Papain-like protease regulates SARS-CoV-2 viral spread and innate immunity

[1]  Y. Hu,et al.  [Asymptomatic infection of COVID-19 and its challenge to epidemic prevention and control]. , 2020, Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi.

[2]  A. Shanker,et al.  Whole-genome sequence analysis and homology modelling of the main protease and non-structural protein 3 of SARS-CoV-2 reveal an aza-peptide and a lead inhibitor with possible antiviral properties , 2020, New Journal of Chemistry.

[3]  Yu Wai Chen,et al.  Simeprevir Potently Suppresses SARS-CoV-2 Replication and Synergizes with Remdesivir , 2020, bioRxiv.

[4]  Ian A. Durie,et al.  Characterization and Noncovalent Inhibition of the Deubiquitinase and deISGylase Activity of SARS-CoV-2 Papain-Like Protease , 2020, ACS infectious diseases.

[5]  S. Ciesek,et al.  Proteomics of SARS-CoV-2-infected host cells reveals therapy targets , 2020, Nature.

[6]  R. Schwartz,et al.  Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19 , 2020, Cell.

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

[8]  Benjamin J. Polacco,et al.  A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing , 2020, Nature.

[9]  Zongyang Lv,et al.  Activity profiling and structures of inhibitor-bound SARS-CoV-2-PLpro protease provides a framework for anti-COVID-19 drug design , 2020, bioRxiv.

[10]  Björn Rotter,et al.  Optimized qRT-PCR Approach for the Detection of Intra- and Extra-Cellular SARS-CoV-2 RNAs , 2020, bioRxiv.

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

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

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

[14]  Hyeshik Chang,et al.  The Architecture of SARS-CoV-2 Transcriptome , 2020, Cell.

[15]  Hualiang Jiang,et al.  Structure of Mpro from COVID-19 virus and discovery of its inhibitors , 2020, bioRxiv.

[16]  Kai Zhao,et al.  A pneumonia outbreak associated with a new coronavirus of probable bat origin , 2020, Nature.

[17]  E. Holmes,et al.  Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding , 2020, The Lancet.

[18]  B. Schulman,et al.  NEDD8 nucleates a multivalent cullin-RING-UBE2D ubiquitin ligation assembly , 2020, Nature.

[19]  Victor M Corman,et al.  Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR , 2020, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[20]  C. Münch,et al.  Functional Translatome Proteomics Reveal Converging and Dose-Dependent Regulation by mTORC1 and eIF2α , 2019, Molecular cell.

[21]  Karthik Srinivasan,et al.  Decoupling deISGylating and deubiquitinating activities of the MERS virus papain-like protease , 2019, Antiviral Research.

[22]  Mark N. Wass,et al.  Doxorubicin-loaded human serum albumin nanoparticles overcome transporter-mediated drug resistance in drug-adapted cancer cells , 2019, bioRxiv.

[23]  Gerbrand J. van der Heden van Noort,et al.  Profiling DUBs and Ubl-specific proteases with activity-based probes , 2019, Methods in Enzymology.

[24]  Fredrik Levander,et al.  NormalyzerDE: Online Tool for Improved Normalization of Omics Expression Data and High-Sensitivity Differential Expression Analysis. , 2018, Journal of proteome research.

[25]  Christian Drosten,et al.  The papain-like protease determines a virulence trait that varies among members of the SARS-coronavirus species , 2018, PLoS pathogens.

[26]  S. Pegan,et al.  Structurally Guided Removal of DeISGylase Biochemical Activity from Papain-Like Protease Originating from Middle East Respiratory Syndrome Coronavirus , 2017, Journal of Virology.

[27]  Shao-Cong Sun,et al.  NF-κB signaling in inflammation , 2017, Signal Transduction and Targeted Therapy.

[28]  A. Mesecar,et al.  Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species , 2017, Journal of Molecular Biology.

[29]  K. Knobeloch,et al.  Structural basis of the specificity of USP18 toward ISG15 , 2017, Nature Structural &Molecular Biology.

[30]  Marco Y. Hein,et al.  The Perseus computational platform for comprehensive analysis of (prote)omics data , 2016, Nature Methods.

[31]  Christopher D. Lima,et al.  Recognition of Lys48-Linked Di-ubiquitin and Deubiquitinating Activities of the SARS Coronavirus Papain-like Protease , 2016, Molecular Cell.

[32]  Gerbrand J. van der Heden van Noort,et al.  Non-hydrolyzable Diubiquitin Probes Reveal Linkage-Specific Reactivity of Deubiquitylating Enzymes Mediated by S2 Pockets , 2016, Cell chemical biology.

[33]  José A. Dianes,et al.  2016 update of the PRIDE database and its related tools , 2015, Nucleic Acids Res..

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

[35]  Paul Robustelli,et al.  Water dispersion interactions strongly influence simulated structural properties of disordered protein states. , 2015, The journal of physical chemistry. B.

[36]  Brian L. Mark,et al.  Crystal Structure of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Papain-like Protease Bound to Ubiquitin Facilitates Targeted Disruption of Deubiquitinating Activity to Demonstrate Its Role in Innate Immune Suppression , 2014, The Journal of Biological Chemistry.

[37]  S. Vogel,et al.  An essential role for IFN-β in the induction of IFN-stimulated gene expression by LPS in macrophages , 2014, Journal of leukocyte biology.

[38]  K. Knobeloch,et al.  Molecular characterization of ubiquitin‐specific protease 18 reveals substrate specificity for interferon‐stimulated gene 15 , 2014, The FEBS journal.

[39]  Michael W. Wilson,et al.  X-ray Structural and Biological Evaluation of a Series of Potent and Highly Selective Inhibitors of Human Coronavirus Papain-like Proteases , 2014, Journal of medicinal chemistry.

[40]  Andrew R. Jones,et al.  ProteomeXchange provides globally co-ordinated proteomics data submission and dissemination , 2014, Nature Biotechnology.

[41]  Andy Kilianski,et al.  Cell-based antiviral screening against coronaviruses: Developing virus-specific and broad-spectrum inhibitors , 2013, Antiviral Research.

[42]  H. Mootz,et al.  Covalent inhibition of SUMO and ubiquitin-specific cysteine proteases by an in situ thiol-alkyne addition. , 2013, Bioorganic & medicinal chemistry.

[43]  A. Scholten,et al.  On Terminal Alkynes That Can React with Active-Site Cysteine Nucleophiles in Proteases , 2013, Journal of the American Chemical Society.

[44]  H. Ren,et al.  DNA-PK is a DNA sensor for IRF-3-dependent innate immunity , 2012, eLife.

[45]  Matthias Peter,et al.  Structural basis for a reciprocal regulation between SCF and CSN. , 2012, Cell reports.

[46]  R. Best,et al.  Residue-specific α-helix propensities from molecular simulation. , 2012, Biophysical journal.

[47]  P. Zwart,et al.  Towards automated crystallographic structure refinement with phenix.refine , 2012, Acta crystallographica. Section D, Biological crystallography.

[48]  Herwig P. Moll,et al.  The differential activity of interferon-α subtypes is consistent among distinct target genes and cell types , 2011, Cytokine.

[49]  Debbie C. Mulhearn,et al.  Severe acute respiratory syndrome coronavirus papain-like novel protease inhibitors: design, synthesis, protein-ligand X-ray structure and biological evaluation. , 2010, Journal of medicinal chemistry.

[50]  Yufei Shan,et al.  Positive Regulation of Interferon Regulatory Factor 3 Activation by Herc5 via ISG15 Modification , 2010, Molecular and Cellular Biology.

[51]  R. Dror,et al.  Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.

[52]  Katrina Sleeman,et al.  Structure-based design, synthesis, and biological evaluation of a series of novel and reversible inhibitors for the severe acute respiratory syndrome-coronavirus papain-like protease. , 2009, Journal of medicinal chemistry.

[53]  G. Hummer,et al.  Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. , 2009, The journal of physical chemistry. B.

[54]  R. Johnston,et al.  Severe Acute Respiratory Syndrome Coronavirus Papain-Like Protease Ubiquitin-Like Domain and Catalytic Domain Regulate Antagonism of IRF3 and NF-κB Signaling , 2009, Journal of Virology.

[55]  Wentao Fu,et al.  A noncovalent class of papain-like protease/deubiquitinase inhibitors blocks SARS virus replication , 2008, Proceedings of the National Academy of Sciences.

[56]  Zhongbin Chen,et al.  Regulation of IRF-3-dependent Innate Immunity by the Papain-like Protease Domain of the Severe Acute Respiratory Syndrome Coronavirus , 2007, Journal of Biological Chemistry.

[57]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[58]  V. Hornak,et al.  Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.

[59]  R. Medzhitov,et al.  Type I interferons in host defense. , 2006, Immunity.

[60]  Sachiko Sato,et al.  Galectin-1 Acts as a Soluble Host Factor That Promotes HIV-1 Infectivity through Stabilization of Virus Attachment to Host Cells1 , 2005, The Journal of Immunology.

[61]  John Bechill,et al.  Identification of Severe Acute Respiratory Syndrome Coronavirus Replicase Products and Characterization of Papain-Like Protease Activity , 2004, Journal of Virology.

[62]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[63]  M. Mann,et al.  Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. , 2003, Analytical chemistry.

[64]  L. F. Ng,et al.  Identification of a Novel Cleavage Activity of the First Papain-Like Proteinase Domain Encoded by Open Reading Frame 1a of the Coronavirus Avian Infectious Bronchitis Virus and Characterization of the Cleavage Products , 2000, Journal of Virology.

[65]  H. Chapman,et al.  Cross-class inhibition of the cysteine proteinases cathepsins K, L, and S by the serpin squamous cell carcinoma antigen 1: a kinetic analysis. , 1998, Biochemistry.

[66]  T. Takahashi,et al.  Squamous cell carcinoma antigen is a potent inhibitor of cysteine proteinase cathepsin L , 1995, FEBS letters.

[67]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[68]  Denis J. Evans,et al.  The Nose–Hoover thermostat , 1985 .

[69]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[70]  S. Nosé A unified formulation of the constant temperature molecular dynamics methods , 1984 .

[71]  T. Mosmann Rapid colorimetric assay for cellular growth and survival: application to proliferation and cytotoxicity assays. , 1983, Journal of immunological methods.

[72]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[73]  P. Langridge,et al.  BMC Molecular Biology BioMed Central , 2006 .

[74]  Karen N. Allen,et al.  research papers Acta Crystallographica Section D Biological , 2003 .

[75]  W. Delano The PyMOL Molecular Graphics System , 2002 .