Discovering New Medicines Targeting Helicases: Challenges and Recent Progress

Crute, 2002, Herpes Simplex Virus Helicase-Primase Inhibitors Are Active in Animal Models of Human Disease, Nat. Med., 8, 386, 10.1038/nm0402-386 Kleymann, 2002, New Helicase-Primase Inhibitors as Drug Candidates for the Treatment of Herpes Simplex Disease, Nat. Med., 8, 392, 10.1038/nm0402-392 Wang, 2012, PubChem’s BioAssay Database, Nucleic Acids Res., 40, D400, 10.1093/nar/gkr1132 Delagoutte, 2002, Helicase Mechanisms and the Coupling of Helicases within Macromolecular Machines. Part I: Structures and Properties of Isolated Helicases, Q. Rev. Biophys., 35, 431, 10.1017/S0033583502003852 Delagoutte, 2003, Helicase Mechanisms and the Coupling of Helicases within Macromolecular Machines. Part II: Integration of Helicases into Cellular Processes, Q. Rev. Biophys., 36, 1, 10.1017/S0033583502003864 Pyle, 2008, Translocation and Unwinding Mechanisms of RNA and DNA Helicases, Annu. Rev. Biophys., 37, 317, 10.1146/annurev.biophys.37.032807.125908 Kwong, 2005, Viral and Cellular RNA Helicases as Antiviral Targets, Nat. Rev. Drug Discov., 4, 845, 10.1038/nrd1853 Frick, 2006, Understanding Helicases as a Means of Virus Control, Curr. Pharm. Des., 12, 1315, 10.2174/138161206776361147 Singleton, 2007, Structure and Mechanism of Helicases and Nucleic Acid Translocases, Annu. Rev. Biochem., 76, 23, 10.1146/annurev.biochem.76.052305.115300 Bolton, 2008, PubChem: Integrated Platform of Small Molecules and Biological Activities, Annu. Rep. Comp. Chem., 4, 217 Belon, 2008, Monitoring Helicase Activity with Molecular Beacons, BioTechniques, 45, 433, 10.2144/000112834 Xi, 2007, Helicases as Antiviral and Anticancer Drug Targets, Curr. Med. Chem., 14, 883, 10.2174/092986707780362998 Frick, 2003, Helicases as Antiviral Drug Targets, Drug News Perspect., 16, 355, 10.1358/dnp.2003.16.6.829307 van Brabant, 2000, DNA Helicases, Genomic Instability, and Human Genetic Disease, Annu. Rev. Genomics Hum. Genet., 1, 409, 10.1146/annurev.genom.1.1.409 Gupta, 2008, Helicases as Prospective Targets for Anti-Cancer Therapy, Anticancer Agents Med. Chem., 8, 390, 10.2174/187152008784220339 Aggarwal, 2009, Hitting the Bull’s Eye: Novel Directed Cancer Therapy through Helicase-Targeted Synthetic Lethality, J. Cell. Biochem., 106, 758, 10.1002/jcb.22048 Kleymann, 2003, New Antiviral Drugs That Target Herpesvirus Helicase Primase Enzymes, Herpes, 10, 46 Kleymann, 2004, Helicase Primase: Targeting the Achilles Heel of Herpes Simplex Viruses, Antivir. Chem. Chemother., 15, 135, 10.1177/095632020401500303 Field, 2013, The Helicase-Primase Complex as a Target for Effective Herpesvirus Antivirals, Adv. Exp. Med. Biol., 767, 145, 10.1007/978-1-4614-5037-5_7 Bretner, 2004, Inhibitors of the NTPase/Helicases of Hepatitis C and Related Flaviviridae Viruses, Acta Pol. Pharm., 61, 26 Frick, 2007, The Hepatitis C Virus NS3 Protein: A Model RNA Helicase and Potential Drug Target, Curr. Issues Mol. Biol., 9, 1 Belon, 2009, Helicase Inhibitors as Specifically Targeted Antiviral Therapy for Hepatitis C, Future Virol., 4, 277, 10.2217/fvl.09.7 Belon, 2011, NS3 Helicase Inhibitors, 237 Hanson, 2012, Identification and Analysis of Inhibitors Targeting the Hepatitis C Virus NS3 Helicase, Methods Enzymol., 511, 463, 10.1016/B978-0-12-396546-2.00021-8 Lescar, 2008, Towards the Design of Antiviral Inhibitors against Flaviviruses: The Case for the Multifunctional NS3 Protein from Dengue Virus as a Target, Antiviral Res., 80, 94, 10.1016/j.antiviral.2008.07.001 Chu, 2009, RecQ Helicases: Multifunctional Genome Caretakers, Nat. Rev. Cancer, 9, 644, 10.1038/nrc2682 Suhasini, 2013, DNA Helicases Associated with Genetic Instability, Cancer, and Aging, Adv. Exp. Med. Biol., 767, 123, 10.1007/978-1-4614-5037-5_6 Suhasini, A. N., Brosh, R. M. J. Disease-Causing Missense Mutations in Human DNA Helicase Disorders. Mutat. Res., in press. Larsen, 2013, RecQ Helicases: Conserved Guardians of Genomic Integrity, Adv. Exp. Med. Biol., 767, 161, 10.1007/978-1-4614-5037-5_8 Singleton, 2000, Crystal Structure of T7 Gene 4 Ring Helicase Indicates a Mechanism for Sequential Hydrolysis of Nucleotides, Cell, 101, 589, 10.1016/S0092-8674(00)80871-5 Li, 2003, Structure of the Replicative Helicase of the Oncoprotein SV40 Large Tumour Antigen, Nature, 423, 512, 10.1038/nature01691 Skordalakes, 2006, Structural Insights into RNA-Dependent Ring Closure and ATPase Activation by the Rho Termination Factor, Cell, 127, 553, 10.1016/j.cell.2006.08.051 Eoff, 2006, Intermediates Revealed in the Kinetic Mechanism for DNA Unwinding by a Monomeric Helicase, Nat. Struct. Mol. Biol., 13, 242, 10.1038/nsmb1055 Wong, 1992, DNA-Induced Dimerization of the Escherichia coli rep Helicase: Allosteric Effects of Single-Stranded and Duplex DNA, J. Biol. Chem., 267, 7596, 10.1016/S0021-9258(18)42558-6 Sikora, 2008, Hepatitis C Virus NS3 Helicase Forms Oligomeric Structures That Exhibit Optimal DNA Unwinding Activity In Vitro, J. Biol. Chem., 283, 11516, 10.1074/jbc.M708125200 Singleton, 2004, Crystal Structure of RecBCD Enzyme Reveals a Machine for Processing DNA Breaks, Nature, 432, 187, 10.1038/nature02988 Story, 1992, The Structure of the E. coli recA Protein Monomer and Polymer, Nature, 355, 318, 10.1038/355318a0 Lohman, 2008, Non-hexameric DNA Helicases and Translocases: Mechanisms and Regulation, Nat. Rev. Mol. Cell Biol., 9, 391, 10.1038/nrm2394 Yao, 1997, Structure of the Hepatitis C Virus RNA Helicase Domain, Nat. Struct. Biol., 4, 463, 10.1038/nsb0697-463 Velankar, 1999, Crystal Structures of Complexes of PcrA DNA Helicase with a DNA Substrate Indicate an Inchworm Mechanism, Cell, 97, 75, 10.1016/S0092-8674(00)80716-3 Soultanas, 2000, DNA Helicases: ‘Inching Forward’, Curr. Opin. Struct. Biol., 10, 124, 10.1016/S0959-440X(99)00059-7 Gu, 2010, Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal a Ratchet Translocation Mechanism, Proc. Natl. Acad. Sci. U. S. A., 107, 521, 10.1073/pnas.0913380107 Appleby, 2011, Visualizing ATP-Dependent RNA Translocation by the NS3 Helicase from HCV, J. Mol. Biol., 405, 1139, 10.1016/j.jmb.2010.11.034 Morris, 1999, DNA Helicases Displace Streptavidin from Biotin-Labeled Oligonucleotides, Biochemistry, 38, 5164, 10.1021/bi9822269 Fischer, 2004, Mechanism of ATP-Dependent Translocation of E.coli UvrD Monomers along Single-Stranded DNA, J. Mol. Biol., 344, 1287, 10.1016/j.jmb.2004.10.005 Gorbalenya, 1993, Helicases: Amino Acid Sequence Comparisons and Structure-Function Relationships, Curr. Opin. Struct. Biol., 3, 419, 10.1016/S0959-440X(05)80116-2 Iyer, 2004, Evolutionary History and Higher Order Classification of AAA+ ATPases, J. Struct. Biol., 146, 11, 10.1016/j.jsb.2003.10.010 Gilhooly, 2013, Superfamily 1 Helicases, Front. Biosci., 5, 206, 10.2741/S367 Byrd, 2012, Superfamily 2 helicases, Front. Biosci., 17, 2070, 10.2741/4038 Keum, 2012, Development of Chemical Inhibitors of the SARS Coronavirus: Viral Helicase as a Potential Target, Biochem. Pharmacol., 84, 1351, 10.1016/j.bcp.2012.08.012 Henn, 2012, ATP Utilization and RNA Conformational Rearrangement by DEAD-box Proteins, Annu. Rev. Biophys., 41, 247, 10.1146/annurev-biophys-050511-102243 Bennett, 2004, Structure and Function of RecQ DNA Helicases, Crit. Rev. Biochem. Mol. Biol., 39, 79, 10.1080/10409230490460756 Enemark, 2006, Mechanism of DNA Translocation in a Replicative Hexameric Helicase, Nature, 442, 270, 10.1038/nature04943 White, 2011, Small Molecule Inhibitors of the Human Papillomavirus E1-E2 Interaction, Curr. Top. Microbiol. Immunol., 348, 61 Itsathitphaisarn, 2012, The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation, Cell, 151, 267, 10.1016/j.cell.2012.09.014 Rajendran, 2000, Multiple-Step Kinetic Mechanism of DNA-Independent ATP Binding and Hydrolysis by Escherichia coli Replicative Helicase DnaB Protein: Quantitative Analysis Using the Rapid Quench-Flow Method, J. Mol. Biol., 303, 773, 10.1006/jmbi.2000.4124 Kaper, 2004, Pathogenic Escherichia coli, Nat. Rev. Microbiol., 2, 123, 10.1038/nrmicro818 Bereket, 2012, Update on Bacterial Nosocomial Infections, Eur. Rev. Med. Pharmacol. Sci., 16, 1039 Enright, 2002, The Evolutionary History of Methicillin-Resistant Staphylococcus aureus (MRSA), Proc. Natl. Acad. Sci. U. S. A., 99, 7687, 10.1073/pnas.122108599 Eggleston, 1996, A Helicase Assay Based on the Displacement of Fluorescent, Nucleic Acid–Binding Ligands, Nucleic Acids Res., 24, 1179, 10.1093/nar/24.7.1179 Dillingham, 2003, RecBCD Enzyme Is a Bipolar DNA Helicase, Nature, 423, 893, 10.1038/nature01673 Anderson, 1997, The Translocating RecBCD Enzyme Stimulates Recombination by Directing RecA Protein onto ssDNA in a Chi-Regulated Manner, Cell, 90, 77, 10.1016/S0092-8674(00)80315-3 Court, 2007, The Crystal Structure of Lambda-Gam Protein Suggests a Model for RecBCD Inhibition, J. Mol. Biol., 371, 25, 10.1016/j.jmb.2007.05.037 Cromie, 2009, Phylogenetic Ubiquity and Shuffling of the Bacterial RecBCD and AddAB Recombination Complexes, J. Bacteriol., 191, 5076, 10.1128/JB.00254-09 Cernik, 2008, The Treatment of Herpes Simplex Infections: An Evidence-Based Review, Arch. Intern. Med., 168, 1137, 10.1001/archinte.168.11.1137 Marintcheva, 2001, A Tale of Two HSV-1 Helicases: Roles of Phage and Animal Virus Helicases in DNA Replication and Recombination, Prog. Nucleic Acid Res. Mol. Biol., 70, 77, 10.1016/S0079-6603(01)70014-1 Muylaert, 2011, Replication and Recombination of Herpes Simplex Virus DNA, J. Biol. Chem., 286, 15619, 10.1074/jbc.R111.233981 Hartman, 2008, Update on PML: Lessons from the HIV Uninfected and New Insights in Pathogenesis and Treatment, Curr. HIV/AIDS Rep., 5, 112, 10.1007/s11904-008-0018-0 Fanning, 1992, Structure and Function of Simian Virus 40 Large Tumor Antigen, Annu. Rev. Biochem., 61, 55, 10.1146/annurev.bi.61.070192.000415 zur Hausen, 2002, Papillomaviruses and Cancer: From Basic Studies to Clinical Application, Nat. Rev. Cancer, 2, 342, 10.1038/nrc798 Chène, 2009, NS3 Helicases as Drug Targets, RNA, 2, 2 Wu, 2005, Structure of the Flavivirus Helicase: Implications for Catalytic Activity, Protein Interactions, and Proteolytic Processing, J. Virol., 79, 10268, 10.1128/JVI.79.16.10268-10277.2005 Mastrangelo, 2007, Crystal Structure and Activity of Kunjin Virus NS3 Helicase; Protease and Helicase Domain Assembly in the Full Length NS3 Protein, J. Mol. Biol., 372, 444, 10.1016/j.jmb.2007.06.055 De Colibus, 2007, Purification and Crystallization of Kokobera Virus Helicase, Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 63, 193, 10.1107/S1744309107005283 Tomei, 1993, NS3 is a Serine Protease Required for Processing of Hepatitis C Virus Polyprotein, J. Virol., 67, 4017, 10.1128/jvi.67.7.4017-4026.1993 Yao, 1999, Molecular Views of Viral Polyprotein Processing Revealed by the Crystal Structure of the Hepatitis C Virus Bifunctional Protease-Helicase, Structure, 7, 1353, 10.1016/S0969-2126(00)80025-8 Luo, 2008, Crystal Structure of the NS3 Protease-Helicase from Dengue Virus, J. Virol., 82, 173, 10.1128/JVI.01788-07 Assenberg, 2009, Crystal Structure of a Novel Conformational State of the Flavivirus NS3 Protein: Implications for Polyprotein Processing and Viral Replication, J. Virol., 83, 12895, 10.1128/JVI.00942-09 Wengler, 1993, The NS 3 Nonstructural Protein of Flaviviruses Contains an RNA Triphosphatase Activity, Virology, 197, 265, 10.1006/viro.1993.1587 Spahn, 2001, Hepatitis C Virus IRES RNA-Induced Changes in the Conformation of the 40S Ribosomal Subunit, Science, 291, 1959, 10.1126/science.1058409 Edlin, 2011, Perspective: Test and Treat This Silent Killer, Nature, 474, S18, 10.1038/474S18a McHutchison, 2004, Understanding Hepatitis C, Am. J. Manag. Care, 10, S21 Lange, 2010, Review Article: Specifically Targeted Anti-viral Therapy for Hepatitis C—A New Era in Therapy, Aliment Pharmacol. Ther., 32, 14, 10.1111/j.1365-2036.2010.04317.x Garber, 2011, Hepatitis C: Move Over Interferon, Nat. Biotechnol., 29, 963, 10.1038/nbt.2031 Mackenzie, 2004, Emerging Flaviviruses: The Spread and Resurgence of Japanese Encephalitis, West Nile and Dengue Viruses, Nat. Med., 10, S98, 10.1038/nm1144 Al-Ahdal, 2012, Coronavirus Respiratory Illness in Saudi Arabia, J. Infect. Dev. Ctries., 6, 692, 10.3855/jidc.3084 Ivanov, 2004, Human Coronavirus 229E Nonstructural Protein 13: Characterization of Duplex-Unwinding, Nucleoside Triphosphatase, and RNA 5′-Triphosphatase Activities, J. Virol., 78, 7833, 10.1128/JVI.78.14.7833-7838.2004 Reddy, 2000, Sam68, RNA Helicase A and Tap Cooperate in the Post-transcriptional Regulation of Human Immunodeficiency Virus and Type D Retroviral mRNA, Oncogene, 19, 3570, 10.1038/sj.onc.1203676 Roy, 2006, Association of RNA Helicase A with Human Immunodeficiency Virus Type 1 Particles, J. Biol. Chem., 281, 12625, 10.1074/jbc.M510596200 Cocude, 2003, A Novel Cellular RNA Helicase, RH116, Differentially Regulates Cell Growth, Programmed Cell Death and Human Immunodeficiency Virus Type 1 Replication, J. Gen. Virol., 84, 3215, 10.1099/vir.0.19300-0 Sharma, 2007, The Werner Syndrome Helicase Is a Cofactor for HIV-1 Long Terminal Repeat Transactivation and Retroviral Replication, J. Biol. Chem., 282, 12048, 10.1074/jbc.M608104200 Yedavalli, 2004, Requirement of DDX3 DEAD Box RNA Helicase for HIV-1 Rev-RRE Export Function, Cell, 119, 381, 10.1016/j.cell.2004.09.029 Fang, 2004, A DEAD Box Protein Facilitates HIV-1 Replication as a Cellular Co-factor of Rev, Virology, 330, 471, 10.1016/j.virol.2004.09.039 Fang, 2005, The RNA Helicase DDX1 Is Involved in Restricted HIV-1 Rev Function in Human Astrocytes, Virology, 336, 299, 10.1016/j.virol.2005.03.017 Ma, 2008, The Requirement of the DEAD-Box Protein DDX24 for the Packaging of Human Immunodeficiency Virus Type 1 RNA, Virology, 375, 253, 10.1016/j.virol.2008.01.025 Sharma, 2005, DNA Helicases as Targets for Anti-Cancer Drugs, Curr. Med. Chem. Anticancer Agents, 5, 183, 10.2174/1568011053765985 Hu, 2009, Recql5 Plays an Important Role in DNA Replication and Cell Survival after Camptothecin Treatment, Mol. Biol. Cell, 20, 114, 10.1091/mbc.e08-06-0565 Lu, 2011, A Blm-Recql5 Partnership in Replication Stress Response, J. Mol. Cell Biol., 3, 31, 10.1093/jmcb/mjq056 Yu, 1996, Positional Cloning of the Werner’s Syndrome Gene, Science, 272, 258, 10.1126/science.272.5259.258 Gray, 1997, The Werner Syndrome Protein Is a DNA Helicase, Nat. Genet., 17, 100, 10.1038/ng0997-100 Kitao, 1999, Mutations in RECQL4 Cause a Subset of Cases of Rothmund-Thomson Syndrome, Nat. Genet., 22, 82, 10.1038/8788 Kellermayer, 2005, A Patient with Rothmund-Thomson Syndrome and All Features of RAPADILINO, Arch. Dermatol., 141, 617, 10.1001/archderm.141.5.617 Van Maldergem, 2006, Revisiting the Craniosynostosis-Radial Ray Hypoplasia Association: Baller-Gerold Syndrome Caused by Mutations in the RECQL4 Gene, J. Med. Genet., 43, 148, 10.1136/jmg.2005.031781 Cheng, 2012, Targeting Werner Syndrome Protein Sensitizes U-2 OS Osteosarcoma Cells to Selenium-Induced DNA Damage Response and Necrotic Death, Biochem. Biophys. Res. Commun., 420, 24, 10.1016/j.bbrc.2012.02.104 Blander, 2000, The Werner Syndrome Protein Contributes to Induction of p53 by DNA Damage, FASEB J., 14, 2138, 10.1096/fj.00-0171fje Jin, C., Rajabi, H., Rodrigo, C. M., Porco, J. A. J., Kufe, D. Targeting the eIF4A RNA Helicase Blocks Translation of the MUC1-C Oncoprotein. Oncogene, in press. Ishaq, 2008, Knockdown of Cellular RNA Helicase DDX3 by Short Hairpin RNAs Suppresses HIV-1 Viral Replication without Inducing Apoptosis, Mol. Biotechnol., 39, 231, 10.1007/s12033-008-9040-0 Bolinger, 2010, RNA Helicase A Modulates Translation of HIV-1 and Infectivity of Progeny Virions, Nucleic Acids Res., 38, 1686, 10.1093/nar/gkp1075 Goh, 2004, Cellular RNA Helicase p68 Relocalization and Interaction with the Hepatitis C Virus (HCV) NS5B Protein and the Potential Role of p68 in HCV RNA Replication, J. Virol., 78, 5288, 10.1128/JVI.78.10.5288-5298.2004 Grandori, 2003, Werner Syndrome Protein Limits MYC-Induced Cellular Senescence, Genes Dev., 17, 1569, 10.1101/gad.1100303 Futami, 2007, Increased Chemotherapeutic Activity of Camptothecin in Cancer Cells by siRNA-Induced Silencing of WRN Helicase, Biol. Pharm. Bull., 30, 1958, 10.1248/bpb.30.1958 Masuda, 2012, Association of Epigenetic Inactivation of the WRN Gene with Anticancer Drug Sensitivity in Cervical Cancer Cells, Oncol. Rep., 28, 1146, 10.3892/or.2012.1912 Artsaenko, 2003, Abrogation of Hepatitis C Virus NS3 Helicase Enzymatic Activity by Recombinant Human Antibodies, J. Gen. Virol., 84, 2323, 10.1099/vir.0.19299-0 Prabhu, 2004, Inhibition of Hepatitis C Virus Nonstructural Protein, Helicase Activity, and Viral Replication by a Recombinant Human Antibody Clone, Am. J. Pathol., 165, 1163, 10.1016/S0002-9440(10)63377-9 Hwang, 2004, Isolation of Specific and High-Affinity RNA Aptamers against NS3 Helicase Domain of Hepatitis C Virus, RNA, 10, 1277, 10.1261/rna.7100904 Umehara, 2005, Rational Design of Dual-Functional Aptamers That Inhibit the Protease and Helicase Activities of HCV NS3, J. Biochem., 137, 339, 10.1093/jb/mvi042 Fukuda, 2004, An RNA Ligand Inhibits Hepatitis C Virus NS3 Protease and Helicase Activities, Biochem. Biophys. Res. Commun., 325, 670, 10.1016/j.bbrc.2004.10.089 Koresawa, 2004, High-Throughput Screening with Quantitation of ATP Consumption: A Universal Non-Radioisotope, Homogeneous Assay for Protein Kinase, Assay Drug Dev. Technol., 2, 153, 10.1089/154065804323056495 Simoni, 2002, The Determination of Phosphorus and the Discovery of Phosphocreatine and ATP: The Work of Fiske and SubbaRow, J. Biol. Chem., 277, 21e, 10.1016/S0021-9258(20)85219-3 Lanzetta, 1979, An Improved Assay for Nanomole Amounts of Inorganic Phosphate, Anal. Biochem., 100, 95, 10.1016/0003-2697(79)90115-5 Frick, 2007, Role of Divalent Metal Cations in ATP Hydrolysis Catalyzed by the Hepatitis C Virus NS3 Helicase: Magnesium Provides a Bridge for ATP to Fuel Unwinding, J. Mol. Biol., 365, 1017, 10.1016/j.jmb.2006.10.023 Funk, 2004, Development of High-Throughput Screens for Discovery of Kinesin Adenosine Triphosphatase Modulators, Anal. Biochem., 329, 68, 10.1016/j.ab.2004.02.032 Miyata, 2010, High-Throughput Screen for Escherichia coli Heat Shock Protein 70 (Hsp70/DnaK): ATPase Assay in Low Volume by Exploiting Energy Transfer, J. Biomol. Screen., 15, 1211, 10.1177/1087057110380571 Seguin, 2012, A Screen for Modulators of Large T Antigen’s ATPase Activity Uncovers Novel Inhibitors of Simian Virus 40 and BK Virus Replication, Antiviral Res., 96, 70, 10.1016/j.antiviral.2012.07.012 Suzich, 1993, Hepatitis C Virus NS3 Protein Polynucleotide-Stimulated Nucleoside Triphosphatase and Comparison with the Related Pestivirus and Flavivirus Enzymes, J. Virol., 67, 6152, 10.1128/jvi.67.10.6152-6158.1993 Rieger, 1997, A Continuous Spectrophotometric Assay for Aspartate Transcarbamylase and ATPases, Anal. Biochem., 246, 86, 10.1006/abio.1996.9962 Ndjomou, 2012, Fluorescent Primuline Derivatives Inhibit Hepatitis C Virus NS3-Catalyzed RNA Unwinding, Peptide Hydrolysis and Viral Replicase Formation, Antiviral Res., 96, 245, 10.1016/j.antiviral.2012.08.006 Seguin, 2012, High-Throughput Screening Identifies a Bisphenol Inhibitor of SV40 Large T Antigen ATPase Activity, J. Biomol. Screen., 17, 194, 10.1177/1087057111421630 Sivaraja, 1998, High-Throughput Screening Assay for Helicase Enzymes, Anal. Biochem., 265, 22, 10.1006/abio.1998.2875 Kyono, 1998, Detection of Hepatitis C Virus Helicase Activity Using the Scintillation Proximity Assay System, Anal. Biochem., 257, 120, 10.1006/abio.1998.2560 Earnshaw, 2001, FlashPlate Scintillation Proximity Assays for Characterization and Screening of DNA Polymerase, Primase, and Helicase Activities, J Biomol. Screen, 6, 39, 10.1177/108705710100600106 Hicham Alaoui-Ismaili, 2000, A Novel High Throughput Screening Assay for HCV NS3 Helicase Activity, Antiviral Res., 46, 181, 10.1016/S0166-3542(00)00085-1 Zhang, 2001, Development of a Novel Helicase Assay Using Electrochemiluminescence, Anal. Biochem., 293, 31, 10.1006/abio.2001.5093 Hsu, 1998, An ELISA for RNA Helicase Activity: Application as an Assay of the NS3 Helicase of Hepatitis C Virus, Biochem. Biophys. Res. Commun., 253, 594, 10.1006/bbrc.1998.9813 Houston, 1994, Spectrophotometric Assay for Enzyme-Mediated Unwinding of Double-Stranded DNA, Proc. Natl. Acad. Sci. U. S. A., 91, 5471, 10.1073/pnas.91.12.5471 Bjornson, 1994, Single-Turnover Kinetics of Helicase-Catalyzed DNA Unwinding Monitored Continuously by Fluorescence Energy Transfer, Biochemistry, 33, 14306, 10.1021/bi00251a044 Boguszewska-Chachulska, 2004, Direct Fluorometric Measurement of Hepatitis C Virus Helicase Activity, FEBS Lett., 567, 253, 10.1016/j.febslet.2004.04.072 Tani, 2010, Real-Time Monitoring of RNA Helicase Activity Using Fluorescence Resonance Energy Transfer In Vitro, Biochem. Biophys. Res. Commun., 393, 131, 10.1016/j.bbrc.2010.01.100 Xu, 2003, Simultaneously Monitoring DNA Binding and Helicase-Catalyzed DNA Unwinding by Fluorescence Polarization, Nucleic Acids Res., 31, e70, 10.1093/nar/gng070 Earnshaw, 1999, Time-Resolved Fluorescence Energy Transfer DNA Helicase Assays for High Throughput Screening, J. Biomol. Screen., 4, 239, 10.1177/108705719900400505 Tyagi, 1996, Molecular Beacons: Probes That Fluoresce upon Hybridization, Nat. Biotechnol., 14, 303, 10.1038/nbt0396-303 Li, 2012, Optimization of Potent Hepatitis C Virus NS3 Helicase Inhibitors Isolated from the Yellow Dyes Thioflavine S and Primuline, J. Med. Chem., 55, 3319, 10.1021/jm300021v Baumeister, 2007, Superior Efficacy of Helicase-Primase Inhibitor BAY 57-1293 for Herpes Infection and Latency in the Guinea Pig Model of Human Genital Herpes Disease, Antivir. Chem. Chemother., 18, 35, 10.1177/095632020701800104 Kaufman, 2008, Efficacy of a Helicase-Primase Inhibitor in Animal Models of Ocular Herpes Simplex Virus Type 1 Infection, J. Ocul. Pharmacol. Ther., 24, 34, 10.1089/jop.2007.0084 Biswas, 2007, Detection of HSV-1 Variants Highly Resistant to the Helicase-Primase Inhibitor BAY 57-1293 at High Frequency in 2 of 10 Recent Clinical Isolates of HSV-1, J. Antimicrob. Chemother., 60, 274, 10.1093/jac/dkm182 Biswas, 2008, A Single Drug-Resistance Mutation in HSV-1 UL52 Primase Points to a Difference between Two Helicase-Primase Inhibitors in Their Mode of Interaction with the Antiviral Target, J. Antimicrob. Chemother., 61, 1044, 10.1093/jac/dkn057 Chono, 2010, ASP2151, a Novel Helicase-Primase Inhibitor, Possesses Antiviral Activity against Varicella-Zoster Virus and Herpes Simplex Virus Types 1 and 2, J. Antimicrob. Chemother., 65, 1733, 10.1093/jac/dkq198 Katsumata, 2011, Effect of ASP2151, a Herpesvirus Helicase-Primase Inhibitor, in a Guinea Pig Model of Genital Herpes, Molecules, 16, 7210, 10.3390/molecules16097210 Himaki, 2012, Efficacy of ASP2151, a Helicase-Primase Inhibitor, against Thymidine Kinase-Deficient Herpes Simplex Virus Type 2 Infection In Vitro and In Vivo, Antiviral Res., 93, 301, 10.1016/j.antiviral.2011.11.015 Chono, 2012, Characterization of Virus Strains Resistant to the Herpes Virus Helicase-Primase Inhibitor ASP2151 (Amenamevir), Biochem. Pharmacol., 84, 459, 10.1016/j.bcp.2012.05.020 Tyring, 2012, ASP2151 for the Treatment of Genital Herpes: A Randomized, Double-Blind, Placebo- and Valacyclovir-Controlled, Dose-Finding Study, J. Infect. Dis., 205, 1100, 10.1093/infdis/jis019 Katsumata, 2012, Susceptibility of Herpes Simplex Virus Isolated from Genital Herpes Lesions to ASP2151, a Novel Helicase-Primase Inhibitor, Antimicrob. Agents Chemother., 56, 3587, 10.1128/AAC.00133-12 Borowski, 2000, ATP-Binding Domain of NTPase/Helicase as a Target for Hepatitis C Antiviral Therapy, Acta Biochim. Pol., 47, 173, 10.18388/abp.2000_4075 Yedavalli, 2008, Ring Expanded Nucleoside Analogues Inhibit RNA Helicase and Intracellular Human Immunodeficiency Virus Type 1 Replication, J. Med. Chem., 51, 5043, 10.1021/jm800332m White, 2005, Biphenylsulfonacetic Acid Inhibitors of the Human Papillomavirus Type 6 E1 Helicase Inhibit ATP Hydrolysis by an Allosteric Mechanism Involving Tyrosine 486, Antimicrob. Agents Chemother., 49, 4834, 10.1128/AAC.49.12.4834-4842.2005 Radi, 2012, Discovery of the First Small Molecule Inhibitor of Human DDX3 Specifically Designed to Target the RNA Binding Site: Towards the Next Generation HIV-1 Inhibitors, Bioorg. Med. Chem. Lett., 22, 2094, 10.1016/j.bmcl.2011.12.135 Chen, 2009, Structure-Based Discovery of Triphenylmethane Derivatives as Inhibitors of Hepatitis C Virus Helicase, J. Med. Chem., 52, 2716, 10.1021/jm8011905 Mukherjee, 2012, Identification and Analysis of Hepatitis C Virus NS3 Helicase Inhibitors Using Nucleic Acid Binding Assays, Nucleic Acids Res., 40, 8607, 10.1093/nar/gks623 D’Abramo, 2011, Small Molecule Inhibitors of Human Papillomavirus Protein-Protein Interactions, Open Virol. J., 5, 80, 10.2174/1874357901105010080 Faucher, 2004, Discovery of Small-Molecule Inhibitors of the ATPase Activity of Human Papillomavirus E1 Helicase, J. Med. Chem., 47, 18, 10.1021/jm034206x Walker, 1982, Distantly Related Sequences in the Alpha- and Beta-Subunits of ATP Synthase, Myosin, Kinases and Other ATP-Requiring Enzymes and a Common Nucleotide Binding Fold, EMBO J., 1, 945, 10.1002/j.1460-2075.1982.tb01276.x Lee, 2009, Investigation of the Pharmacophore Space of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) NTPase/Helicase by Dihydroxychromone Derivatives, Bioorg. Med. Chem. Lett., 19, 4538, 10.1016/j.bmcl.2009.07.009 Kim, 2011, 2,6-Bis-arylmethyloxy-5-hydroxychromones with Antiviral Activity against Both Hepatitis C Virus (HCV) and SARS-Associated Coronavirus (SCV), Eur. J. Med. Chem., 46, 5698, 10.1016/j.ejmech.2011.09.005 Kwok, 2001, Allosteric Interaction of Minor Groove Binding Ligands with UL9-DNA Complexes, Biochemistry, 40, 12628, 10.1021/bi0109865 Brosh, 2000, Potent Inhibition of Werner and Bloom Helicases by DNA Minor Groove Binding Drugs, Nucleic Acids Res., 28, 2420, 10.1093/nar/28.12.2420 Ali, 2007, Inhibition of Simian Virus 40 Large T Antigen Helicase Activity by Fluoroquinolones, Antivir. Ther., 12, 1, 10.1177/135965350701200104 Khan, 2012, Fluoroquinolones Inhibit HCV by Targeting Its Helicase, Antivir. Ther., 17, 467, 10.3851/IMP1937 Xu, 2001, Flavones Inhibit the Hexameric Replicative Helicase RepA, Nucleic Acids Res., 29, 5058, 10.1093/nar/29.24.5058 Yu, 2012, Identification of Myricetin and Scutellarein as Novel Chemical Inhibitors of the SARS Coronavirus Helicase, nsP13, Bioorg. Med. Chem. Lett., 22, 4049, 10.1016/j.bmcl.2012.04.081 Griep, 2007, Myricetin Inhibits Escherichia coli DnaB Helicase but Not Primase, Bioorg. Med. Chem., 15, 7203, 10.1016/j.bmc.2007.07.057 Sharma, 2011, Non-B DNA Secondary Structures and Their Resolution by RecQ Helicases, J. Nucleic Acids, 2011, 724215, 10.4061/2011/724215 Wu, 2001, Substrate-Specific Inhibition of RecQ Helicase, Nucleic Acids Res., 29, 1765, 10.1093/nar/29.8.1765 Yang, 2007, Inhibition of SARS Coronavirus Helicase by Bismuth Complexes, Chem. Commun. (Camb)., 42, 4413, 10.1039/b709515e Boger, 2001, A Simple, High-Resolution Method for Establishing DNA Binding Affinity and Sequence Selectivity, J. Am. Chem. Soc., 123, 5878, 10.1021/ja010041a Boger, 2001, Thiazole Orange as the Fluorescent Intercalator in a High Resolution Fid Assay for Determining DNA Binding Affinity and Sequence Selectivity of Small Molecules, Bioorg. Med. Chem., 9, 2511, 10.1016/S0968-0896(01)00243-7 Phoon, 2001, Biological Evaluation of Hepatitis C Virus Helicase Inhibitors, Bioorg. Med. Chem. Lett., 11, 1647, 10.1016/S0960-894X(01)00263-3 Belon, 2010, Mechanism and Specificity of a Symmetrical Benzimidazolephenylcarboxamide Helicase Inhibitor, Biochemistry, 49, 1822, 10.1021/bi901974a Tunitskaya, 2011, Inhibition of the Helicase Activity of the HCV NS3 Protein by Symmetrical Dimeric Bis-benzimidazoles, Bioorg. Med. Chem. Lett., 21, 5331, 10.1016/j.bmcl.2011.07.018 Belon, 2010, Thioflavin S Inhibits Hepatitis C Virus RNA Replication and the Viral Helicase with a Novel Mechanism, FASEB J., 24, lb202 Li, K., Frankowski, K. J., Hanson, A. M., Ndjomou, J., Shanahan, M. A., Mukherjee, S., Shadrick, W. R., Sweeney, N. L., Belon, C. A., Neuenswander, B., et al. Hepatitis C Virus NS3 Helicase Inhibitor Discovery. In Probe Reports from the NIH Molecular Libraries Program, in press. Graham, 1969, Fluorescence Staining for the Determination of Cell Viability, Appl Microbiol, 17, 489, 10.1128/am.17.3.489-490.1969 Novac, 2004, Inhibitors of Protein Synthesis Identified by a High Throughput Multiplexed Translation Screen, Nucleic Acids Res., 32, 902, 10.1093/nar/gkh235 Tan, 2012, Small Molecule Inhibition of RISC Loading, ACS Chem. Biol., 7, 403, 10.1021/cb200253h McKay, 2006, Triaminotriazine DNA Helicase Inhibitors with Antibacterial Activity, Bioorg. Med. Chem. Lett., 16, 1286, 10.1016/j.bmcl.2005.11.076 Aiello, 2009, Discovery, Characterization and Comparison of Inhibitors of Bacillus anthracis and Staphylococcus aureus Replicative DNA Helicases, Bioorg. Med. Chem., 17, 4466, 10.1016/j.bmc.2009.05.014 Li, 2012, Coumarin-Based Inhibitors of Bacillus anthracis and Staphylococcus aureus Replicative DNA Helicase: Chemical Optimization, Biological Evaluation, and Antibacterial Activities, J. Med. Chem., 55, 10896, 10.1021/jm300922h Aggarwal, 2011, Inhibition of Helicase Activity by a Small Molecule Impairs Werner Syndrome Helicase (WRN) Function in the Cellular Response to DNA Damage or Replication Stress, Proc. Natl. Acad. Sci. U. S. A., 108, 1525, 10.1073/pnas.1006423108 Nguyen, 2013, A Small Molecule Inhibitor of the BLM Helicase Modulates Chromosome Stability in Human Cells, Chem. Biol., 20, 55, 10.1016/j.chembiol.2012.10.016 Adedeji, 2012, Severe Acute Respiratory Syndrome Coronavirus Replication Inhibitor That Interferes with the Nucleic Acid Unwinding of the Viral Helicase, Antimicrob. Agents Chemother., 56, 4718, 10.1128/AAC.00957-12 Grell, 1998, Repaglinide and Related Hypoglycemic Benzoic Acid Derivatives, J. Med. Chem., 41, 5219, 10.1021/jm9810349 Wright, 2009, Inhibition of Simian Virus 40 Replication by Targeting the Molecular Chaperone Function and ATPase Activity of T Antigen, Virus Res., 141, 71, 10.1016/j.virusres.2008.12.018 Mousseau, 2011, Dimerization-Driven Interaction of Hepatitis C Virus Core Protein with NS3 Helicase, J. Gen. Virol., 92, 101, 10.1099/vir.0.023325-0 Saalau-Bethell, 2012, Discovery of an Allosteric Mechanism for the Regulation of HCV NS3 Protein Function, Nat. Chem. Biol., 8, 920, 10.1038/nchembio.1081 Bordeleau, 2006, Functional Characterization of IRESes by an Inhibitor of the RNA Helicase eIF4A, Nat. Chem. Biol., 2, 213, 10.1038/nchembio776 Lindqvist, 2008, Selective Pharmacological Targeting of a DEAD Box RNA Helicase, PLoS One, 3, e1583, 10.1371/journal.pone.0001583 Bordeleau, 2005, Stimulation of Mammalian Translation Initiation Factor eIF4A Activity by a Small Molecule Inhibitor of Eukaryotic Translation, Proc. Natl. Acad. Sci. U. S. A., 102, 10460, 10.1073/pnas.0504249102 Bordeleau, 2006, RNA-Mediated Sequestration of the RNA Helicase eIF4A by Pateamine A Inhibits Translation Initiation, Chem. Biol., 13, 1287, 10.1016/j.chembiol.2006.10.005 Bordeleau, 2008, Therapeutic Suppression of Translation Initiation Modulates Chemosensitivity in a Mouse Lymphoma Model, J. Clin. Invest., 118, 2651 Amundsen, 2012, Small-Molecule Inhibitors of Bacterial AddAB and RecBCD Helicase-Nuclease DNA Repair Enzymes, ACS Chem. Biol., 7, 879, 10.1021/cb300018x Wang, 2004, Crystal Structure of the E2 Transactivation Domain of Human Papillomavirus Type 11 Bound to a Protein Interaction Inhibitor, J. Biol. Chem., 279, 6976, 10.1074/jbc.M311376200 Kandil, 2009, Discovery of a Novel HCV Helicase Inhibitor by a De Novo Drug Design Approach, Bioorg. Med. Chem. Lett., 19, 2935, 10.1016/j.bmcl.2009.04.074 Mastrangelo, 2012, Ivermectin is a Potent Inhibitor of Flavivirus Replication Specifically Targeting NS3 Helicase Activity: New Prospects for an Old Drug, J. Antimicrob. Chemother., 67, 1884, 10.1093/jac/dks147 Hogbom, 2007, Crystal Structure of Conserved Domains 1 and 2 of the Human DEAD-box Helicase DDX3X in Complex with the Mononucleotide AMP, J. Mol. Biol., 372, 150, 10.1016/j.jmb.2007.06.050 Maga, 2008, Pharmacophore Modeling and Molecular Docking Led to the Discovery of Inhibitors of Human Immunodeficiency Virus–1 Replication Targeting the Human Cellular Aspartic Acid–Glutamic Acid–Alanine–Aspartic Acid Box Polypeptide 3, J. Med. Chem., 51, 6635, 10.1021/jm8008844 Ha, 2012, Single-Molecule Views of Protein Movement on Single-Stranded DNA, Annu. Rev. Biophys., 41, 295, 10.1146/annurev-biophys-042910-155351 Goudreau, 2007, Optimization and Determination of the Absolute Configuration of a Series of Potent Inhibitors of Human Papillomavirus Type-11 E1-E2 Protein-Protein Interaction: A Combined Medicinal Chemistry, NMR and Computational Chemistry Approach, Bioorg. Med. Chem., 15, 2690, 10.1016/j.bmc.2007.01.036