In silico structural elucidation of Nipah virus L protein and targeting RNA-dependent RNA polymerase domain by nucleoside analogs

A dual mechanism of action of AT-527 against SARS-CoV-2 polymerase

(2022) Ashleigh Shannon et al.   Nature Communications

Molecular dynamics simulations and MM-GBSA reveal novel guanosine derivatives against SARS-CoV-2 RNA dependent RNA polymerase

(2022) Abdo A. Elfiky et al.   RSC Advances

AT-752, a double prodrug of a guanosine nucleotide analog, inhibits yellow fever virus in a hamster model

(2022) Kai Lin et al.   PLoS Neglected Tropical Diseases

Pharmacokinetics and Safety of the Nucleoside Analog Antiviral Drug Galidesivir Administered to Healthy Adult Subjects

(2022) Amanda Mathis et al.   Clinical Pharmacology in Drug Development

Multidimensional in silico strategy for identification of natural polyphenols-based SARS-CoV-2 main protease (Mpro) inhibitors to unveil a hope against COVID-19

(2022) Şevki Adem et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Interference of Chaga mushroom terpenoids with the attachment of SARS-CoV-2; in silico perspective

(2022) Wael M. Elshemey et al.   COMPUTERS IN BIOLOGY AND MEDICINE

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

DEMO2: Assemble multi-domain protein structures by coupling analogous template alignments with deep-learning inter-domain restraint prediction

(2022) Xiaogen Zhou et al.   NUCLEIC ACIDS RESEARCH

Investigating the structure-activity relationship of marine polycyclic batzelladine alkaloids as promising inhibitors for SARS-CoV-2 main protease (Mpro)

(2022) Alaa M. Elgohary et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Dual targeting of RdRps of SARS-CoV-2 and the mucormycosis-causing fungus: an in silico perspective

(2022) Abdo A Elfiky   Future Microbiology

Structural insights into RNA polymerases of negative-sense RNA viruses

(2021) Aartjan J. W. te Velthuis et al.   NATURE REVIEWS MICROBIOLOGY

Mechanism of SARS-CoV-2 polymerase stalling by remdesivir

(2021) Goran Kokic et al.   Nature Communications

Broad-Spectrum Antiviral Strategies and Nucleoside Analogues

(2021) Robert J. Geraghty et al.   Viruses-Basel

Strategy, Progress, and Challenges of Drug Repurposing for Efficient Antiviral Discovery

(2021) Xinlei Li et al.   Frontiers in Pharmacology

Evaluation of AT-752, a double prodrug of a guanosine nucleotide analog with in vitro and in vivo activity against dengue and other flaviviruses

(2021) Steven S. Good et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings

(2021) Jerome Eberhardt et al.   Journal of Chemical Information and Modeling

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

CryoEM structure of the Nipah virus nucleocapsid assembly

(2021) De-Sheng Ker et al.   PLoS Pathogens

An update on the progress of galidesivir (BCX4430), a broad-spectrum antiviral

(2021) Justin G. Julander et al.   ANTIVIRAL RESEARCH

gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS

(2021) Mario S. Valdés-Tresanco et al.   Journal of Chemical Theory and Computation

Structure of a rabies virus polymerase complex from electron cryo-microscopy

(2020) Joshua A. Horwitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of a paramyxovirus polymerase complex reveals a unique methyltransferase-CTD conformation

(2020) Ryan Abdella et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nipah Virus: Past Outbreaks and Future Containment

(2020) Vinod Soman Pillai et al.   Viruses-Basel

Anti-norovirus activity of C7-modified 4-amino-pyrrolo[2,1-f][1,2,4]triazine C-nucleosides

(2020) Qingfeng Li et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study

(2020) Abdo A. Elfiky   LIFE SCIENCES

Remdesivir: First Approval

(2020) Yvette N. Lamb   DRUGS

A combination of AT-527, a pan-genotypic guanosine nucleotide prodrug, and daclatasvir was well-tolerated and effective in HCV-infected subjects

(2020) Ounisha Mungur et al.   JOURNAL OF HEPATOLOGY

Structures of the Mononegavirales Polymerases

(2020) Bo Liang   JOURNAL OF VIROLOGY

Targeting the RdRp of Emerging RNA Viruses: The Structure-Based Drug Design Challenge

(2020) Francesca Picarazzi et al.   MOLECULES

Post-lockdown SARS-CoV-2 nucleic acid screening in nearly ten million residents of Wuhan, China

(2020) Shiyi Cao et al.   Nature Communications

Remdesivir Is Effective in Combating COVID-19 because It Is a Better Substrate than ATP for the Viral RNA-Dependent RNA Polymerase

(2020) Tyler L. Dangerfield et al.   iScience

First experience of ribavirin postexposure prophylaxis for Nipah virus, tried during the 2018 outbreak in Kerala, India

(2019) Sayantan Banerjee et al.   JOURNAL OF INFECTION

Remdesivir (GS-5734) protects African green monkeys from Nipah virus challenge

(2019) Michael K. Lo et al.   Science Translational Medicine

End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

(2019) Ercheng Wang et al.   CHEMICAL REVIEWS

RNA Synthesis and Capping by Non-segmented Negative Strand RNA Viral Polymerases: Lessons From a Prototypic Virus

(2019) Tomoaki Ogino et al.   Frontiers in Microbiology

Safety, pharmacokinetics and antiviral activity of AT-527, a novel purine nucleotide prodrug, in HCV-infected subjects with and without cirrhosis

(2019) Elina Berliba et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Structure of the Respiratory Syncytial Virus Polymerase Complex

(2019) Morgan S.A. Gilman et al.   CELL

Discovery of a non-nucleoside RNA polymerase inhibitor for blocking Zika virus replication through in silico screening

(2018) Aryamav Pattnaik et al.   ANTIVIRAL RESEARCH

Nipah Virus Infection

(2018) Brenda S. P. Ang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution

(2018) Sangita Venkataraman et al.   Viruses-Basel

Favipiravir (T-705) protects against Nipah virus infection in the hamster model

(2018) Brian E. Dawes et al.   Scientific Reports

Emerging trends of Nipah virus: A review

(2018) Vikrant Sharma et al.   REVIEWS IN MEDICAL VIROLOGY

TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries

(2018) Thibault Tubiana et al.   Journal of Chemical Information and Modeling

Molecular dynamics and MM/GBSA-integrated protocol probing the correlation between biological activities and binding free energies of HIV-1 TAR RNA inhibitors

(2017) Saikiran Reddy Peddi et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

RNA elongation by respiratory syncytial virus polymerase is calibrated by conserved region V

(2017) Molly R. Braun et al.   PLoS Pathogens

Computational protein–ligand docking and virtual drug screening with the AutoDock suite

(2016) Stefano Forli et al.   Nature Protocols

Mericitabine and Either Boceprevir or Telaprevir in Combination with Peginterferon Alfa-2a plus Ribavirin for Patients with Chronic Hepatitis C Genotype 1 Infection and Prior Null Response: The Randomized DYNAMO 1 and DYNAMO 2 Studies

(2016) Heiner Wedemeyer et al.   PLoS One

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

X-ray structure and activities of an essential Mononegavirales L-protein domain

(2015) Guido C. Paesen et al.   Nature Communications

Putative Domain-Domain Interactions in the Vesicular Stomatitis Virus L Polymerase Protein Appendage Region

(2014) J. B. Ruedas et al.   JOURNAL OF VIROLOGY

Protection against filovirus diseases by a novel broad-spectrum nucleoside analogue BCX4430

(2014) Travis K. Warren et al.   NATURE

Characterization of Hepatitis C Virus (HCV) Quasispecies Dynamics upon Short-Term Dual Therapy with the HCV NS5B Nucleoside Polymerase Inhibitor Mericitabine and the NS3/4 Protease Inhibitor Danoprevir

(2012) S. Le Pogam et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Recent progress in structure-based anti-influenza drug design

(2012) Juan Du et al.   DRUG DISCOVERY TODAY

Therapeutics for filovirus infection: traditional approaches and progress towardsin silicodrug design

(2012) Amy C Shurtleff et al.   Expert Opinion on Drug Discovery

INX-08189, a Phosphoramidate Prodrug of 6-O-Methyl-2′-C-Methyl Guanosine, Is a Potent Inhibitor of Hepatitis C Virus Replication with Excellent Pharmacokinetic and Pharmacodynamic Properties

(2011) John H. Vernachio et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions

(2011) Maxim V. Shapovalov et al.   STRUCTURE

Open Babel: An open chemical toolbox

(2011) Noel M O'Boyle et al.   Journal of Cheminformatics

Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

(2010) Freddie R Salsbury Jr   CURRENT OPINION IN PHARMACOLOGY

Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase

(2010) P. Gong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combined chloroquine and ribavirin treatment does not prevent death in a hamster model of Nipah and Hendra virus infection

(2009) A. N. Freiberg et al.   JOURNAL OF GENERAL VIROLOGY

Antiviral Compounds Discovered by Virtual Screening of Small−Molecule Libraries against Dengue Virus E Protein

(2008) Zhigang Zhou et al.   ACS Chemical Biology

Debio 025, a Cyclophilin Binding Molecule, Is Highly Efficient in Clearing Hepatitis C Virus (HCV) Replicon-Containing Cells When Used Alone or in Combination with Specifically Targeted Antiviral Therapy for HCV (STAT-C) Inhibitors

(2008) L. Coelmont et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY