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Balakrishnan A, Price E, Luu C, Shaul J, Wartchow C, Cantwell J, Vo T, DiDonato M, Spraggon G, Hekmat-Nejad M. Biochemical Characterization of Respiratory Syncytial Virus RNA-Dependent RNA Polymerase Complex. ACS Infect Dis 2020; 6:2800-2811. [PMID: 32886480 DOI: 10.1021/acsinfecdis.0c00554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
RNA-dependent RNA polymerases (RdRPs) from nonsegmented negative strand (NNS) RNA viruses perform both mRNA transcription and genome replication, and these activities are regulated by their interactions with RNA and other accessory proteins within the ribonucleoprotein (RNP) complex. Detailed biochemical characterization of these enzymatic activities and their regulation is essential for understanding the life cycles of many pathogenic RNA viruses and for antiviral drug discovery. We developed biochemical and biophysical kinetic methods to study the RNA synthesis and RNA binding activities of respiratory syncytial virus (RSV) L/P RdRP. We determined that the intact L protein is essential for RdRP activity, and in truncated L protein constructs, RdRP activity is abrogated due to their deficiency in RNA template binding. These results are in agreement with the observation of an RNA template-binding tunnel at the interface of RdRP and capping domains in RSV and vesicular stomatitis virus (VSV) L protein cryo-EM structures. We also describe nonradiometric assays for measuring RNA binding and RNA polymerization activity of RSV RdRP, which are amenable to compound screening and profiling.
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Affiliation(s)
- Anand Balakrishnan
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Edmund Price
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Catherine Luu
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Jacob Shaul
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Charles Wartchow
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - John Cantwell
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
| | - Todd Vo
- Structural Biology and Protein Sciences, Genomics Institute of the Novartis Research Foundation, La Jolla, California 92121, United States
| | - Michael DiDonato
- Structural Biology and Protein Sciences, Genomics Institute of the Novartis Research Foundation, La Jolla, California 92121, United States
| | - Glen Spraggon
- Structural Biology and Protein Sciences, Genomics Institute of the Novartis Research Foundation, La Jolla, California 92121, United States
| | - Mohammad Hekmat-Nejad
- Infectious Diseases, Novartis Institutes for Biomedical Research, Emeryville, California 94608, United States
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2
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Ludeke B, Fearns R. The respiratory syncytial virus polymerase can perform RNA synthesis with modified primers and nucleotide analogs. Virology 2019; 540:66-74. [PMID: 31739186 DOI: 10.1016/j.virol.2019.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/03/2019] [Accepted: 11/03/2019] [Indexed: 12/29/2022]
Abstract
Respiratory syncytial virus (RSV) is significant for public health, capable of causing respiratory tract disease in infants, the elderly and the immunocompromised. The RSV polymerase is an attractive target for antiviral drug development, but as yet, there is no high throughput assay for analyzing RSV polymerase activity, specifically. In this study, using a primer elongation assay as a basis, we analyzed the tolerance of the RSV polymerase for modifications at the 5' end of the primer, and nucleotide analogs. The RSV polymerase was found to accept primers containing 5' biotin or digoxygenin modifications, and nucleotide analogs that are reactive or fluorescent, including 5-ethynyl UTP, 8-azido ATP, 2-amino PTP, and thieno-GTP. These findings provide a menu of options for developing non-isotopic high throughput assays for RSV polymerase RNA synthesis activity, and yield insight regarding the molecular biology of the polymerase complex.
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Affiliation(s)
- Barbara Ludeke
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Rachel Fearns
- Department of Microbiology, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
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Nasiri AH, Nasiri HR. Polymerase assays for lead discovery: An overall review of methodologies and approaches. Anal Biochem 2018; 563:40-50. [PMID: 30291837 DOI: 10.1016/j.ab.2018.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/26/2018] [Accepted: 09/30/2018] [Indexed: 12/18/2022]
Abstract
Polymerases represent an attractive molecular target for antibacterial drug development, antiviral intervention and cancer therapy. Over the past decade, academic groups and scientists from pharmaceutical industry have developed a large plethora of different functional assays to monitor the enzymatic reaction catalyzed by polymerases. These assays were used to enable high-throughput screening (HTS) for lead discovery purposes, as well as hit-to-lead (H2L) drug profiling activities. In both cases the choice of the assay technology is critical and to the best of our knowledge, there is no review available to help scientists to choose the most suitable assay. This review summarizes the most common functional assays developed to monitor the enzymatic activity of polymerases and discusses the advantages and disadvantages of each assay. Assays are presented and evaluated in term of cost, ease of use, high-throughput screening compatibility and liability towards delivering false positives and false negatives.
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Affiliation(s)
- Amir H Nasiri
- Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, D-60438, Frankfurt am Main, Germany; CARD Center of Aptamer Research and Development, Gerhard-Domagk-Str.1, 53121, Bonn, Germany
| | - Hamid R Nasiri
- Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, D-60438, Frankfurt am Main, Germany; Sysmex-inostics GmbH, Falkenried 88, CiM centrum für innovative medizin Haus A, 20251, Hamburg, Germany.
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Abstract
The persistence of West Nile virus (WNV) infections throughout the USA since its inception in 1999 and its continuous spread throughout the globe calls for an urgent need of effective treatments and prevention measures. Although the licensing of several WNV vaccines for veterinary use provides a proof of concept, similar efforts on the development of an effective vaccine for humans remain still unsuccessful. Increased understanding of biology and pathogenesis of WNV together with recent technological advancements have raised hope that an effective WNV vaccine may be available in the near future. In addition, rapid progress in the structural and functional characterization of WNV and other flaviviral proteins have provided a solid base for the design and development of several classes of inhibitors as potential WNV therapeutics. Moreover, the therapeutic monoclonal antibodies demonstrate an excellent efficacy against WNV in animal models and represent a promising class of WNV therapeutics. However, there are some challenges as to the design and development of a safe and efficient WNV vaccine or therapeutic. In this chapter, we discuss the current approaches, progress, and challenges toward the development of WNV vaccines, therapeutic antibodies, and antiviral drugs.
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SYBR Green II Dye-Based Real-Time Assay for Measuring Inhibitor Activity Against HIV-1 Reverse Transcriptase. Mol Biotechnol 2017; 58:619-625. [PMID: 27376894 DOI: 10.1007/s12033-016-9961-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
There are arrays of in vitro assays to quantify the activity of HIV-1 reverse transcriptase (HIV-1 RT). These assays utilize either chemically customized/labelled nucleotides, or TaqMan probes, or radiolabeled nucleotides/primers. Although several real-time PCR assays exist commercially for measuring the RT activity, which are usually used for quantifying the viral titres, these assays are not optimized for measuring the inhibitory concentrations (IC50) of HIV-1 RT inhibitors. Moreover, a recently established inorganic pyrophosphate-coupled enzyme assay cannot be employed for studying nonphosphorylated nucleoside reverse transcriptase inhibitors (NRTIs). In the present study, we have developed a novel one-step assay with native nucleotide substrates and SYBR Green II dye to determine IC50 values of triphosphorylated NRTIs against HIV-1 RT. Using exact batches of wild-type and mutant RT, and triphosphorylated NRTIs, we showed that our method gave IC50 values for inhibitors similar to that of an earlier published colorimetric assay with BrdUTP substrate (CABS). Our assay should be suitable for high-throughput screening of antiretroviral drugs and could also be suitable for studying drug resistance profiles. Additionally, we also used our assay to study inhibition by AZT in its nonphosphorylated form by supplementing the reaction mixture with necessary kinases and ATP.
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Analysis of Ribonucleotide 5'-Triphosphate Analogs as Potential Inhibitors of Zika Virus RNA-Dependent RNA Polymerase by Using Nonradioactive Polymerase Assays. Antimicrob Agents Chemother 2017; 61:AAC.01967-16. [PMID: 27993851 DOI: 10.1128/aac.01967-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 12/13/2016] [Indexed: 01/20/2023] Open
Abstract
Zika virus (ZIKV) is an emerging human pathogen that is spreading rapidly through the Americas and has been linked to the development of microcephaly and to a dramatically increased number of Guillain-Barré syndrome cases. Currently, no vaccine or therapeutic options for the prevention or treatment of ZIKV infections exist. In the study described in this report, we expressed, purified, and characterized full-length nonstructural protein 5 (NS5) and the NS5 polymerase domain (NS5pol) of ZIKV RNA-dependent RNA polymerase. Using purified NS5, we developed an in vitro nonradioactive primer extension assay employing a fluorescently labeled primer-template pair. Both purified NS5 and NS5pol can carry out in vitro RNA-dependent RNA synthesis in this assay. Our results show that Mn2+ is required for enzymatic activity, while Mg2+ is not. We found that ZIKV NS5 can utilize single-stranded DNA but not double-stranded DNA as a template or a primer to synthesize RNA. The assay was used to compare the efficiency of incorporation of analog 5'-triphosphates by the ZIKV polymerase and to calculate their discrimination versus that of natural ribonucleotide triphosphates (rNTPs). The 50% inhibitory concentrations for analog rNTPs were determined in an alternative nonradioactive coupled-enzyme assay. We determined that, in general, 2'-C-methyl- and 2'-C-ethynyl-substituted analog 5'-triphosphates were efficiently incorporated by the ZIKV polymerase and were also efficient chain terminators. Derivatives of these molecules may serve as potential antiviral compounds to be developed to combat ZIKV infection. This report provides the first characterization of ZIKV polymerase and demonstrates the utility of in vitro polymerase assays in the identification of potential ZIKV inhibitors.
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Kocabas F, Turan RD, Aslan GS. Fluorometric RdRp assay with self-priming RNA. Virus Genes 2015; 50:498-504. [PMID: 25749997 DOI: 10.1007/s11262-015-1187-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 02/27/2015] [Indexed: 10/23/2022]
Abstract
There is an outmost need for the identification of specific antiviral compounds. Current antivirals lack specificity, making them susceptible to off-target effects, and highlighting importance of development of assays to discover antivirals targeting viral specific proteins. Previous studies for identification of inhibitors of RNA-dependent RNA polymerase (RdRp) mostly relied on radioactive methods. This study describes a fluorometric approach to assess in vitro activity of viral RdRp for drug screening. Using readily available DNA- and RNA-specific fluorophores, we determined an optimum fluorometric approach that could be used in antiviral discovery specifically for RNA viruses by targeting RdRp. Here, we show that double-stranded RNA could be successfully distinguished from single-stranded RNA. In addition, we provide a strategy based on self-priming RNA to assess RdRp activity.
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Affiliation(s)
- Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, 34755, Istanbul, Turkey,
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Holler TP, Parkinson T, Pryde DC. Targeting the non-structural proteins of hepatitis C virus: beyond hepatitis C virus protease and polymerase. Expert Opin Drug Discov 2013; 4:293-314. [PMID: 23489127 DOI: 10.1517/17460440902762802] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Chronic hepatitis C virus (HCV) infection is a main cause of cirrhosis of the liver and hepatocellular carcinoma. The standard of care is a combination of pegylated interferon with ribavirin, a regimen that has undesirable side effects and is frequently ineffective. Compounds targeting HCV protease and polymerase are in late-stage clinical trials and have been extensively reviewed elsewhere. OBJECTIVE To review and evaluate the progress towards finding novel HCV antivirals targeting HCV proteins beyond the already precedented NS3 protease and NS5B polymerase. METHODS Searches of CAplus and Medline databases were combined with information from key conferences. This review focuses on NS2/3 serine protease, NS3 helicase activity and the non-structural proteins 4A, 4B and 5A. CONCLUSIONS Use of the replicon model of HCV replication and biochemical assays of specific targets has allowed screening of vast libraries of compounds, but resulted in clinical candidates from only NS4A and NS5A. The field is hindered by a lack of good chemical matter that inhibits the remaining enzymes from HCV, and a lack of understanding of the functions of non-structural proteins 4A, 4B and 5A in the replication of HCV.
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Affiliation(s)
- Tod P Holler
- Associate Research Fellow Pfizer Global Research and Development, Antiviral Biology, Ramsgate Road, Sandwich, Kent CT13 9NJ, UK +44 130 464 6387 ; +44 130 465 1819 ;
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An efficient colorimetric assay for RNA synthesis by viral RNA-dependent RNA polymerases, using thermostable pyrophosphatase. Anal Biochem 2013; 434:284-6. [DOI: 10.1016/j.ab.2012.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 11/26/2012] [Accepted: 11/27/2012] [Indexed: 11/19/2022]
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Hepatitis C virus replication is modulated by the interaction of nonstructural protein NS5B and fatty acid synthase. J Virol 2013; 87:4994-5004. [PMID: 23427160 DOI: 10.1128/jvi.02526-12] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Hepatitis C virus (HCV) nonstructural protein 5B (NS5B) is an RNA-dependent RNA polymerase (RdRp) that acts as a key player in the HCV replication complex. Understanding the interplay between the viral and cellular components of the HCV replication complex could provide new insight for prevention of the progression of HCV-associated hepatocellular carcinoma (HCC). In this study, the NS5B protein was used as the bait in a pulldown assay to screen for NS5B-interacting proteins that are present in Huh7 hepatoma cell lysates. After mass spectrophotometric analysis, fatty acid synthase (FASN) was found to interact with NS5B. Coimmunoprecipitation and double staining assays further confirmed the direct binding between NS5B and FASN. The domain of NS5B that interacts with FASN was also determined. Moreover, FASN was associated with detergent-resistant lipid rafts and colocalized with NS5B in active HCV replication complexes. In addition, overexpression of FASN enhanced HCV expression in Huh7/Rep-Feo cells, while transfection of FASN small interfering RNA (siRNA) or treatment with FASN-specific inhibitors decreased HCV replication and viral production. Notably, FASN directly increased HCV NS5B RdRp activity in vitro. These results together indicate that FASN interacts with NS5B and modulates HCV replication through a direct increase of NS5B RdRp activity. FASN may thereby serve as a target for the treatment of HCV infection and the prevention of HCV-associated HCC progression.
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Wiesler SC, Werner F, Weinzierl ROJ. Promoter independent abortive transcription assays unravel functional interactions between TFIIB and RNA polymerase. Methods Mol Biol 2013; 977:217-227. [PMID: 23436365 DOI: 10.1007/978-1-62703-284-1_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
TFIIB-like general transcription factors are required for transcription initiation by all eukaryotic and archaeal RNA polymerases (RNAPs). TFIIB facilitates both recruitment and post-recruitment steps of initiation; in particular, TFIIB stimulates abortive initiation. X-ray crystallography of TFIIB-RNAP II complexes shows that the TFIIB linker region penetrates the RNAP active center, yet the impact of this arrangement on RNAP activity and underlying mechanisms remains elusive. Promoter-independent abortive initiation assays exploit the intrinsic ability of RNAP enzymes to initiate transcription from nicked DNA templates and record the formation of the first phosphodiester bonds. These assays can be used to measure the effect of transcription factors such as TFIIB and RNAP mutations on abortive transcription.
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Affiliation(s)
- Simone C Wiesler
- Department of Life Sciences, Imperial College London, London, UK
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12
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Deore RR, Chen GS, Chang PT, Chern TR, Lai SY, Chuang MH, Lin JH, Kung FL, Chen CS, Chiou CT, Chern JW. Discovery of N-Arylalkyl-3-hydroxy-4-oxo-3,4-dihydroquinazolin-2-carboxamide Derivatives as HCV NS5B Polymerase Inhibitors. ChemMedChem 2012; 7:850-60. [DOI: 10.1002/cmdc.201200058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Indexed: 11/06/2022]
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13
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Cauchon E, Falgueyret JP, Auger A, Melnyk RA. A high-throughput continuous assay for screening and characterization of inhibitors of HIV reverse-transcriptase DNA polymerase activity. ACTA ACUST UNITED AC 2011; 16:518-24. [PMID: 21474837 DOI: 10.1177/1087057111402201] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The authors have devised a continuous fluorescence-based assay to measure HIV reverse transcriptase (RT) polymerase activity for both high-throughput screening (HTS) and mechanistic characterization of inhibitors. The designed substrate is composed of a recessed DNA primer annealed to a DNA template that is labeled at the 5'-terminus with a donor fluorophore (AlexaFluor 488). RT-catalyzed incorporation of an acceptor-labeled deoxyuridine (dUTP-AlexaFluor 555) at the 3'-terminus of the fully extended DNA primer juxtaposes donor and acceptor fluorophores, resulting in robust fluorescence resonance energy transfer that can be monitored kinetically in real time. The assay is sensitive, permitting the use of low enzyme concentrations (<0.5 nM), and can be miniaturized for use in 384-well HTS mode. The authors further show that this assay is capable of evaluating inhibitor mechanism of action by confirming the binding mechanism of a set of nonnucleoside RT inhibitors. Given the versatility and the lack of requirement for costly platforms or radioactivity, this assay may serve to accelerate and streamline the discovery and characterization process for future antiviral agents.
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Affiliation(s)
- Elizabeth Cauchon
- Department of In Vitro Sciences, Merck Frosst Centre for Therapeutic Research, 16711 Trans Canada Highway, Kirkland, Quebec, Canada
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14
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Durk RC, Singh K, Cornelison CA, Rai DK, Matzek KB, Leslie MD, Schafer E, Marchand B, Adedeji A, Michailidis E, Dorst CA, Moran J, Pautler C, Rodriguez LL, McIntosh MA, Rieder E, Sarafianos SG. Inhibitors of foot and mouth disease virus targeting a novel pocket of the RNA-dependent RNA polymerase. PLoS One 2010; 5:e15049. [PMID: 21203539 PMCID: PMC3006429 DOI: 10.1371/journal.pone.0015049] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 10/25/2010] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Foot-and-Mouth Disease Virus (FMDV) is a picornavirus that infects cloven-hoofed animals and leads to severe losses in livestock production. In the case of an FMD outbreak, emergency vaccination requires at least 7 days to trigger an effective immune response. There are currently no approved inhibitors for the treatment or prevention of FMDV infections. METHODOLOGY/PRINCIPAL FINDINGS Using a luciferase-based assay we screened a library of compounds and identified seven novel inhibitors of 3Dpol, the RNA-dependent RNA polymerase of FMDV. The compounds inhibited specifically 3Dpol (IC(50)s from 2-17 µM) and not other viral or bacterial polymerases. Enzyme kinetic studies on the inhibition mechanism by compounds 5D9 and 7F8 showed that they are non-competitive inhibitors with respect to NTP and nucleic acid substrates. Molecular modeling and docking studies into the 3Dpol structure revealed an inhibitor binding pocket proximal to, but distinct from the 3Dpol catalytic site. Residues surrounding this pocket are conserved among all 60 FMDV subtypes. Site directed mutagenesis of two residues located at either side of the pocket caused distinct resistance to the compounds, demonstrating that they indeed bind at this site. Several compounds inhibited viral replication with 5D9 suppressing virus production in FMDV-infected cells with EC(50) = 12 µM and EC(90) = 20 µM). SIGNIFICANCE We identified several non-competitive inhibitors of FMDV 3Dpol that target a novel binding pocket, which can be used for future structure-based drug design studies. Such studies can lead to the discovery of even more potent antivirals that could provide alternative or supplementary options to contain future outbreaks of FMD.
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Affiliation(s)
- Ryan C. Durk
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Kamalendra Singh
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Ceili A. Cornelison
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Devendra K. Rai
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Kayla B. Matzek
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Maxwell D. Leslie
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Elizabeth Schafer
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, Greenport, New York, United States of America
| | - Bruno Marchand
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Adeyemi Adedeji
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Eleftherios Michailidis
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Christopher A. Dorst
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Jennifer Moran
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Christie Pautler
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Luis L. Rodriguez
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, Greenport, New York, United States of America
| | - Mark A. McIntosh
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
| | - Elizabeth Rieder
- Foreign Animal Disease Research Unit, United States Department of Agriculture, Agricultural Research Service, Plum Island Animal Disease Center, Greenport, New York, United States of America
| | - Stefan G. Sarafianos
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, United States of America
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Real-time bioluminescent assay for inhibitors of RNA and DNA polymerases and other ATP-dependent enzymes. Anal Biochem 2010; 408:226-34. [PMID: 20727342 DOI: 10.1016/j.ab.2010.08.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 08/04/2010] [Accepted: 08/12/2010] [Indexed: 11/20/2022]
Abstract
Viral polymerases are important targets for drug development. However, current methods used to identify and characterize inhibitors of polymerases are time-consuming, use radiolabeled reagents, and are cost-inefficient. Here we present a bioluminescent assay for the identification and characterization of inhibitors of polymerases, as well as other ATP-dependent enzymes, that monitors the decrease of ATP or dATP in real time, allowing detection of enzyme inhibition based on differences in ATP/dATP consumption. The assay works with a variety of RNA and DNA polymerases, using both RNA and DNA templates. The assay measures changes in substrate concentration in real time and provides a faster alternative for kinetic studies of inhibition. Michaelis-Menten plots were obtained from a single reaction, yielding K(m) values that compared well with literature values. The assay could identify the mechanism of inhibition and determine inhibition constants (K(i)) for a weak competitive inhibitor of Klenow fragment and two strong noncompetitive inhibitors of HIV-1 reverse transcriptase with one series of inhibitor concentrations, reducing the total number of experiments that would normally be needed. The assay is also sensitive enough to detect a weak inhibitor with K(i)>100 μM, making it a viable technique for fragment-based drug discovery.
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16
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Zhang C, Wu Y, Sun Y, Hong C, Xiang K, Guo Y, Bartlam M, Lou Z. A novel non-radioactive assay for HIV-RT (RdDp) based on pyrosequencing for high-throughput drug screening. Protein Cell 2010; 1:284-90. [PMID: 21203975 DOI: 10.1007/s13238-010-0031-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 01/15/2010] [Indexed: 11/28/2022] Open
Abstract
Current in vitro assays for the activity of HIV-RT (reverse transcriptase) require radio-labeled or chemically modified nucleotides to detect reaction products. However, these assays are inherently end-point measurements and labor intensive. Here we describe a novel non-radioactive assay based on the principle of pyrosequencing coupled-enzyme system to monitor the activity of HIV-RT by indirectly measuring the release of pyrophosphate (PP(i)), which is generated during nascent strand synthesis. The results show that our assay could monitor HIV-RT activity with high sensitivity and is suitable for rapid high-throughput drug screening targeting anti-HIV therapies due to its high speed and convenience. Moreover, this assay can be used to measure primase activity in an easy and sensitive manner, which suggests that this novel approach could be wildly used to analyze the activity of PP(i)-generated and ATP-free enzyme reactions.
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Affiliation(s)
- Chang Zhang
- Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China
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Efficient Colorimetric Assay of RNA Polymerase Activity Using Inorganic Pyrophosphatase and Ammonium Molybdate. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.10.2485] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Prosdocimo DA, Douglas DC, Romani AM, O'Neill WC, Dubyak GR. Autocrine ATP release coupled to extracellular pyrophosphate accumulation in vascular smooth muscle cells. Am J Physiol Cell Physiol 2009; 296:C828-39. [PMID: 19193865 DOI: 10.1152/ajpcell.00619.2008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Extracellular inorganic pyrophosphate (PP(i)) is a potent suppressor of physiological calcification in bone and pathological calcification in blood vessels. Ectonucleotide pyrophosphatase/phosphodiesterases (eNPPs) generate PP(i) via the hydrolysis of ATP released into extracellular compartments by poorly understood mechanisms. Here we report that cultured vascular smooth muscle cells (VSMC) from rat aorta generate extracellular PP(i) via an autocrine mechanism that involves ATP release tightly coupled to eNPP activity. The nucleotide analog beta,gamma-methylene ATP (MeATP or AMPPCP) was used to selectively suppress ATP metabolism by eNPPs but not the CD39-type ecto-ATPases. In the absence of MeATP, VSMC generated extracellular PP(i) to accumulate >or=600 nM within 2 h while steadily maintaining extracellular ATP at 1 nM. Conversely, the presence of MeATP completely suppressed PP(i) accumulation while increasing ATP accumulation. Probenecid, which inhibits PP(i) efflux dependent on ANK, a putative PP(i) transporter or transport regulator, reduced extracellular PP(i) accumulation by approximately twofold. This indicates that autocrine ATP release coupled to eNPP activity comprises >or=50% of the extracellular PP(i)-generating capacity of VSMC. The accumulation of extracellular PP(i) and ATP was markedly attenuated by reduced temperature but was insensitive to brefeldin A, which suppresses constitutive exocytosis of Golgi-derived secretory vesicles. The magnitude of extracellular PP(i) accumulation in VSMC cultures increased with time postplating, suggesting that ATP release coupled to PP(i) generation is upregulated as cultured VSMC undergo contact-inhibition of proliferation or deposit extracellular matrix.
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Affiliation(s)
- Domenick A Prosdocimo
- Dept. of Physiology, Case Western Reserve Univ. School of Medicine, 2109 Adelbert Rd., Cleveland, OH 44106, USA
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Wang YK, Rigat KL, Roberts SB, Gao M. A homogeneous, solid-phase assay for hepatitis C virus RNA-dependent RNA polymerase. Anal Biochem 2006; 359:106-11. [PMID: 17054898 DOI: 10.1016/j.ab.2006.09.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Revised: 09/14/2006] [Accepted: 09/14/2006] [Indexed: 10/24/2022]
Abstract
Discovery and development of effective antiviral agents to combat hepatitis C virus (HCV) is the focus of intensive research both in academia and in pharmaceutical companies. One of the HCV nonstructural proteins, NS5B (an RNA-dependent RNA polymerase), represents an attractive target in light of the clinical success of human immunodeficiency virus reverse transcriptase inhibitors. To identify and evaluate NS5B inhibitors, we developed a homogeneous, solid-phase, high-throughput biochemical assay for detecting NS5B enzymatic activity. In this assay, a biotinylated oligo(dT(12)) primer was immobilized onto streptavidin-coated scintillation proximity assay (SPA) beads, and after addition of homopolymeric A template, NS5B enzyme, and radiolabeled uridine 5'-triphosphate, the primer-dependent RNA synthesis occurred on beads. Optimization of the on-bead reaction resulted in the use of significantly less RNA template and NS5B enzyme while producing a faster steady state reaction rate compared to the solution-phase or off-bead SPA. The newly developed solid-phase assay is functionally comparable to the solution-phase assay as similar potencies of HCV NS5B inhibitors tested were obtained with the two assays. Furthermore, the solid-phase assay offers the advantage of delaying initiation, mimicking a physical preincubation step required for evaluating time-dependent inhibitors.
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Affiliation(s)
- Ying-Kai Wang
- Department of Virology, Bristol Myers Squibb Co. Pharmaceutical Research Institute, Wallingford, CT 06067, USA.
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