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Detailed Computational Study of the Active Site of the Hepatitis C Viral RNA Polymerase to Aid Novel Drug Design

https://doi.org/10.1021/ci4003969
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/hep.20819openalex-snapshot
Consensus Proposals for a Unified System of Nomenclature of Hepatitis C Virus Genotypes *
inferredcites →https://doi.org/10.1002/hep.510240552openalex-snapshot
The "gold-standard," accuracy, and the current concepts: Hepatitis C virus genotype and viremia
inferredcites →https://doi.org/10.1002/jcc.20035openalex-snapshot
Development and testing of a general amber force field
inferredcites →https://doi.org/10.1002/jcc.21366openalex-snapshot
How to obtain statistically converged MM/GBSA results
inferredcites →https://doi.org/10.1002/jmv.22010openalex-snapshot
Prevalence of and risk factors for hepatitis C virus infection among blood donors in Chengdu, China
inferredcites →https://doi.org/10.1002/prot.20384openalex-snapshot
MM/PBSA analysis of molecular dynamics simulations of bovine β‐lactoglobulin: Free energy gradients in conformational transitions?
inferredcites →https://doi.org/10.1002/prot.21123openalex-snapshot
Comparison of multiple Amber force fields and development of improved protein backbone parameters
inferredcites →https://doi.org/10.1006/jcph.1999.6201openalex-snapshot
NAMD2: Greater Scalability for Parallel Molecular Dynamics
inferredcites →https://doi.org/10.1007/s10822-010-9373-1openalex-snapshot
Homology modeling and metabolism prediction of human carboxylesterase-2 using docking analyses by GriDock: a parallelized tool based on AutoDock 4.0
inferredcites →https://doi.org/10.1016/j.antiviral.2011.05.003openalex-snapshot
Activity and the metabolic activation pathway of the potent and selective hepatitis C virus pronucleotide inhibitor PSI-353661
inferredcites →https://doi.org/10.1016/j.bmc.2012.03.049openalex-snapshot
Hepatitis C RNA-dependent RNA polymerase inhibitors: A review of structure–activity and resistance relationships; different scaffolds and mutations
inferredcites →https://doi.org/10.1016/j.bmcl.2010.11.068openalex-snapshot
Quinolones as HCV NS5B polymerase inhibitors
inferredcites →https://doi.org/10.1016/j.chembiol.2010.05.019openalex-snapshot
Discovery and Characterization of the Laulimalide-Microtubule Binding Mode by Mass Shift Perturbation Mapping
inferredcites →https://doi.org/10.1016/j.cld.2011.05.003openalex-snapshot
The HCV NS5B Nucleoside and Non-Nucleoside Inhibitors
inferredcites →https://doi.org/10.1016/j.cld.2012.09.007openalex-snapshot
Nucleoside/Nucleotide Analogue Polymerase Inhibitors in Development
inferredcites →https://doi.org/10.1016/j.jmgm.2009.12.003openalex-snapshot
Ensemble-based virtual screening reveals dual-inhibitors for the p53–MDM2/MDMX interactions
inferredcites →https://doi.org/10.1016/j.jmgm.2010.12.003openalex-snapshot
Relaxed complex scheme suggests novel inhibitors for the lyase activity of DNA polymerase beta
inferredcites →https://doi.org/10.1021/ar000033jopenalex-snapshot
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
inferredcites →https://doi.org/10.1021/jm030424eopenalex-snapshot
Structure−Activity Relationship of Purine Ribonucleosides for Inhibition of Hepatitis C Virus RNA-Dependent RNA Polymerase
inferredcites →https://doi.org/10.1021/jm040068fopenalex-snapshot
Structure−Activity Relationship of Heterobase-Modified 2‘-C-Methyl Ribonucleosides as Inhibitors of Hepatitis C Virus RNA Replication
inferredcites →https://doi.org/10.1021/jm049081qopenalex-snapshot
Validation and Use of the MM-PBSA Approach for Drug Discovery
inferredcites →https://doi.org/10.1021/jm0495172openalex-snapshot
Synthesis and Evaluation ofS-Acyl-2-thioethyl Esters of Modified Nucleoside 5‘-Monophosphates as Inhibitors of Hepatitis C Virus RNA Replication
inferredcites →https://doi.org/10.1038/13305openalex-snapshot
Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site.
inferredcites →https://doi.org/10.1038/nature05610openalex-snapshot
Patterns of somatic mutation in human cancer genomes
inferredcites →https://doi.org/10.1038/nbt1358openalex-snapshot
A quantitative analysis of kinase inhibitor selectivity
inferredcites →https://doi.org/10.1056/nejmoa020047openalex-snapshot
Peginterferon Alfa-2a plus Ribavirin for Chronic Hepatitis C Virus Infection
inferredcites →https://doi.org/10.1073/pnas.0507603102openalex-snapshot
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
inferredcites →https://doi.org/10.1074/jbc.m210914200openalex-snapshot
Inhibition of Hepatitis C Virus RNA Replication by 2′-Modified Nucleoside Analogs
inferredcites →https://doi.org/10.1074/jbc.m510195200openalex-snapshot
The Novel Nucleoside Analog R1479 (4′-Azidocytidine) Is a Potent Inhibitor of NS5B-dependent RNA Synthesis and Hepatitis C Virus Replication in Cell Culture
inferredcites →https://doi.org/10.1074/jbc.m708929200openalex-snapshot
2′-Deoxy-4′-azido Nucleoside Analogs Are Highly Potent Inhibitors of Hepatitis C Virus Replication Despite the Lack of 2′-α-Hydroxyl Groups
inferredcites →https://doi.org/10.1093/nar/gkm276openalex-snapshot
PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
inferredcites →https://doi.org/10.1111/j.1365-2893.2009.01115.xopenalex-snapshot
Epidemic hepatitis C virus infection in Egypt: estimates of past incidence and future morbidity and mortality
inferredcites →https://doi.org/10.1111/j.1365-2893.2011.01526.xopenalex-snapshot
New developments in HCV therapy
inferredcites →https://doi.org/10.1111/j.1478-3231.2011.02494.xopenalex-snapshot
Hepatitis C virus infection in USA: an estimate of true prevalence
inferredcites →https://doi.org/10.1124/mol.112.082347openalex-snapshot
Small Molecule Inhibitors of ERCC1-XPF Protein-Protein Interaction Synergize Alkylating Agents in Cancer Cells
inferredcites →https://doi.org/10.1126/science.2523562openalex-snapshot
Isolation of a cDNA cLone Derived from a Blood-Borne Non-A, Non-B Viral Hepatitis Genome
inferredcites →https://doi.org/10.1128/aac.00312-12openalex-snapshot
Preclinical Characterization of JTK-853, a Novel Nonnucleoside Inhibitor of the Hepatitis C Virus RNA-Dependent RNA Polymerase
inferredcites →https://doi.org/10.1128/aac.00399-10openalex-snapshot
PSI-7851, a Pronucleotide of β- d -2′-Deoxy-2′-Fluoro-2′- C -Methyluridine Monophosphate, Is a Potent and Pan-Genotype Inhibitor of Hepatitis C Virus Replication
inferredcites →https://doi.org/10.1128/aac.00433-06openalex-snapshot
General Catalytic Deficiency of Hepatitis C Virus RNA Polymerase with an S282T Mutation and Mutually Exclusive Resistance towards 2′-Modified Nucleotide Analogues
inferredcites →https://doi.org/10.1128/aac.00444-08openalex-snapshot
Selected Replicon Variants with Low-Level In Vitro Resistance to the Hepatitis C Virus NS5B Polymerase Inhibitor PSI-6130 Lack Cross-Resistance with R1479
inferredcites →https://doi.org/10.1128/aac.48.10.3944-3953.2004openalex-snapshot
A 7-Deaza-Adenosine Analog Is a Potent and Selective Inhibitor of Hepatitis C Virus Replication with Excellent Pharmacokinetic Properties
inferredcites →https://doi.org/10.1128/jvi.00386-12openalex-snapshot
Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA
inferredcites →https://doi.org/10.1128/jvi.00459-12openalex-snapshot
Two Crucial Early Steps in RNA Synthesis by the Hepatitis C Virus Polymerase Involve a Dual Role of Residue 405
inferredcites →https://doi.org/10.1128/jvi.67.3.1385-1395.1993openalex-snapshot
Expression and identification of hepatitis C virus polyprotein cleavage products
inferredcites →https://doi.org/10.1128/jvi.77.3.2029-2037.2003openalex-snapshot
Hepatitis C Virus RNA Synthesis in a Cell-Free System Isolated from Replicon-Containing Hepatoma Cells
inferredcites →https://doi.org/10.1371/journal.pone.0011955openalex-snapshot
Virtual Screening for HIV Protease Inhibitors: A Comparison of AutoDock 4 and Vina
inferredcites →https://doi.org/10.1371/journal.pone.0027651openalex-snapshot
Effects of Temperature on the p53-DNA Binding Interactions and Their Dynamical Behavior: Comparing the Wild Type to the R248Q Mutant
inferredcites →https://doi.org/10.1371/journal.pone.0051329openalex-snapshot
Virtual Screening and Biological Evaluation of Inhibitors Targeting the XPA-ERCC1 Interaction
inferredcites →https://doi.org/10.1517/13543784.2010.500285openalex-snapshot
New NS5B polymerase inhibitors for hepatitis C
inferredcites →https://doi.org/10.1586/14787210.6.4.463openalex-snapshot
Resistance mechanisms in HCV: from evolution to intervention
inferredcites →https://doi.org/10.2174/092986711798347234openalex-snapshot
Current Perspective of HCV NS5B Inhibitors: A Review
inferredcites →https://doi.org/10.2174/157489106778777664openalex-snapshot
Recent Patents on Nucleoside and Nucleotide Inhibitors for HCV
inferredcites →https://doi.org/10.4155/fmc.12.10openalex-snapshot
Progress In The Development Of Anti-Hepatitis C Virus Nucleoside And Nucleotide Prodrugs

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1002/wcms.1306openalex-snapshot
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inferred← citeshttps://doi.org/10.1007/978-1-4939-7756-7_6openalex-snapshot
Molecular Dynamics Simulation and Prediction of Druggable Binding Sites
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Role of R292K mutation in influenza H7N9 neuraminidase toward oseltamivir susceptibility: MD and MM/PB(GB)SA study
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2018.01.008openalex-snapshot
Quantum molecular modeling of hepatitis C virus inhibition through non-structural protein 5B polymerase receptor binding of C5-arylidene rhodanines
inferred← citeshttps://doi.org/10.1016/j.drudis.2015.01.003openalex-snapshot
The impact of molecular dynamics on drug design: applications for the characterization of ligand–macromolecule complexes
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Human PD-1 binds differently to its human ligands: A comprehensive modeling study
inferred← citeshttps://doi.org/10.1016/j.jmgm.2015.09.010openalex-snapshot
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inferred← citeshttps://doi.org/10.1016/j.jmgm.2017.10.015openalex-snapshot
Natural products used as a chemical library for protein–protein interaction targeted drug discovery
inferred← citeshttps://doi.org/10.1016/j.jmgm.2024.108842openalex-snapshot
Combining machine learning, molecular dynamics, and free energy analysis for (5HT)-2A receptor modulator classification
inferred← citeshttps://doi.org/10.1016/j.toxlet.2014.08.007openalex-snapshot
A human ether-á-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity
inferred← citeshttps://doi.org/10.1021/ci400631nopenalex-snapshot
A Refined Model of the HCV NS5A Protein Bound to Daclatasvir Explains Drug-Resistant Mutations and Activity against Divergent Genotypes
inferred← citeshttps://doi.org/10.1039/c8cp01843jopenalex-snapshot
Prediction of the binding mode and resistance profile for a dual-target pyrrolyl diketo acid scaffold against HIV-1 integrase and reverse-transcriptase-associated ribonuclease H
inferred← citeshttps://doi.org/10.1039/c8ra07346eopenalex-snapshot
Targeting HCV polymerase: a structural and dynamic perspective into the mechanism of selective covalent inhibition
inferred← citeshttps://doi.org/10.1039/d0cp00831aopenalex-snapshot
The application of the MM/GBSA method in the binding pose prediction of FGFR inhibitors
inferred← citeshttps://doi.org/10.1053/j.gastro.2014.07.019openalex-snapshot
Daclatasvir-Like Inhibitors of NS5A Block Early Biogenesis of Hepatitis C Virus–Induced Membranous Replication Factories, Independent of RNA Replication
inferred← citeshttps://doi.org/10.1080/07391102.2021.1930162openalex-snapshot
A ‘deep dive’ into the SARS-Cov-2 polymerase assembly: identifying novel allosteric sites and analyzing the hydrogen bond networks and correlated dynamics
inferred← citeshttps://doi.org/10.1080/17460441.2017.1291628openalex-snapshot
Applications of computer-aided approaches in the development of hepatitis C antiviral agents
inferred← citeshttps://doi.org/10.1371/journal.pone.0191905openalex-snapshot
Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel
inferred← citeshttps://doi.org/10.2147/dddt.s133944openalex-snapshot
Modeling the human Nav1.5 sodium channel: structural and mechanistic insights of ion permeation and drug blockade
inferred← citeshttps://doi.org/10.23860/diss-shen-yuanjun-2017openalex-snapshot
CES Involved Inhibition and Regulation
inferred← citeshttps://doi.org/10.3390/molecules27144530openalex-snapshot
The Inhibitory Potential of 2′-dihalo Ribonucleotides against HCV: Molecular Docking, Molecular Simulations, MM-BPSA, and DFT Studies
inferred← citeshttps://doi.org/10.4172/2376-0419.1000e127openalex-snapshot
Immune Checkpoints Inhibitors: A Single Antiviral and Anticancer Magic Bullet
inferred← citeshttps://doi.org/10.4172/2376-0419.1000e131openalex-snapshot
Modelling Off-target Interactions (I): Cardiotoxicity
inferred← citeshttps://doi.org/10.4172/2376-0419.1000e141openalex-snapshot
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