Viral Polymerases: Structures, Functions and Roles as Antiviral Drug Targets

Cover\nViral Polymerases\nCopyright\nList of Contributors\nPreface\n1 RNA-Dependent RNA Polymerases and Their Emerging Roles in Antiviral Therapy\n	1.1 Introduction\n	1.2 RNA Polymerase\n		1.2.1 DNA-Dependent RNA Polymerases\n		1.2.2 RNA-Dependent RNA Polymerases\n	1.3 Structure of Viral RNA-Dependent RNA Polymerases\n		1.3.1 Structural Flexibility\n		1.3.2 Divalent Metal Ions\n	1.4 Mechanism of Enzyme Action\n		1.4.1 Two Metal Ion Mechanism\n		1.4.2 Initiation of RNA Synthesis\n			1.4.2.1 De Novo Initiation Mechanism\n			1.4.2.2 Primer-Dependent Initiation\n	1.5 Structures of Different Viral RdRPs\n		1.5.1 Hepatitis C Virus\n		1.5.2 Poliovirus\n		1.5.3 Influenza A Virus\n			1.5.3.1 Polymerase Basic 1 Subdomain\n			1.5.3.2 Polymerase Basic 2 Subdomain\n			1.5.3.3 Polymerase Acidic Subdomain\n		1.5.4 Dengue Virus\n		1.5.5 Zika Virus\n		1.5.6 Japanese Encephalitis Virus\n		1.5.7 Human Rhinoviruses\n	1.6 Enzyme-Ligand Interaction Strategies (Drug Design and Development)\n	1.7 Synthetic Inhibitors of RdRPs\n		1.7.1 Nucleoside Inhibitors\n			1.7.1.1 Purine Nucleoside Inhibitors\n			1.7.1.2 Pyrimidine Nucleoside Inhibitors\n			1.7.1.3 Miscellaneous Nucleoside Inhibitors\n		1.7.2 Nonnucleoside Inhibitors\n			1.7.2.1 Active Site Inhibitors\n			1.7.2.2 Allosteric Site Inhibitors\n				1.7.2.2.1 Anthranilic Acid Derivatives\n				1.7.2.2.2 Benzimidazole Derivatives\n				1.7.2.2.3 Benzothiadiazine Derivatives\n				1.7.2.2.4 Indole Derivatives\n				1.7.2.2.5 Proline Sulfonamide Derivatives\n				1.7.2.2.6 Pyrrolidine Diacid Derivatives\n				1.7.2.2.7 Pyridobenzothiazole Derivatives\n			1.7.2.3 Miscellaneous\n	1.8 Conclusion\n	1.9 Future Prospective\n	References\n2 Structure–Function Relationship of Negative-Stranded Viral RNA Polymerases: Prospectives for Antiviral Therapy\n	2.1 Introduction\n	2.2 Polyprotein Processing\n	2.3 Genome Organization of Polymerase of segmented negative-strand RNA Viruses\n	2.4 Mechanism of Capping by RdRps\n	2.5 Structures of L-Proteins (Polymerases)\n		2.5.1 Structures of SNS RNA Virus L-Proteins (Polymerases)\n			2.5.1.1 La Crosse Orthobunyavirus RNA Polymerase (L-Protein)\n			2.5.1.2 Influenza Virus (H3N2) RNA Polymerase\n			2.5.1.3 Lymphocytic Choriomeningitis Virus RNA Polymerase (L-Protein)\n			2.5.1.4 Avian Influenza Virus (H5N1) RNA Polymerase\n		2.5.2 Structure of NNS RNA Virus L-Proteins (Polymerases)\n	2.6 Activity Assays\n		2.6.1 Mini-Replicon Assay\n		2.6.2 Nuclease Activity and Thermal Stability Assay\n		2.6.3 UV Cross-Linking Assays for Nucleotide Binding\n		2.6.4 Band Shift Assay for RNA Binding\n		2.6.5 Fluorescence-Based Assay\n	2.7 Inhibition Studies\n		2.7.1 Synergistic Action of Favipiravir and Ribavirin\n		2.7.2 Neutral Red Uptake Assay for Assessing Inhibition of Viral Replication by Antiviral Compounds\n		2.7.3 Negative-Strand Viral Replication Inhibition Through Gene Silencing approaches\n		2.7.4 Exploration of Antiviral Agents for Influenza in Clinical Trials\n		2.7.5 Targeting of Viral RNA in Eukaryotic Cells Through Cas9\n		2.7.6 Novel Sugar-Modified Nucleosides Inhibitors Against Human RSV Polymerase\n	2.8 Conclusion\n	References\n	Further Reading\n3 RNA-Dependent RNA Polymerase of Alphaviruses: A Potential Target for the Design of Drugs Against Alphaviruses\n	3.1 Introduction\n	3.2 Genome Structure\n	3.3 Viral Life Cycle\n	3.4 Replication Complexes in Alphavirus\n	3.5 Structure of RNA-Dependent RNA Polymerases\n		3.5.1 Divalent Metal Binding Site\n		3.5.2 Nucleotide Binding Site\n	3.6 Initiation of Replication\n		3.6.1 Primer-Independent Initiation\n		3.6.2 Primer-Dependent Initiation\n	3.7 Polymerase Activity of Alphaviral RdRP\n		3.7.1 Promoter Recognition by the Polymerase\n			3.7.1.1 5′ end\n			3.7.1.2 3′ end\n			3.7.1.3 SG Promoter\n		3.7.2 Temperature Sensitivity of Polymerase\n		3.7.3 Fidelity of RdRP\n	3.8 Inhibitors Against Replication of Alphaviruses\n	3.9 Conclusions\n	References\n4 DNA-Dependent DNA Polymerases as Drug Targets in Herpesviruses and Poxviruses\n	4.1 Introduction\n	4.2 DNA Viruses: Mechanisms of Genomic DNA Replication\n		4.2.1 Bidirectional and Rolling Circle Replication\n		4.2.2 Single-Stranded DNA Formation Through Strand Displacement Replication\n	4.3 Herpesviruses\n		4.3.1 Types and Classification\n		4.3.2 Herpesvirus DNA Polymerase Structure\n		4.3.3 DNA Polymerase Properties: Processivity and Nucleotide Specificity\n	4.4 Antiviral Drugs Targeting Herpesvirus DNA Polymerases\n		4.4.1 Approved Drugs\n		4.4.2 Resistance to Approved Drugs Targeting Herpesvirus Replication\n		4.4.3 Drugs in Preclinical and Clinical Development\n	4.5 Poxviruses\n		4.5.1 Poxvirus DNA Polymerase\n		4.5.2 Drugs Targeting Poxvirus DNA Polymerases\n	4.6 Conclusions\n	References\n5 Poliovirus Polymerase: An Effective Target for Design and Development of Antipolio Drugs\n	5.1 Introduction\n	5.2 Poliovirus RNA-Dependent RNA Polymerase\n		5.2.1 Structure\n			5.2.1.1 The Palm Subdomain and Its Motifs\n			5.2.1.2 Fingers Subdomain\n			5.2.1.3 Thumb Subdomain\n				5.2.1.3.1 Roles of Subdomains\n			5.2.1.4 Metal Ions\n		5.2.2 Function\n	5.3 Isolation, Purification, and Characterization of Poliovirus RNA Polymerase\n		5.3.1 Isolation From HeLa cells\n		5.3.2 Recombinant Baculovirus Infected Insect Cells\n		5.3.3 Escherichia coli Transformed With an Expression Plasmid Containing 3Dpol Sequences\n	5.4 RNA-Dependent RNA Polymerase Inhibitors\n	5.5 Conclusions and Future Perspective\n	References\n6 Studies on HIV-1 Polymerase and Its Inhibitors\n	6.1 Introduction\n	6.2 Structure of Reverse Transcriptase\n	6.3 Role and Mechanism of Action of HIV-1 RT\n	6.4 HIV-1 RT Inhibitors\n	6.5 Binding of NNRTIs With the Receptor\n	6.6 Theoretical Studies\n	6.7 RNH Inhibitors\n	6.8 HIV-1 Capsid and Its Role on Reverse Transcription Regulation and Control of Entry of RT Inhibitors\n	6.9 Conclusions\n	References\n	Further Reading\n7 A Focus on Ebola Virus Polymerase: Structure, Functions and Antiviral Therapies\n	7.1 Introduction\n		7.1.1 History and Epidemiology\n		7.1.2 Transmission and Pathology\n	7.2 Structure and Genome\n	7.3 Replication\n	7.4 L-Protein\n		7.4.1 RNA-Dependent RNA Polymerase Domain\n		7.4.2 Capping Domain\n		7.4.3 Methyl Transferase Domain\n		7.4.4 Connector and C-Terminal Domains\n		7.4.5 Domain Organization\n		7.4.6 L-Protein in Virus Replication\n	7.5 Antiviral Strategies\n		7.5.1 Brincidofovir (CMX-001)\n		7.5.2 Lamivudine (BCH-189)\n		7.5.3 Favipiravir (T-705)\n		7.5.4 Immucillin A (BCX4430)\n		7.5.5 The FGI (Functional Genetics Inc.) Compounds\n		7.5.6 Neplanocin A (3-deazaneplanocin A)\n		7.5.7 Bioinformatics Approach to Drug Discovery\n	7.6 Ebola Vaccine\n	7.7 Conclusions\n	References\n8 Hepatitis C Virus NS5B RNA-Dependent RNA Polymerase Inhibitor: An Integral Part of HCV Antiviral Therapy\n	8.1 Introduction\n	8.2 The HCV Genome and Viral Replication\n	8.3 Development of HCV-Specific DAA drugs Targeting the NS3 Protease\n	8.4 Development of HCV-Specific DAA drugs Targeting NS5A\n	8.5 Structural and Functional Studies of HCV RNA Polymerase\n	8.6 Initiation of HCV Replication by NS5B Polymerase\n	8.7 Direct-Acting Antivirals Targeting the HCV RNA Polymerase\n		8.7.1 Nucleos(t)ide Inhibitors\n		8.7.2 Nonnucleos(t)ide Inhibitors\n			8.7.2.1 Thumb 1 inhibitors\n			8.7.2.2 Thumb 2 Inhibitors\n			8.7.2.3 Palm 1 Inhibitors\n			8.7.2.4 Palm 2 Inhibitors\n	8.8 Conclusions\n	Acknowledgments\n	References\n	Further Reading\n9 HBV Polymerase as a Target for Development of Anti-HBV Drugs\n	9.1 Introduction\n	9.2 Structure and Biology of HBV\n		9.2.1 Structure\n		9.2.2 Genome\n			9.2.2.1 Size of Genome\n			9.2.2.2 Encoding\n			9.2.2.3 Genotypes\n	9.3 Life Cycle of HBV\n		9.3.1 Attachment\n		9.3.2 Penetration\n		9.3.3 Uncoating\n		9.3.4 Replication\n		9.3.5 Assembly\n		9.3.6 Release\n	9.4 Structure of HBV Polymerase\n		9.4.1 TP Domain\n		9.4.2 Spacer Domain\n		9.4.3 RT Domain\n		9.4.4 RNase H Domain\n	9.5 Multiple Roles of HBV Polymerase\n	9.6 A Potential Target for Anti-HBV Drugs\n		9.6.1 HBV Mutants\n	9.7 Need for New Drugs\n		9.7.1 Sites of Action for New Drugs\n	9.8 Present Status of Drugs Used Against HBV\n		9.8.1 Rational Synthetic Drugs\n		9.8.2 Empirical Indigenous Drugs\n			9.8.2.1 Choices\n	9.9 Recent Studies on HP Inhibitors\n	9.10 Conclusions\n	Acknowledgment\n	References\n	Further Reading\n10 Polymerases of Coronaviruses: Structure, Function, and Inhibitors\n	10.1 Introduction\n	10.2 Structure of HCoV RdRP\n	10.3 Function of HCoV RdRP\n	10.4 Clinical Therapies for HCoV Infections\n		10.4.1 Approaches to Identify the Suitable Treatment for SARS\n		10.4.2 RNA-Dependent RNA Polymerase Inhibitors\n		10.4.3 Marketed RdRP Inhibitors\n		10.4.4 Preclinical RdRP Inhibitors\n		10.4.5 Design of SARS-CoV RdRP Inhibitors\n			10.4.5.1 Nucleoside Analog Inhibitors\n			10.4.5.2 Nonnucleoside Analog Inhibitors\n	10.5 Conclusions\n	References\n11 Rhinovirus RNA Polymerase: Structure, Function, and Inhibitors\n	11.1 Introduction\n	11.2 Classification\n	11.3 Structural Features of HRV Polymerase\n		11.3.1 Crystal Structure of HRV 3Dpol\n		11.3.2 Description of Individual Domains\n		11.3.3 Potassium Binding Site\n		11.3.4 Metal Binding at the Active Site\n		11.3.5 Modeling of Duplex Oligonucleotide for HRV 3Dpol\n		11.3.6 Potential Oligomerization Interfaces\n		11.3.7 Conformational Analysis Showing the Flexibility of the Enzyme\n		11.3.8 Role of Motif D as Fidelity Checkpoint\n	11.4 Biochemical Characterization of 3Dpol\n		11.4.1 Optimization of the HRV16 Polymerase Reaction Conditions\n		11.4.2 HRV16 3D Polymerase Activity on Homopolymeric and Heteropolymeric Templates\n		11.4.3 Kinetic Analysis of HRV16 Polymerase\n		11.4.4 Substrate Specificity of HRV16 3D polymerase\n	11.5 Functions of HRV Polymerase\n		11.5.1 RNA Replication\n			11.5.1.1 Initiation\n			11.5.1.2 Elongation\n				11.5.1.2.1 RNA Interactions in the Active Site\n				11.5.1.2.2 Two Proton Transfer Mechanism in the Transition State for Nucleotidyl Transfer and Formation of Phosphodiester Bond\n				11.5.1.2.3 Downstream and Upstream Template RNA Interactions\n				11.5.1.2.4 Translocation Step\n			11.5.1.3 Termination\n		11.5.2 Mechanism of VPg Uridylation by 3Dpol\n	11.6 Inhibitors of Rhinovirus Polymerase\n		11.6.1 Zinc\n		11.6.2 Gliotoxin\n		11.6.3 Nucleoside and Nonnucleoside Analogs\n		11.6.4 Quercetin\n		11.6.5 2-Furylmercury Chloride (2-FMC)\n		11.6.6 Pyrrolidine Dithiocarbamate\n		11.6.7 Favipiravir\n	11.7 Conclusion\n	References\n12 Herpesvirus Polymerase Inhibitors\n	12.1 Introduction\n	12.2 Classification of Herpesviruses\n	12.3 Herpes Simplex Virus\n		12.3.1 Transmission\n		12.3.2 Structure\n	12.4 Polymerases in Herpesviruses\n		12.4.1 HSV-1 Polymerase\n		12.4.2 HSV-1 Polymerase and DNA Replication\n	12.5 HSV Polymerase Inhibitors\n		12.5.1 Nucleoside Inhibitors\n			12.5.1.1 Acyclovir and Valacyclovir\n			12.5.1.2 Gancilovir and Penciclovir\n			12.5.1.3 Famciclovir\n			12.5.1.4 Sorivudine and Brivudine\n		12.5.2 Nonnucleoside Allosteric Inhibitors\n			12.5.2.1 Foscarnet\n			12.5.2.2 Cidofovir\n			12.5.2.3 Brincidofovir\n			12.5.2.4 4-Oxo-Dihydroquinolines\n	12.6 Mechanism of Drug Actions\n	12.7 Vaccines for HSV Infection\n	12.8 Drug Resistance\n	12.9 Future Anti-HSV Drugs\n	12.10 Conclusions\n	References\n	Further Reading\n13 Zika Virus Polymerase: Structure, Function, and Inhibitors\n	13.1 Introduction\n	13.2 ZIKA Virus: Structure and Function\n	13.3 ZIKV Polymerase\n	13.4 ZIKV NS5 Inhibitors\n		13.4.1 RdRP Inhibitors\n		13.4.2 MTase Inhibitors\n	13.5 Other ZIKV Replication Inhibitors\n		13.5.1 NS3 Helicase Inhibitors\n		13.5.2 Natural Inhibitors From Marine Algae\n	13.6 FDA Approved Inhibitors\n	13.7 Conclusions\n	References\n	Further Reading\n14 Dengue Virus Polymerase: A Crucial Target for Antiviral Drug Discovery\n	14.1 Introduction\n	14.2 Dengue Virus Life Cycle\n	14.3 Structure of DENV Protein\n	14.4 Anti-DENV Agents\n	14.5 DENV RdRP Inhibitors\n		14.5.1 Nucleoside/Nucleotide Inhibitors\n		14.5.2 Nonnucleoside/Nonnucleotide Inhibitors\n	14.6 Crystal Structures of DENV RdRP Inhibitors\n	14.7 Atomistic-Level and Molecular Dynamics Studies of Dengue Virus Interactions and Key Mechanisms for the Cell Membrane E...\n	14.8 Conclusions\n	References\n	Further Reading\n15 Adenovirus DNA Polymerase: Structure, Function, and Prospects in Diagnostics and Therapeutics\n	15.1 Introduction\n	15.2 DNA Polymerases\n		15.2.1 Family B DNA Polymerases\n		15.2.2 Adenovirus DNA Polymerase\n		15.2.3 Structure of Adenovirus DNA Polymerase\n		15.2.4 Processivity\n	15.3 Protein–Protein Interactions of Adenovirus Polymerase\n	15.4 Functions of Adenovirus DNA Polymerase\n	15.5 The Mechanism of Adenovirus Replication\n	15.6 Diagnosis and THERAPEUTIC Prospects\n		15.6.1 Prospects in Diagnosis\n		15.6.2 Prospects in Therapeutics\n	15.7 Conclusions\n	References\n	Further Reading\nIndex\nBack Cover