1
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Hostachy S, Wang H, Zong G, Franke K, Riley AM, Schmieder P, Potter BVL, Shears SB, Fiedler D. Fluorination Influences the Bioisostery of Myo-Inositol Pyrophosphate Analogs. Chemistry 2023; 29:e202302426. [PMID: 37773020 PMCID: PMC7615343 DOI: 10.1002/chem.202302426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/14/2023] [Accepted: 09/28/2023] [Indexed: 09/30/2023]
Abstract
Inositol pyrophosphates (PP-IPs) are densely phosphorylated messenger molecules involved in numerous biological processes. PP-IPs contain one or two pyrophosphate group(s) attached to a phosphorylated myo-inositol ring. 5PP-IP5 is the most abundant PP-IP in human cells. To investigate the function and regulation by PP-IPs in biological contexts, metabolically stable analogs have been developed. Here, we report the synthesis of a new fluorinated phosphoramidite reagent and its application for the synthesis of a difluoromethylene bisphosphonate analog of 5PP-IP5 . Subsequently, the properties of all currently reported analogs were benchmarked using a number of biophysical and biochemical methods, including co-crystallization, ITC, kinase activity assays and chromatography. Together, the results showcase how small structural alterations of the analogs can have notable effects on their properties in a biochemical setting and will guide in the choice of the most suitable analog(s) for future investigations.
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Affiliation(s)
- Sarah Hostachy
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Huanchen Wang
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Guangning Zong
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Katy Franke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Andrew M. Riley
- Medicinal Chemistry & Drug Discovery Department of PharmacologyUniversity of OxfordOxfordOX1 3QTUK
| | - Peter Schmieder
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
| | - Barry V. L. Potter
- Medicinal Chemistry & Drug Discovery Department of PharmacologyUniversity of OxfordOxfordOX1 3QTUK
| | - Stephen B. Shears
- Inositol Signaling GroupNational Institutes of HealthResearch Triangle ParkNorth Carolina27709USA
| | - Dorothea Fiedler
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)Robert-Rössle-Straße 1013125BerlinGermany
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Str. 212489BerlinGermany
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2
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Shevchuk M, Wang Q, Pajkert R, Xu J, Mei H, Röschenthaler G, Han J. Recent Advances in Synthesis of Difluoromethylene Phosphonates for Biological Applications. Adv Synth Catal 2021. [DOI: 10.1002/adsc.202001464] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Michael Shevchuk
- Department of Life Sciences and Chemistry Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany
| | - Qian Wang
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
| | - Romana Pajkert
- Department of Life Sciences and Chemistry Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany
| | - Jingcheng Xu
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
| | - Haibo Mei
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
| | - Gerd‐Volker Röschenthaler
- Department of Life Sciences and Chemistry Jacobs University Bremen gGmbH Campus Ring 1 28759 Bremen Germany
| | - Jianlin Han
- Jiangsu Co–Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering Nanjing Forestry University Nanjing 210037 People's Republic of China
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3
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Merkel K, Loska B, Welch C, Mehl GH, Kocot A. The role of intermolecular interactions in stabilizing the structure of the nematic twist-bend phase. RSC Adv 2021; 11:2917-2925. [PMID: 35424219 PMCID: PMC8693785 DOI: 10.1039/d0ra10481g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
The understanding of the relationship between molecular structure and the formation of the nematic twist-bend phase is still at an early stage of development. This is mainly related to molecular geometry, while the correlation between the nematic twist-bend phase and the electronic structure is ambiguous. To explore the electronic effect on properties and stabilization of the nematic twist-bend phase we investigated 2′,3′-difluoro-4,4′′-dipentyl-p-terphenyl dimers (DTC5Cn). We used polarized fourier transform infrared spectroscopy, which can, at least in principle, provide information about the ordering in the twist-bend phase. All dimers show a significant drop in the average value of the transition dipole moment for parallel dipoles at the transition from the nematic to the twist-bend phase, and an increase for perpendicular dipoles, despite remaining unchanged for the monomer. Density functional theory calculations were used to determine the geometric and electronic properties of the hydrogen bonded complexes. We have provided experimental and theoretical evidence of stabilization of the nematic twist-bend phase by arrays of multiple hydrogen bonds (XF⋯HX, X–benzene ring). Stabilization of the nematic twist-band phase by arrays of multiple nonspecific short-range intermolecular interactions.![]()
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Affiliation(s)
- Katarzyna Merkel
- Institute of Materials Engineering, University of Silesia 75 Pułku Piechoty 1A 41-500 Chorzów Poland
| | - Barbara Loska
- Institute of Materials Engineering, University of Silesia 75 Pułku Piechoty 1A 41-500 Chorzów Poland
| | - Chris Welch
- Department of Chemistry, University of Hull Hull HU6 7RX UK
| | - Georg H Mehl
- Department of Chemistry, University of Hull Hull HU6 7RX UK
| | - Antoni Kocot
- Institute of Materials Engineering, University of Silesia 75 Pułku Piechoty 1A 41-500 Chorzów Poland
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4
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Setterholm NA, Haratipour P, Kashemirov BA, McKenna CE, Joyce GF. Kinetic Effects of β,γ-Modified Deoxynucleoside 5'-Triphosphate Analogues on RNA-Catalyzed Polymerization of DNA. Biochemistry 2020; 60:1-5. [PMID: 33356161 DOI: 10.1021/acs.biochem.0c00779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently described DNA polymerase ribozyme, obtained by in vitro evolution, provides the opportunity to investigate mechanistic features of RNA catalysis using methods that previously had only been applied to DNA polymerase proteins. Insight can be gained into the transition state of the DNA polymerization reaction by studying the behavior of various β,γ-bridging substituted methylene (CXY; X, Y = H, halo, methyl) or imido (NH) dNTP analogues that differ with regard to the pKa4 of the bisphosphonate or imidodiphosphate leaving group. The apparent rate constant (kpol) of the polymerase ribozyme was determined for analogues of dGTP and dCTP that span a broad range of acidities for the leaving group, ranging from 7.8 for the CF2-bisphosphonate to 11.6 for the CHCH3-bisphosphonate. A Brønsted plot of log(kpol) versus pKa4 of the leaving group demonstrates linear free energy relationships (LFERs) for dihalo-, monohalo-, and non-halogen-substituted analogues of the dNTPs, with negative slopes, as has been observed for DNA polymerase proteins. The unsubstituted dNTPs have a faster catalytic rate than would be predicted from consideration of the linear free energy relationship alone, presumably due to a relatively more favorable interaction of the β,γ-bridging oxygen within the active site. Although the DNA polymerase ribozyme is considerably slower than DNA polymerase proteins, it exhibits a similar LFER fingerprint, suggesting mechanistic commonality pertaining to the buildup of negative charge in the transition state, despite the very different chemical compositions of the two catalysts.
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Affiliation(s)
- Noah A Setterholm
- The Salk Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Pouya Haratipour
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Gerald F Joyce
- The Salk Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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5
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Haratipour P, Minard C, Nakhjiri M, Negahbani A, Chamberlain BT, Osuna J, Upton TG, Zhao M, Kashemirov BA, McKenna CE. Completing the β,γ-CXY-dNTP Stereochemical Probe Toolkit: Synthetic Access to the dCTP Diastereomers and 31P and 19F NMR Correlations with Absolute Configurations. J Org Chem 2020; 85:14592-14609. [PMID: 33125847 DOI: 10.1021/acs.joc.0c01204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleoside 5'-triphosphate (dNTP) analogues in which the β,γ-oxygen is mimicked by a CXY group (β,γ-CXY-dNTPs) have provided information about DNA polymerase catalysis and fidelity. Definition of CXY stereochemistry is important to elucidate precise binding modes. We previously reported the (R)- and (S)-β,γ-CHX-dGTP diastereomers (X = F, Cl), prepared via P,C-dimorpholinamide CHCl (6a, 6b) and CHF (7a, 7b) bisphosphonates (BPs) equipped with an (R)-mandelic acid as a chiral auxiliary, with final deprotection using H2/Pd. This method also affords the β,γ-CHCl-dTTP (11a, 11b), β,γ-CHF (12a, 12b), and β,γ-CHCl (13a, 13b) dATP diastereomers as documented here, but the reductive deprotection step is not compatible with dCTP or the bromo substituent in β,γ-CHBr-dNTP analogues. To complete assembly of the toolkit, we describe an alternative synthetic strategy featuring ethylbenzylamine or phenylglycine-derived chiral BP synthons incorporating a photolabile protecting group. After acid-catalyzed removal of the (R)-(+)-α-ethylbenzylamine auxiliary, coupling with activated dCMP and photochemical deprotection, the individual diastereomers of β,γ-CHBr- (33a, 33b), β,γ-CHCl- (34a, 34b), β,γ-CHF-dCTP (35a, 35b) were obtained. The β,γ-CH(CH3)-dATPs (44a, 44b) were obtained using a methyl (R)-(-)-phenylglycinate auxiliary. 31P and 19F NMR Δδ values are correlated with CXY stereochemistry and pKa2-4 values for 13 CXY-bisphosphonic acids and imidodiphosphonic acid are tabulated.
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Affiliation(s)
- Pouya Haratipour
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Corinne Minard
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Maryam Nakhjiri
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Amirsoheil Negahbani
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Brian T Chamberlain
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Jorge Osuna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Thomas G Upton
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Michelle Zhao
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
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6
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Batra VK, Alnajjar KS, Sweasy JB, McKenna CE, Goodman MF, Wilson SH. Revealing an Internal Stabilization Deficiency in the DNA Polymerase β K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography. Biochemistry 2020; 59:955-963. [PMID: 31999437 DOI: 10.1021/acs.biochem.9b01072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human DNA polymerase (pol) β cancer variant K289M has altered polymerase activity in vitro, and the structure of wild-type pol β reveals that the K289 side chain contributes to a network of stabilizing interactions in a C-terminal region of the enzyme distal to the active site. Here, we probed the capacity of the K289M variant to tolerate strain introduced within the C-terminal region and active site. Strain was imposed by making use of a dGTP analogue containing a CF2 group substitution for the β-γ bridging oxygen atom. The ternary complex structure of the K289M variant displays an alteration in the C-terminal region, whereas the structure of wild-type pol β is not altered in the presence of the dGTP CF2 analogue. The alteration in the K289M variant impacts the active site, because the enzyme in the ternary complex fails to adopt the normal open to closed conformational change and assembly of the catalytically competent active site. These results reveal the importance of the K289-mediated stabilizing network in the C-terminal region of pol β and suggest an explanation for why the K289M cancer variant is deficient in polymerase activity even though the position 289 side chain is distal to the active site.
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Affiliation(s)
- Vinod K Batra
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, North Carolina 27709, United States
| | - Khadijeh S Alnajjar
- Department of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Joann B Sweasy
- Department of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Charles E McKenna
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062, United States
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-0371, United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T. W. Alexander Drive, Research Triangle Park, North Carolina 27709, United States
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7
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
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8
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Tarasenko KV, Romanenko VD, Sorochinsky AE. Condensation of diethyl fluoromethylphosphonate with esters: An alternative synthetic route to diethyl α-fluoro-β-ketophosphonates. J Fluor Chem 2018. [DOI: 10.1016/j.jfluchem.2018.04.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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9
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Batra VK, Oertell K, Beard WA, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH. Mapping Functional Substrate-Enzyme Interactions in the pol β Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs. Biochemistry 2018; 57:3934-3944. [PMID: 29874056 DOI: 10.1021/acs.biochem.8b00418] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report high-resolution crystal structures of DNA polymerase (pol) β in ternary complex with a panel of incoming dNTPs carrying acidity-modified 5'-triphosphate groups. These novel dNTP analogues have a variety of halomethylene substitutions replacing the bridging oxygen between Pβ and Pγ of the incoming dNTP, whereas other analogues have alkaline substitutions at the bridging oxygen. Use of these analogues allows the first systematic comparison of effects of 5'-triphosphate acidity modification on active site structures and the rate constant of DNA synthesis. These ternary complex structures with incoming dATP, dTTP, and dCTP analogues reveal the enzyme's active site is not grossly altered by the acidity modifications of the triphosphate group, yet with analogues of all three incoming dNTP bases, subtle structural differences are apparent in interactions around the nascent base pair and at the guanidinium groups of active site arginine residues. These results are important for understanding how acidity modification of the incoming dNTP's 5'-triphosphate can influence DNA polymerase activity and the significance of interactions at arginines 183 and 149 in the active site.
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Affiliation(s)
- Vinod K Batra
- Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences, National Institutes of Health , 111 T. W. Alexander Drive , Research Triangle Park , North Carolina 27709 , United States
| | - Keriann Oertell
- Department of Biological Sciences , University of Southern California , Los Angeles , California 90089-0371 , United States
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences, National Institutes of Health , 111 T. W. Alexander Drive , Research Triangle Park , North Carolina 27709 , United States
| | - Boris A Kashemirov
- Department of Chemistry , University of Southern California , Los Angeles , California 90089-1062 , United States
| | - Charles E McKenna
- Department of Chemistry , University of Southern California , Los Angeles , California 90089-1062 , United States
| | - Myron F Goodman
- Department of Biological Sciences , University of Southern California , Los Angeles , California 90089-0371 , United States
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory , National Institute of Environmental Health Sciences, National Institutes of Health , 111 T. W. Alexander Drive , Research Triangle Park , North Carolina 27709 , United States
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10
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Feldman AW, Fischer EC, Ledbetter MP, Liao JY, Chaput JC, Romesberg FE. A Tool for the Import of Natural and Unnatural Nucleoside Triphosphates into Bacteria. J Am Chem Soc 2018; 140:1447-1454. [PMID: 29338214 DOI: 10.1021/jacs.7b11404] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Nucleoside triphosphates play a central role in biology, but efforts to study these roles have proven difficult because the levels of triphosphates are tightly regulated in a cell and because individual triphosphates can be difficult to label or modify. In addition, many synthetic biology efforts are focused on the development of unnatural nucleoside triphosphates that perform specific functions in the cellular environment. In general, both of these efforts would be facilitated by a general means to directly introduce desired triphosphates into cells. Previously, we demonstrated that recombinant expression of a nucleoside triphosphate transporter from Phaeodactylum tricornutum (PtNTT2) in Escherichia coli functions to import triphosphates that are added to the media. Here, to explore the generality and utility of this approach, we report a structure-activity relationship study of PtNTT2. Using a conventional competitive uptake inhibition assay, we characterize the effects of nucleobase, sugar, and triphosphate modification, and then develop an LC-MS/MS assay to directly measure the effects of the modifications on import. Lastly, we use the transporter to import radiolabeled or 2'-fluoro-modified triphosphates and quantify their incorporation into DNA and RNA. The results demonstrate the general utility of the PtNTT2-mediated import of natural or modified nucleoside triphosphates for different molecular or synthetic biology applications.
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Affiliation(s)
- Aaron W Feldman
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Emil C Fischer
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Michael P Ledbetter
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Jen-Yu Liao
- Department of Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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11
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Fluorine NMR spectroscopy and computational calculations for assessing intramolecular hydrogen bond involving fluorine and for characterizing the dynamic of a fluorinated molecule. J Fluor Chem 2017. [DOI: 10.1016/j.jfluchem.2017.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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12
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Alnajjar KS, Negahbani A, Nakhjiri M, Krylov IS, Kashemirov BA, McKenna CE, Goodman MF, Sweasy JB. DNA Polymerase β Cancer-Associated Variant I260M Exhibits Nonspecific Selectivity toward the β-γ Bridging Group of the Incoming dNTP. Biochemistry 2017; 56:5449-5456. [PMID: 28862868 DOI: 10.1021/acs.biochem.7b00713] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The hydrophobic hinge region of DNA polymerase β (pol β) is located between the fingers and palm subdomains. The hydrophobicity of the hinge region is important for maintaining the geometry of the binding pocket and for the selectivity of the enzyme. Various cancer-associated pol β variants in the hinge region have reduced fidelity resulting from a decreased discrimination at the level of dNTP binding. Specifically, I260M, a prostate cancer-associated variant of pol β, has been shown to have a reduced discrimination during dNTP binding and also during nucleotidyl transfer. To test whether fidelity of the I260M variant is dependent on leaving group chemistry, we employed a toolkit comprising dNTP bisphosphonate analogues modified at the β-γ bridging methylene to modulate leaving group (pCXYp mimicking PPi) basicity. Construction of linear free energy relationship plots for the dependence of log(kpol) on leaving group pKa4 revealed that I260M catalyzes dNMP incorporation with a marked negative dependence on leaving group basicity, consistent with a chemical transition state, during both correct and incorrect incorporation. Additionally, we provide evidence that I260M fidelity is altered in the presence of some of the analogues, possibly resulting from a lack of coordination between the fingers and palm subdomains in the presence of the I260M mutation.
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Affiliation(s)
- Khadijeh S Alnajjar
- Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine , New Haven, Connecticut 06520, United States
| | - Amirsoheil Negahbani
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Maryam Nakhjiri
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Ivan S Krylov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Boris A Kashemirov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Charles E McKenna
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Myron F Goodman
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Joann B Sweasy
- Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine , New Haven, Connecticut 06520, United States
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13
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Ni F, Kung A, Duan Y, Shah V, Amador CD, Guo M, Fan X, Chen L, Chen Y, McKenna CE, Zhang C. Remarkably Stereospecific Utilization of ATP α,β-Halomethylene Analogues by Protein Kinases. J Am Chem Soc 2017; 139:7701-7704. [PMID: 28535041 DOI: 10.1021/jacs.7b03266] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
ATP analogues containing a CXY group in place of the α,β-bridging oxygen atom are powerful chemical probes for studying ATP-dependent enzymes. A limitation of such probes has been that conventional synthetic methods generate a mixture of diastereomers when the bridging carbon substitution is nonequivalent (X ≠ Y). We report here a novel method based on derivatization of a bisphosphonate precursor with a d-phenylglycine chiral auxiliary that enables preparation of the individual diastereomers of α,β-CHF-ATP and α,β-CHCl-ATP, which differ only in the configuration at the CHX carbon. When tested on a dozen divergent protein kinases, these individual diastereomers exhibit remarkable diastereospecificity (up to over 1000-fold) in utilization by the enzymes. This high selectivity can be exploited in an enzymatic approach to obtain the otherwise inaccessible diastereomers of α,β-CHBr-ATP. The crystal structure of a tyrosine kinase Src bound to α,β-CHX-ADP establishes the absolute configuration of the CHX carbon and helps clarify the origin of the remarkable diastereospecificity observed. We further synthesized the individual diastereomers of α,β-CHF-γ-thiol-ATP and demonstrated their utility in labeling a wide spectrum of kinase substrates. The novel ATP substrate analogues afforded by these two complementary strategies should have broad application in the study of the structure and function of ATP-dependent enzymes.
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Affiliation(s)
- Feng Ni
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Loker Hydrocarbon Research Institute, University of Southern California , Los Angeles, California 90089, United States
| | - Alvin Kung
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Loker Hydrocarbon Research Institute, University of Southern California , Los Angeles, California 90089, United States
| | - Yankun Duan
- Department of Infectious Diseases & Hunan Key Laboratory of Viral Hepatitis, XiangYa Hospital, Central South University , Changsha, Hunan 410008, China.,Molecular & Computational Biology Program, Department of Biological Sciences, University of Southern California , Los Angeles, California 90089, United States
| | - Vivek Shah
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Carolina D Amador
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Ming Guo
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University , Changsha, Hunan 410008, China
| | - Xuegong Fan
- Department of Infectious Diseases & Hunan Key Laboratory of Viral Hepatitis, XiangYa Hospital, Central South University , Changsha, Hunan 410008, China
| | - Lin Chen
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Molecular & Computational Biology Program, Department of Biological Sciences, University of Southern California , Los Angeles, California 90089, United States
| | - Yongheng Chen
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University , Changsha, Hunan 410008, China
| | - Charles E McKenna
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Chao Zhang
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States.,Loker Hydrocarbon Research Institute, University of Southern California , Los Angeles, California 90089, United States
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14
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Dutta AK, Captain I, Jessen HJ. New Synthetic Methods for Phosphate Labeling. Top Curr Chem (Cham) 2017; 375:51. [DOI: 10.1007/s41061-017-0135-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/27/2017] [Indexed: 12/12/2022]
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15
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Alnajjar KS, Garcia-Barboza B, Negahbani A, Nakhjiri M, Kashemirov B, McKenna C, Goodman MF, Sweasy JB. A Change in the Rate-Determining Step of Polymerization by the K289M DNA Polymerase β Cancer-Associated Variant. Biochemistry 2017; 56:2096-2105. [PMID: 28326765 DOI: 10.1021/acs.biochem.6b01230] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
K289M is a variant of DNA polymerase β (pol β) that has previously been identified in colorectal cancer. The expression of this variant leads to a 16-fold increase in mutation frequency at a specific site in vivo and a reduction in fidelity in vitro in a sequence context-specific manner. Previous work shows that this reduction in fidelity results from a decreased level of discrimination against incorrect nucleotide incorporation at the level of polymerization. To probe the transition state of the K289M mutator variant of pol β, single-turnover kinetic experiments were performed using β,γ-CXY dGTP analogues with a wide range of leaving group monoacid dissociation constants (pKa4), including a corresponding set of novel β,γ-CXY dCTP analogues. Surprisingly, we found that the values of the log of the catalytic rate constant (kpol) for correct insertion by K289M, in contrast to those of wild-type pol β, do not decrease with increased leaving group pKa4 for analogues with pKa4 values of <11. This suggests that one of the relative rate constants differs for the K289M reaction in comparison to that of the wild type (WT). However, a plot of log(kpol) values for incorrect insertion by K289M versus pKa4 reveals a linear correlation with a negative slope, in this respect resembling kpol values for misincorporation by the WT enzyme. We also show that some of these analogues improve the fidelity of K289M. Taken together, our data show that Lys289 critically influences the catalytic pathway of pol β.
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Affiliation(s)
- Khadijeh S Alnajjar
- Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine , New Haven, Connecticut 06520, United States
| | - Beatriz Garcia-Barboza
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Amirsoheil Negahbani
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Maryam Nakhjiri
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Boris Kashemirov
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Charles McKenna
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Myron F Goodman
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Joann B Sweasy
- Department of Therapeutic Radiology and Department of Genetics, Yale University School of Medicine , New Haven, Connecticut 06520, United States
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16
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Feldman AW, Dien VT, Romesberg FE. Chemical Stabilization of Unnatural Nucleotide Triphosphates for the in Vivo Expansion of the Genetic Alphabet. J Am Chem Soc 2017; 139:2464-2467. [PMID: 28170246 DOI: 10.1021/jacs.6b12731] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We have developed an unnatural base pair (UBP) and a semisynthetic organism (SSO) that imports the constituent unnatural nucleoside triphosphates and uses them to replicate DNA containing the UBP. However, propagation of the UBP is at least in part limited by the stability of the unnatural triphosphates, which are degraded by cellular and secreted phosphatases. To circumvent this problem, we now report the synthesis and evaluation of unnatural triphosphates with their β,γ-bridging oxygen replaced with a difluoromethylene moiety, yielding dNaMTPCF2 and dTPT3TPCF2. We find that although dNaMTPCF2 cannot support in vivo replication, likely due to poor polymerase recognition, dTPT3TPCF2 can, and moreover, its increased stability can contribute to increased UBP retention. The data demonstrate the promise of this chemical approach to SSO optimization, and suggest that other modifications should be sought that confer phosphatase resistance without interfering with polymerase recognition.
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Affiliation(s)
- Aaron W Feldman
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vivian T Dien
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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17
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Graton J, Compain G, Besseau F, Bogdan E, Watts JM, Mtashobya L, Wang Z, Weymouth-Wilson A, Galland N, Le Questel JY, Linclau B. Influence of Alcohol β-Fluorination on Hydrogen-Bond Acidity of Conformationally Flexible Substrates. Chemistry 2016; 23:2811-2819. [DOI: 10.1002/chem.201604940] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Jerome Graton
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Guillaume Compain
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Francois Besseau
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Elena Bogdan
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Joseph M. Watts
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Lewis Mtashobya
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Zhong Wang
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
| | - Alex Weymouth-Wilson
- Dextra Laboratories Ltd; The Science and Technology Centre; Earley Gate, Whiteknights Road Reading RG6 6BZ UK
| | - Nicolas Galland
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230; Faculté des Sciences et des Techniques; Université de Nantes; 2, rue de la Houssinière, BP 92208 44322 Nantes Cedex 3 France
| | - Bruno Linclau
- Chemistry; University of Southampton; Highfield Southampton SO17 1BJ UK
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18
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Dalvit C, Vulpetti A. Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions, Chemical Properties, and Ligand/Protein Fluorine NMR Screening. Chemistry 2016; 22:7592-601. [DOI: 10.1002/chem.201600446] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Claudio Dalvit
- Faculty of Science University of Neuchâtel 2000 Neuchâtel Switzerland
- Sanofi, LG-CR/SDI/SBB 94403 Vitry-sur-Seine France
| | - Anna Vulpetti
- Novartis Institutes for Biomedical Research, Global Discovery Chemistry, CADD 4002 Basel Switzerland
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19
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Rapp M, Margas-Musielak K, Koroniak H. Synthesis and spectral properties of fluorinated α,β-epoxyphosphonates. J Fluor Chem 2015. [DOI: 10.1016/j.jfluchem.2015.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Kadina AP, Kashemirov BA, Oertell K, Batra VK, Wilson SH, Goodman MF, McKenna CE. Two Scaffolds from Two Flips: (α,β)/(β,γ) CH2/NH "Met-Im" Analogues of dTTP. Org Lett 2015; 17:2586-9. [PMID: 25970636 PMCID: PMC4672865 DOI: 10.1021/acs.orglett.5b00799] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel α,β-CH2 and β,γ-NH (1a) or α,β-NH and β,γ-CH2 (1b) "Met-Im" dTTPs were synthesized via monodemethylation of triethyl-dimethyl phosphorimido-bisphosphonate synthons (4a, 4b), formed via a base-induced [1,3]-rearrangement of precursors (3a, 3b) in a reaction with dimethyl or diethyl phosphochloridate. Anomerization during final bromotrimethylsilane (BTMS) deprotection after Mitsunobu conjugation with dT was avoided by microwave conditions. 1a was 9-fold more potent in inhibiting DNA polymerase β, attributed to an NH-group interaction with R183 in the active site.
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Affiliation(s)
- Anastasia P. Kadina
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Keriann Oertell
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Vinod K. Batra
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, United States
| | - Myron F. Goodman
- Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
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21
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Hwang CS, Kung A, Kashemirov BA, Zhang C, McKenna CE. 5'-β,γ-CHF-ATP diastereomers: synthesis and fluorine-mediated selective binding by c-Src protein kinase. Org Lett 2015; 17:1624-7. [PMID: 25781066 PMCID: PMC4892180 DOI: 10.1021/ol503765n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The first preparation of the individual β,γ-CHF-ATP stereoisomers 12a and 12b is reported. Configurationally differing solely by the orientation of the C-F fluorine, 12a and 12b have discrete (31)P (202 MHz, pH 10.9, ΔδPα 6 Hz, ΔδPβ 4 Hz) and (19)F NMR (470 MHz, pH 9.8, ΔδF 25 Hz) spectral signatures and exhibit a 6-fold difference in IC50 values for c-Src kinase, attributed to a unique interaction of the (S)-fluorine of bound 12b with R388 in the active site.
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Affiliation(s)
- Candy S. Hwang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Alvin Kung
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
| | - Chao Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Loker Hydrocarbon Research Institute, University of Southern California, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
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22
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Panigrahi K, Applegate GA, Malik G, Berkowitz DB. Combining a Clostridial enzyme exhibiting unusual active site plasticity with a remarkably facile sigmatropic rearrangement: rapid, stereocontrolled entry into densely functionalized fluorinated phosphonates for chemical biology. J Am Chem Soc 2015; 137:3600-9. [PMID: 25719907 DOI: 10.1021/jacs.5b00022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Described is an efficient stereocontrolled route into valuable, densely functionalized fluorinated phosphonates that takes advantage of (i) a Clostridial enzyme to set the absolute stereochemistry and (ii) a new [3,3]-sigmatropic rearrangement of the thiono-Claisen variety that is among the fastest sigmatropic rearrangements yet reported. Here, a pronounced rate enhancement is achieved by distal fluorination. This rearrangement is completely stereoretentive, parlaying the enzymatically established β-C-O stereochemistry in the substrate into the δ-C-S stereochemistry in the product. The final products are of interest to chemical biology, with a platform for Zn-aminopeptidase A inhibitors being constructed here. The enzyme, Clostridium acetobutylicum (CaADH), recently expressed by our group, reduces a spectrum of γ,δ-unsaturated β-keto-α,α-difluorophosphonate esters (93-99% ee; 10 examples). The resultant β-hydroxy-α,α-difluorophosphonates possess the "L"-stereochemistry, opposite to that previously observed for the CaADH-reduction of ω-keto carboxylate esters ("D"), indicating an unusual active site plasticity. For the thiono-Claisen rearrangement, a notable structure-reactivity relationship is observed. Measured rate constants vary by over 3 orders of magnitude, depending upon thiono-ester structure. Temperature-dependent kinetics reveal an unusually favorable entropy of activation (ΔS(‡) = 14.5 ± 0.6 e.u.). Most notably, a 400-fold rate enhancement is seen upon fluorination of the distal arene ring, arising from favorable enthalpic (ΔΔH(‡) = -2.3 kcal/mol) and entropic (ΔΔS(‡) = 4 e.u., i.e. 1.2 kcal/mol at rt) contributions. The unusual active site plasticity seen here is expected to drive structural biology studies on CaADH, while the exceptionally facile sigmatropic rearrangement is expected to drive computational studies to elucidate its underlying entropic and enthalpic basis.
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Affiliation(s)
- Kaushik Panigrahi
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Gregory A Applegate
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Guillaume Malik
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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23
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Dalvit C, Invernizzi C, Vulpetti A. Fluorine as a hydrogen-bond acceptor: experimental evidence and computational calculations. Chemistry 2014; 20:11058-68. [PMID: 25044441 DOI: 10.1002/chem.201402858] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Indexed: 12/19/2022]
Abstract
Hydrogen-bonding interactions play an important role in many chemical and biological systems. Fluorine acting as a hydrogen-bond acceptor in intermolecular and intramolecular interactions has been the subject of many controversial discussions and there are different opinions about it. Recently, we have proposed a correlation between the propensity of fluorine to be involved in hydrogen bonds and its (19)F NMR chemical shift. We now provide additional experimental and computational evidence for this correlation. The strength of hydrogen-bond complexes involving the fluorine moieties CH2F, CHF2, and CF3 was measured and characterized in simple systems by using established and novel NMR methods and compared to the known hydrogen-bond complex formed between acetophenone and p-fluorophenol. Implications of these results for (19)F NMR screening are analyzed in detail. Computed values of the molecular electrostatic potential at the different fluorine atoms and the analysis of the electron density topology at bond critical points correlate well with the NMR results.
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Affiliation(s)
- Claudio Dalvit
- University of Neuchâtel, Faculty of Science, 2000 Neuchâtel (Switzerland).
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24
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Zhang Z, Eloge J, Florián J. Quantum mechanical analysis of nonenzymatic nucleotidyl transfer reactions: kinetic and thermodynamic effects of β-γ bridging groups of dNTP substrates. Biochemistry 2014; 53:4180-91. [PMID: 24901652 PMCID: PMC4081047 DOI: 10.1021/bi5003713] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Rate (k) and equilibrium
(K)
constants for the reaction of tetrahydrofuranol with a series of Mg2+ complexes of methyl triphosphate analogues, CH3O-P(O2)-O-P(O2)-X-PO34–, X = O, CH2, CHCH3, C(CH3)2, CFCH3, CHF, CHCl, CHBr, CFCl, CF2,
CCl2, and CBr2, forming phosphate diester and
pyrophosphate or bisphosphonate in aqueous solution were evaluated
by B3LYP/TZVP//HF/6-31G* quantum chemical calculations and Langevin
dipoles and polarized continuum solvation models. The calculated log k and log K values were found to depend
linearly on the experimental pKa4 of the
conjugate acid of the corresponding pyrophosphate or bisphosphonate
leaving group. The calculated slopes of these Brønsted linear
free energy relationships were βlg = −0.89
and βeq = −0.93, respectively. The studied
compounds also followed the linear relationship Δlog k = 0.8Δlog K, which became less
steep, Δlog k = 0.6Δlog K, after the range of studied compounds was extended to include analogues
that were doubly protonated on γ-phosphate, CH3O-P(O2)-O-P(O2)-X-PO3H22–. The scissile Pα–Olg bond length
in studied methyl triphosphate analogues slightly increases with decreasing
pKa of the leaving group; concomitantly,
the CH3OPα(O2) moiety becomes
more positive. These structural effects indicate that substituents
with low pKa can facilitate both Pα–Olg bond breaking and the Pα–Onuc bond forming process, thus explaining the
large negative βlg calculated for the transition
state geometry that has significantly longer Pα–Onuc distance than the Pα–Olg distance.
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Affiliation(s)
- Zheng Zhang
- Department of Chemistry and Biochemistry, Loyola University Chicago , 6525 N. Sheridan Road, Chicago, Illinois 60626, United States
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25
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Hwang C, Kashemirov BA, McKenna CE. On the observation of discrete fluorine NMR spectra for uridine 5'-β,γ-fluoromethylenetriphosphate diastereomers at basic pH. J Org Chem 2014; 79:5315-9. [PMID: 24819695 PMCID: PMC4059216 DOI: 10.1021/jo500452b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Indexed: 11/28/2022]
Abstract
Jakeman et al. recently reported the inability to distinguish the diastereomers of uridine 5'-β,γ-fluoromethylenetriphosphate (β,γ-CHF-UTP, 1) by (19)F NMR under conditions we previously prescribed for the resolution of the corresponding β,γ-CHF-dGTP spectra, stating further that 1 decomposed under these basic conditions. Here we show that the (19)F NMR spectra of 1 (~1:1 diastereomer mixture prepared by coupling of UMP-morpholidate with fluoromethylenebis(phosphonic acid)) in D2O at pH 10 are indeed readily distinguishable. 1 in this solution was stable for 24 h at rt.
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Affiliation(s)
- Candy
S. Hwang
- Department of Chemistry, University of
Southern California, Los Angeles, California 90089, United States
| | - Boris A. Kashemirov
- Department of Chemistry, University of
Southern California, Los Angeles, California 90089, United States
| | - Charles E. McKenna
- Department of Chemistry, University of
Southern California, Los Angeles, California 90089, United States
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26
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Oertell K, Chamberlain BT, Wu Y, Ferri E, Kashemirov BA, Beard WA, Wilson SH, McKenna CE, Goodman MF. Transition state in DNA polymerase β catalysis: rate-limiting chemistry altered by base-pair configuration. Biochemistry 2014; 53:1842-8. [PMID: 24580380 PMCID: PMC3985788 DOI: 10.1021/bi500101z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
Kinetics
studies of dNTP analogues having pyrophosphate-mimicking
β,γ-pCXYp leaving groups with variable X and Y substitution
reveal striking differences in the chemical transition-state energy
for DNA polymerase β that depend on all aspects of base-pairing
configurations, including whether the incoming dNTP is a purine or
pyrimidine and if base-pairings are right (T•A and G•C)
or wrong (T•G and G•T). Brønsted plots of the catalytic
rate constant (log(kpol)) versus pKa4 for the leaving group exhibit linear free
energy relationships (LFERs) with negative slopes ranging from −0.6
to −2.0, consistent with chemical rate-determining transition-states
in which the active-site adjusts to charge-stabilization demand during
chemistry depending on base-pair configuration. The Brønsted
slopes as well as the intercepts differ dramatically and provide the
first direct evidence that dNTP base recognition by the enzyme–primer–template
complex triggers a conformational change in the catalytic region of
the active-site that significantly modifies the rate-determining chemical
step.
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Affiliation(s)
- Keriann Oertell
- Department of Biological Sciences and ‡Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California , University Park Campus, Los Angeles, California 90089-0744, United States
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27
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Beaton SA, Jiang PM, Melong JC, Loranger MW, Mohamady S, Veinot TI, Jakeman DL. The effect of bisphosphonate acidity on the activity of a thymidylyltransferase. Org Biomol Chem 2014; 11:5473-80. [PMID: 23857455 DOI: 10.1039/c3ob41017j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Thymidylyltransferases (thymidine diphospho pyrophosphorylases) are nucleotidylyltransferases that play key roles in the biosynthesis of carbohydrate components within bacterial cell walls and in the biosynthesis of glycosylated natural products. They catalyze the formation of sugar nucleotides concomitant with the release of pyrophosphate. Protein engineering of thymidylyltransferases has been an approach for the production of a variety of non-physiological sugar nucleotides. In this work, we have explored chemical approaches towards modifying the activity of the thymidylyltransferase (Cps2L) cloned from S. pneumoniae, through the use of chemically synthesized 'activated' nucleoside triphosphates with enhanced leaving groups, or by switching the metal ion co-factor specificity. Within a series of phosphonate-containing nucleoside triphosphate analogues, thymidylyltransferase activity is enhanced based on the acidity of the leaving group and a Brønsted-type analysis indicated that leaving group departure is rate limiting. We have also determined IC50 values for a series of bisphosphonates as inhibitors of thymidylyltransferases. No correlation between the acidity of the inhibitors (pKa) and the magnitude of enzyme inhibition was found.
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Affiliation(s)
- Stephen A Beaton
- Department of Chemistry, Dalhousie University, 1459 Oxford St., Halifax, Nova Scotia B3H 4R2, Canada
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28
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Downey AM, Cairo CW. Synthesis of α-brominated phosphonates and their application as phosphate bioisosteres. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00255e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A review of the synthesis and biological activity of α-bromo-phosphonate groups as phosphate bioisosteres.
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Affiliation(s)
- A. Michael Downey
- Alberta Glycomics Centre
- Department of Chemistry
- University of Alberta
- Edmonton, Canada
| | - Christopher W. Cairo
- Alberta Glycomics Centre
- Department of Chemistry
- University of Alberta
- Edmonton, Canada
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29
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Dalvit C, Ko SY, Vulpetti A. Application of the rule of shielding in the design of novel fluorinated structural motifs and peptidomimetics. J Fluor Chem 2013. [DOI: 10.1016/j.jfluchem.2013.01.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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30
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Hollenstein M. Nucleoside triphosphates--building blocks for the modification of nucleic acids. Molecules 2012; 17:13569-91. [PMID: 23154273 PMCID: PMC6268876 DOI: 10.3390/molecules171113569] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 11/07/2012] [Accepted: 11/09/2012] [Indexed: 11/16/2022] Open
Abstract
Nucleoside triphosphates are moldable entities that can easily be functionalized at various locations. The enzymatic polymerization of these modified triphosphate analogues represents a versatile platform for the facile and mild generation of (highly) functionalized nucleic acids. Numerous modified triphosphates have been utilized in a broad palette of applications spanning from DNA-tagging and -labeling to the generation of catalytic nucleic acids. This review will focus on the recent progress made in the synthesis of modified nucleoside triphosphates as well as on the understanding of the mechanisms underlying their polymerase acceptance. In addition, the usefulness of chemically altered dNTPs in SELEX and related methods of in vitro selection will be highlighted, with a particular emphasis on the generation of modified DNA enzymes (DNAzymes) and DNA-based aptamers.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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31
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Oertell K, Wu Y, Zakharova VM, Kashemirov BA, Shock DD, Beard WA, Wilson SH, McKenna CE, Goodman MF. Effect of β,γ-CHF- and β,γ-CHCl-dGTP halogen atom stereochemistry on the transition state of DNA polymerase β. Biochemistry 2012; 51:8491-501. [PMID: 23043620 DOI: 10.1021/bi3010335] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Recently, we synthesized the first individual β,γ-CHX-dGTP diastereomers [(R)- or (S)-CHX, where X is F or Cl] and determined their structures in ternary complexes with DNA polymerase β (pol β). We now report stereospecificity by pol β on the mixed β,γ-CHX diastereomer pairs using nuclear magnetic resonance and on the separate diastereomers using transient kinetics. For both the F and Cl diastereomers, the R isomer is favored over the S isomer for G·C correct incorporation, with stereospecificities [(k(pol)/K(d))(R)/(k(pol)/K(d))(S)] of 3.8 and 6.3, respectively, and also for G·T misincorporation, with stereospecificities of 11 and 7.8, respectively. Stereopreference for the (R)-CHF-dGTP diastereomer was abolished for k(pol) but not K(d) with mutant pol β (R183A). These compounds constitute a new class of stereochemical probes for active site interactions involving halogen atoms. As Arg183 is unique in family X pols, the design of CXY deoxyribonucleotide analogues to enhance interaction is a possible strategy for inhibiting BER selectively in cancer cells.
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Affiliation(s)
- Keriann Oertell
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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32
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Strenkowska M, Wanat P, Ziemniak M, Jemielity J, Kowalska J. Preparation of synthetically challenging nucleotides using cyanoethyl P-imidazolides and microwaves. Org Lett 2012; 14:4782-5. [PMID: 22966945 DOI: 10.1021/ol302071f] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We describe a general method for the elongation of nucleoside oligophosphate chains by means of cyanoethyl (CE) phosphorimidazolides. Though the method requires a phosphorylation and subsequent deprotection reaction, both steps could be achieved in one pot without isolation/purification of the initial phosphorylation product. We have also found that pyrophosphate bond formation by this method is significantly accelerated by microwave irradiation.
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Affiliation(s)
- Malwina Strenkowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Zwirki i Wigury 93, 02-089 Warsaw, Poland
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Vulpetti A, Dalvit C. Fluorine local environment: from screening to drug design. Drug Discov Today 2012; 17:890-7. [DOI: 10.1016/j.drudis.2012.03.014] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 02/19/2012] [Accepted: 03/26/2012] [Indexed: 12/21/2022]
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Wu Y, Zakharova VM, Kashemirov BA, Goodman MF, Batra VK, Wilson SH, McKenna CE. β,γ-CHF- and β,γ-CHCl-dGTP diastereomers: synthesis, discrete 31P NMR signatures, and absolute configurations of new stereochemical probes for DNA polymerases. J Am Chem Soc 2012; 134:8734-7. [PMID: 22397499 PMCID: PMC3595068 DOI: 10.1021/ja300218x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deoxynucleoside 5'-triphosphate analogues in which the β,γ-bridging oxygen has been replaced with a CXY group are useful chemical probes to investigate DNA polymerase catalytic and base-selection mechanisms. A limitation of such probes has been that conventional synthetic methods generate a mixture of diastereomers when the bridging carbon substitution is nonequivalent (X ≠ Y). We report here a general solution to this long-standing problem with four examples of β,γ-CXY dNTP diastereomers: (S)- and (R)-β,γ-CHCl-dGTP (12a-1/12a-2) and (S)- and (R)-β,γ-CHF-dGTP (12b-1/12b-2). Central to their preparation was conversion of the prochiral parent bisphosphonic acids to the P,C-dimorpholinamide derivatives 7 of their (R)-mandelic acid monoesters, which provided access to the individual diastereomers 7a-1, 7a-2, 7b-1, and 7b-2 by preparative HPLC. Selective acidic hydrolysis of the P-N bond then afforded "portal" diastereomers, which were readily coupled to morpholine-activated dGMP. Removal of the chiral auxiliary by H(2) (Pd/C) gave the four individual diastereomeric nucleotides 12, which were characterized by (31)P, (1)H, and (19)F NMR spectroscopy and by mass spectrometry. After treatment with Chelex-100 to remove traces of paramagnetic ions, at pH ~10 the diastereomer pairs 12a,b exhibit discrete P(α) and P(β)(31)P resonances. The more upfield P(α) and more downfield P(β) resonances (and also the more upfield (19)F NMR resonance in 12b) are assigned to the R configuration at the P(β)-CHX-P(γ) carbons on the basis of the absolute configurations of the individual diastereomers as determined from the X-ray crystallographic structures of their ternary complexes with DNA and polymerase β.
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Affiliation(s)
- Yue Wu
- Department of Chemistry, University of Southern California, Los Angeles, California 90089
| | - Valeria M. Zakharova
- Department of Chemistry, University of Southern California, Los Angeles, California 90089
| | - Boris A. Kashemirov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089
| | - Myron F. Goodman
- Department of Chemistry, University of Southern California, Los Angeles, California 90089
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| | - Vinod K. Batra
- 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
| | - Charles E. McKenna
- Department of Chemistry, University of Southern California, Los Angeles, California 90089
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Chamberlain BT, Batra VK, Beard WA, Kadina AP, Shock DD, Kashemirov BA, McKenna CE, Goodman MF, Wilson SH. Stereospecific formation of a ternary complex of (S)-α,β-fluoromethylene-dATP with DNA pol β. Chembiochem 2012; 13:528-30. [PMID: 22315190 DOI: 10.1002/cbic.201100738] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Indexed: 11/07/2022]
Abstract
The influence of water: crystallization of (R/S)-α,β-CHF-dATP with the preorganized pol β-DNA complex shows that (S)-α,β-CHF-dATP is preferentially bound to the active site with the C=F fluorine proximal to a structural water bound to Asp276.
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Affiliation(s)
- Brian T Chamberlain
- Departments of Chemistry and Biology, University of Southern California, Los Angeles, CA 90089, USA
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Dalvit C, Vulpetti A. Intermolecular and intramolecular hydrogen bonds involving fluorine atoms: implications for recognition, selectivity, and chemical properties. ChemMedChem 2012; 7:262-72. [PMID: 22262517 DOI: 10.1002/cmdc.201100483] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 12/02/2011] [Indexed: 11/06/2022]
Abstract
A correlation between 19F NMR isotropic chemical shift and close intermolecular F⋅⋅⋅H-X contacts (with X=N or O) has been identified upon analysis of the X-ray crystal structures of fluorinated molecules listed in the Cambridge Structural Database (CSD). An optimal F⋅⋅⋅X distance involving primary and shielded secondary fluorine atoms in hydrogen-bond formation along with a correlation between F⋅⋅⋅H distance and F⋅⋅⋅H-X angle were also derived from the analysis. The hydrogen bonds involving fluorine are relevant, not only for the recognition mechanism and stabilization of a preferred conformation, but also for improvement in the permeability of the molecules, as shown with examples taken from a proprietary database. Results of an analysis of the small number of fluorine-containing natural products listed in the Protein Data Bank (PDB) appear to strengthen the derived correlation between 19F NMR isotropic chemical shift and interactions involving fluorine (also known as the "rule of shielding") and provides a hypothesis for the recognition mechanism and catalytic activity of specific enzymes. Novel chemical scaffolds, based on the rule of shielding, have been designed for recognizing distinct structural motifs present in proteins. It is envisaged that this approach could find useful applications in drug design for the efficient optimization of chemical fragments or promising compounds by increasing potency and selectivity against the desired biomolecular target.
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Affiliation(s)
- Claudio Dalvit
- Department of Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, 2000 Neuchâtel, Swizerland.
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Forget SM, Bhattasali D, Hart VC, Cameron TS, Syvitski RT, Jakeman DL. Synthesis and enzymatic evaluation of ketose phosphonates: the interplay between mutarotation, monofluorination and acidity. Chem Sci 2012. [DOI: 10.1039/c2sc01077a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Chamberlain BT, Upton TG, Kashemirov BA, McKenna CE. α-Azido bisphosphonates: synthesis and nucleotide analogues. J Org Chem 2011; 76:5132-6. [PMID: 21462930 PMCID: PMC3112310 DOI: 10.1021/jo200045a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first examples of α-azido bisphosphonates [(RO)(2)P(O)](2)CXN(3) (1, R = i-Pr, X = Me; 2, R = i-Pr, X = H; 3, R = H, X = Me; 4, R = H, X = H) and corresponding β,γ-CXN(3) dGTP (5-6) and α,β-CXN(3) dATP (7-8) analogues are described. The individual diastereomers of 7 (7a/b) were obtained by HPLC separation of the dADP synthetic precursor (14a/b).
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Affiliation(s)
- Brian T Chamberlain
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, USA
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40
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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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41
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Chamberlain BT, Osuna J, Kashemirov BA, McKenna CE. Synthesis and Sensing of Bisphosphonophosphate Alkyl Monoesters: A Novel Class of Compounds for the Study of Nucleoside 5′-Triphosphate Chemistry. PHOSPHORUS SULFUR 2011; 186:966-967. [DOI: 10.1080/10426507.2010.526675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Brian T. Chamberlain
- a Department of Chemistry , University of Southern California , Los Angeles , California , USA
| | - Jorge Osuna
- a Department of Chemistry , University of Southern California , Los Angeles , California , USA
| | - Boris A. Kashemirov
- a Department of Chemistry , University of Southern California , Los Angeles , California , USA
| | - Charles E. McKenna
- a Department of Chemistry , University of Southern California , Los Angeles , California , USA
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Partha SK, Sadeghi-Khomami A, Slowski K, Kotake T, Thomas NR, Jakeman DL, Sanders DAR. Chemoenzymatic synthesis, inhibition studies, and X-ray crystallographic analysis of the phosphono analog of UDP-Galp as an inhibitor and mechanistic probe for UDP-galactopyranose mutase. J Mol Biol 2010; 403:578-90. [PMID: 20850454 DOI: 10.1016/j.jmb.2010.08.053] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 08/27/2010] [Accepted: 08/30/2010] [Indexed: 12/01/2022]
Abstract
UDP (uridine diphosphate) galactopyranose mutase (UGM) is involved in the cell wall biosynthesis of many pathogenic microorganisms. UGM catalyzes the reversible conversion of UDP-α-D-galactopyranose into UDP-α-D-galactofuranose, with the latter being the precursor of galactofuranose (Galf) residues in cell walls. Glycoconjugates of Galf are essential components in the cell wall of various pathogenic bacteria, including Mycobacterium tuberculosis, the causative agent of tuberculosis. The absence of Galf in humans and its bacterial requirement make UGM a potential target for developing novel antibacterial agents. In this article, we report the synthesis, inhibitory activity, and X-ray crystallographic studies of UDP-phosphono-galactopyranose, a nonhydrolyzable C-glycosidic phosphonate. This is the first report on the synthesis of a phosphonate analog of UDP-α-D-galactopyranose by a chemoenzymatic phosphoryl coupling method. The phosphonate was evaluated against three bacterial UGMs and showed only moderate inhibition. We determined the crystal structure of the phosphonate analog bound to Deinococcus radiodurans UGM at 2.6 Å resolution. The phosphonate analog is bound in a novel conformation not observed in UGM-substrate complex structures or in other enzyme-sugar nucleotide phosphonate complexes. This complex structure provides a structural basis for the observed micromolar inhibition towards UGM. Steric clashes, loss of electrostatic stabilization between an active-site arginine (Arg305) and the phosphonate analog, and a 180° flip of the hexose moiety account for the differences in the binding orientations of the isosteric phosphonate analog and the physiological substrate. This provides new insight into the ability of a sugar-nucleotide-binding enzyme to orient a substrate analog in an unexpected geometry and should be taken into consideration in designing such enzyme inhibitors.
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Surya Prakash GK, Zibinsky M, Upton TG, Kashemirov BA, McKenna CE, Oertell K, Goodman MF, Batra VK, Pedersen LC, Beard WA, Shock DD, Wilson SH, Olah GA. Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Proc Natl Acad Sci U S A 2010; 107:15693-8. [PMID: 20724659 PMCID: PMC2936638 DOI: 10.1073/pnas.1007430107] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is difficult to overestimate the importance of nucleoside triphosphates in cellular chemistry: They are the building blocks for DNA and RNA and important sources of energy. Modifications of biologically important organic molecules with fluorine are of great interest to chemists and biologists because the size and electronegativity of the fluorine atom can be used to make defined structural alterations to biologically important molecules. Although the concept of nonhydrolyzable nucleotides has been around for some time, the progress in the area of modified triphosphates was limited by the lack of synthetic methods allowing to access bisCF(2)-substituted nucleotide analogs-one of the most interesting classes of nonhydrolyzable nucleotides. These compounds have "correct" polarity and the smallest possible steric perturbation compared to natural nucleotides. No other known nucleotides have these advantages, making bisCF(2)-substituted analogs unique. Herein, we report a concise route for the preparation of hitherto unknown highly acidic and polybasic bis(difluoromethylene)triphosphoric acid 1 using a phosphorous(III)/phosphorous(V) interconversion approach. The analog 1 compared to triphosphoric acid is enzymatically nonhydrolyzable due to substitution of two bridging oxygen atoms with CF(2) groups, maintaining minimal perturbations in steric bulkiness and overall polarity of the triphosphate polyanion. The fluorinated triphosphoric acid 1 was used for the preparation of the corresponding fluorinated deoxynucleotides (dNTPs). One of these dNTP analogs (dT) was demonstrated to fit into DNA polymerase beta (DNA pol beta) binding pocket by obtaining a 2.5 A resolution crystal structure of a ternary complex with the enzyme. Unexpected dominating effect of triphosphate/Mg(2+) interaction over Watson-Crick hydrogen bonding was found and discussed.
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Affiliation(s)
- G. K. Surya Prakash
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Mikhail Zibinsky
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Thomas G. Upton
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Boris A. Kashemirov
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Charles E. McKenna
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Keriann Oertell
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Myron F. Goodman
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
| | - Vinod K. Batra
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - William A. Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - David D. Shock
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709
| | - George A. Olah
- Loker Hydrocarbon Research Institute, Department of Chemistry and Department of Biology, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661; and
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