Structure of SARS-CoV2 PLpro bound to a covalent inhibitor

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Potent and selective covalent inhibition of the papain-like protease from SARS-CoV-2.

Sanders, B.C.Pokhrel, S.Labbe, A.D.Mathews, I.I.Cooper, C.J.Davidson, R.B.Phillips, G.Weiss, K.L.Zhang, Q.O'Neill, H.Kaur, M.Schmidt, J.G.Reichard, W.Surendranathan, S.Parvathareddy, J.Phillips, L.Rainville, C.Sterner, D.E.Kumaran, D.Andi, B.Babnigg, G.Moriarty, N.W.Adams, P.D.Joachimiak, A.Hurst, B.L.Kumar, S.Butt, T.R.Jonsson, C.B.Ferrins, L.Wakatsuki, S.Galanie, S.Head, M.S.Parks, J.M.

(2023) Nat Commun 14: 1733-1733

  • DOI: https://doi.org/10.1038/s41467-023-37254-w
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we design a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibits PLpro with k inact /K I  = 9,600 M -1 s -1 , achieves sub-μM EC 50 values against three SARS-CoV-2 variants in mammalian cell lines, and does not inhibit a panel of human deubiquitinases (DUBs) at >30 μM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validates our design strategy and establishes the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.

  • Organizational Affiliation

    Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. sandersbc@ornl.gov.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease nsp3319Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: (PDB Primary Data), 3.4.22 (PDB Primary Data)
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.195 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.33α = 90
b = 112.33β = 90
c = 217.33γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30GM133894
Department of Energy (DOE, United States)United StatesAC02-76SF00515

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-05
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description