101
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Cormanich RA, Freitas MP, Tormena CF, Rittner R. The F⋯HO intramolecular hydrogen bond forming five-membered rings hardly appear in monocyclic organofluorine compounds. RSC Adv 2012. [DOI: 10.1039/c2ra00039c] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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102
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Vorobyeva DV, Sokolova NV, Nenajdenko VG, Peregudov AS, Osipov SN. Synthesis of CF3-containing tetrapeptide surrogates via Ugi reaction/dipolar cycloaddition sequence. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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103
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Schneider HJ. Hydrogen bonds with fluorine. Studies in solution, in gas phase and by computations, conflicting conclusions from crystallographic analyses. Chem Sci 2012. [DOI: 10.1039/c2sc00764a] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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104
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Forconi M, Schwans JP, Porecha RH, Sengupta RN, Piccirilli JA, Herschlag D. 2'-Fluoro substituents can mimic native 2'-hydroxyls within structured RNA. ACTA ACUST UNITED AC 2011; 18:949-54. [PMID: 21867910 DOI: 10.1016/j.chembiol.2011.07.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 06/20/2011] [Accepted: 07/06/2011] [Indexed: 10/17/2022]
Abstract
The ability of fluorine in a C-F bond to act as a hydrogen bond acceptor is controversial. To test such ability in complex RNA macromolecules, we have replaced native 2'-OH groups with 2'-F and 2'-H groups in two related systems, the Tetrahymena group I ribozyme and the ΔC209 P4-P6 RNA domain. In three cases the introduced 2'-F mimics the native 2'-OH group, suggesting that the fluorine atom can accept a hydrogen bond. In each of these cases the native hydroxyl group interacts with a purine exocyclic amine. Our results give insight about the properties of organofluorine and suggest a possible general biochemical signature for tertiary interactions between 2'-hydroxyl groups and exocyclic amino groups within RNA.
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Affiliation(s)
- Marcello Forconi
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
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105
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Topczewski JJ, Callahan MP, Kodet JG, Inbarasu JD, Mente NR, Beutler JA, Wiemer DF. Relevance of the C-5 position to schweinfurthin induced cytotoxicity. Bioorg Med Chem 2011; 19:7570-81. [PMID: 22055715 PMCID: PMC3232010 DOI: 10.1016/j.bmc.2011.10.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Revised: 10/05/2011] [Accepted: 10/10/2011] [Indexed: 11/20/2022]
Abstract
The schweinfurthins are an intriguing group of anti-proliferative agents that display low nanomolar activities against several cell types, including the human-derived glioblastoma cell line SF-295, but have little impact on other cell lines even at micromolar concentrations. This activity has inspired the synthesis of seven of the natural schweinfurthins, all with the correct absolute stereochemistry, and a variety of analogues designed to probe different facets of the pharmacophore. Reported herein is the synthesis of several new schweinfurthin analogues varied at the C-5 position along with data on their biological activity in the NCI 60 cell-line assay.
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Affiliation(s)
| | | | - John G. Kodet
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - Jery D. Inbarasu
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - Nolan R. Mente
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
| | - John A. Beutler
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - David F. Wiemer
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1294, USA
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106
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Fortuna CG, Barresi V, Bonaccorso C, Consiglio G, Failla S, Trovato-Salinaro A, Musumarra G. Design, synthesis and in vitro antitumour activity of new heteroaryl ethylenes. Eur J Med Chem 2011; 47:221-7. [PMID: 22119128 DOI: 10.1016/j.ejmech.2011.10.060] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/24/2011] [Accepted: 10/25/2011] [Indexed: 10/15/2022]
Abstract
Almond and VolSurf + modelling procedures allowed the structural design of new di- and mono-heteroaryl-ethylenes. The structural modifications suggested by the molecular modelling were verified by the synthesis of the designed molecules and by the evaluation of their in vitro activities against two lung tumour cell lines, A549 and H226. 2-{(E)-2-[5'-(Dibutylamino)-2,2'-bithien-5-yl]vinyl}-1-methylquinolinium iodide exhibited in vitro antiproliferative activity two orders of magnitude higher than that of the most active compound previously synthesized in our laboratory.
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Affiliation(s)
- Cosimo G Fortuna
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, Viale A. Doria 6 95125, Catania, Italy.
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107
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Wallnoefer HG, Liedl KR, Fox T. A GRID-Derived Water Network Stabilizes Molecular Dynamics Computer Simulations of a Protease. J Chem Inf Model 2011; 51:2860-7. [DOI: 10.1021/ci200138u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Hannes G. Wallnoefer
- Computational Chemistry, Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co., KG, 88397 Biberach, Germany
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
| | - Thomas Fox
- Computational Chemistry, Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co., KG, 88397 Biberach, Germany
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108
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Targeting the Large Subunit of Human Ribonucleotide Reductase for Cancer Chemotherapy. Pharmaceuticals (Basel) 2011; 4:1328-1354. [PMID: 23115527 PMCID: PMC3483043 DOI: 10.3390/ph4101328] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ribonucleotide reductase (RR) is a crucial enzyme in de novo DNA synthesis, where it catalyses the rate determining step of dNTP synthesis. RRs consist of a large subunit called RR1 (α), that contains two allosteric sites and one catalytic site, and a small subunit called RR2 (β), which houses a tyrosyl free radical essential for initiating catalysis. The active form of mammalian RR is an αnβm hetero oligomer. RR inhibitors are cytotoxic to proliferating cancer cells. In this brief review we will discuss the three classes of RR, the catalytic mechanism of RR, the regulation of the dNTP pool, the substrate selection, the allosteric activation, inactivation by ATP and dATP, and the nucleoside drugs that target RR. We will also discuss possible strategies for developing a new class of drugs that disrupts the RR assembly.
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109
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Giuffredi GT, Jennings LE, Bernet B, Gouverneur V. Facile synthesis of 4-deoxy-4-fluoro-α-d-talopyranoside, 4-deoxy-4-fluoro-α-d-idopyranoside and 2,4-dideoxy-2,4-difluoro-α-d-talopyranoside. J Fluor Chem 2011. [DOI: 10.1016/j.jfluchem.2011.05.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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110
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Cappel D, Wahlström R, Brenk R, Sotriffer CA. Probing the Dynamic Nature of Water Molecules and Their Influences on Ligand Binding in a Model Binding Site. J Chem Inf Model 2011; 51:2581-94. [DOI: 10.1021/ci200052j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Daniel Cappel
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians University Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Rickard Wahlström
- College of Life Sciences, Division of Chemical Biology and Drug Discovery, James Black Centre, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Ruth Brenk
- College of Life Sciences, Division of Chemical Biology and Drug Discovery, James Black Centre, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
| | - Christoph A. Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians University Würzburg, Am Hubland, D-97074 Würzburg, Germany
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111
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Scerba MT, Leavitt CM, Diener ME, DeBlase AF, Guasco TL, Siegler MA, Bair N, Johnson MA, Lectka T. NH+–F Hydrogen Bonding in a Fluorinated “Proton Sponge” Derivative: Integration of Solution, Solid-State, Gas-Phase, and Computational Studies. J Org Chem 2011; 76:7975-84. [DOI: 10.1021/jo2015328] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Michael T. Scerba
- Department of Chemistry, New Chemistry Building, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Christopher M. Leavitt
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Matthew E. Diener
- Department of Chemistry, New Chemistry Building, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Andrew F. DeBlase
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Timothy L. Guasco
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Maxime A. Siegler
- Department of Chemistry, New Chemistry Building, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Nathaniel Bair
- Department of Chemistry, New Chemistry Building, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Mark A. Johnson
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520, United States
| | - Thomas Lectka
- Department of Chemistry, New Chemistry Building, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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112
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Abstract
The term “hydrogen bond” has been used in the literature for nearly a century now. While its importance has been realized by physicists, chemists, biologists, and material scientists, there has been a continual debate about what this term means. This debate has intensified following some important experimental results, especially in the last decade, which questioned the basis of the traditional view on hydrogen bonding. Most important among them are the direct experimental evidence for a partial covalent nature and the observation of a blue-shift in stretching frequency following X–H···Y hydrogen bond formation (XH being the hydrogen bond donor and Y being the hydrogen bond acceptor). Considering the recent experimental and theoretical advances, we have proposed a new definition of the hydrogen bond, which emphasizes the need for evidence. A list of criteria has been provided, and these can be used as evidence for the hydrogen bond formation. This list is followed by some characteristics that are observed in typical hydrogen-bonding environments.
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113
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Giuffredi GT, Bernet B, Gouverneur V. De Novo Synthesis of Racemic 4-Deoxy-4,4-difluoro- and 2,4-Dideoxy-2,4,4-trifluorohexosides. European J Org Chem 2011. [DOI: 10.1002/ejoc.201100565] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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114
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Dalvit C, Vulpetti A. Fluorine-protein interactions and ¹⁹F NMR isotropic chemical shifts: An empirical correlation with implications for drug design. ChemMedChem 2011; 6:104-14. [PMID: 21117131 DOI: 10.1002/cmdc.201000412] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
An empirical correlation between the fluorine isotropic chemical shifts, measured by ¹⁹F NMR spectroscopy, and the type of fluorine-protein interactions observed in crystal structures is presented. The CF, CF₂, and CF₃ groups present in fluorinated ligands found in the Protein Data Bank were classified according to their ¹⁹F NMR chemical shifts and their close intermolecular contacts with the protein atoms. Shielded fluorine atoms, i.e., those with increased electron density, are observed primarily in close contact to hydrogen bond donors within the protein structure, suggesting the possibility of intermolecular hydrogen bond formation. Deshielded fluorines are predominantly found in close contact with hydrophobic side chains and with the carbon of carbonyl groups of the protein backbone. Correlation between the ¹⁹F NMR chemical shift and hydrogen bond distance, both derived experimentally and computed through quantum chemical methods, is also presented. The proposed "rule of shielding" provides some insight into and guidelines for the judicious selection of appropriate fluorinated moieties to be inserted into a molecule for making the most favorable interactions with the receptor.
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Affiliation(s)
- Claudio Dalvit
- Italian Institute of Technology, Drug Discovery and Development Department, Genova, Italy.
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115
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Broccatelli F, Carosati E, Neri A, Frosini M, Goracci L, Oprea TI, Cruciani G. A novel approach for predicting P-glycoprotein (ABCB1) inhibition using molecular interaction fields. J Med Chem 2011; 54:1740-51. [PMID: 21341745 DOI: 10.1021/jm101421d] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
P-glycoprotein (Pgp or ABCB1) is an ABC transporter protein involved in intestinal absorption, drug metabolism, and brain penetration, and its inhibition can seriously alter a drug's bioavailability and safety. In addition, inhibitors of Pgp can be used to overcome multidrug resistance. Given this dual purpose, reliable in silico procedures to predict Pgp inhibition are of great interest. A large and accurate literature collection yielded more than 1200 structures; a model was then constructed using various molecular interaction field-based technologies, considering pharmacophoric features and those physicochemical properties related to membrane partitioning. High accuracy was demonstrated internally with two different validation sets and, moreover, using a number of molecules, for which Pgp inhibition was not experimentally available but was evaluated in-house. All of the validations confirmed the robustness of the model and its suitability to help medicinal chemists in drug discovery. The information derived from the model was rationalized as a pharmacophore for competitive Pgp inhibition.
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Affiliation(s)
- Fabio Broccatelli
- Laboratory of Chemometrics, Department of Chemistry, University of Perugia, Via Elce di Sotto 10, I-06123 Perugia, Italy
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116
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Sarkisov PD, Butusov OB, Meshalkin VP. Computer-aided tools for molecular systems engineering and wavelet-morphometric analysis of the texture of nanomaterials. THEORETICAL FOUNDATIONS OF CHEMICAL ENGINEERING 2011. [DOI: 10.1134/s004057951101009x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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117
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Vulpetti A, Schiering N, Dalvit C. Combined use of computational chemistry, NMR screening, and X-ray crystallography for identification and characterization of fluorophilic protein environments. Proteins 2011; 78:3281-91. [PMID: 20886466 DOI: 10.1002/prot.22836] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
(19)F NMR screening of fluorinated fragments with different Local Environment of Fluorine, a.k.a. LEF library, is an experimental methodology which, beyond providing useful starting fragments for fragment-based drug discovery projects, offers, in combination with crystal and computational analysis, an approach for the identification of fluorophilic hot-spots in the proteins of interest. The application of this approach in the identification of fluorinated fragments binding to the serine protease trypsin, and the X-ray structures of the complexes are presented. The specific nature of the observed fluorine-protein interactions is discussed and compared with the interactions detected for other fluorinated ligands reported in the protein data bank. The presence of similar 3D arrangements of protein atoms at the fluorine sub-sites is identified with a newly developed tool. In this approach, protein sub-sites are extracted around each fluorine contained in the protein data bank and compared with the query of interest by using a pharmacophoric description.
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Affiliation(s)
- Anna Vulpetti
- Global Chemistry Discovery, Novartis Institutes for Biomedical Research, CH-4002 Basel, Switzerland.
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118
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Chatzopoulou M, Mamadou E, Juskova M, Koukoulitsa C, Nicolaou I, Stefek M, Demopoulos VJ. Structure–activity relations on [1-(3,5-difluoro-4-hydroxyphenyl)-1H-pyrrol-3-yl]phenylmethanone. The effect of methoxy substitution on aldose reductase inhibitory activity and selectivity. Bioorg Med Chem 2011; 19:1426-33. [DOI: 10.1016/j.bmc.2011.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 12/29/2010] [Accepted: 01/05/2011] [Indexed: 12/21/2022]
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119
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120
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Dikundwar AG, Venkateswarlu C, Piltz RO, Chandrasekaran S, Guru Row TN. Crystal structures of fluorinated aryl biscarbonates and a biscarbamate: a counterpoise between weak intermolecular interactions and molecular symmetry. CrystEngComm 2011. [DOI: 10.1039/c0ce00537a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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121
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Rojas-Aguirre Y, Yépez-Mulia L, Castillo I, López-Vallejo F, Soria-Arteche O, Hernández-Campos A, Castillo R, Hernández-Luis F. Studies on 6-chloro-5-(1-naphthyloxy)-2-(trifluoromethyl)-1H-benzimidazole/2-hydroxypropyl-β-cyclodextrin association: Characterization, molecular modeling studies, and in vivo anthelminthic activity. Bioorg Med Chem 2011; 19:789-97. [DOI: 10.1016/j.bmc.2010.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/25/2010] [Accepted: 12/04/2010] [Indexed: 10/18/2022]
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122
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Brincat JP, Carosati E, Sabatini S, Manfroni G, Fravolini A, Raygada JL, Patel D, Kaatz GW, Cruciani G. Discovery of novel inhibitors of the NorA multidrug transporter of Staphylococcus aureus. J Med Chem 2010; 54:354-65. [PMID: 21141825 DOI: 10.1021/jm1011963] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Four novel inhibitors of the NorA efflux pump of Staphylococcus aureus, discovered through a virtual screening process, are reported. The four compounds belong to different chemical classes and were tested for their in vitro ability to block the efflux of a well-known NorA substrate, as well as for their ability to potentiate the effect of ciprofloxacin (CPX) on several strains of S. aureus, including a NorA overexpressing strain. Additionally, the MIC values of each of the compounds individually are reported. A structure-activity relationship study was also performed on these novel chemotypes, revealing three new compounds that are also potent NorA inhibitors. The virtual screening procedure employed FLAP, a new methodology based on GRID force field descriptors.
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123
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Rational quantitative structure-activity relationship (RQSAR) screen for PXR and CAR isoform-specific nuclear receptor ligands. Chem Biol Interact 2010; 188:512-25. [PMID: 20869355 DOI: 10.1016/j.cbi.2010.09.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 12/11/2022]
Abstract
Constitutive androstane receptor (CAR) and pregnane X receptor (PXR) are closely related orphan nuclear receptor proteins that share several ligands and target overlapping sets of genes involved in homeostasis and all phases of drug metabolism. CAR and PXR are involved in the development of certain diseases, including diabetes, metabolic syndrome and obesity. Ligand screens for these receptors so far have typically focused on steroid hormone analogs with pharmacophore-based approaches, only to find relatively few new hits. Multiple CAR isoforms have been detected in human liver, with the most abundant being the constitutively active reference, CAR1, and the ligand-dependent isoform CAR3. It has been assumed that any compound that binds CAR1 should also activate CAR3, and so CAR3 can be used as a ligand-activated surrogate for CAR1 studies. The possibility of CAR3-specific ligands has not, so far, been addressed. To investigate the differences between CAR1, CAR3 and PXR, and to look for more CAR ligands that may be of use in quantitative structure-activity relationship (QSAR) studies, we performed a luciferase transactivation assay screen of 60 mostly non-steroid compounds. Known active compounds with different core chemistries were chosen as starting points and structural variants were rationally selected for screening. Distinct differences in agonist versus inverse agonist/antagonist effects were seen in 49 compounds that had some ligand effect on at least one receptor and 18 that had effects on all three receptors; eight were CAR1 ligands only, three were CAR3 only ligands and four affected PXR only. This work provides evidence for new CAR ligands, some of which have CAR3-specific effects, and provides observational data on CAR and PXR ligands with which to inform in silico strategies. Compounds that demonstrated unique activity on any one receptor are potentially valuable diagnostic tools for the investigation of in vivo molecular targets.
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124
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On the catalytic role of the active site residue E121 of E. coli l-aspartate oxidase. Biochimie 2010; 92:1335-42. [DOI: 10.1016/j.biochi.2010.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 06/16/2010] [Indexed: 11/18/2022]
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125
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Dong M, Kirchberger T, Huang X, Yang ZJ, Zhang LR, Guse AH, Zhang LH. Trifluoromethylated cyclic-ADP-ribose mimic: synthesis of 8-trifluoromethyl-N(1)-[(5''-O-phosphorylethoxy)methyl]-5'-O-phosphorylinosine-5',5''-cyclic pyrophosphate (8-CF(3)-cIDPRE) and its calcium release activity in T cells. Org Biomol Chem 2010; 8:4705-15. [PMID: 20740240 DOI: 10.1039/c0ob00090f] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A convenient trifluoromethylation method was firstly applied to the synthesis of 8- CF(3)-purine nucleosides. On the basis of this method, new protection and deprotection strategies were developed for the successful synthesis of the trifluoromethylated cyclic-ADP-ribose mimic, 8-CF(3)-cIDPRE 1. Using intact, fura-2-loaded Jurkat T cells compound 1 and 2',3'-O-isopropylidene 8-CF(3)-cIDPRE 14 were characterized as membrane-permeant cADPR agonists. Contrary to the 8-substituted cADPR analogues that mainly act as antagonists of cADPR in cells, 8-substituted cIDPRE derivatives were shown to be Ca(2+) mobilizing agonists. Here we report that even compound 1, the 8-substituted cIDPRE with the strong electron withdrawing CF(3) group, behaves as an agonist in T cells. Interestingly, also the partially protected 2',3'-O-isopropylidene 8-CF(3)-cIDPRE activated Ca(2+) signaling indicating only a minor role for the hydroxyl groups of the southern ribose of cADPR for its biological activity. To our knowledge 8-CF(3)-cIDPRE 1 is the first reported fluoro substituted cADPR mimic and 8-CF(3)-cIDPRE 1 and compound 14 are promising molecular probes for elucidating the mode of action of cADPR.
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Affiliation(s)
- Min Dong
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
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126
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Affiliation(s)
- Caterina Bissantz
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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127
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Pieroni M, Dimovska M, Brincat JP, Sabatini S, Carosati E, Massari S, Kaatz GW, Fravolini A. From 6-aminoquinolone antibacterials to 6-amino-7-thiopyranopyridinylquinolone ethyl esters as inhibitors of Staphylococcus aureus multidrug efflux pumps. J Med Chem 2010; 53:4466-80. [PMID: 20446747 DOI: 10.1021/jm1003304] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thiopyranopyridine moiety was synthesized as a new heterocyclic base to be inserted at the C-7 position of selected quinolone nuclei followed by a determination of antibacterial activity against strains of Staphylococcus aureus. Selected thiopyranopyridinylquinolones showed significant antimicrobial activity, including strains having mutations in gyrA and grlA as well as other strains overexpressing the NorA multidrug (MDR) efflux pump. Most derivatives did not appear to be NorA substrates. The effect of the thiopyranopyridinyl substituent on making these quinolones poor substrates for NorA was investigated further. Several quinolone ester intermediates, devoid of any intrinsic antibacterial activity, were tested for their abilities to inhibit the activities of NorA (MFS family) and MepA (MATE family) S. aureus MDR efflux pumps. Selected quinolone esters were capable of inhibiting both MDR pumps more efficiently than the reference compound reserpine. Moreover, they also were able to restore, and even enhance, the activity of ciprofloxacin toward some genetically modified resistant S. aureus strains.
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Affiliation(s)
- Marco Pieroni
- Dipartimento di Chimica e Tecnologia del Farmaco, Università degli Studi di Perugia, 06123 Perugia, Italy
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128
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Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE. Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. J Am Chem Soc 2010; 132:7617-25. [PMID: 20465217 PMCID: PMC2891752 DOI: 10.1021/ja909370k] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta,gamma-fluoromethylene analogues of nucleotides are considered to be useful mimics of the natural substrates, but direct structural evidence defining their active site interactions has not been available, including the influence of the new chiral center introduced at the CHF carbon, as in beta,gamma-fluoromethylene-dGTP, which forms an active site complex with DNA polymerase beta, a repair enzyme that plays an important role in base excision repair (BER) and oncogenesis. We report X-ray crystallographic results for a series of beta,gamma-CXY dGTP analogues, where X,Y = H, F, Cl, Br, and/or CH(3). For all three R/S monofluorinated analogues examined (CHF, 3/4; CCH(3)F, 13/14; CClF 15/16), a single CXF-diastereomer (3, 13, 16) is observed in the active site complex, with the CXF fluorine atom at a approximately 3 A (bonding) distance to a guanidinium N of Arg183. In contrast, for the CHCl, CHBr, and CHCH(3) analogues, both diasteromers (6/7, 8/9, 10/11) populate the dGTP site in the enzyme complex about equally. The structures of the bound dichloro (5) and dimethyl (12) analogue complexes indicate little to no steric effect on the placement of the bound nucleotide backbone. The results suggest that introduction of a single fluorine atom at the beta,gamma-bridging carbon atom of these dNTP analogues enables a new, stereospecific interaction within the preorganized active site complex that is unique to fluorine. The results also provide the first diverse structural data set permitting an assessment of how closely this class of dNTP analogues mimics the conformation of the parent nucleotide within the active site complex.
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Affiliation(s)
- Vinod K. Batra
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - William A. Beard
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - Samuel H. Wilson
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - Boris A. Kashemirov
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| | - Thomas G. Upton
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| | - Myron F. Goodman
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| | - Charles E. McKenna
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
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129
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Design and synthesis of novel series of pyrrole based chemotypes and their evaluation as selective aldose reductase inhibitors. A case of bioisosterism between a carboxylic acid moiety and that of a tetrazole. Bioorg Med Chem 2010; 18:2107-2114. [DOI: 10.1016/j.bmc.2010.02.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 02/02/2010] [Accepted: 02/05/2010] [Indexed: 11/21/2022]
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130
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Gedeck P, Kramer C, Ertl P. Computational analysis of structure-activity relationships. PROGRESS IN MEDICINAL CHEMISTRY 2010; 49:113-60. [PMID: 20855040 DOI: 10.1016/s0079-6468(10)49004-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Peter Gedeck
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1, Novartis Campus, CH-4056 Basel, Switzerland
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131
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Thakur TS, Kirchner MT, Bläser D, Boese R, Desiraju GR. C–H⋯F–C hydrogen bonding in 1,2,3,5-tetrafluorobenzene and other fluoroaromatic compounds and the crystal structure of alloxan revisited. CrystEngComm 2010. [DOI: 10.1039/b925082d] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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132
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The phosphorylation specificity of B-RAF WT, B-RAF D594V, B-RAF V600E and B-RAF K601E kinases: an in silico study. J Mol Graph Model 2009; 28:598-603. [PMID: 20093060 DOI: 10.1016/j.jmgm.2009.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 12/14/2009] [Accepted: 12/15/2009] [Indexed: 12/30/2022]
Abstract
Phosphorylation of the B-RAF kinase is an essential process in tumour induction and maintenance in several cancers. Herein the phosphorylation specificity of the activation segment of the wild type B-RAF kinase and the B-RAF(D594V), B-RAF(V600E) and B-RAF(K601E) mutants was examined by molecular dynamics (MD) simulations and GRID molecular interaction field analysis. According to our analysis, Thr599 and Ser602 were the only residues in the activation segment in B-RAF(WT) that were well exposed to ATP binding, which is in agreement with the experimental results, and provide a molecular basis of the observed phosphorylation. The phosphorylation specificity was altered significantly for each of the three different mutants studied due to the large conformational changes and subsequent alterations in the electrostatic forces between several residues for each of these mutants. Thus the analysis revealed limited phosphorylation potential of the non-active B-RAF(D594V) mutant and several potential ATP binding sites were identified for the highly active B-RAF(V600E) mutant. The Lys601 residue, which is specific to RAF and not present in the activation segment of other similar kinases, was identified to potentially be of major importance to the observed differences in the phosphorylation specificity of the mutants. Our results indicate that Lys601 might be a specific ATP coordinating residue, contributing to the B-RAF phosphorylation specificity. The overall results can be helpful for the understanding of the B-RAF phosphorylation processes on a molecular level.
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133
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Lu Y, Wang Y, Xu Z, Yan X, Luo X, Jiang H, Zhu W. C-X...H contacts in biomolecular systems: how they contribute to protein-ligand binding affinity. J Phys Chem B 2009; 113:12615-21. [PMID: 19708644 DOI: 10.1021/jp906352e] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydrogen bond acceptor capability of halogens has long been underappreciated in the field of biology. In this work, we have surveyed structures of protein complexes with halogenated ligands to characterize geometrical preferences of C-X...H contacts and contributions of such interactions to protein-ligand binding affinity. Notably, F...H interactions in biomolecules exhibit a remarkably different behavior as compared to three other kinds of X...H (X = Cl, Br, I) interactions, which has been rationalized by means of ab initio calculations using simple model systems. The C-X...H contacts in biological systems are characterized as weak hydrogen bonding interactions. Furthermore, the electrophile "head on" and nucleophile "side on" interactions of halogens have been extensively investigated through the examination of interactions in protein structures and a two-layer ONIOM-based QM/MM method. In biomolecular systems, C-X...H contacts are recognized as secondary interaction contributions to C-X...O halogen bonds that play important roles in conferring specificity and affinity for halogenated ligands. The results presented here are within the context of their potential applications in drug design, including relevance to the development of accurate force fields for halogens.
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Affiliation(s)
- Yunxiang Lu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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134
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Sciabola S, Stanton RV, Mills JE, Flocco MM, Baroni M, Cruciani G, Perruccio F, Mason JS. High-Throughput Virtual Screening of Proteins Using GRID Molecular Interaction Fields. J Chem Inf Model 2009; 50:155-69. [DOI: 10.1021/ci9003317] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simone Sciabola
- Pfizer Research Technology Center, Cambridge, Massachusetts 02139, Pfizer Global Research and Development, Ramsgate Road, Kent CT13 9NJ, Sandwich, United Kingdom, Molecular Discovery Limited, 215 Marsh Road, HA5 5NE, Pinner, Middlesex, United Kingdom, Laboratory of Chemometrics, University of Perugia, Via Elce di Sotto, 10 I-60123, Perugia, Italy, Syngenta, Schaffhauserstrasse, 4332 Stein AG, Switzerland, Lundbeck A/S, Ottiliavej 9, DK-25000, Copenhagen, Denmark
| | - Robert V. Stanton
- Pfizer Research Technology Center, Cambridge, Massachusetts 02139, Pfizer Global Research and Development, Ramsgate Road, Kent CT13 9NJ, Sandwich, United Kingdom, Molecular Discovery Limited, 215 Marsh Road, HA5 5NE, Pinner, Middlesex, United Kingdom, Laboratory of Chemometrics, University of Perugia, Via Elce di Sotto, 10 I-60123, Perugia, Italy, Syngenta, Schaffhauserstrasse, 4332 Stein AG, Switzerland, Lundbeck A/S, Ottiliavej 9, DK-25000, Copenhagen, Denmark
| | - James E. Mills
- Pfizer Research Technology Center, Cambridge, Massachusetts 02139, Pfizer Global Research and Development, Ramsgate Road, Kent CT13 9NJ, Sandwich, United Kingdom, Molecular Discovery Limited, 215 Marsh Road, HA5 5NE, Pinner, Middlesex, United Kingdom, Laboratory of Chemometrics, University of Perugia, Via Elce di Sotto, 10 I-60123, Perugia, Italy, Syngenta, Schaffhauserstrasse, 4332 Stein AG, Switzerland, Lundbeck A/S, Ottiliavej 9, DK-25000, Copenhagen, Denmark
| | - Maria M. Flocco
- Pfizer Research Technology Center, Cambridge, Massachusetts 02139, Pfizer Global Research and Development, Ramsgate Road, Kent CT13 9NJ, Sandwich, United Kingdom, Molecular Discovery Limited, 215 Marsh Road, HA5 5NE, Pinner, Middlesex, United Kingdom, Laboratory of Chemometrics, University of Perugia, Via Elce di Sotto, 10 I-60123, Perugia, Italy, Syngenta, Schaffhauserstrasse, 4332 Stein AG, Switzerland, Lundbeck A/S, Ottiliavej 9, DK-25000, Copenhagen, Denmark
| | - Massimo Baroni
- Pfizer Research Technology Center, Cambridge, Massachusetts 02139, Pfizer Global Research and Development, Ramsgate Road, Kent CT13 9NJ, Sandwich, United Kingdom, Molecular Discovery Limited, 215 Marsh Road, HA5 5NE, Pinner, Middlesex, United Kingdom, Laboratory of Chemometrics, University of Perugia, Via Elce di Sotto, 10 I-60123, Perugia, Italy, Syngenta, Schaffhauserstrasse, 4332 Stein AG, Switzerland, Lundbeck A/S, Ottiliavej 9, DK-25000, Copenhagen, Denmark
| | - Gabriele Cruciani
- Pfizer Research Technology Center, Cambridge, Massachusetts 02139, Pfizer Global Research and Development, Ramsgate Road, Kent CT13 9NJ, Sandwich, United Kingdom, Molecular Discovery Limited, 215 Marsh Road, HA5 5NE, Pinner, Middlesex, United Kingdom, Laboratory of Chemometrics, University of Perugia, Via Elce di Sotto, 10 I-60123, Perugia, Italy, Syngenta, Schaffhauserstrasse, 4332 Stein AG, Switzerland, Lundbeck A/S, Ottiliavej 9, DK-25000, Copenhagen, Denmark
| | - Francesca Perruccio
- Pfizer Research Technology Center, Cambridge, Massachusetts 02139, Pfizer Global Research and Development, Ramsgate Road, Kent CT13 9NJ, Sandwich, United Kingdom, Molecular Discovery Limited, 215 Marsh Road, HA5 5NE, Pinner, Middlesex, United Kingdom, Laboratory of Chemometrics, University of Perugia, Via Elce di Sotto, 10 I-60123, Perugia, Italy, Syngenta, Schaffhauserstrasse, 4332 Stein AG, Switzerland, Lundbeck A/S, Ottiliavej 9, DK-25000, Copenhagen, Denmark
| | - Jonathan S. Mason
- Pfizer Research Technology Center, Cambridge, Massachusetts 02139, Pfizer Global Research and Development, Ramsgate Road, Kent CT13 9NJ, Sandwich, United Kingdom, Molecular Discovery Limited, 215 Marsh Road, HA5 5NE, Pinner, Middlesex, United Kingdom, Laboratory of Chemometrics, University of Perugia, Via Elce di Sotto, 10 I-60123, Perugia, Italy, Syngenta, Schaffhauserstrasse, 4332 Stein AG, Switzerland, Lundbeck A/S, Ottiliavej 9, DK-25000, Copenhagen, Denmark
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135
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Carosati E, Budriesi R, Ioan P, Cruciani G, Fusi F, Frosini M, Saponara S, Gasparrini F, Ciogli A, Villani C, Stephens PJ, Devlin FJ, Spinelli D, Chiarini A. Stereoselective Behavior of the Functional Diltiazem Analogue 1-[(4-Chlorophenyl)sulfonyl]-2-(2-thienyl)pyrrolidine, a New L-Type Calcium Channel Blocker. J Med Chem 2009; 52:6637-48. [DOI: 10.1021/jm9008696] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emanuele Carosati
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italy
| | - Roberta Budriesi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Pierfranco Ioan
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Gabriele Cruciani
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italy
| | - Fabio Fusi
- Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Maria Frosini
- Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Simona Saponara
- Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Francesco Gasparrini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università “La Sapienza”, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Alessia Ciogli
- Dipartimento di Chimica e Tecnologie del Farmaco, Università “La Sapienza”, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Claudio Villani
- Dipartimento di Chimica e Tecnologie del Farmaco, Università “La Sapienza”, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Philip J. Stephens
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482
| | - Frank J. Devlin
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482
| | - Domenico Spinelli
- Dipartimento di Chimica “G. Ciamician”, Università degli Studi di Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Alberto Chiarini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy
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136
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Zhou P, Zou J, Tian F, Shang Z. Fluorine Bonding — How Does It Work In Protein−Ligand Interactions? J Chem Inf Model 2009; 49:2344-55. [DOI: 10.1021/ci9002393] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Zhou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Jianwei Zou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Feifei Tian
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Zhicai Shang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
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137
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Vulpetti A, Hommel U, Landrum G, Lewis R, Dalvit C. Design and NMR-Based Screening of LEF, a Library of Chemical Fragments with Different Local Environment of Fluorine. J Am Chem Soc 2009; 131:12949-59. [DOI: 10.1021/ja905207t] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Anna Vulpetti
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Ulrich Hommel
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Gregory Landrum
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Richard Lewis
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
| | - Claudio Dalvit
- Novartis Institute for Biomedical Research, Novartis Pharma AG, CH-4002 Basel, Switzerland, Italian Institute of Technology, Via Morego 30, 16163 Genova, Italy
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138
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Abstract
Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.
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Affiliation(s)
- Hans-Jörg Schneider
- Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken, Deutschland.
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139
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140
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Budriesi R, Cosimelli B, Ioan P, Ugenti MP, Carosati E, Frosini M, Fusi F, Spisani R, Saponara S, Cruciani G, Novellino E, Spinelli D, Chiarini A. L-Type Calcium Channel Blockers: From Diltiazem to 1,2,4-Oxadiazol-5-ones via Thiazinooxadiazol-3-one Derivatives. J Med Chem 2009; 52:2352-62. [DOI: 10.1021/jm801351u] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberta Budriesi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Barbara Cosimelli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Pierfranco Ioan
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Maria Paola Ugenti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Emanuele Carosati
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Maria Frosini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Fabio Fusi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Raffaella Spisani
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Simona Saponara
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Gabriele Cruciani
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Ettore Novellino
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Domenico Spinelli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
| | - Alberto Chiarini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli, Italy, Dipartimento di Chimica, Università di Perugia, via Elce di Sotto 8, 06123 Perugia, Italy, Dipartimento di Neuroscienze, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy, Dipartimento di Chimica Organica “A. Mangini”, Università degli
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Matter H, Nazaré M, Güssregen S, Will D, Schreuder H, Bauer A, Urmann M, Ritter K, Wagner M, Wehner V. Evidence for CCl/CBr⋅⋅⋅π Interactions as an Important Contribution to Protein-Ligand Binding Affinity. Angew Chem Int Ed Engl 2009; 48:2911-6. [DOI: 10.1002/anie.200806219] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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142
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Matter H, Nazaré M, Güssregen S, Will D, Schreuder H, Bauer A, Urmann M, Ritter K, Wagner M, Wehner V. Evidence for CCl/CBr⋅⋅⋅π Interactions as an Important Contribution to Protein-Ligand Binding Affinity. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806219] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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143
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La Motta C, Sartini S, Mugnaini L, Salerno S, Simorini F, Taliani S, Marini AM, Da Settimo F, Lavecchia A, Novellino E, Antonioli L, Fornai M, Blandizzi C, Del Tacca M. Exploiting the Pyrazolo[3,4-d]pyrimidin-4-one Ring System as a Useful Template To Obtain Potent Adenosine Deaminase Inhibitors. J Med Chem 2009; 52:1681-92. [DOI: 10.1021/jm801427r] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Concettina La Motta
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Stefania Sartini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Laura Mugnaini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Silvia Salerno
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Francesca Simorini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Sabrina Taliani
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Anna Maria Marini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Federico Da Settimo
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Antonio Lavecchia
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Ettore Novellino
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Luca Antonioli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Matteo Fornai
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Corrado Blandizzi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
| | - Mario Del Tacca
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, Via Bonanno, 6, 56126 Pisa, Italy, Dipartimento di Chimica Farmaceutica e Tossicologica, Università di Napoli “Federico II”, Via D. Montesano, 49, 80131 Napoli, Italy, and Centro Interdipartimentale di Ricerche di Farmacologia Clinica e Terapia Sperimentale, Via Roma 55, 56126 Pisa, Italy
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Chapter 4 Case History: Chantix™/Champix™ (Varenicline Tartrate), a Nicotinic Acetylcholine Receptor Partial Agonist as a Smoking Cessation Aid. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2009. [DOI: 10.1016/s0065-7743(09)04404-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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145
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Manam RR, McArthur KA, Chao TH, Weiss J, Ali JA, Palombella VJ, Groll M, Lloyd GK, Palladino MA, Neuteboom STC, Macherla VR, Potts BCM. Leaving Groups Prolong the Duration of 20S Proteasome Inhibition and Enhance the Potency of Salinosporamides. J Med Chem 2008; 51:6711-24. [PMID: 18939815 DOI: 10.1021/jm800548b] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Rama Rao Manam
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Katherine A. McArthur
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Ta-Hsiang Chao
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Jeffrey Weiss
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Janid A. Ali
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Vito J. Palombella
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Michael Groll
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - G. Kenneth Lloyd
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Michael A. Palladino
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Saskia T. C. Neuteboom
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Venkat R. Macherla
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
| | - Barbara C. M. Potts
- Nereus Pharmaceuticals, Inc., 10480 Wateridge Circle, San Diego, California 92121, Infinity Pharmaceuticals, 780 Memorial Drive, Cambridge, Massachusetts 02139, and Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, Garching D-85747, Germany
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146
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Comparative docking studies of labdane-type diterpenes with forskolin at the active site of adenylyl cyclase. Bioorg Med Chem 2008; 16:8237-43. [DOI: 10.1016/j.bmc.2008.07.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Revised: 07/03/2008] [Accepted: 07/16/2008] [Indexed: 11/21/2022]
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147
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Carosati E, Budriesi R, Ioan P, Ugenti MP, Frosini M, Fusi F, Corda G, Cosimelli B, Spinelli D, Chiarini A, Cruciani G. Discovery of Novel and Cardioselective Diltiazem-like Calcium Channel Blockers via Virtual Screening. J Med Chem 2008; 51:5552-65. [DOI: 10.1021/jm800151n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emanuele Carosati
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Roberta Budriesi
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Pierfranco Ioan
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Maria P. Ugenti
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Maria Frosini
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Fabio Fusi
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Gaetano Corda
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Barbara Cosimelli
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Domenico Spinelli
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Alberto Chiarini
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
| | - Gabriele Cruciani
- Dipartimento di Chimica, Università degli Studi di Perugia, Via Elce di Sotto 10, 06123 Perugia, Italia, Dipartimento di Scienze Farmaceutiche, Università degli Studi di Bologna, Via Belmeloro 6, 40126 Bologna, Italia, Dipartimento di Scienze Biomediche, Sezione di Farmacologia, Fisiologia e Tossicologia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italia, Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, Via Montesano 49, 80131 Napoli,
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Pugazhendhi D, Watson KA, Mills S, Botting N, Pope GS, Darbre PD. Effect of sulphation on the oestrogen agonist activity of the phytoestrogens genistein and daidzein in MCF-7 human breast cancer cells. J Endocrinol 2008; 197:503-15. [PMID: 18492816 PMCID: PMC2386535 DOI: 10.1677/joe-07-0384] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The phytoestrogens genistein, daidzein and the daidzein metabolite equol have been shown previously to possess oestrogen agonist activity. However, following consumption of soya diets, they are found in the body not only as aglycones but also as metabolites conjugated at their 4'- and 7-hydroxyl groups with sulphate. This paper describes the effects of monosulphation on the oestrogen agonist properties of these three phytoestrogens in MCF-7 human breast cancer cells in terms of their relative ability to compete with [(3)H]oestradiol for binding to oestrogen receptor (ER), to induce a stably transfected oestrogen-responsive reporter gene (ERE-CAT) and to stimulate cell growth. In no case did sulphation abolish activity. The 4'-sulphation of genistein reduced oestrogen agonist activity to a small extent in whole-cell assays but increased the relative binding affinity to ER. The 7-sulphation of genistein, and also of equol, reduced oestrogen agonist activity substantially in all assays. By contrast, the position of monosulphation of daidzein acted in an opposing manner on oestrogen agonist activity. Sulphation at the 4'-position of daidzein resulted in a modest reduction in oestrogen agonist activity but sulphation of daidzein at the 7-position resulted in an increase in oestrogen agonist activity. Molecular modelling and docking studies suggested that the inverse effects of sulphation could be explained by the binding of daidzein into the ligand-binding domain of the ER in the opposite orientation compared with genistein and equol. This is the first report of sulphation enhancing activity of an isoflavone and inverse effects of sulphation between individual phytoestrogens.
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Affiliation(s)
- D Pugazhendhi
- School of Biological SciencesThe University of ReadingReading, RG6 6AJUK
| | - K A Watson
- School of Biological SciencesThe University of ReadingReading, RG6 6AJUK
- Structural Biology UnitThe BioCentre, University of ReadingReading, RG6 6ASUK
| | - S Mills
- School of Biological SciencesThe University of ReadingReading, RG6 6AJUK
| | - N Botting
- School of ChemistryUniversity of St AndrewsSt Andrews, Fife, KY16 9STUK
| | - G S Pope
- School of Biological SciencesThe University of ReadingReading, RG6 6AJUK
| | - P D Darbre
- School of Biological SciencesThe University of ReadingReading, RG6 6AJUK
- (Correspondence should be addressed to P D Darbre; )
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149
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Halogenated ligands and their interactions with amino acids: implications for structure-activity and structure-toxicity relationships. J Mol Graph Model 2008; 27:170-7. [PMID: 18524655 DOI: 10.1016/j.jmgm.2008.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 04/02/2008] [Accepted: 04/03/2008] [Indexed: 11/24/2022]
Abstract
The properties of chemicals are rooted in their molecular structure. It follows that structural analysis of specific interactions between ligands and biomolecules at the molecular level is invaluable for defining structure-activity relationships (SARs) and structure-toxicity relationships (STRs). This study has elucidated the structural and molecular basis of interactions of biomolecules with alkyl and aryl halides that are extensively used as components in many commercial pesticides, disinfectants, and drugs. We analyzed the protein structures deposited in Protein Data Bank (PDB) for structural information associated with interactions between halogenated ligands and proteins. This analysis revealed distinct patterns with respect to the nature and structural characteristics of halogen interactions with specific types of atoms and groups in proteins. Fluorine had the highest propensity of interactions for glycine, while chlorine for leucine, bromine for arginine, and iodine for lysine. Chlorine, bromine and iodine had the lowest propensity of interactions for cysteine, while fluorine had a lowest propensity for proline. These trends for highest propensity shifted towards the hydrophobic residues for all the halogens when only interactions with the side chain were considered. Halogens had equal propensities of interaction for the halogen bonding partners (nitrogen and oxygen atoms), albeit with different geometries. The optimal angle for interactions with halogens was approximately 120 degrees for oxygen atoms, and approximately 96 degrees for nitrogen atoms. The distance distributions of halogens with various amino acids were mostly bimodal, and the angle distributions were unimodal. Insights gained from this study have implications for the rational design of safer drugs and commercially important chemicals.
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150
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Krow GR, Gandla D, Guo W, Centafont RA, Lin G, Debrosse C, Sonnet PE, Ross CW, Ramjit HG, Cannon KC. Selectfluor as a nucleofuge in the reactions of azabicyclo[n.2.1]alkane beta-halocarbamic acid esters (n = 2,3). J Org Chem 2008; 73:2122-9. [PMID: 18290657 DOI: 10.1021/jo702155v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability of Selectfluor to act as a nucleofuge for hydrolysis of beta-anti-halides was investigated with N-alkoxycarbonyl derivatives of 6-anti-Y-7-anti-X-2-azabicyclo[2.2.1]heptanes and 4-anti-Y-8-anti-X-6-azabicyclo[3.2.1]octanes. The azabicycles contained X = I or Br groups in the methano bridge and Y = F, Br, Cl, or OH substituents in the larger bridge. The relative reactivities of the halides were a function of the azabicycle, the halide, and its bridge and the addition of Selectfluor or HgF(2) as a nucleofuge. All halide displacements occurred with retention of stereochemistry. Selectfluor with sodium bromide or sodium chloride, but not sodium iodide, competitively oxidized some haloalcohols to haloketones. A significant 15.6 Hz F...HO NMR coupling was observed with 4-anti-fluoro-8-anti-hydroxy-6-azabicyclo[3.2.1]octane.
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Affiliation(s)
- Grant R Krow
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, USA.
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