Screening Malaria-box compounds to identify potential inhibitors against SARS-CoV-2 Mpro, using molecular docking and dynamics simulation studies

[1]  Leonardo Bruno Federico,et al.  Virtual screening, ADME/Tox predictions and the drug repurposing concept for future use of old drugs against the COVID-19 , 2020, Life Sciences.

[2]  Q. Shao.  Effect of conjugated (EK)10 peptide on structural and dynamic properties of ubiquitin protein: a molecular dynamics simulation study. , 2020, Journal of materials chemistry. B.

[3]  T. Jin,et al.  Designing of improved drugs for COVID-19: Crystal structure of SARS-CoV-2 main protease Mpro , 2020, Signal Transduction and Targeted Therapy.

[4]  F. Romanelli,et al.  Rapid repurposing of drugs for COVID-19 , 2020, Science.

[5]  R. D’Aquila,et al.  Broad-spectrum inhibition of coronavirus main and papain-like proteases by HCV drugs , 2020 .

[6]  Z. Jin,et al.  THE CRYSTAL STRUCTURE OF COVID-19 MAIN PROTEASE IN COMPLEX WITH AN INHIBITOR N3 at 1.7 angstrom , 2020 .

[7]  Hualiang Jiang,et al.  Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease , 2020, Science.

[8]  G. Montelione,et al.  Structural Similarity of SARS-CoV2 Mpro and HCV NS3/4A Proteases Suggests New Approaches for Identifying Existing Drugs Useful as COVID-19 Therapeutics , 2020, ChemRxiv : the preprint server for chemistry.

[9]  Bafna Khushboo.  Structural Similarity of SARS-CoV2 Mpro and HCV NS3/4A Proteases Suggests New Approaches for Identifying Existing Drugs Useful as COVID-19 Therapeutics , 2020 .

[10]  Hualiang Jiang,et al.  Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors , 2020, Nature.

[11]  Mandeep R. Mehra,et al.  COVID-19 illness in native and immunosuppressed states: A clinical–therapeutic staging proposal , 2020, The Journal of Heart and Lung Transplantation.

[12]  R. Hilgenfeld,et al.  Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors , 2020, Science.

[13]  Xu Liu,et al.  In Vitro Antiviral Activity and Projection of Optimized Dosing Design of Hydroxychloroquine for the Treatment of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) , 2020, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[14]  Christel Faes,et al.  Estimating the generation interval for COVID-19 based on symptom onset data , 2020, medRxiv.

[15]  G. Chowell,et al.  Estimating the asymptomatic proportion of coronavirus disease 2019 (COVID-19) cases on board the Diamond Princess cruise ship, Yokohama, Japan, 2020 , 2020, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[16]  Yechun Xu,et al.  Structure of Mpro from COVID-19 virus and discovery of its inhibitors , 2020, bioRxiv.

[17]  Mubarak A. Alamri,et al.  Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants , 2020, Journal of Pharmaceutical Analysis.

[18]  Gengfu Xiao,et al.  Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro , 2020, Cell Research.

[19]  R. Kruse.  Therapeutic strategies in an outbreak scenario to treat the novel coronavirus originating in Wuhan, China , 2020, F1000Research.

[20]  Qianyun Liu,et al.  Emerging coronaviruses: Genome structure, replication, and pathogenesis , 2020, Journal of medical virology.

[21]  Kavita Sharma,et al.  Structural and functional alterations of nitric oxide synthase 3 due to missense variants associate with high-altitude pulmonary edema through dynamic study , 2020, Journal of biomolecular structure & dynamics.

[22]  D. Shin,et al.  Inhibition of SARS-CoV 3CL protease by flavonoids , 2019, Journal of enzyme inhibition and medicinal chemistry.

[23]  Asimul Islam,et al.  2/3D-QSAR, molecular docking and MD simulation studies of FtsZ protein targeting benzimidazoles derivatives , 2019, Comput. Biol. Chem..

[24]  Wei Tian,et al.  CASTp 3.0: computed atlas of surface topography of proteins , 2018, Nucleic Acids Res..

[25]  M. I. Hassan,et al.  Designing of phenol-based β−carbonic anhydrase1 inhibitors through QSAR, molecular docking, and MD simulation approach , 2018, 3 Biotech.

[26]  Xiaotao Lu,et al.  Coronavirus Susceptibility to the Antiviral Remdesivir (GS-5734) Is Mediated by the Viral Polymerase and the Proofreading Exoribonuclease , 2018, mBio.

[27]  Radka Svobodová Vařeková,et al.  PDBsum: Structural summaries of PDB entries , 2017, Protein science : a publication of the Protein Society.

[28]  Jiguo Cao,et al.  Parametric functional principal component analysis , 2017, Biometrics.

[29]  Olivier Michielin,et al.  SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules , 2017, Scientific Reports.

[30]  Christopher A Lipinski,et al.  Rule of five in 2015 and beyond: Target and ligand structural limitations, ligand chemistry structure and drug discovery project decisions. , 2016, Advanced drug delivery reviews.

[31]  Ruth Huey,et al.  Computational protein–ligand docking and virtual drug screening with the AutoDock suite , 2016, Nature Protocols.

[32]  Haitao Yang,et al.  Structure of Main Protease from Human Coronavirus NL63: Insights for Wide Spectrum Anti-Coronavirus Drug Design , 2016, Scientific Reports.

[33]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[34]  Jeremy N. Burrows,et al.  The Open Access Malaria Box: A Drug Discovery Catalyst for Neglected Diseases , 2013, PloS one.

[35]  Z. Rao,et al.  The newly emerged SARS-Like coronavirus HCoV-EMC also has an “Achilles’ heel”: current effective inhibitor targeting a 3C-like protease , 2013, Protein & Cell.

[36]  V. Avery,et al.  Development and Optimization of a Novel 384-Well Anti-Malarial Imaging Assay Validated for High-Throughput Screening , 2012, The American journal of tropical medicine and hygiene.

[37]  H. Abdi,et al.  Principal component analysis , 2010 .

[38]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[39]  Z. Rao,et al.  Structures of Two Coronavirus Main Proteases: Implications for Substrate Binding and Antiviral Drug Design , 2007, Journal of Virology.

[40]  Yoko Fukuda,et al.  An Evolutionarily Conserved Mechanism for MicroRNA-223 Expression Revealed by MicroRNA Gene Profiling , 2007, Cell.

[41]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[42]  K. Yuen,et al.  Correction: Design of Wide-Spectrum Inhibitors Targeting Coronavirus Main Proteases , 2005, PLoS Biology.

[43]  M. Hsu,et al.  Mechanism of the Maturation Process of SARS-CoV 3CL Protease , 2005, Journal of Biological Chemistry.

[44]  A. W. Schüttelkopf,et al.  PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. , 2004, Acta crystallographica. Section D, Biological crystallography.

[45]  Jie Liang,et al.  CASTp: Computed Atlas of Surface Topography of proteins , 2003, Nucleic Acids Res..

[46]  Rolf Hilgenfeld,et al.  Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of Anti-SARS Drugs , 2003, Science.

[47]  W. Patrick Walters,et al.  A guide to drug discovery: Designing screens: how to make your hits a hit , 2003, Nature Reviews Drug Discovery.

[48]  Arup K. Ghose,et al.  Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics , 1989, J. Chem. Inf. Comput. Sci..

[49]  M. Stepanova,et al.  Probing oligomerization of amyloid beta peptide in silico. , 2016, Molecular bioSystems.