Neil Wells
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK), Fax: (+44) 23-8059-6805
| | - Zhong Wang
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK), Fax: (+44) 23-8059-6805
| | - Guillaume Compain
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK), Fax: (+44) 23-8059-6805
| | - Clement Q Fontenelle
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ (UK), Fax: (+44) 23-8059-6805
| | - Nicolas Galland
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2, rue de la Houssinière - BP 92208, 44322 NANTES Cedex 3 (France), Fax: (+3) 2-51-12-54-02
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2, rue de la Houssinière - BP 92208, 44322 NANTES Cedex 3 (France), Fax: (+3) 2-51-12-54-02
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Faculté des Sciences et des Techniques, Université de Nantes, 2, rue de la Houssinière - BP 92208, 44322 NANTES Cedex 3 (France), Fax: (+3) 2-51-12-54-02.
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37
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Kasireddy C, Bann JG, Mitchell-Koch KR. Demystifying fluorine chemical shifts: electronic structure calculations address origins of seemingly anomalous (19)F-NMR spectra of fluorohistidine isomers and analogues. Phys Chem Chem Phys 2015; 17:30606-12. [PMID: 26524669 PMCID: PMC4643390 DOI: 10.1039/c5cp05502d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fluorine NMR spectroscopy is a powerful tool for studying biomolecular structure, dynamics, and ligand binding, yet the origins of (19)F chemical shifts are not well understood. Herein, we use electronic structure calculations to describe the changes in (19)F chemical shifts of 2F- and 4F-histidine/(5-methyl)-imidazole upon acid titration. While the protonation of the 2F species results in a deshielded chemical shift, protonation of the 4F isomer results in an opposite, shielded chemical shift. The deshielding of 2F-histidine/(5-methyl)-imidazole upon protonation can be rationalized by concomitant decreases in charge density on fluorine and a reduced dipole moment. These correlations do not hold for 4F-histidine/(5-methyl)-imidazole, however. Molecular orbital calculations reveal that for the 4F species, there are no lone pair electrons on the fluorine until protonation. Analysis of a series of 4F-imidazole analogues, all with delocalized fluorine electron density, indicates that the deshielding of (19)F chemical shifts through substituent effects correlates with increased C-F bond polarity. In summary, the delocalization of fluorine electrons in the neutral 4F species, with gain of a lone pair upon protonation may help explain the difficulty in developing a predictive framework for fluorine chemical shifts. Ideas debated by chemists over 40 years ago, regarding fluorine's complex electronic effects, are shown to have relevance for understanding and predicting fluorine NMR spectra.
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Affiliation(s)
- Chandana Kasireddy
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, USA.
| | - James G Bann
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, USA.
| | - Katie R Mitchell-Koch
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, USA.
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38
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Sharaf NG, Gronenborn AM. (19)F-modified proteins and (19)F-containing ligands as tools in solution NMR studies of protein interactions. Methods Enzymol 2015; 565:67-95. [PMID: 26577728 DOI: 10.1016/bs.mie.2015.05.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
(19)F solution NMR is a powerful and versatile tool to study protein structure and protein-ligand interactions due to the favorable NMR characteristics of the (19)F atom, its absence in naturally occurring biomolecules, and small size. Protocols to introduce (19)F atoms into both proteins and their ligands are readily available and offer the ability to conduct protein-observe (using (19)F-labeled proteins) or ligand-observe (using (19)F-containing ligands) NMR experiments. This chapter provides two protocols for the (19)F-labeling of proteins, using an Escherichia coli expression system: (i) amino acid type-specific incorporation of (19)F-modified amino acids and (ii) site-specific incorporation of (19)F-modified amino acids using recombinantly expressed orthogonal amber tRNA/tRNA synthetase pairs. In addition, we discuss several applications, involving (19)F-modified proteins and (19)F-containing ligands.
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Affiliation(s)
- Naima G Sharaf
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Angela M Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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39
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Ye L, Larda ST, Li YFF, Manglik A, Prosser RS. A comparison of chemical shift sensitivity of trifluoromethyl tags: optimizing resolution in ¹⁹F NMR studies of proteins. JOURNAL OF BIOMOLECULAR NMR 2015; 62:97-103. [PMID: 25813845 PMCID: PMC6675403 DOI: 10.1007/s10858-015-9922-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/16/2015] [Indexed: 05/16/2023]
Abstract
The elucidation of distinct protein conformers or states by fluorine ((19)F) NMR requires fluorinated moieties whose chemical shifts are most sensitive to subtle changes in the local dielectric and magnetic shielding environment. In this study we evaluate the effective chemical shift dispersion of a number of thiol-reactive trifluoromethyl probes [i.e. 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA), N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA), 3-bromo-1,1,1-trifluoropropan-2-ol (BTFP), 1-bromo-3,3,4,4,4-pentafluorobutan-2-one (BPFB), 3-bromo-1,1,1-trifluoropropan-2-one (BTFA), and 2,2,2-trifluoroethyl-1-thiol (TFET)] under conditions of varying polarity. In considering the sensitivity of the (19)F NMR chemical shift to the local environment, a series of methanol/water mixtures were prepared, ranging from relatively non-polar (MeOH:H2O = 4) to polar (MeOH:H2O = 0.25). (19)F NMR spectra of the tripeptide, glutathione ((2S)-2-amino-4-{[(1R)-1-[(carboxymethyl)carbamoyl]-2-sulfanylethyl]carbamoyl}butanoic acid), conjugated to each of the above trifluoromethyl probes, revealed that the BTFMA tag exhibited a significantly greater range of chemical shift as a function of solvent polarity than did either BTFA or TFET. DFT calculations using the B3LYP hybrid functional and the 6-31G(d,p) basis set, confirmed the observed trend in chemical shift dispersion with solvent polarity.
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Affiliation(s)
- Libin Ye
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - Sacha Thierry Larda
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - Yi Feng Frank Li
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
| | - Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - R. Scott Prosser
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Road North, Mississauga, ON L5L 1C6, Canada
- Department of Biochemistry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
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40
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Hwang CS, Kung A, Kashemirov BA, Zhang C, McKenna CE. 5'-β,γ-CHF-ATP diastereomers: synthesis and fluorine-mediated selective binding by c-Src protein kinase. Org Lett 2015; 17:1624-7. [PMID: 25781066 PMCID: PMC4892180 DOI: 10.1021/ol503765n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The first preparation of the individual β,γ-CHF-ATP stereoisomers 12a and 12b is reported. Configurationally differing solely by the orientation of the C-F fluorine, 12a and 12b have discrete (31)P (202 MHz, pH 10.9, ΔδPα 6 Hz, ΔδPβ 4 Hz) and (19)F NMR (470 MHz, pH 9.8, ΔδF 25 Hz) spectral signatures and exhibit a 6-fold difference in IC50 values for c-Src kinase, attributed to a unique interaction of the (S)-fluorine of bound 12b with R388 in the active site.
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Affiliation(s)
- Candy S. Hwang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Alvin Kung
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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41
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Istrate A, Medvecky M, Leumann CJ. 2'-Fluorination of tricyclo-DNA controls furanose conformation and increases RNA affinity. Org Lett 2015; 17:1950-3. [PMID: 25837683 DOI: 10.1021/acs.orglett.5b00662] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The synthesis of 2'-fluoro tricyclo-DNA pyrimidine nucleosides with fluorine in the ribo-configuration and their incorporation into oligodeoxynucleotides was accomplished. Unlike the parent tc-T nucleoside, the 2'F-RNA-tc-T unit occurs in the 2'-exo conformation in the crystal. Specifically, F-RNA-tc-T was found to stabilize duplexes with RNA by +2 to +4 °C in Tm/mod. F-RNA-tc-nucleosides mix well with the DNA backbone and thus open up possibilities of using shorter and mixed-(DNA/tc-DNA) backbone oligonucleotides for therapeutic applications.
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Affiliation(s)
- Alena Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Michal Medvecky
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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42
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Medvecky M, Istrate A, Leumann CJ. Synthesis and properties of 6'-fluoro-tricyclo-DNA. J Org Chem 2015; 80:3556-65. [PMID: 25767996 DOI: 10.1021/acs.joc.5b00184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The synthesis of the two fluorinated tricyclic nucleosides 6'-F-tc-T and 6'-F-tc-5(Me)C, as well as the corresponding building blocks for oligonucleotide assembly, was accomplished. An X-ray analysis of N(4)-benzoylated 6'-F-tc-(5Me)C reavealed a 2'-exo (north) conformation of the furanose ring, characterizing it as an RNA mimic. In contrast to observations in the bicyclo-DNA series, no short contact between the fluorine atom and the H6 of the base, reminiscent of a nonclassical F···H hydrogen bond, could be observed. Tm measurements of modified oligodeoxynucleotides with complementary RNA showed slightly sequence-dependent duplex stabilization profiles with maximum ΔTm/mod values of +4.5 °C for 6'-F-tc-(5Me)C and +1 °C for 6'-F-tc-T. In comparison with parent tc-modified oligonucleotides, no relevant changes in Tm were detected, attributing the fluorine substituent a neutral role in RNA affinity. A structural analysis of duplexes with DNA and RNA by CD-spectroscopy revealed a shift from B- to A-type conformation induced by the 6'-F-tc-nucleosides. This is not a specific "fluorine effect", as the same is also observed for the parent tc-modifications. The two fluorinated tc-nucleosides were also incorporated into a pure tricyclo-DNA backbone and showed no discrimination in Tm with complementary RNA, demonstrating that 6'-F substitution is also compatible within fully modified tc-oligonucleotides.
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Affiliation(s)
- Michal Medvecky
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Alena Istrate
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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43
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Xing L, Blakemore DC, Narayanan A, Unwalla R, Lovering F, Denny RA, Zhou H, Bunnage ME. Fluorine in Drug Design: A Case Study with Fluoroanisoles. ChemMedChem 2015; 10:715-26. [DOI: 10.1002/cmdc.201402555] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/09/2015] [Indexed: 11/05/2022]
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44
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Mtashobya L, Quiquempoix L, Linclau B. The synthesis of mono- and difluorinated 2,3-dideoxy-d-glucopyranoses. J Fluor Chem 2015. [DOI: 10.1016/j.jfluchem.2014.08.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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45
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Sukach VA, Resetnic AA, Tkachuk VM, Lin Z, Kortz U, Vovk MV, Röschenthaler GV. Synthesis of Trifluoromethylated Analogues of 4,5-Dihydroorotic Acid. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403495] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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van Straaten KE, Kuttiyatveetil JRA, Sevrain CM, Villaume SA, Jiménez-Barbero J, Linclau B, Vincent SP, Sanders DAR. Structural basis of ligand binding to UDP-galactopyranose mutase from Mycobacterium tuberculosis using substrate and tetrafluorinated substrate analogues. J Am Chem Soc 2015; 137:1230-44. [PMID: 25562380 DOI: 10.1021/ja511204p] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
UDP-Galactopyranose mutase (UGM) is a flavin-containing enzyme that catalyzes the reversible conversion of UDP-galactopyranose (UDP-Galp) to UDP-galactofuranose (UDP-Galf) and plays a key role in the biosynthesis of the mycobacterial cell wall galactofuran. A soluble, active form of UGM from Mycobacterium tuberculosis (MtUGM) was obtained from a dual His6-MBP-tagged MtUGM construct. We present the first complex structures of MtUGM with bound substrate UDP-Galp (both oxidized flavin and reduced flavin). In addition, we have determined the complex structures of MtUGM with inhibitors (UDP and the dideoxy-tetrafluorinated analogues of both UDP-Galp (UDP-F4-Galp) and UDP-Galf (UDP-F4-Galf)), which represent the first complex structures of UGM with an analogue in the furanose form, as well as the first structures of dideoxy-tetrafluorinated sugar analogues bound to a protein. These structures provide detailed insight into ligand recognition by MtUGM and show an overall binding mode similar to those reported for other prokaryotic UGMs. The binding of the ligand induces conformational changes in the enzyme, allowing ligand binding and active-site closure. In addition, the complex structure of MtUGM with UDP-F4-Galf reveals the first detailed insight into how the furanose moiety binds to UGM. In particular, this study confirmed that the furanoside adopts a high-energy conformation ((4)E) within the catalytic pocket. Moreover, these investigations provide structural insights into the enhanced binding of the dideoxy-tetrafluorinated sugars compared to unmodified analogues. These results will help in the design of carbohydrate mimetics and drug development, and show the enormous possibilities for the use of polyfluorination in the design of carbohydrate mimetics.
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Affiliation(s)
- Karin E van Straaten
- Department of Chemistry, University of Saskatchewan , 110 Science Place, Saskatoon S7N 5C9, Canada
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47
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Dugovic B, Leumann CJ. A 6′-fluoro-substituent in bicyclo-DNA increases affinity to complementary RNA presumably by CF–HC pseudohydrogen bonds. J Org Chem 2014; 79:1271-9. [PMID: 24422513 DOI: 10.1021/jo402690j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The synthesis of a novel bicyclic thymidine analogue carrying a β-fluoro substituent at C6′ (6′F-bcT) has been achieved. Key steps of the synthesis were an electrophilic fluorination/stereospecific hydrogenation sequence of a bicyclo sugar intermediate, followed by an N-iodo-succinimide-induced stereoselective nucleosidation. A corresponding phosphoramidite building block was then prepared and used for oligonucleotide synthesis. Tm measurements of oligonucleotides with single and double incorporations showed a remarkable stabilization of duplex formation particularly with RNA as complement without compromising pairing selectivity. Increases in Tm were in the range of +1–2 °C compared to thymidine and +1–3 °C compared to a standard bc-T residue. Structural investigations of the 6′F-bcT nucleoside by X-ray crystallography showed an in-line arrangement of the fluorine substituent with H6 of thymine, however, with a distance that is relatively long for a nonclassical CF–HC hydrogen bond. In contrast, structural investigations in solution by 1H and 13C NMR clearly showed scalar coupling of fluorine with H6 and C6 of the nucleobase, indicating the existence of at least weak electrostatic interactions. On the basis of these results, we put forward the hypothesis that these weak CF–HC6 electrostatic interactions increase duplex stability by orienting and partially freezing torsion angle χ of the 6′F-bcT nucleoside.
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Dalvit C, Invernizzi C, Vulpetti A. Fluorine as a hydrogen-bond acceptor: experimental evidence and computational calculations. Chemistry 2014; 20:11058-68. [PMID: 25044441 DOI: 10.1002/chem.201402858] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Indexed: 12/19/2022]
Abstract
Hydrogen-bonding interactions play an important role in many chemical and biological systems. Fluorine acting as a hydrogen-bond acceptor in intermolecular and intramolecular interactions has been the subject of many controversial discussions and there are different opinions about it. Recently, we have proposed a correlation between the propensity of fluorine to be involved in hydrogen bonds and its (19)F NMR chemical shift. We now provide additional experimental and computational evidence for this correlation. The strength of hydrogen-bond complexes involving the fluorine moieties CH2F, CHF2, and CF3 was measured and characterized in simple systems by using established and novel NMR methods and compared to the known hydrogen-bond complex formed between acetophenone and p-fluorophenol. Implications of these results for (19)F NMR screening are analyzed in detail. Computed values of the molecular electrostatic potential at the different fluorine atoms and the analysis of the electron density topology at bond critical points correlate well with the NMR results.
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Affiliation(s)
- Claudio Dalvit
- University of Neuchâtel, Faculty of Science, 2000 Neuchâtel (Switzerland).
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Leung EWW, Yagi H, Harjani JR, Mulcair MD, Scanlon MJ, Baell JB, Norton RS. 19F NMR as a Probe of Ligand Interactions with the iNOS Binding site of SPRY Domain-Containing SOCS Box Protein 2. Chem Biol Drug Des 2014; 84:616-25. [DOI: 10.1111/cbdd.12355] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/12/2014] [Accepted: 04/29/2014] [Indexed: 01/17/2023]
Affiliation(s)
- Eleanor W. W. Leung
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Hiromasa Yagi
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Jitendra R. Harjani
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Mark D. Mulcair
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Martin J. Scanlon
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Jonathan B. Baell
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
| | - Raymond S. Norton
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University; Parkville Victoria 3052 Australia
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50
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Chatzopoulou M, Patsilinakos A, Vallianatou T, Prnova MS, Žakelj S, Ragno R, Stefek M, Kristl A, Tsantili-Kakoulidou A, Demopoulos VJ. Decreasing acidity in a series of aldose reductase inhibitors: 2-Fluoro-4-(1H-pyrrol-1-yl)phenol as a scaffold for improved membrane permeation. Bioorg Med Chem 2014; 22:2194-207. [DOI: 10.1016/j.bmc.2014.02.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/06/2014] [Accepted: 02/13/2014] [Indexed: 12/28/2022]
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