Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors

Journal Article · · Progress in Biophysics and Molecular Biology
Not Available
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231; AC02-06CH11357; AC02-76SF00515; SC0012704
OSTI ID:
1766903
Alternate ID(s):
OSTI ID: 1808955
OSTI ID: 1810840
OSTI ID: 1812927
OSTI ID: 1813416
Journal Information:
Progress in Biophysics and Molecular Biology, Journal Name: Progress in Biophysics and Molecular Biology Journal Issue: C Vol. 163; ISSN 0079-6107
Publisher:
ElsevierCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (75)

UCSF Chimera?A visualization system for exploratory research and analysis journal January 2004
An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families journal March 1996
T-coffee: a novel method for fast and accurate multiple sequence alignment 1 1Edited by J. Thornton journal September 2000
Cancer patients in SARS-CoV-2 infection: a nationwide analysis in China journal March 2020
Genomic evidence for reinfection with SARS-CoV-2: a case study journal January 2021
Targeting Allostery with Avatars to Design Inhibitors Assessed by Cell Activity: Dissecting MRE11 Endo- and Exonuclease Activities book January 2018
PARG has a robust endo-glycohydrolase activity that releases protein-free poly(ADP-ribose) chains journal June 2020
Imbalanced Host Response to SARS-CoV-2 Drives Development of COVID-19 journal May 2020
Synthesis and biological evaluation of novel xanthine derivatives as potential apoptotic antitumor agents journal August 2019
Update on therapeutic approaches and emerging therapies for SARS-CoV-2 virus journal September 2020
Cytokine release syndrome in severe COVID-19: interleukin-6 receptor antagonist tocilizumab may be the key to reduce mortality journal May 2020
Sequence homology between human PARP14 and the SARS-CoV-2 ADP ribose 1’-phosphatase journal August 2020
A Family of Evolution–Entropy Hybrid Methods for Ranking Protein Residues by Importance journal March 2004
Superoxide Dismutase from the Eukaryotic Thermophile Alvinella pompejana: Structures, Stability, Mechanism, and Insights into Amyotrophic Lateral Sclerosis journal February 2009
DNA Double-Strand Break Repair Pathway Choice Is Directed by Distinct MRE11 Nuclease Activities journal January 2014
Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor journal December 2016
Viral Macrodomains: Unique Mediators of Viral Replication and Pathogenesis journal July 2018
Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions journal March 2013
Molecular Basis for ADP-Ribose Binding to the Mac1 Domain of SARS-CoV-2 nsp3 journal June 2020
Structural, Biophysical, and Biochemical Elucidation of the SARS-CoV-2 Nonstructural Protein 3 Macro Domain journal September 2020
Caffeine-Based Gold(I) N -Heterocyclic Carbenes as Possible Anticancer Agents: Synthesis and Biological Properties journal December 2013
Synthesis of Dimeric ADP-Ribose and Its Structure with Human Poly(ADP-ribose) Glycohydrolase journal March 2015
The reactivity of anti-peptide antibodies is a function of the atomic mobility of sites in a protein journal November 1984
The structure and catalytic mechanism of a poly(ADP-ribose) glycohydrolase journal September 2011
Anchored plasticity opens doors for selective inhibitor design in nitric oxide synthase journal October 2008
PARP9 and PARP14 cross-regulate macrophage activation via STAT1 ADP-ribosylation journal October 2016
PARP9-DTX3L ubiquitin ligase targets host histone H2BJ and viral 3C protease to enhance interferon signaling and control viral infection journal December 2015
Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element journal May 2012
A family of macrodomain proteins reverses cellular mono-ADP-ribosylation journal March 2013
Selective small molecule PARG inhibitor causes replication fork stalling and cancer cell death journal December 2019
A pneumonia outbreak associated with a new coronavirus of probable bat origin journal February 2020
Identifying SARS-CoV-2 related coronaviruses in Malayan pangolins journal March 2020
In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication journal August 2020
The use of phosphate bioisosteres in medicinal chemistry and chemical biology journal January 2012
Clinical Characteristics of Coronavirus Disease 2019 in China journal April 2020
ADP-ribosylhydrolase activity of Chikungunya virus macrodomain is critical for virus replication and virulence journal January 2017
The ARTT motif and a unified structural understanding of substrate recognition in ADP-ribosylating bacterial toxins and eukaryotic ADP-ribosyltransferases journal January 2001
PyETV: a PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes journal October 2010
UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches journal November 2014
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms journal May 2018
Molecular Evolutionary Genetics Analysis (MEGA) for macOS journal January 2020
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal September 1997
MUSCLE: multiple sequence alignment with high accuracy and high throughput journal March 2004
AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints journal July 2005
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee journal July 2006
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins journal January 2007
XRCC1 promotes replication restart, nascent fork degradation and mutagenic DNA repair in BRCA2-deficient cells journal August 2020
Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential journal November 2020
PARP and PARG inhibitors in cancer treatment journal February 2020
(ADP-ribosyl)hydrolases: structure, function, and biology journal February 2020
Coot model-building tools for molecular graphics journal November 2004
New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection journal November 2008
electronic Ligand Builder and Optimization Workbench ( eLBOW ): a tool for ligand coordinate and restraint generation journal September 2009
XDS journal January 2010
Overview of the CCP 4 suite and current developments journal March 2011
Phaser.MRage : automated molecular replacement journal October 2013
The Stanford Automated Mounter: pushing the limits of sample exchange at the SSRL macromolecular crystallography beamlines journal February 2016
Crystal structures of SARS-CoV-2 ADP-ribose phosphatase: from the apo form to ligand complexes journal July 2020
Polder maps: improving OMIT maps by excluding bulk solvent journal February 2017
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix journal October 2019
Drug Discovery Strategies for SARS-CoV-2 journal July 2020
Targeting dePARylation selectively suppresses DNA repair–defective and PARP inhibitor–resistant malignancies journal April 2019
Structural basis for allosteric PARP-1 retention on DNA breaks journal April 2020
Poly(ADP-Ribose) (PAR) Binding to Apoptosis-Inducing Factor Is Critical for PAR Polymerase-1-Dependent Cell Death (Parthanatos) journal April 2011
The nsp3 Macrodomain Promotes Virulence in Mice with Coronavirus-Induced Encephalitis journal November 2014
The Conserved Coronavirus Macrodomain Promotes Virulence and Suppresses the Innate Immune Response during Severe Acute Respiratory Syndrome Coronavirus Infection journal December 2016
Both ADP-Ribosyl-Binding and Hydrolase Activities of the Alphavirus nsP3 Macrodomain Affect Neurovirulence in Mice journal February 2020
Macrodomains: Structure, Function, Evolution, and Catalytic Activities journal June 2016
The MRE11–RAD50–NBS1 Complex Conducts the Orchestration of Damage Signaling and Outcomes to Stress in DNA Replication and Repair journal June 2018
Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability journal January 2013
Structures of the Human Poly (ADP-Ribose) Glycohydrolase Catalytic Domain Confirm Catalytic Mechanism and Explain Inhibition by ADP-HPD Derivatives journal December 2012
The coronavirus macrodomain is required to prevent PARP-mediated inhibition of virus replication and enhancement of IFN expression journal May 2019
A Putative Role of de-Mono-ADP-Ribosylation of STAT1 by the SARS-CoV-2 Nsp3 Protein in the Cytokine Storm Syndrome of COVID-19 journal June 2020
PARP14 Controls the Nuclear Accumulation of a Subset of Type I IFN–Inducible Proteins journal March 2018
Collaboration gets the most out of software journal September 2013