7KG8

Structure of human PARG complexed with PARG-061


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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

Brosey, C.A.Houl, J.H.Katsonis, P.Balapiti-Modarage, L.P.F.Bommagani, S.Arvai, A.Moiani, D.Bacolla, A.Link, T.Warden, L.S.Lichtarge, O.Jones, D.E.Ahmed, Z.Tainer, J.A.

(2021) Prog Biophys Mol Biol 163: 171-186

  • DOI: 10.1016/j.pbiomolbio.2021.02.002
  • Primary Citation of Related Structures:  
    7KFP, 7KG1, 7KG0, 7KG6, 7KG3, 7KG7, 7KG8, 7KXB, 7LG7

  • PubMed Abstract: 
  • Arrival of the novel SARS-CoV-2 has launched a worldwide effort to identify both pre-approved and novel therapeutics targeting the viral proteome, highlighting the urgent need for efficient drug discovery strategies. Even with effective vaccines, infection is possible, and at-risk populations would benefit from effective drug compounds that reduce the lethality and lasting damage of COVID-19 infection ...

    Arrival of the novel SARS-CoV-2 has launched a worldwide effort to identify both pre-approved and novel therapeutics targeting the viral proteome, highlighting the urgent need for efficient drug discovery strategies. Even with effective vaccines, infection is possible, and at-risk populations would benefit from effective drug compounds that reduce the lethality and lasting damage of COVID-19 infection. The CoV-2 MacroD-like macrodomain (Mac1) is implicated in viral pathogenicity by disrupting host innate immunity through its mono (ADP-ribosyl) hydrolase activity, making it a prime target for antiviral therapy. We therefore solved the structure of CoV-2 Mac1 from non-structural protein 3 (Nsp3) and applied structural and sequence-based genetic tracing, including newly determined A. pompejana MacroD2 and GDAP2 amino acid sequences, to compare and contrast CoV-2 Mac1 with the functionally related human DNA-damage signaling factor poly (ADP-ribose) glycohydrolase (PARG). Previously, identified targetable features of the PARG active site allowed us to develop a pharmacologically useful PARG inhibitor (PARGi). Here, we developed a focused chemical library and determined 6 novel PARGi X-ray crystal structures for comparative analysis. We applied this knowledge to discovery of CoV-2 Mac1 inhibitors by combining computation and structural analysis to identify PARGi fragments with potential to bind the distal-ribose and adenosyl pockets of the CoV-2 Mac1 active site. Scaffold development of these PARGi fragments has yielded two novel compounds, PARG-345 and PARG-329, that crystallize within the Mac1 active site, providing critical structure-activity data and a pathway for inhibitor optimization. The reported structural findings demonstrate ways to harness our PARGi synthesis and characterization pipeline to develop CoV-2 Mac1 inhibitors targeting the ADP-ribose active site. Together, these structural and computational analyses reveal a path for accelerating development of antiviral therapeutics from pre-existing drug optimization pipelines.


    Organizational Affiliation

    Department of Molecular and Cellular Oncology, M. D. Anderson Cancer Center, Houston, TX, 77030, USA; Department of Cancer Biology, M.D. Anderson Cancer Center, Houston, TX, 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. Electronic address: JTainer@mdanderson.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly(ADP-ribose) glycohydrolaseA531Homo sapiensMutation(s): 6 
Gene Names: PARG
EC: 3.2.1.143
UniProt & NIH Common Fund Data Resources
Find proteins for Q86W56 (Homo sapiens)
Explore Q86W56 
Go to UniProtKB:  Q86W56
PHAROS:  Q86W56
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
WDM (Subject of Investigation/LOI)
Query on WDM

Download Ideal Coordinates CCD File 
B [auth A]1,3-dimethyl-8-{[2-(morpholin-4-yl)-2-oxoethyl]sulfanyl}-6-sulfanylidene-1,3,6,7-tetrahydro-2H-purin-2-one
C13 H17 N5 O3 S2
KRPVEFPMIUNCJW-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC

Download Ideal Coordinates CCD File 
I [auth A]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], H [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.408α = 90
b = 89.201β = 90
c = 93.877γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA200231

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references