1
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Yuan Z, Britton R. Development and application of decatungstate catalyzed C-H 18F- and 19F-fluorination, fluoroalkylation and beyond. Chem Sci 2023; 14:12883-12897. [PMID: 38023504 PMCID: PMC10664588 DOI: 10.1039/d3sc04027e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Over the past few decades, photocatalytic C-H functionalization reactions have received increasing attention due to the often mild reaction conditions and complementary selectivities to conventional functionalization processes. Now, photocatalytic C-H functionalization is a widely employed tool, supporting activities ranging from complex molecule synthesis to late-stage structure-activity relationship studies. In this perspective, we will discuss our efforts in developing a photocatalytic decatungstate catalyzed C-H fluorination reaction as well as its practical application realized through collaborations with industry partners at Hoffmann-La Roche and Merck, and extension to radiofluorination with radiopharmaceutical chemists and imaging experts at TRIUMF and the BC Cancer Agency. Importantly, we feel that our efforts address a question of utility posed by Professor Tobias Ritter in "Late-Stage Fluorination: Fancy Novelty or Useful Tool?" (ACIE, 2015, 54, 3216). In addition, we will discuss decatungstate catalyzed C-H fluoroalkylation and the interesting electrostatic effects observed in decatungstate-catalyzed C-H functionalization. We hope this perspective will inspire other researchers to explore the use of decatungstate for the purposes of photocatalytic C-H functionalization and further advance the exploitation of electrostatic effects for both rate acceleration and directing effects in these reactions.
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Affiliation(s)
- Zheliang Yuan
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S2 Canada
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University Jinhua Zhejiang 321004 China
| | - Robert Britton
- Department of Chemistry, Simon Fraser University Burnaby British Columbia V5A 1S2 Canada
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2
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Islam B, Colby DA. Transient Formation of Hemiketals from Pentafluoro- gem-diols in the Presence of Alcohols. J Fluor Chem 2023; 270:110162. [PMID: 37546180 PMCID: PMC10399912 DOI: 10.1016/j.jfluchem.2023.110162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Pentafluoro-gem-diols have emerged as a source of reactive intermediates for synthesizing fluorinated molecules. When pentafluoro-gem-diols were exposed to alcohols as solvents, the formation of transient hemiketals was detected by 19F NMR. The conversion rates to hemiketals were found to be higher with primary alcohols than with secondary or fluorinated alcohols. These findings provide valuable insight for developing novel techniques to construct intricate fluorinated structures using pentafluoro-gem-diols.
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Affiliation(s)
- Baharul Islam
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, U.S.A
| | - David A Colby
- Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, U.S.A
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3
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Watson PR, Bai P, Wang C, Cragin AD, Hooker JM, Christianson DW. Aromatic Ring Fluorination Patterns Modulate Inhibitory Potency of Fluorophenylhydroxamates Complexed with Histone Deacetylase 6. Biochemistry 2022; 61:1945-1954. [PMID: 36073962 PMCID: PMC9489680 DOI: 10.1021/acs.biochem.2c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bavarostat (EKZ-001) is a selective inhibitor of histone deacetylase 6 (HDAC6) that contains a meta-fluorophenylhydroxamate Zn2+-binding group. The recently determined crystal structure of its complex with HDAC6 from Danio rerio (zebrafish) revealed that the meta-fluoro substituent binds exclusively in an aromatic crevice defined by F583 and F643 rather than being oriented out toward solvent. To explore the binding of inhibitor C-F groups in this fluorophilic crevice, we now report a series of 10 simple fluorophenylhydroxamates bearing one or more fluorine atoms with different substitution patterns. Inhibitory potencies against human and zebrafish HDAC6 range widely from 121 to >30,000 nM. The best inhibitory potency is measured for meta-difluorophenylhydroxamate (5) with IC50 = 121 nM against human HDAC6; the worst inhibitory potencies are measured for ortho-fluorophenylhydroxamate (1) as well as fluorophenylhydroxamates 4, 7, 9, and 10, although there are some variations in activity trends against human and zebrafish HDAC6. These studies show that aromatic ring fluorination at the meta position(s) does not improve inhibitory activity against human HDAC6 relative to the nonfluorinated parent compound phenylhydroxamate (IC50 = 120 nM), but meta-fluorination does not seriously compromise inhibitory activity either. Crystal structures of selected zebrafish HDAC6-fluorophenylhydroxamate complexes reveal that the fluoroaromatic ring is uniformly accommodated in the F583-F643 aromatic crevice, so ring fluorination does not perturb the inhibitor binding conformation. However, hydroxamate-Zn2+ coordination is bidentate for some inhibitors and monodentate for others. These studies will inform design strategies underlying the design of 18F-labeled HDAC6 inhibitors intended for positron emission tomography.
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Affiliation(s)
- Paris R. Watson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - Ping Bai
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129 United States
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129 United States
| | - Abigail D. Cragin
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - Jacob M. Hooker
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129 United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
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4
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Karges J, Stokes RW, Cohen SM. Computational Prediction of the Binding Pose of Metal-Binding Pharmacophores. ACS Med Chem Lett 2022; 13:428-435. [PMID: 35300086 PMCID: PMC8919381 DOI: 10.1021/acsmedchemlett.1c00584] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/14/2022] [Indexed: 01/22/2023] Open
Abstract
Computational modeling of inhibitors for metalloenzymes in virtual drug development campaigns has proven challenging. To overcome this limitation, a technique for predicting the binding pose of metal-binding pharmacophores (MBPs) is presented. Using a combination of density functional theory (DFT) calculations and docking using a genetic algorithm, inhibitor binding was evaluated in silico and compared with inhibitor-enzyme cocrystal structures. The predicted binding poses were found to be consistent with the cocrystal structures. The computational strategy presented represents a useful tool for predicting metalloenzyme-MBP interactions.
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Affiliation(s)
- Johannes Karges
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Ryjul W Stokes
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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5
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Small-molecule MDM2/X inhibitors and PROTAC degraders for cancer therapy: advances and perspectives. Acta Pharm Sin B 2020; 10:1253-1278. [PMID: 32874827 PMCID: PMC7452049 DOI: 10.1016/j.apsb.2020.01.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/31/2019] [Accepted: 12/26/2019] [Indexed: 12/26/2022] Open
Abstract
Blocking the MDM2/X–P53 protein–protein interaction has been widely recognized as an attractive therapeutic strategy for the treatment of cancers. Numerous small-molecule MDM2 inhibitors have been reported since the release of the structure of the MDM2–P53 interaction in 1996, SAR405838, NVP-CGM097, MK-8242, RG7112, RG7388, DS-3032b, and AMG232 currently undergo clinical evaluation for cancer therapy. This review is intended to provide a comprehensive and updated overview of MDM2 inhibitors and proteolysis targeting chimera (PROTAC) degraders with a particular focus on how these inhibitors or degraders are identified from starting points, strategies employed, structure–activity relationship (SAR) studies, binding modes or co-crystal structures, biochemical data, mechanistic studies, and preclinical/clinical studies. Moreover, we briefly discuss the challenges of designing MDM2/X inhibitors for cancer therapy such as dual MDM2/X inhibition, acquired resistance and toxicity of P53 activation as well as future directions.
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6
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Appalanaidu K, Dadmal TL, Patil SM, Jagadeesh Babu N, Laxmikanth Rao J, Kumbhare RM. An Efficient One‐Shot Metal‐Free Electrophilic Fluorination of 2‐Iminothiazolidine‐4‐one. ChemistrySelect 2020. [DOI: 10.1002/slct.202000189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Killari Appalanaidu
- Fluoro AgrochemicalsDivision CSIR-Indian Institute of Chemical Technology, Tarnaka Hyderabad 500607 India
| | - Tulshiram L. Dadmal
- Department of Chemistry Government of Maharashtra's, IsmailYusuf College, Jogeshwari (E) Mumbai 400060 India
| | - Suvarna M. Patil
- Fluoro AgrochemicalsDivision CSIR-Indian Institute of Chemical Technology, Tarnaka Hyderabad 500607 India
| | - N. Jagadeesh Babu
- InstitutionLaboratory of X-ray Crystallography CSIR-Indian Institute of Chemical Technology Hyderabad 500607 India
| | - J. Laxmikanth Rao
- Dept. Of Catalysis and fine chemical CSIR-Indian Institute of Chemical Technology Hyderabad 500607 India
| | - Ravindra M. Kumbhare
- Fluoro AgrochemicalsDivision CSIR-Indian Institute of Chemical Technology, Tarnaka Hyderabad 500607 India
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7
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Osko JD, Porter NJ, Reddy PAN, Xiao YC, Rokka J, Jung M, Hooker JM, Salvino JM, Christianson DW. Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J Med Chem 2020; 63:295-308. [PMID: 31793776 PMCID: PMC6952581 DOI: 10.1021/acs.jmedchem.9b01540] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Inhibition of histone deacetylase 6 (HDAC6) has emerged as a promising therapeutic strategy for the treatment of cancer, chemotherapy-induced peripheral neuropathy, and neurodegenerative disease. The recent X-ray crystal structure determination of HDAC6 enables an understanding of structural features directing affinity and selectivity in the active site. Here, we present the X-ray crystal structures of five HDAC6-inhibitor complexes that illuminate key molecular features of the inhibitor linker and capping groups that facilitate and differentiate binding to HDAC6. In particular, aromatic and heteroaromatic linkers nestle within an aromatic cleft defined by F583 and F643, and different aromatic linkers direct the capping group toward shallow pockets defined by the L1 loop, the L2 loop, or somewhere in between these pockets. These results expand our understanding of factors contributing to the selective inhibition of HDAC6, particularly regarding interactions that can be targeted in the region of the L2 pocket.
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Affiliation(s)
- Jeremy D. Osko
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | - Nicholas J. Porter
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
| | | | - You-Cai Xiao
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, United States
| | - Johanna Rokka
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Manfred Jung
- Institute of Pharmaceutical Sciences, University of Freiburg, Albertstraße 25, 79104 Freiburg, Germany
| | - Jacob M. Hooker
- Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Joseph M. Salvino
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, United States
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, PA 19104-6323, United States
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8
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Abstract
The article discusses the basic properties of fluorine atom that have made it so useful in drug development. It presents several examples of therapeutically useful drugs acting against many life-threatening diseases along with the mechanism as to how fluorine influences the drug activity. It has been pointed out that fluorine, due to its ability to increase the lipophilicity of the molecule, greatly affects the hydrophobic interaction between the drug molecule and the receptor. Because of its small size, it hardly produces any steric effect, rather due to electronic properties enters into electrostatic and hydrogen-bond interactions. Thus, it greatly affects the drug-receptor interaction and leads to increase the activity of the drugs.
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Affiliation(s)
- Satya Prakash Gupta
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, Meerut 250005, India
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9
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Thermodynamic, kinetic, and structural parameterization of human carbonic anhydrase interactions toward enhanced inhibitor design. Q Rev Biophys 2019; 51:e10. [PMID: 30912486 DOI: 10.1017/s0033583518000082] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The aim of rational drug design is to develop small molecules using a quantitative approach to optimize affinity. This should enhance the development of chemical compounds that would specifically, selectively, reversibly, and with high affinity interact with a target protein. It is not yet possible to develop such compounds using computational (i.e., in silico) approach and instead the lead molecules are discovered in high-throughput screening searches of large compound libraries. The main reason why in silico methods are not capable to deliver is our poor understanding of the compound structure-thermodynamics and structure-kinetics correlations. There is a need for databases of intrinsic binding parameters (e.g., the change upon binding in standard Gibbs energy (ΔGint), enthalpy (ΔHint), entropy (ΔSint), volume (ΔVintr), heat capacity (ΔCp,int), association rate (ka,int), and dissociation rate (kd,int)) between a series of closely related proteins and a chemically diverse, but pharmacophoric group-guided library of compounds together with the co-crystal structures that could help explain the structure-energetics correlations and rationally design novel compounds. Assembly of these data will facilitate attempts to provide correlations and train data for modeling of compound binding. Here, we report large datasets of the intrinsic thermodynamic and kinetic data including over 400 primary sulfonamide compound binding to a family of 12 catalytically active human carbonic anhydrases (CA). Thermodynamic parameters have been determined by the fluorescent thermal shift assay, isothermal titration calorimetry, and by the stopped-flow assay of the inhibition of enzymatic activity. Kinetic measurements were performed using surface plasmon resonance. Intrinsic thermodynamic and kinetic parameters of binding were determined by dissecting the binding-linked protonation reactions of the protein and sulfonamide. The compound structure-thermodynamics and kinetics correlations reported here helped to discover compounds that exhibited picomolar affinities, hour-long residence times, and million-fold selectivities over non-target CA isoforms. Drug-lead compounds are suggested for anticancer target CA IX and CA XII, antiglaucoma CA IV, antiobesity CA VA and CA VB, and other isoforms. Together with 85 X-ray crystallographic structures of 60 compounds bound to six CA isoforms, the database should be of help to continue developing the principles of rational target-based drug design.
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10
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Chen D, Li Y, Guo W, Li Y, Savidge T, Li X, Fan X. The shielding effect of metal complexes on the binding affinities of ligands to metalloproteins. Phys Chem Chem Phys 2019; 21:205-216. [DOI: 10.1039/c8cp06555a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The contributions of metal–ligand interactions to the ligand binding affinities are largely reduced by the shielding effects of metal complexes.
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Affiliation(s)
- Deliang Chen
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Yibao Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Wei Guo
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Yongdong Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Tor Savidge
- Department of Pathology & Immunology
- Baylor College of Medicine
- Houston
- USA
- Texas Children's Microbiome Center
| | - Xun Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
| | - Xiaolin Fan
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry
- Chemistry and Chemical Engineering College
- Gannan Normal University
- Ganzhou
- P. R. China
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11
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Abstract
The role of π-π interactions in controlling the reactivity and selectivity of a chemical reaction is only recently being explored, even though their ubiquitous role in the structural aspects is well known. We have studied Bergman cyclisation focusing on the effect of π-π interactions on the activation barrier and the variation of π-π interactions along the reaction coordinate. We used enediyne substrates that contain phenyl groups connected to the reaction centres (C1 and C6 atoms), separated by 0, 1 and 2 linker groups. The main difference between the substrates is that the Ph groups enjoy different flexibility to accommodate the changes occurring during the progress of the reaction. The path length of the minimum energy path is increased - shortest in the least flexible substrate (a) and longer in the more flexible ones (c, d and e). We calculated the interaction between the Ph groups, the π-π interaction, using BP86-D3BJ, B3LYP-D3BJ, M06-2X, B2PLYP-D3BJ, SCS-MP2, and SAPT. The BP86-D3BJ was found to be sufficiently accurate with a mean absolute deviation of 0.26 kcal mol(-1) with respect to the SAPT2+3 values. The variation in the π-π interaction shows different behaviour in a-e, and this can be correlated with the flexibility of the Ph groups to orient themselves to maintain the optimal relative orientation while conforming to the changes in the reaction coordinate. We analysed the relative orientation of the phenyl groups using certain geometric parameters that showed that when Ph groups can attain a relative orientation close to that of the free dimer, the interaction is maximum. Energy decomposition analysis using SAPT showed that the dispersive interaction is the major contributor (50-60%) to the attractive forces. The π-π interactions influenced the overall activation energy, either by destabilising the substrates or by stabilising the TS - resulting in a variation of about 3.5 kcal mol(-1) in activation energies in a-e. The effect of substituents of different electronic nature was assessed which showed that electron donating and electron withdrawing substituents increase the π-π interactions; however, the TS is more stabilised and hence activation energies are increased.
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Affiliation(s)
- Saibal Jana
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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12
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Lu X, Sun J, Liu Y, Shao J, Ma L, Zhang S, Zhao J, Shao Y, Zhang HL, Wang Z, Shao X. Decorating tetrathiafulvalene (TTF) with fluorinated phenyls through sulfur bridges: facile synthesis, properties, and aggregation through fluorine interactions. Chemistry 2014; 20:9650-6. [PMID: 24981731 DOI: 10.1002/chem.201402327] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Indexed: 11/12/2022]
Abstract
Tetrathiafulvalene derivatives (TTF1-TTF9) bearing fluorinated phenyl groups attached through the sulfur bridges have been synthesized by employing a copper-mediated C-S coupling reaction of C6 H5-x Fx I (x=1, 2, 5) and a zinc-thiolate complex, (TBA)2 [Zn(DMIT)2 ] (TBA=tetrabutyl ammonium, DMIT=1,3-dithiole-2-thione-4,5-dithiolate), as the key step. Particularly, the selective synthesis of C6 F5 -substituted (TTF8) and C6 F4 -fused (TTF9) TTFs from C6 F5 I is disclosed. The physicochemical properties and crystal structures of these TTFs are fully investigated by UV/Vis absorption spectra, cyclic voltammetry, molecular orbital calculation, and single-crystal X-ray diffraction. The exchange of hydrogen versus fluorine on the peripheral phenyl groups show a notable influence on both the electronic and crystallographic natures of the resulting TTFs: 1) lowering both the HOMO and the LUMO energy levels, 2) modulating the electrochemical properties by regioselective and/or the degree of fluorination, 3) enhancing the driving forces of stacking by multiple fluorine interactions (F⋅⋅⋅S, CF⋅⋅⋅π/πF , CF⋅⋅⋅FC, and CF⋅⋅⋅H). This work indicates that the decoration with fluorinated phenyls holds promise to produce functional TTFs with novel electronic and aggregation features.
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Affiliation(s)
- Xiaofeng Lu
- State Key Laboratory of Applied Organic Chemistry & School of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, Gansu Province (P.R. China)
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13
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Wang JL, Xu JS, Wang DY, Wang H, Li ZT, Zhang DW. Anti-parallel sheet structures of side-chain-free γ-, δ-, and ε-dipeptides stabilized by benzene–pentafluorobenzene stacking. CrystEngComm 2014. [DOI: 10.1039/c3ce42060d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Benzene–pentafluorobenzene stacking can guide ω-amino acid dipeptides to arrange in an anti-parallel manner.
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Affiliation(s)
- Ji-Liang Wang
- Department of Chemistry
- Fudan University
- Shanghai 200433, China
| | - Jia-Su Xu
- Department of Chemistry
- Fudan University
- Shanghai 200433, China
| | - Dong-Yun Wang
- Department of Chemistry
- Fudan University
- Shanghai 200433, China
| | - Hui Wang
- Department of Chemistry
- Fudan University
- Shanghai 200433, China
| | - Zhan-Ting Li
- Department of Chemistry
- Fudan University
- Shanghai 200433, China
| | - Dan-Wei Zhang
- Department of Chemistry
- Fudan University
- Shanghai 200433, China
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14
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Liang T, Neumann CN, Ritter T. Introduction of fluorine and fluorine-containing functional groups. Angew Chem Int Ed Engl 2013; 52:8214-64. [PMID: 23873766 DOI: 10.1002/anie.201206566] [Citation(s) in RCA: 1953] [Impact Index Per Article: 177.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Indexed: 01/20/2023]
Abstract
Over the past decade, the most significant, conceptual advances in the field of fluorination were enabled most prominently by organo- and transition-metal catalysis. The most challenging transformation remains the formation of the parent C-F bond, primarily as a consequence of the high hydration energy of fluoride, strong metal-fluorine bonds, and highly polarized bonds to fluorine. Most fluorination reactions still lack generality, predictability, and cost-efficiency. Despite all current limitations, modern fluorination methods have made fluorinated molecules more readily available than ever before and have begun to have an impact on research areas that do not require large amounts of material, such as drug discovery and positron emission tomography. This Review gives a brief summary of conventional fluorination reactions, including those reactions that introduce fluorinated functional groups, and focuses on modern developments in the field.
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Affiliation(s)
- Theresa Liang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
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16
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Wu S, Pan D, Cao C, Wang Q, Chen FX. Diastereoselective and Enantioselective Epoxidation of Acyclic β-Trifluoromethyl-β,β-Disubstituted Enones by Hydrogen Peroxide with a Pentafluorinated Quinidine-Derived Phase-Transfer Catalyst. Adv Synth Catal 2013. [DOI: 10.1002/adsc.201300249] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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17
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De Simone G, Alterio V, Supuran CT. Exploiting the hydrophobic and hydrophilic binding sites for designing carbonic anhydrase inhibitors. Expert Opin Drug Discov 2013; 8:793-810. [DOI: 10.1517/17460441.2013.795145] [Citation(s) in RCA: 209] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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18
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Bereau T, Kramer C, Monnard FW, Nogueira ES, Ward TR, Meuwly M. Scoring Multipole Electrostatics in Condensed-Phase Atomistic Simulations. J Phys Chem B 2013; 117:5460-71. [DOI: 10.1021/jp400593c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Tristan Bereau
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Christian Kramer
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Fabien W. Monnard
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Elisa S. Nogueira
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Thomas R. Ward
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, 4056 Basel, Switzerland
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D'Antonio EL, Ullman B, Roberts SC, Dixit UG, Wilson ME, Hai Y, Christianson DW. Crystal structure of arginase from Leishmania mexicana and implications for the inhibition of polyamine biosynthesis in parasitic infections. Arch Biochem Biophys 2013; 535:163-76. [PMID: 23583962 DOI: 10.1016/j.abb.2013.03.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 02/06/2023]
Abstract
Arginase from parasitic protozoa belonging to the genus Leishmania is a potential drug target for the treatment of leishmaniasis because this binuclear manganese metalloenzyme catalyzes the first committed step in the biosynthesis of polyamines that enable cell growth and survival. The high resolution X-ray crystal structures of the unliganded form of Leishmania mexicana arginase (LmARG) and four inhibitor complexes are now reported. These complexes include the reactive substrate analogue 2(S)-amino-6-boronohexanoic acid (ABH) and the hydroxylated substrate analogue nor-N(ω)-hydroxy-l-arginine (nor-NOHA), which are the most potent arginase inhibitors known to date. Comparisons of the LmARG structure with that of the archetypal arginase, human arginase I, reveal that all residues important for substrate binding and catalysis are strictly conserved. However, three regions of tertiary structure differ between the parasitic enzyme and the human enzyme corresponding to the G62 - S71, L161 - C172, and I219 - V230 segments of LmARG. Additionally, variations are observed in salt link interactions that stabilize trimer assembly in LmARG. We also report biological studies in which we demonstrate that localization of LmARG to the glycosome, a unique subcellular organelle peculiar to Leishmania and related parasites, is essential for robust pathogenesis.
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Affiliation(s)
- Edward L D'Antonio
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, PA 19104-6323, USA
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20
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Snyder SE, Huang BS, Chu YW, Lin HS, Carey JR. The Effects of Substituents on the Geometry of π-π Interactions. Chemistry 2012; 18:12663-71. [DOI: 10.1002/chem.201202253] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Indexed: 11/07/2022]
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21
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Pace CJ, Zheng H, Mylvaganam R, Kim D, Gao J. Stacked Fluoroaromatics as Supramolecular Synthons for Programming Protein Dimerization Specificity. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201105857] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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22
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Pace CJ, Zheng H, Mylvaganam R, Kim D, Gao J. Stacked fluoroaromatics as supramolecular synthons for programming protein dimerization specificity. Angew Chem Int Ed Engl 2011; 51:103-7. [PMID: 22105859 DOI: 10.1002/anie.201105857] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Indexed: 11/06/2022]
Affiliation(s)
- Christopher J Pace
- Department of Chemistry, Merkert Chemistry Center, Boston College, 2609 Beacon street, Chestnut Hill, MA 02467, USA
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23
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Huang Y, Wolf S, Koes D, Popowicz GM, Camacho CJ, Holak TA, Dömling A. Exhaustive fluorine scanning toward potent p53-Mdm2 antagonists. ChemMedChem 2011; 7:49-52. [PMID: 21954050 DOI: 10.1002/cmdc.201100428] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Yijun Huang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
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24
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Kumar Seth S, Dey B, Kar T, Mukhopadhyay S. Experimental observation of supramolecular carbonyl–π/π–π/π–carbonyl assemblies of CuII complex of iminodiacetate and dipyridylamine. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.03.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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25
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Cozier GE, Leese MP, Lloyd MD, Baker MD, Thiyagarajan N, Acharya KR, Potter BVL. Structures of Human Carbonic Anhydrase II/Inhibitor Complexes Reveal a Second Binding Site for Steroidal and Nonsteroidal Inhibitors,. Biochemistry 2010; 49:3464-76. [DOI: 10.1021/bi902178w] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gyles E. Cozier
- Medicinal Chemistry, Department of Pharmacy and Pharmacology
| | - Mathew P. Leese
- Medicinal Chemistry, Department of Pharmacy and Pharmacology
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26
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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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27
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Biswas C, Drew MGB, Escudero D, Frontera A, Ghosh A. Anion-π, Lone-Pair-π, π-π and Hydrogen-Bonding Interactions in a CuIIComplex of 2-Picolinate and Protonated 4,4′-Bipyridine: Crystal Structure and Theoretical Studies. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900110] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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28
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Choudhury SR, Dey B, Das S, Gamez P, Robertazzi A, Chan KT, Lee HM, Mukhopadhyay S. Supramolecular Lone Pair−π/π−π/π−Anion Assembly in a Mg(II)−Malonate−2-Aminopyridine−Nitrate Ternary System. J Phys Chem A 2009; 113:1623-7. [DOI: 10.1021/jp810191t] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Somnath Ray Choudhury
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India, Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands, CNR-INFM SLACS and Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato, Italy, and Department of Chemistry, National Changhua University of Education, Changhua, Taiwan 50058
| | - Biswajit Dey
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India, Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands, CNR-INFM SLACS and Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato, Italy, and Department of Chemistry, National Changhua University of Education, Changhua, Taiwan 50058
| | - Suranjana Das
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India, Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands, CNR-INFM SLACS and Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato, Italy, and Department of Chemistry, National Changhua University of Education, Changhua, Taiwan 50058
| | - Patrick Gamez
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India, Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands, CNR-INFM SLACS and Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato, Italy, and Department of Chemistry, National Changhua University of Education, Changhua, Taiwan 50058
| | - Arturo Robertazzi
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India, Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands, CNR-INFM SLACS and Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato, Italy, and Department of Chemistry, National Changhua University of Education, Changhua, Taiwan 50058
| | - Kai-Ting Chan
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India, Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands, CNR-INFM SLACS and Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato, Italy, and Department of Chemistry, National Changhua University of Education, Changhua, Taiwan 50058
| | - Hon Man Lee
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India, Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands, CNR-INFM SLACS and Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato, Italy, and Department of Chemistry, National Changhua University of Education, Changhua, Taiwan 50058
| | - Subrata Mukhopadhyay
- Department of Chemistry, Jadavpur University, Kolkata 700 032, India, Leiden Institute of Chemistry, Leiden University, Post Office Box 9502, 2300 RA Leiden, The Netherlands, CNR-INFM SLACS and Dipartimento di Fisica, Università di Cagliari, S.P. Monserrato-Sestu Km 0.700, I-09042 Monserrato, Italy, and Department of Chemistry, National Changhua University of Education, Changhua, Taiwan 50058
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Abbate F, Casini A, Scozzafava A, Supuran CT. Carbonic Anhydrase Inhibitors: X-ray Crystallographic Structure of the Adduct of Human Isozyme II with the Perfluorobenzoyl Analogue of Methazolamide. Implications for the Drug Design of Fluorinated Inhibitors. J Enzyme Inhib Med Chem 2008; 18:303-8. [PMID: 14567544 DOI: 10.1080/1475636031000119337] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The X-ray crystal structure for the adduct of human carbonic anhydrase (hCA) II with 4-methyl-5-perfluorophenylcarboximido-delta2-1,3,4-thiadiazoline-2-sulfonamide (PFMZ), a topically acting antiglaucoma sulfonamide, has been resolved at a resolution of 1.8 A. This compound is almost 10 times more effective as a hCA II inhibitor (KI of 1.5 nM) compared to the lead molecule, methazolamide, a clinically used drug (KI of 14 nM). Its binding to the enzyme active site is similar to that of other sulfonamide inhibitors, considering the interactions of the sulfonamide zinc anchoring group and thiadiazoline ring contacts, but differs considerably when the perfluorobenzoylimino fragment of the molecule is analyzed. Indeed, several unprecedented strong hydrogen bonds involving the imino nitrogen, carbonyl oxygen, a fluorine atom in the ortho position of the inhibitor, and two water molecules, as well as Gln 92 of the enzyme active site were seen. A stacking interaction of the perfluorophenyl ring of the inhibitor and the aromatic ring of Phe 131 was also observed for the first time in a CA-sulfonamide adduct. All these findings prove that more potent CA inhibitors incorporating perfluoroaryl/alkyl tails may be designed, with potentially improved antiglaucoma properties, in view of the new types of interactions seen here between the enzyme and the perfluorobenzoylated analogue of methazolamide.
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Affiliation(s)
- Francesco Abbate
- Università degli Studi di Firenze, Polo Scientifico, Dipartimento di Chimica, Laboratorio di Chimica Bioinorganica, Via della Lastruccia, 3, Rm. 188, 1-50019 Sesto Fiorentino, Firenze, Italy
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30
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Krishnamurthy VM, Kaufman GK, Urbach AR, Gitlin I, Gudiksen KL, Weibel DB, Whitesides GM. Carbonic anhydrase as a model for biophysical and physical-organic studies of proteins and protein-ligand binding. Chem Rev 2008; 108:946-1051. [PMID: 18335973 PMCID: PMC2740730 DOI: 10.1021/cr050262p] [Citation(s) in RCA: 555] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Vijay M. Krishnamurthy
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George K. Kaufman
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Adam R. Urbach
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Irina Gitlin
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Katherine L. Gudiksen
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - Douglas B. Weibel
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
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31
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Amini A, Shrimpton PJ, Muggleton SH, Sternberg MJE. A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming. Proteins 2008; 69:823-31. [PMID: 17910057 DOI: 10.1002/prot.21782] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Despite the increased recent use of protein-ligand and protein-protein docking in the drug discovery process due to the increases in computational power, the difficulty of accurately ranking the binding affinities of a series of ligands or a series of proteins docked to a protein receptor remains largely unsolved. This problem is of major concern in lead optimization procedures and has lead to the development of scoring functions tailored to rank the binding affinities of a series of ligands to a specific system. However, such methods can take a long time to develop and their transferability to other systems remains open to question. Here we demonstrate that given a suitable amount of background information a new approach using support vector inductive logic programming (SVILP) can be used to produce system-specific scoring functions. Inductive logic programming (ILP) learns logic-based rules for a given dataset that can be used to describe properties of each member of the set in a qualitative manner. By combining ILP with support vector machine regression, a quantitative set of rules can be obtained. SVILP has previously been used in a biological context to examine datasets containing a series of singular molecular structures and properties. Here we describe the use of SVILP to produce binding affinity predictions of a series of ligands to a particular protein. We also for the first time examine the applicability of SVILP techniques to datasets consisting of protein-ligand complexes. Our results show that SVILP performs comparably with other state-of-the-art methods on five protein-ligand systems as judged by similar cross-validated squares of their correlation coefficients. A McNemar test comparing SVILP to CoMFA and CoMSIA across the five systems indicates our method to be significantly better on one occasion. The ability to graphically display and understand the SVILP-produced rules is demonstrated and this feature of ILP can be used to derive hypothesis for future ligand design in lead optimization procedures. The approach can readily be extended to evaluate the binding affinities of a series of protein-protein complexes.
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Affiliation(s)
- Ata Amini
- Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London SW7 2AY, United Kingdom
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32
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Wan CQ, Chen XD, Mak TCW. Supramolecular frameworks assembled via intermolecular lone pair-aromatic interaction between carbonyl and pyridyl groups. CrystEngComm 2008. [DOI: 10.1039/b718823d] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Kohmoto S, Tsuyuki R, Masu H, Azumaya I, Kishikawa K. Polymorphism-dependent fluorescence of 9,10-bis(pentafluorobenzoyloxy)anthracene. Tetrahedron Lett 2008. [DOI: 10.1016/j.tetlet.2007.11.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Abstract
Fluorine substituents have become a widespread and important drug component, their introduction facilitated by the development of safe and selective fluorinating agents. Organofluorine affects nearly all physical and adsorption, distribution, metabolism, and excretion properties of a lead compound. Its inductive effects are relatively well understood, enhancing bioavailability, for example, by reducing the basicity of neighboring amines. In contrast, exploration of the specific influence of carbon-fluorine single bonds on docking interactions, whether through direct contact with the protein or through stereoelectronic effects on molecular conformation of the drug, has only recently begun. Here, we review experimental progress in this vein and add complementary analysis based on comprehensive searches in the Cambridge Structural Database and the Protein Data Bank.
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Affiliation(s)
- Klaus Müller
- Pharmaceuticals Division, Discovery Chemistry, F. Hoffmann-La Roche, CH-4070 Basel, Switzerland.
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35
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Alterio V, De Simone G, Monti SM, Scozzafava A, Supuran CT. Carbonic anhydrase inhibitors: Inhibition of human, bacterial, and archaeal isozymes with benzene-1,3-disulfonamides—Solution and crystallographic studies. Bioorg Med Chem Lett 2007; 17:4201-7. [PMID: 17540563 DOI: 10.1016/j.bmcl.2007.05.045] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2007] [Revised: 05/09/2007] [Accepted: 05/12/2007] [Indexed: 10/23/2022]
Abstract
Three benzene-1,3-disulfonamide derivatives were investigated for their interaction with 12 mammalian alpha-carbonic anhydrases (CAs, EC 4.2.1.1), and three bacterial/archaeal CAs belonging to the alpha-, beta-, and gamma-CA class, respectively. X-ray crystal structure of the three inhibitors in complex with the dominant human isozyme CA II revealed a particular binding mode within the cavity. The sulfonamide group in meta-position to the Zn(2+)-coordinated SO(2)NH(2) moiety was oriented toward the hydrophilic side of the active site cleft, establishing hydrogen bonds with His64, Asn67, Gln92, and Thr200. The plane of the phenyl moiety of the inhibitors was rotated by 45 degrees and tilted by 10 degrees with respect to its most recurrent orientation in other CA II-sulfonamide complexes.
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Affiliation(s)
- Vincenzo Alterio
- Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy
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36
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37
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Lee EC, Kim D, Jurecka P, Tarakeshwar P, Hobza P, Kim KS. Understanding of Assembly Phenomena by Aromatic−Aromatic Interactions: Benzene Dimer and the Substituted Systems. J Phys Chem A 2007; 111:3446-57. [PMID: 17429954 DOI: 10.1021/jp068635t] [Citation(s) in RCA: 512] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted pi systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several pi-pi systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure is likely to be slightly more stable (D0 approximately equal to 2.4-2.5 kcal/mol) if quadruple excitations are included in the coupled cluster calculations. The presence of substituents on the aromatic ring, irrespective of their electron withdrawing or donating nature, leads to an increase in the binding energy, and the displaced-stacked conformations are more stabilized than the T-shaped conformers. This explains the wide prevalence of displaced stacked structures in organic crystals. Despite that the dispersion energy is dominating, the substituent as well as the conformational effects are correlated to the electrostatic interaction. This electrostatic origin implies that the substituent effect would be reduced in polar solution, but important in apolar media, in particular, for assembling processes.
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Affiliation(s)
- Eun Cheol Lee
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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Kim KH. Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers? J Comput Aided Mol Des 2007; 21:63-86. [PMID: 17334823 DOI: 10.1007/s10822-007-9106-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 01/09/2007] [Indexed: 11/30/2022]
Abstract
A lead optimization is usually carried out by structure-activity relationship (SAR) and/or quantitative structure-activity relationship (QSAR) studies. One of the assumptions in SAR and QSAR studies is that similar analogs bind to the same binding site in a similar binding mode. One often observes that there are outliers, especially in QSAR. However, most QSAR studies are carried out focusing their attention to the development of QSAR and leave the outliers without much attention. We searched a number of ligand-bound X-ray crystal structures from the protein structure database to find evidences that could indicate a possible source of outliers in SAR or QSAR. Our results show that unusual binding mode could be a source of outliers.
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Affiliation(s)
- Ki Hwan Kim
- Hope Drug Discovery Research Laboratory, 260 Southgate Drive, Vernon Hills, IL 60061, USA.
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39
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Lucassen ACB, Zubkov T, Shimon LJW, van der Boom ME. Design, synthesis and crystal structure of a multiple donor–acceptor halogen bonded stilbazole: assembly of unimolecular interconnected helices. CrystEngComm 2007. [DOI: 10.1039/b704569g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Jude KM, Banerjee AL, Haldar MK, Manokaran S, Roy B, Mallik S, Srivastava DK, Christianson DW. Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors reveal the molecular basis of high affinity. J Am Chem Soc 2006; 128:3011-8. [PMID: 16506782 PMCID: PMC2527509 DOI: 10.1021/ja057257n] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The atomic-resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors are reported. Each inhibitor contains a benzenesulfonamide prong and a cupric iminodiacetate (IDA-Cu(2+)) prong separated by linkers of different lengths and compositions. The ionized NH(-) group of each benzenesulfonamide coordinates to the active site Zn(2+) ion; the IDA-Cu(2+) prong of the tightest-binding inhibitor, BR30, binds to H64 of CAII and H200 of CAI. This work provides the first evidence verifying the structural basis of nanomolar affinity measured for two-prong inhibitors targeting the carbonic anhydrases.
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Affiliation(s)
- Kevin M. Jude
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Abir L. Banerjee
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Manas K. Haldar
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816
| | - Sumathra Manokaran
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - Bidhan Roy
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816
| | - Sanku Mallik
- Department of Chemistry, University of Central Florida, Orlando, Florida 32816
| | - D. K. Srivastava
- Department of Chemistry, Biochemistry and Molecular Biology, North Dakota State University, Fargo, North Dakota 58105
| | - David W. Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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41
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Gautrot JE, Hodge P, Cupertino D, Helliwell M. Experimental evidence for carbonyl–π electron cloud interactions. NEW J CHEM 2006. [DOI: 10.1039/b608628d] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Lee EC, Hong BH, Lee JY, Kim JC, Kim D, Kim Y, Tarakeshwar P, Kim KS. Substituent Effects on the Edge-to-Face Aromatic Interactions. J Am Chem Soc 2005; 127:4530-7. [PMID: 15783237 DOI: 10.1021/ja037454r] [Citation(s) in RCA: 171] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The edge-to-face interactions for either axially or facially substituted benzenes are investigated by using ab initio calculations. The predicted maximum energy difference between substituted and unsubstituted systems is approximately 0.7 kcal/mol (approximately 1.2 kcal/mol if substituents are on both axially and facially substituted positions). In the case of axially substituted aromatic systems, the electron density at the para position is an important stabilizing factor, and thus the stabilization/destabilization by substitution is highly correlated to the electrostatic energy. This results in its subsequent correlation with the polarization and charge transfer. Thus, the stabilization/destabilization by substitution is represented by the sum of electrostatic energy and induction energy. On the other hand, the facially substituted aromatic system depends on not only the electron-donating ability responsible for the electrostatic energy but also the dispersion interaction and exchange repulsion. Although the dispersion energy is the most dominating interaction in both axial and facial substitutions, it is almost canceled by the exchange repulsion in the axial substitution, whereas in the facial substitution, together with the exchange repulsion it augments the electrostatic energy. The systems with electron-accepting substituents (NO2, CN, Br, Cl, F) favor the axial substituent conformation, while those with electron-donating substituents (NH2, CH3, OH) favor the facial substituent conformation. The interactions for the T-shape complex systems of an aromatic ring with other counterpart such as H2, H2O, HCl, and HF are also studied.
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Affiliation(s)
- Eun Cheol Lee
- National Creative Research Initiative Center for Superfunctional Materials, Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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Kontoyianni M, Sokol GS, McClellan LM. Evaluation of library ranking efficacy in virtual screening. J Comput Chem 2005; 26:11-22. [PMID: 15526325 DOI: 10.1002/jcc.20141] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We present the results of a comprehensive study in which we explored how the docking procedure affects the performance of a virtual screening approach. We used four docking engines and applied 10 scoring functions to the top-ranked docking solutions of seeded databases against six target proteins. The scores of the experimental poses were placed within the total set to assess whether the scoring function required an accurate pose to provide the appropriate rank for the seeded compounds. This method allows a direct comparison of library ranking efficacy. Our results indicate that the LigandFit/Ligscore1 and LigandFit/GOLD docking/scoring combinations, and to a lesser degree FlexX/FlexX, Glide/Ligscore1, DOCK/PMF (Tripos implementation), LigandFit1/Ligscore2 and LigandFit/PMF (Tripos implementation) were able to retrieve the highest number of actives at a 10% fraction of the database when all targets were looked upon collectively. We also show that the scoring functions rank the observed binding modes higher than the inaccurate poses provided that the experimental poses are available. This finding stresses the discriminatory ability of the scoring algorithms, when better poses are available, and suggests that the number of false positives can be lowered with conformers closer to bioactive ones.
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Affiliation(s)
- Maria Kontoyianni
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Computer Assisted Drug Discovery, Welsh and McKean Roads, P.O. Box 776, Spring House, Pennsylvania 19477, USA.
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Abbate F, Casini A, Scozzafava A, Supuran CT. Carbonic anhydrase inhibitors: X-ray crystallographic structure of the adduct of human isozyme II with a topically acting antiglaucoma sulfonamide. Bioorg Med Chem Lett 2004; 14:2357-61. [PMID: 15081040 DOI: 10.1016/j.bmcl.2004.01.096] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Revised: 01/23/2004] [Accepted: 01/26/2004] [Indexed: 10/26/2022]
Abstract
The X-ray crystal structure for the adduct of human carbonic anhydrase (hCA) II with a topically acting antiglaucoma sulfonamide (the 2-N,N-diethylaminoethylamide of 5-(4-carboxybenzenesulfonamido-1,3,4-thiadiazole-2-sulfonamide), has been resolved at a resolution of 1.6A. This compound is a very potent inhibitor of the physiologically most relevant isozyme hCA II for the secretion of aqueous humor within the eye K(I) of 1.4 nM), and in animal models of glaucoma showed very effective intraocular pressure (IOP) lowering after topical administration. Surprisingly, the inhibitor bound within the enzyme active site is in the sulfonylimido-4H- delta(2)-1,3,4-thiadiazoline tautomeric form. The inhibitor is directly bound to the Zn(II) ion of the enzyme through the deprotonated primary sulfonamide moiety, participating to the classical hydrogen bond network involving residues of the zinc-binding function and Thr 199 and Glu 106. The 1,3,4-thiadiazoline fragment of the inhibitor makes two hydrogen bonds with the active site residue Thr 200, the secondary sulfonamide moiety makes two hydrogen bonds involving a water molecule and the residue Gln 92, whereas the phenyl ring of the inhibitor participates to an edge-to-face interaction with the phenyl ring of Phe 131, the two cycles being almost perfectly perpendicular to each other. The tertiary amine fragment of the carboxamido tail and the carboxamido moiety itself make hydrogen bonds with water molecules present at the rim of the active site entrance and van der Waals contacts with His 4, Trp 5, and Phe 20. All these multiple interactions never evidenced previously in CA-sulfonamide complexes, explain the very high affinity of this inhibitor for the hCA II active site and may allow further optimization of this class of inhibitors.
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Affiliation(s)
- Francesco Abbate
- Bruker-AXS s.r.l., Milano, via G Pascoli 70/3, I-20133 Milano, Italy
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Böhm HJ, Banner D, Bendels S, Kansy M, Kuhn B, Müller K, Obst-Sander U, Stahl M. Fluorine in medicinal chemistry. Chembiochem 2004; 5:637-43. [PMID: 15122635 DOI: 10.1002/cbic.200301023] [Citation(s) in RCA: 1190] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Fluorinated compounds are synthesized in pharmaceutical research on a routine basis and many marketed compounds contain fluorine. The present review summarizes some of the most frequently employed strategies for using fluorine substituents in medicinal chemistry. Quite often, fluorine is introduced to improve the metabolic stability by blocking metabolically labile sites. However, fluorine can also be used to modulate the physicochemical properties, such as lipophilicity or basicity. It may exert a substantial effect on the conformation of a molecule. Increasingly, fluorine is used to enhance the binding affinity to the target protein. Recent 3D-structure determinations of protein complexes with bound fluorinated ligands have led to an improved understanding of the nonbonding protein-ligand interactions that involve fluorine.
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Affiliation(s)
- Hans-Joachim Böhm
- Discovery Research, Pharmaceuticals Division, Roche, CH 4070 Basel, Switzerland.
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Pastorekova S, Casini A, Scozzafava A, Vullo D, Pastorek J, Supuran CT. Carbonic anhydrase inhibitors: the first selective, membrane-impermeant inhibitors targeting the tumor-associated isozyme IX. Bioorg Med Chem Lett 2004; 14:869-73. [PMID: 15012984 DOI: 10.1016/j.bmcl.2003.12.029] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2003] [Revised: 12/03/2003] [Accepted: 12/03/2003] [Indexed: 01/15/2023]
Abstract
The inhibition of the tumor-associated transmembrane carbonic anhydrase IX (CA IX) isozyme possessing an extracellular active site has been investigated with a series of positively-charged, pyridinium derivatives of sulfanilamide, homosulfanilamide and 4-aminoethylbenzenesulfonamide. Inhibition data for the physiologically relevant isozymes I and II (cytosolic forms) and IV (membrane-bound) were also provided for comparison. A very interesting inhibition profile against CA IX with these sulfonamides has been observed. Several nanomolar (K(i)'s in the range of 6-54 nM) CA IX inhibitors have also been detected. Because CA IX is a highly active isozyme predominantly expressed in tumor tissues with bad prognosis of disease progression, this finding is very promising for the potential design of CA IX-specific inhibitors with applications as anti-tumor agents. This is the first report of inhibitors that may selectively target CA IX, due to their membrane-impermeability and high affinity for this clinically relevant isozyme.
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Affiliation(s)
- Silvia Pastorekova
- Institute of Virology, Slovak Academy of Sciences, Dubravska cesta 9, 842 45 Bratislava, Slovak Republic
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Sakai T, Korenaga T, Washio N, Nishio Y, Minami S, Ema T. Synthesis of Enantiomerically Pure (R,R)- and (S,S)-1,2-Bis(pentafluorophenyl)ethane-1,2-diamine and Evaluation of the pKaValue by Ab Initio Calculations. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2004. [DOI: 10.1246/bcsj.77.1001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abbate F, Winum JY, Potter BVL, Casini A, Montero JL, Scozzafava A, Supuran CT. Carbonic anhydrase inhibitors: X-ray crystallographic structure of the adduct of human isozyme II with EMATE, a dual inhibitor of carbonic anhydrases and steroid sulfatase. Bioorg Med Chem Lett 2004; 14:231-4. [PMID: 14684333 DOI: 10.1016/j.bmcl.2003.09.064] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The X-ray crystal structure for the adduct of human carbonic anhydrase II (hCA II) with estrone-3-O-sulfamate (EMATE), an antiendocrine agent showing both CA and estrone sulfatase inhibitory properties, has been resolved at a resolution of 1.5A. Its binding to the enzyme is similar to that of other sulfamates/sulfonamides, considering the interactions of the zinc anchoring group, but differs considerably when the steroidal scaffold of the inhibitor is analyzed. This part of the inhibitor interacts only within the hydrophobic half of the CA active site, interacting with residues Val 121, Phe 131, Val 135 and Pro 202, and leaving the hydrophilic half able to accommodate several water molecules not present in the uncomplexed enzyme. In addition, a very short bond of 1.78A between the zinc ion and the coordinated nitrogen atom of the sulfamate moiety is observed, which may explain the high affinity of this inhibitor for hCA II (K(i) of 10nM).
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Affiliation(s)
- Francesco Abbate
- Università degli Studi di Firenze, Polo Scientifico, Dipartimento di Chimica, Laboratorio di Chimica Bioinorganica, Via della Lastruccia 3, Rm. 188, I-50019 Sesto Fiorentino, Florence, Italy
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Metwally E, Ismail HA, Davison JS, Mathison R. A tree-based algorithm for determining the effects of solvation on the structure of salivary gland tripeptide NH3+-D-PHE-D-GLU-GLY-COO-. Biophys J 2003; 85:1503-11. [PMID: 12944268 PMCID: PMC1303327 DOI: 10.1016/s0006-3495(03)74583-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A D-enantiomeric analog of the submandibular gland rat-1 tripeptide FEG (Seq: NH(3)(+)-Phe-Glu-Gly-COO(-)) called feG (Seq: NH(3)(+)-D-Phe-D-Glu-Gly-COO(-)) was examined by molecular dynamics simulations in water. Previous in vacuo simulations suggested a conformation consisting predominantly of interactions between the Phe side chain and glutamyl-carboxyl group and a carboxyl/amino termini interaction. The solvated peptide was simulated using two approaches which were compared-a single 400-ns simulation and a "simulation tree." The "tree" approach utilized 45 10-ns simulations with different conformations used as initial structures for given trajectories. We demonstrate that multiple short duration simulations are able to describe the same conformational space as that described by longer simulations. Furthermore, previously described in vacuo interactions were confirmed with amendments: the previously described head-to-tail arrangement of the amino and carboxyl termini, was not observed; the interaction between the glutamyl carboxyl and Phe side chain describes only one of a continuum of conformations present wherein the aromatic residue remains in close proximity to the glutamyl carbonyl group, and also interacts with either of the two available carboxyl groups. Finally, utilizing only two separate 10-ns trajectories, we were able to better describe the conformational space than a single 60-ns trajectory, realizing a threefold decrease in the computational complexity of the problem.
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Affiliation(s)
- Essam Metwally
- Department of Physiology and Biophysics, The University of Calgary, Calgary, Alberta, Canada.
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