1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Schäkel L, Schmies CC, Idris RM, Luo X, Lee SY, Lopez V, Mirza S, Vu TH, Pelletier J, Sévigny J, Namasivayam V, Müller CE. Nucleotide Analog ARL67156 as a Lead Structure for the Development of CD39 and Dual CD39/CD73 Ectonucleotidase Inhibitors. Front Pharmacol 2020; 11:1294. [PMID: 33013365 PMCID: PMC7508162 DOI: 10.3389/fphar.2020.01294] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/04/2020] [Indexed: 12/21/2022] Open
Abstract
Nucleoside triphosphate diphosphohydrolase1 (NTPDase1, CD39) inhibitors have potential as novel drugs for the (immuno)therapy of cancer. They increase the extracellular concentration of immunostimulatory ATP and reduce the formation of AMP, which can be further hydrolyzed by ecto-5'-nucleotidase (CD73) to immunosuppressive, cancer-promoting adenosine. In the present study, we synthesized analogs and derivatives of the standard CD39 inhibitor ARL67156, a nucleotide analog which displays a competitive mechanism of inhibition. Structure-activity relationships were analyzed at the human enzyme with respect to substituents in the N 6- and C8-position of the adenine core, and modifications of the triphosph(on)ate chain. Capillary electrophoresis coupled to laser-induced fluorescence detection employing a fluorescent-labeled ATP derivative was employed to determine the compounds' potency. Selected inhibitors were additionally evaluated in an orthogonal, malachite green assay versus the natural substrate ATP. The most potent CD39 inhibitors of the present series were ARL67156 and its derivatives 31 and 33 with Ki values of around 1 µM. Selectivity studies showed that all three nucleotide analogs additionally blocked CD73 acting as dual-target inhibitors. Docking studies provided plausible binding modes to both targets. The present study provides a full characterization of the frequently applied CD39 inhibitor ARL67156, presents structure-activity relationships, and provides a basis for future optimization towards selective CD39 and dual CD39/CD73 inhibitors.
Collapse
Affiliation(s)
- Laura Schäkel
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Constanze C Schmies
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Riham M Idris
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Xihuan Luo
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Sang-Yong Lee
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Vittoria Lopez
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Salahuddin Mirza
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - The Hung Vu
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Julie Pelletier
- Centre de Recherche du CHU de Québec - Université Laval, Québec City, QC, Canada
| | - Jean Sévigny
- Centre de Recherche du CHU de Québec - Université Laval, Québec City, QC, Canada.,Départment de Microbiologie-Infectiologie et d'Immunologie, Faculté de Médecine, Université Laval, Quebec City, QC, Canada
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Bonn, Germany
| |
Collapse
|
4
|
Alnajjar KS, Krylov IS, Negahbani A, Haratipour P, Kashemirov BA, Huang J, Mahmoud M, McKenna CE, Goodman MF, Sweasy JB. A pre-catalytic non-covalent step governs DNA polymerase β fidelity. Nucleic Acids Res 2020; 47:11839-11849. [PMID: 31732732 PMCID: PMC7145665 DOI: 10.1093/nar/gkz1076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 10/23/2019] [Accepted: 11/07/2019] [Indexed: 12/27/2022] Open
Abstract
DNA polymerase β (pol β) selects the correct deoxyribonucleoside triphosphate for incorporation into the DNA polymer. Mistakes made by pol β lead to mutations, some of which occur within specific sequence contexts to generate mutation hotspots. The adenomatous polyposis coli (APC) gene is mutated within specific sequence contexts in colorectal carcinomas but the underlying mechanism is not fully understood. In previous work, we demonstrated that a somatic colon cancer variant of pol β, K289M, misincorporates deoxynucleotides at significantly increased frequencies over wild-type pol β within a mutation hotspot that is present several times within the APC gene. Kinetic studies provide evidence that the rate-determining step of pol β catalysis is phosphodiester bond formation and suggest that substrate selection is governed at this step. Remarkably, we show that, unlike WT, a pre-catalytic step in the K289M pol β kinetic pathway becomes slower than phosphodiester bond formation with the APC DNA sequence but not with a different DNA substrate. Based on our studies, we propose that pre-catalytic conformational changes are of critical importance for DNA polymerase fidelity within specific DNA sequence contexts.
Collapse
Affiliation(s)
- Khadijeh S Alnajjar
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Ivan S Krylov
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Amirsoheil Negahbani
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Pouya Haratipour
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Boris A Kashemirov
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Ji Huang
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Mariam Mahmoud
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Charles E McKenna
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Myron F Goodman
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Joann B Sweasy
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA.,University of Arizona Cancer Center, Tucson, AZ 85724, USA
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Romanenko VD. α-Heteroatom-substituted gem-Bisphosphonates: Advances in the Synthesis and Prospects for Biomedical Application. CURR ORG CHEM 2019. [DOI: 10.2174/1385272823666190401141844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Functionalized gem-bisphosphonic acid derivatives being pyrophosphate isosteres are of great synthetic and biological interest since they are currently the most important class of drugs developed for the treatment of diseases associated with the disorder of calcium metabolism, including osteoporosis, Paget’s disease, and hypercalcemia. In this article, we will try to give an in-depth overview of the methods for obtaining α- heteroatom-substituted methylenebisphosphonates and acquaint the reader with the synthetic strategies that are used to develop biologically important compounds of this type.
Collapse
Affiliation(s)
- Vadim D. Romanenko
- V. P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, 1-Murmanska Street, Kyiv-94, 02660, Ukraine
| |
Collapse
|
7
|
Oertell K, Florián J, Haratipour P, Crans DC, Kashemirov BA, Wilson SH, McKenna CE, Goodman MF. A Transition-State Perspective on Y-Family DNA Polymerase η Fidelity in Comparison with X-Family DNA Polymerases λ and β. Biochemistry 2019; 58:1764-1773. [PMID: 30839203 DOI: 10.1021/acs.biochem.9b00087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deoxynucleotide misincorporation efficiencies can span a wide 104-fold range, from ∼10-2 to ∼10-6, depending principally on polymerase (pol) identity and DNA sequence context. We have addressed DNA pol fidelity mechanisms from a transition-state (TS) perspective using our "tool-kit" of dATP- and dGTP-β,γ substrate analogues in which the pyrophosphate leaving group (p Ka4 = 8.9) has been replaced by a series of bisphosphonates covering a broad acidity range spanning p Ka4 values from 7.8 (CF2) to 12.3 [C(CH3)2]. Here, we have used a linear free energy relationship (LFER) analysis, in the form of a Brønsted plot of log( kpol) versus p Ka4, for Y-family error-prone pol η and X-family pols λ and β to determine the extent to which different electrostatic active site environments alter kpol values. The apparent chemical rate constant ( kpol) is the rate-determining step for the three pols. The pols each exhibit a distinct catalytic signature that differs for formation of right (A·T) and wrong (G·T) incorporations observed as changes in slopes and displacements of the Brønsted lines, in relation to a reference LFER. Common to this signature among all three pols is a split linear pattern in which the analogues containing two halogens show kpol values that are systematically lower than would be predicted from their p Ka4 values measured in aqueous solution. We discuss how metal ions and active site amino acids are responsible for causing "effective" p Ka4 values that differ for dihalo and non-dihalo substrates as well as for individual R and S stereoisomers for CHF and CHCl.
Collapse
Affiliation(s)
- 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
| | - Jan Florián
- Department of Chemistry and Biochemistry , Loyola University Chicago , 1032 West Sheridan Road , Chicago , Illinois 60660 , 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
| | - Debbie C Crans
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , 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
| | - 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
| | - 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
| | - 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.,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
| |
Collapse
|
8
|
Haratipour P, Minard C, Nakhjiri M, Negahbani A, Kashemirov BA, McKenna CE. New Chirally Modified Bisphosphonates for Synthesis of Individual Beta,Gamma-CHX-Deoxynucleotide Diastereomers. PHOSPHORUS SULFUR 2019; 194:329-330. [PMID: 32377060 DOI: 10.1080/10426507.2018.1540482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Individual diastereomers of CXY bisphosphonate analogues of dNTPs or NTPs are useful chemical stereoprobes to investigate interactions within the chiral active site environment of enzymes such as polymerases and kinases. We previously reported synthetic access to β,γ-CHX-dGTPs (X = F or Cl) via a bisphosphonate synthon with an (R)-methyl mandelate auxiliary and have extended this approach to dTTP and dATP analogues. As removal of the chiral auxiliary by (Pd/C) hydrogenolysis is incompatible with the cytosine heterocycle and also with X = Br, we have now designed bisphosphonate synthons using (R)-(+)-α-ethylbenzylamine or methyl (R)-(-)-phenylglycine auxiliaries and equipped with an o-nitrobenzyl ester protecting group allowing photochemical deprotection. These new synthons have made possible the first syntheses of individual dCTP and monobromo-substituted dNTP β,γ-CHX diastereomers.
Collapse
Affiliation(s)
- Pouya Haratipour
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, U.S.A
| | - Corinne Minard
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, U.S.A
| | - Maryam Nakhjiri
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, U.S.A
| | - Amirsoheil Negahbani
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, U.S.A
| | - Boris A Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, U.S.A
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, U.S.A
| |
Collapse
|
9
|
Zhao Q, Yang W, Qin T, Huang Z. Moonlighting Phosphatase Activity of Klenow DNA Polymerase in the Presence of RNA. Biochemistry 2018; 57:5127-5135. [PMID: 30059615 DOI: 10.1021/acs.biochem.8b00688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RNA is a key player in the cellular central dogma, including RNA transcription and protein synthesis. However, it is unknown whether RNA can directly interfere with DNA synthesis. Recently, we have found in vitro that while binding to DNA polymerase nonspecifically, RNA can transform DNA polymerase to display a moonlighting activity, dNTP phosphatase, in turn interfering with DNA synthesis. This phosphatase activity removes the γ-phosphate from dNTPs (generating dNDPs) and subsequently removes the β-phosphate from the formed dNDPs (generating dNMPs), confirmed by the noncleavable α,β-CH2-dGTP and β,γ-CH2-dGTP analogues. We also found that dGTP is the best substrate for the phosphatase, and the dNTP phosphatase activity is sensitive to the reaction medium. In addition, we have revealed that RNA can tune the activity of closely related proteins and give rise to new catalytic functions with subtle differences. Moreover, we have demonstrated in vitro that at the lower dNTP level, this phosphatase can directly inhibit DNA synthesis by dNTP depletion, though the phosphatase activity is 690-fold slower than the polymerase activity. Our observation in vitro suggests a plausible strategy for RNA to directly interfere with DNA polymerase and DNA synthesis in vivo.
Collapse
Affiliation(s)
- Qianwei Zhao
- College of Life Sciences , Sichuan University , Chengdu , China
| | - Wen Yang
- College of Life Sciences , Sichuan University , Chengdu , China
| | - Tong Qin
- College of Life Sciences , Sichuan University , Chengdu , China
| | - Zhen Huang
- College of Life Sciences , Sichuan University , Chengdu , China.,Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Oertell K, Kashemirov BA, Negahbani A, Minard C, Haratipour P, Alnajjar KS, Sweasy JB, Batra VK, Beard WA, Wilson SH, McKenna CE, Goodman MF. Probing DNA Base-Dependent Leaving Group Kinetic Effects on the DNA Polymerase Transition State. Biochemistry 2018; 57:3925-3933. [PMID: 29889506 DOI: 10.1021/acs.biochem.8b00417] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We examine the DNA polymerase β (pol β) transition state (TS) from a leaving group pre-steady-state kinetics perspective by measuring the rate of incorporation of dNTPs and corresponding novel β,γ-CXY-dNTP analogues, including individual β,γ-CHF and -CHCl diastereomers with defined stereochemistry at the bridging carbon, during the formation of right (R) and wrong (W) base pairs. Brønsted plots of log kpol versus p Ka4 of the leaving group bisphosphonic acids are used to interrogate the effects of the base identity, the dNTP analogue leaving group basicity, and the precise configuration of the C-X atom in R and S stereoisomers on the rate-determining step ( kpol). The dNTP analogues provide a range of leaving group basicity and steric properties by virtue of monohalogen, dihalogen, or methyl substitution at the carbon atom bridging the β,γ-bisphosphonate that mimics the natural pyrophosphate leaving group in dNTPs. Brønsted plot relationships with negative slopes are revealed by the data, as was found for the dGTP and dTTP analogues, consistent with a bond-breaking component to the TS energy. However, greater multiplicity was shown in the linear free energy relationship, revealing an unexpected dependence on the nucleotide base for both A and C. Strong base-dependent perturbations that modulate TS relative to ground-state energies are likely to arise from electrostatic effects on catalysis in the pol active site. Deviations from a uniform linear Brønsted plot relationship are discussed in terms of insights gained from structural features of the prechemistry DNA polymerase active site.
Collapse
Affiliation(s)
| | | | | | | | | | - Khadijeh S Alnajjar
- Department of Therapeutic Radiology and Department of Genetics , Yale University School of Medicine , New Haven , Connecticut 06520 , United States
| | - Joann B Sweasy
- Department of Therapeutic Radiology and Department of Genetics , Yale University School of Medicine , New Haven , Connecticut 06520 , United States
| | - Vinod K Batra
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle , North Carolina 27709 , United States
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences , National Institutes of Health , Research Triangle , 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 , North Carolina 27709 , United States
| | | | | |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Klvaňa M, Bren U, Florián J. Uniform Free-Energy Profiles of the P-O Bond Formation and Cleavage Reactions Catalyzed by DNA Polymerases β and λ. J Phys Chem B 2016; 120:13017-13030. [PMID: 27992186 PMCID: PMC5217713 DOI: 10.1021/acs.jpcb.6b08581] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
Human
X-family DNA polymerases β (Polβ) and λ
(Polλ) catalyze the nucleotidyl-transfer reaction in the base
excision repair pathway of the cellular DNA damage response. Using
empirical valence bond and free-energy perturbation simulations, we
explore the feasibility of various mechanisms for the deprotonation
of the 3′-OH group of the primer DNA strand, and the subsequent
formation and cleavage of P–O bonds in four Polβ, two
truncated Polλ (tPolλ), and two tPolλ Loop1 mutant
(tPolλΔL1) systems differing in the initial X-ray crystal
structure and nascent base pair. The average calculated activation
free energies of 14, 18, and 22 kcal mol–1 for Polβ,
tPolλ, and tPolλΔL1, respectively, reproduce the
trend in the observed catalytic rate constants. The most feasible
reaction pathway consists of two successive steps: specific base (SB)
proton transfer followed by rate-limiting concerted formation and
cleavage of the P–O bonds. We identify linear free-energy relationships
(LFERs) which show that the differences in the overall activation
and reaction free energies among the eight studied systems are determined
by the reaction free energy of the SB proton transfer. We discuss
the implications of the LFERs and suggest pKa of the 3′-OH group as a predictor of the catalytic
rate of X-family DNA polymerases.
Collapse
Affiliation(s)
- Martin Klvaňa
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor , Smetanova ulica 17, 2000 Maribor, Slovenia.,Department of Chemistry and Biochemistry, Loyola University Chicago , 1032 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Urban Bren
- Laboratory of Physical Chemistry and Chemical Thermodynamics, Faculty of Chemistry and Chemical Technology, University of Maribor , Smetanova ulica 17, 2000 Maribor, Slovenia.,Laboratory for Molecular Modeling, National Institute of Chemistry , Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Jan Florián
- Department of Chemistry and Biochemistry, Loyola University Chicago , 1032 W. Sheridan Road, Chicago, Illinois 60660, United States
| |
Collapse
|
17
|
Chen Z, Meek KN, Rangel AE, Heemstra JM. Synthesis and polymerase incorporation of β,γ-modified α-l-threofuranosyl thymine triphosphate mimics. Bioorg Med Chem Lett 2016; 26:3958-62. [PMID: 27422338 DOI: 10.1016/j.bmcl.2016.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 06/30/2016] [Accepted: 07/02/2016] [Indexed: 01/28/2023]
Abstract
Three β,γ-modified α-l-threofuranosyl nucleoside triphosphates were synthesized. The β,γ-modified tTTPs undergo a single incorporation event with HIV RT but undergo multiple incorporations to form full-length product with engineered thermophilic polymerases.
Collapse
Affiliation(s)
- Zhe Chen
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Kirsten N Meek
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexandra E Rangel
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry and the Center for Cell and Genome Science, University of Utah, Salt Lake City, UT 84112, USA.
| |
Collapse
|
18
|
Hwang CS, Xu L, Wang W, Ulrich S, Zhang L, Chong J, Shin JH, Huang X, Kool ET, McKenna CE, Wang D. Functional interplay between NTP leaving group and base pair recognition during RNA polymerase II nucleotide incorporation revealed by methylene substitution. Nucleic Acids Res 2016; 44:3820-8. [PMID: 27060150 PMCID: PMC4857003 DOI: 10.1093/nar/gkw220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 03/18/2016] [Accepted: 03/21/2016] [Indexed: 02/07/2023] Open
Abstract
RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties in pol II transcription. However, how the triphosphate moiety of substrate influences the rate of P-O bond cleavage and formation during nucleotide incorporation is still unclear. Here, by employing β,γ-bridging atom-'substituted' NTPs, we elucidate how the methylene substitution in the pyrophosphate leaving group affects cognate and non-cognate nucleotide incorporation. Intriguingly, the effect of the β,γ-methylene substitution on the non-cognate UTP/dT scaffold (∼3-fold decrease in kpol) is significantly different from that of the cognate ATP/dT scaffold (∼130-fold decrease in kpol). Removal of the wobble hydrogen bonds in U:dT recovers a strong response to methylene substitution of UTP. Our kinetic and modeling studies are consistent with a unique altered transition state for bond formation and cleavage for UTP/dT incorporation compared with ATP/dT incorporation. Collectively, our data reveals the functional interplay between NTP triphosphate moiety and base pair hydrogen bonding recognition during nucleotide incorporation.
Collapse
Affiliation(s)
- Candy S Hwang
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA
| | - Liang Xu
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Wei Wang
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Sébastien Ulrich
- Department of Chemistry, Stanford University, Stanford, CA 94305-5017, USA Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS, Université Montpellier, ENSCM, Ecole Nationale Supérieure de Chimie de Montpellier, 8 Rue de l'Ecole Normale, 34296 Montpellier cedex 5, France
| | - Lu Zhang
- Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jenny Chong
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Ji Hyun Shin
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| | - Xuhui Huang
- Department of Chemistry, Division of Biomedical Engineering, Center of Systems Biology and Human Health, School of Science and Institute for Advance Study, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305-5017, USA
| | - Charles E McKenna
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-0744, USA
| | - Dong Wang
- Department of Cellular and Molecular Medicine, School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California, San Diego, La Jolla, CA 92093-0625, USA
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Das D, Patra M, Chakrabarti A. Binding of hemin, hematoporphyrin, and protoporphyrin with erythroid spectrin: fluorescence and molecular docking studies. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:171-82. [PMID: 25737232 DOI: 10.1007/s00249-015-1012-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/29/2015] [Accepted: 02/03/2015] [Indexed: 11/27/2022]
Abstract
Free heme has toxic effects, for example lipid peroxidation, DNA damage, and protein aggregation. In severe hemolysis, which occurs during pathological states, for example sickle cell disease, ischemia reperfusion, and malaria, levels of free heme increase inside erythrocytes. The purpose of this study was to investigate whether spectrin, the major erythroid cytoskeleton protein, is involved as an acceptor of free heme. We compared the interactions of three heme derivatives, hemin chloride, hematoporphyrin, and protoporphyrin-IX, with dimeric and tetrameric spectrin. The dissociation constants (K d) for binding to spectrin dimer and tetramer were 0.57 and 1.16 µM respectively. Thermodynamic data associated with this binding revealed the binding to be favored by a positive change in entropy. Although molecular docking studies identified the SH3 domain as the unique binding site of these heme derivatives to erythroid spectrin, experimental results indicated a binding stoichiometry of 1 heme attached to both dimeric and tetrameric spectrin, indicating the common self-associating domain to be the unique binding site. We also noticed heme-induced structural changes in the membrane skeletal protein. Erythroid spectrin could thus act as a potential acceptor of heme, particularly relevant under disease conditions.
Collapse
Affiliation(s)
- Debashree Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, 700064, India
| | | | | |
Collapse
|
22
|
Sengupta C, Basu S. A spectroscopic study to decipher the mode of interaction of some common acridine derivatives with CT DNA within nanosecond and femtosecond time domains. RSC Adv 2015. [DOI: 10.1039/c5ra13035b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Our spectroscopic investigation with acridine derivatives presents the electronic control of their substituents on intercalation, solvation and PET with DNA.
Collapse
Affiliation(s)
- Chaitrali Sengupta
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
| | - Samita Basu
- Chemical Sciences Division
- Saha Institute of Nuclear Physics
- Kolkata 700 064
- India
| |
Collapse
|
23
|
Shakhmin A, Jones JP, Bychinskaya I, Zibinsky M, Oertell K, Goodman MF, Prakash GKS. Preparation of fluorinated RNA nucleotide analogs potentially stable to enzymatic hydrolysis in RNA and DNA polymerase assays. J Fluor Chem 2014; 167:226-230. [PMID: 26279588 DOI: 10.1016/j.jfluchem.2014.07.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Analogs of ribonucleotides (RNA) stable to enzymatic hydrolysis were prepared and characterized. Computational investigations revealed that this class of compounds with a modified triphosphate exhibits the correct polarity and minimal steric effects compared to the natural molecule. Non-hydrolysable properties as well as the ability of the modified nucleotide to be recognized by enzymes were probed by performing single-turnover gap filling assays with T7 RNA polymerase and DNA polymerase β.
Collapse
Affiliation(s)
- Anton Shakhmin
- Loker Hydrocarbon Research Institute, Department of Chemistry, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661, United States
| | - John-Paul Jones
- Loker Hydrocarbon Research Institute, Department of Chemistry, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661, United States
| | - Inessa Bychinskaya
- Loker Hydrocarbon Research Institute, Department of Chemistry, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661, United States
| | - Mikhail Zibinsky
- Loker Hydrocarbon Research Institute, Department of Chemistry, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661, United States
| | - Keriann Oertell
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-1661, United States
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-1661, United States
| | - G K Surya Prakash
- Loker Hydrocarbon Research Institute, Department of Chemistry, University of Southern California, 837 Bloom Walk, Los Angeles, CA 90089-1661, United States
| |
Collapse
|
24
|
Seamon KJ, Hansen EC, Kadina AP, Kashemirov BA, McKenna CE, Bumpus NN, Stivers JT. Small molecule inhibition of SAMHD1 dNTPase by tetramer destabilization. J Am Chem Soc 2014; 136:9822-5. [PMID: 24983818 PMCID: PMC4105058 DOI: 10.1021/ja5035717] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
SAMHD1
is a GTP-activated nonspecific dNTP triphosphohydrolase
that depletes dNTP pools in resting CD4+ T cells and macrophages and
effectively restricts infection by HIV-1. We have designed a nonsubstrate
dUTP analogue with a methylene bridge connecting the α phosphate
and 5′ carbon that potently inhibits SAMHD1. Although pppCH2dU shows apparent competitive inhibition, it acts by a surprising
allosteric mechanism that destabilizes active enzyme tetramer.
Collapse
Affiliation(s)
- Kyle J Seamon
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | | | | | | | | | | | | |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
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.
Collapse
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
| | | | | | | | | | | | | | | | | |
Collapse
|
27
|
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.
Collapse
Affiliation(s)
- Stephen A Beaton
- Department of Chemistry, Dalhousie University, 1459 Oxford St., Halifax, Nova Scotia B3H 4R2, Canada
| | | | | | | | | | | | | |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
|
30
|
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]
|
31
|
Baszczyňski O, Janeba Z. Medicinal Chemistry of Fluorinated Cyclic and Acyclic Nucleoside Phosphonates. Med Res Rev 2013; 33:1304-44. [DOI: 10.1002/med.21296] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ondřej Baszczyňski
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Zlatko Janeba
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i. Flemingovo nám. 2 16610 Prague 6 Czech Republic
| |
Collapse
|
32
|
Guzyr OI, Zasukha SV, Vlasenko YG, Chernega AN, Rozhenko AB, Shermolovich YG. Simple Route to Adducts of (Amino)(aryl)carbene with Phosphorus Pentafluoride. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300563] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
33
|
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.
Collapse
Affiliation(s)
- Keriann Oertell
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
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]
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
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.
Collapse
Affiliation(s)
- Brian T Chamberlain
- Departments of Chemistry and Biology, University of Southern California, Los Angeles, CA 90089, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
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.
Collapse
Affiliation(s)
- Claudio Dalvit
- Department of Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, 2000 Neuchâtel, Swizerland.
| | | |
Collapse
|
38
|
Paul BK, Guchhait N. Exploring the strength, mode, dynamics, and kinetics of binding interaction of a cationic biological photosensitizer with DNA: implication on dissociation of the drug-DNA complex via detergent sequestration. J Phys Chem B 2011; 115:11938-49. [PMID: 21899350 DOI: 10.1021/jp206589e] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The present study aims at exploring a detailed characterization of the binding interaction of a promising cancer cell photosensitizer, harmane (HM), with DNA extracted from herring sperm. The polarity-sensitive prototropic transformation of HM, a naturally occurring, fluorescent, drug-binding alkaloid, β-carboline, is remarkably modified upon interaction with DNA and is manifested through significant modulations on the absorption and emission profiles of HM. From the series of studies undertaken in the present program, for example, absorption; steady-state emission; the effect of chaotrope (urea); iodide ion-induced steady-state fluorescence quenching; circular dichroism (CD); and helix melting from absorption spectroscopy; the mode of binding of HM into the DNA helix has been substantiated to be principally intercalative. Concomitantly, a discernible dependence of the photophysics of the DNA-bound drug on the medium ionic strength indicates that electrostatic attraction should not be ignored in the interaction. Efforts have also been delivered to delineate the dynamical aspects of the interaction, such as modulation in time-resolved fluorescence decay and rotational relaxation dynamics of the drug within the DNA environment. In view of the prospective biological applications of HM, the issue of facile dissociation of intercalated HM from the DNA helix also comprises a crucial prerequisite for the functioning as an effective therapeutic agent. In this context, our results imply that the concept of detergent-sequestered dissociation of the drug from the drug-DNA complex can be a prospective strategy through an appropriate choice of the detergent molecule. The utility of the present work resides in exploring the potential applicability of the fluorescence property of HM for studying its interactions with a relevant biological target, for example, DNA. In addition, the methods and techniques used in the present work can also be exploited to study the interaction of HM with other biological, biomimicking assemblies and drug delivery vehicles, and so forth.
Collapse
Affiliation(s)
- Bijan Kumar Paul
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Calcutta-700009, India
| | | |
Collapse
|
39
|
Paul BK, Guchhait N. Modulation of Prototropic Activity and Rotational Relaxation Dynamics of a Cationic Biological Photosensitizer within the Motionally Constrained Bio-environment of a Protein. J Phys Chem B 2011; 115:10322-34. [DOI: 10.1021/jp2015275] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bijan Kumar Paul
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Calcutta-700009, India
| | - Nikhil Guchhait
- Department of Chemistry, University of Calcutta, 92 A. P. C. Road, Calcutta-700009, India
| |
Collapse
|
40
|
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).
Collapse
Affiliation(s)
- Brian T Chamberlain
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0744, USA
| | | | | | | |
Collapse
|
41
|
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.
Collapse
Affiliation(s)
- Claudio Dalvit
- Italian Institute of Technology, Drug Discovery and Development Department, Genova, Italy.
| | | |
Collapse
|
42
|
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
| |
Collapse
|
43
|
Beier P, Opekar S, Zibinsky M, Bychinskaya I, Prakash GKS. A new route to α-alkyl-α-fluoromethylenebisphosphonates. Org Biomol Chem 2011; 9:4035-8. [DOI: 10.1039/c1ob05095h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
44
|
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.
Collapse
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
| |
Collapse
|
45
|
Batra VK, Pedersen LC, Beard WA, Wilson SH, Kashemirov BA, Upton TG, Goodman MF, McKenna CE. Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. J Am Chem Soc 2010; 132:7617-25. [PMID: 20465217 PMCID: PMC2891752 DOI: 10.1021/ja909370k] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta,gamma-fluoromethylene analogues of nucleotides are considered to be useful mimics of the natural substrates, but direct structural evidence defining their active site interactions has not been available, including the influence of the new chiral center introduced at the CHF carbon, as in beta,gamma-fluoromethylene-dGTP, which forms an active site complex with DNA polymerase beta, a repair enzyme that plays an important role in base excision repair (BER) and oncogenesis. We report X-ray crystallographic results for a series of beta,gamma-CXY dGTP analogues, where X,Y = H, F, Cl, Br, and/or CH(3). For all three R/S monofluorinated analogues examined (CHF, 3/4; CCH(3)F, 13/14; CClF 15/16), a single CXF-diastereomer (3, 13, 16) is observed in the active site complex, with the CXF fluorine atom at a approximately 3 A (bonding) distance to a guanidinium N of Arg183. In contrast, for the CHCl, CHBr, and CHCH(3) analogues, both diasteromers (6/7, 8/9, 10/11) populate the dGTP site in the enzyme complex about equally. The structures of the bound dichloro (5) and dimethyl (12) analogue complexes indicate little to no steric effect on the placement of the bound nucleotide backbone. The results suggest that introduction of a single fluorine atom at the beta,gamma-bridging carbon atom of these dNTP analogues enables a new, stereospecific interaction within the preorganized active site complex that is unique to fluorine. The results also provide the first diverse structural data set permitting an assessment of how closely this class of dNTP analogues mimics the conformation of the parent nucleotide within the active site complex.
Collapse
Affiliation(s)
- Vinod K. Batra
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - William A. Beard
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - Samuel H. Wilson
- Laboratory of Structural Biology, NIEHS, National Institutes of
Health DHHS, Research Triangle Park, North Carolina 27709
| | - Boris A. Kashemirov
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| | - Thomas G. Upton
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| | - Myron F. Goodman
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| | - Charles E. McKenna
- Departments of Chemistry and Biology, University of Southern
California, Los Angeles, California 90089
| |
Collapse
|
46
|
Cavanaugh NA, Beard WA, Wilson SH. DNA polymerase beta ribonucleotide discrimination: insertion, misinsertion, extension, and coding. J Biol Chem 2010; 285:24457-65. [PMID: 20519499 DOI: 10.1074/jbc.m110.132407] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA polymerases must select nucleotides that preserve Watson-Crick base pairing rules and choose substrates with the correct (deoxyribose) sugar. Sugar discrimination represents a great challenge because ribonucleotide triphosphates are present at much higher cellular concentrations than their deoxy-counterparts. Although DNA polymerases discriminate against ribonucleotides, many therapeutic nucleotide analogs that target polymerases have sugar modifications, and their efficacy depends on their ability to be incorporated into DNA. Here, we investigate the ability of DNA polymerase beta to utilize nucleotides with modified sugars. DNA polymerase beta readily inserts dideoxynucleoside triphosphates but inserts ribonucleotides nearly 4 orders of magnitude less efficiently than natural deoxynucleotides. The efficiency of ribonucleotide insertion is similar to that reported for other DNA polymerases. The poor polymerase-dependent insertion represents a key step in discriminating against ribonucleotides because, once inserted, a ribonucleotide is easily extended. Likewise, a templating ribonucleotide has little effect on insertion efficiency or fidelity. In contrast to insertion and extension of a ribonucleotide, the chemotherapeutic drug arabinofuranosylcytosine triphosphate is efficiently inserted but poorly extended. These results suggest that the sugar pucker at the primer terminus plays a crucial role in DNA synthesis; a 3'-endo sugar pucker facilitates nucleotide insertion, whereas a 2'-endo conformation inhibits insertion.
Collapse
Affiliation(s)
- Nisha A Cavanaugh
- Laboratory of Structural Biology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA
| | | | | |
Collapse
|
47
|
McKenna CE, Kashemirov BA, Peterson LW, Goodman MF. Modifications to the dNTP triphosphate moiety: from mechanistic probes for DNA polymerases to antiviral and anti-cancer drug design. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:1223-30. [PMID: 20079885 DOI: 10.1016/j.bbapap.2010.01.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 12/17/2009] [Accepted: 01/04/2010] [Indexed: 11/26/2022]
Abstract
Abnormal replication of DNA is associated with many important human diseases, most notably viral infections and neoplasms. Existing approaches to chemotherapeutics for diseases associated with dysfunctional DNA replication classically involve nucleoside analogues that inhibit polymerase activity due to modification in the nucleobase and/or ribose moieties. These compounds must undergo multiple phosphorylation steps in vivo, converting them into triphosphosphates, in order to inhibit their targeted DNA polymerase. Nucleotide monophosphonates enable bypassing the initial phosphorylation step at the cost of decreased bioavailability. Relatively little attention has been paid to higher nucleotides (corresponding to the natural di- and triphosphate DNA polymerase substrates) as drug platforms due to their expected poor deliverability. However, a better understanding of DNA polymerase mechanism and fidelity dependence on the triphosphate moiety is beginning to emerge, aided by systematic incorporation into this group of substituted methylenebisphosphonate probes. Meanwhile, other bridging, as well as non-bridging, modifications have revealed intriguing possibilities for new drug design. We briefly survey some of this recent work, and argue that the potential of nucleotide-based drugs, and intriguing preliminary progress in this area, warrant acceptance of the challenges that they present with respect to bioavailability and metabolic stability.
Collapse
Affiliation(s)
- Charles E McKenna
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.
| | | | | | | |
Collapse
|
48
|
Gaidamauskas E, Parker H, Kashemirov BA, Holder AA, Saejueng K, McKenna CE, Crans DC. Complexation of bisphosphonates with ytterbium(III): application of phosphate and ATP detection assay based on Yb(3+)-pyrocatechol violet. J Inorg Biochem 2009; 103:1652-7. [PMID: 19850352 DOI: 10.1016/j.jinorgbio.2009.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 08/02/2009] [Accepted: 09/14/2009] [Indexed: 10/20/2022]
Abstract
The coordination chemistry of bisphosphonates with Yb(3+) was investigated to evaluate the potential of the UV-vis based detection method using the Yb(3+)-pyrocatechol complexation reaction as a sensor for bisphosphonates. The complexation chemistry of Yb(3+) with phosphate and ATP analogs was previously described (E. Gaidamauskas, K. Saejueng, A.A. Holder, S. Bharuah, B.A. Kashemirov, D.C. Crans, C.E. McKenna, J. Biol. Inorg. Chem. 13 (2008) 1291-1299), and we here studied the complexation chemistry of bisphosphonates in this system. The spectrophotometric assay yields direct evidence for formation of a 4:3 metal to ligand complex at neutral pH. Direct evidence for Yb(3+):methylenebis(phosphonate) complexes with 1:1 and 1:2 stoichiometry was also obtained by potentiometry at acidic and basic pH. Direct evidence for complex formation was obtained using (1)H NMR spectroscopy although the stoichiometry was not accessed at neutral pH. Our results suggest that the spectroscopic observation of the YbPV complex can be used to conveniently measure concentrations of bisphosphonates down to 2-3 microM.
Collapse
Affiliation(s)
- Ernestas Gaidamauskas
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523-1872, United States
| | | | | | | | | | | | | |
Collapse
|
49
|
Kamerlin SCL, McKenna CE, Goodman MF, Goondman MF, Warshel A. A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases. Biochemistry 2009; 48:5963-71. [PMID: 19391628 DOI: 10.1021/bi900140c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA polymerases make up a family of enzymes responsible for regulating DNA replication and repair, which in turn maintains the integrity of the genome. However, despite intensive kinetic, crystallographic, and computational studies, elucidation of the detailed enzymatic mechanism still presents a significant challenge. We recently developed an alternative strategy for exploring the fidelity and mechanism of DNA polymerases, by probing leaving group effects on nucleotidyl transfer using a series of dGTP bisphosphonate analogues in which the beta,gamma-bridging oxygen was replaced by a series of substituted methylene groups (X = CYZ, where Y and Z = H, halogen, or another substituent). Pre-steady state kinetic measurements of DNA polymerase-catalyzed incorporation of correctly base paired (R) and mispaired (W) analogues demonstrated a strong linear free energy relationship (LFER) between the polymerase rate constant (k(pol)) and the highest pK(a) of the free bisphosphonic acid corresponding to the leaving group. However, unexpectedly, the data segregated into two distinctly different linear correlations depending on the nature of the substituent. The discrepancy between the two lines was considerably greater when the dGTP analogue formed an incorrect (G.T) rather than a correct (G.C) base pair, although the reason for this phenomenon remains unexplained. Here, we have evaluated the complete free energy surfaces for bisphosphonate hydrolysis in aqueous solution and evaluated the corresponding LFER. Our study, which employs several alternative solvation models, finds a split of the calculated LFER for the mono- and dihalogen compounds into two parallel lines, reflecting their behavior in the polymerase-catalyzed condensation reaction. We suggest that the division into two linear subsets may be a generalized solvation phenomenon involving the overall electrostatic interaction between the substrates and their surroundings and would also be observed in polar solvents in the absence of the enzyme, if the reaction in solvent is in fact identical to that of the enzyme. However, the amplified differences between the LFER lines for the incorporation of matched and mismatched deoxynucleotides probably reflects the differences in the electrostatic interaction between the TS charges in the polymerase active site. An understanding of the mechanism of this reaction in solution could thereby provide a steppingstone for understanding the factors governing the fidelity of DNA polymerases.
Collapse
Affiliation(s)
- Shina C L Kamerlin
- Department of Chemistry, University of Southern California, 3620 McClintock Avenue, Los Angeles, California 90089, USA.
| | | | | | | | | |
Collapse
|
50
|
Liang F, Jain N, Hutchens T, Shock DD, Beard WA, Wilson SH, Chiarelli MP, Cho BP. Alpha,beta-methylene-2'-deoxynucleoside 5'-triphosphates as noncleavable substrates for DNA polymerases: isolation, characterization, and stability studies of novel 2'-deoxycyclonucleosides, 3,5'-cyclo-dG, and 2,5'-cyclo-dT. J Med Chem 2008; 51:6460-70. [PMID: 18811136 DOI: 10.1021/jm800692a] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report synthesis and characterization of a complete set of alpha,beta-methylene-2'-dNTPs (alpha,beta-m-dNTP; N = A, C, T, G, 12-15) in which the alpha,beta-oxygen linkage of natural dNTP was replaced by a methylene group. These nucleotides were designed to be noncleavable substrates for DNA polymerases. Synthesis entails preparation of 2'-deoxynucleoside 5'-diphosphate precursors, followed by an enzymatic gamma-phosphorylation. All four synthesized alpha,beta-m-dNTPs were found to be potent inhibitors of polymerase beta, with K i values ranging 1-5 microM. During preparation of the dG and dT derivatives of alpha,beta-methylene diphosphate, we also isolated significant amounts of 3,5'-cyclo-dG (16) and 2,5'-cyclo-dT (17), respectively. These novel 2'-deoxycyclonucleosides were formed via a base-catalyzed intramolecular cyclization (N3 --> C5' and O2 --> C5', respectively). In acidic solution, both 16 and 17 underwent glycolysis, followed by complete depurination. When exposed to alkaline conditions, 16 underwent an oxidative deamination to produce 3,5'- cyclo-2'-deoxyxanthosine (19), whereas 17 was hydrolyzed exclusively to dT.
Collapse
Affiliation(s)
- Fengting Liang
- Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, 41 Lower College Road, Kingston, Rhode Island 02881, USA
| | | | | | | | | | | | | | | |
Collapse
|