8EUA | pdb_00008eua

Structure of SARS-CoV2 PLpro bound to a covalent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8EUA/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-10-18 Released: 2023-04-05 
• Deposition Author(s): Mathews, I.I., Pokhrel, S., Wakatsuki, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.253 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 36977673 
• DOI: https://doi.org/10.1038/s41467-023-37254-w
• Primary Citation Related Structures: 
  8EUA


• 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.

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Organizational Affiliation: 
• Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. [e-mail].
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
Biological Sciences Division, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA.
Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
B-11 Bioenergy and Biome Sciences, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, USA.
Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, TN, USA.
Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, USA.
Progenra Inc., Malvern, PA, USA.
Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
Center for BioMolecular Structure, National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA.
Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA.
Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.
Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Department of Bioengineering, University of California, Berkeley, CA, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA.
Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA. [e-mail].
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, USA.
Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Computational and Data Sciences, Center for Research Acceleration by Digital Innovation, Amgen, Inc., Thosand Oaks, CA, USA.
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.94 kDa 
• Atom Count: 2,553 
• Modeled Residue Count: 311 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Papain-like protease nsp3	A	319	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.19.12 (PDB Primary Data), 3.4.22 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WUK (Subject of Investigation/LOI)	B [auth A]	methyl 4-{2-[3-(2-{[(1R)-1-(naphthalen-1-yl)ethyl]carbamoyl}phenyl)propanoyl]hydrazinyl}-4-oxobutanoate C27 H29 N3 O5 KCRIVPTZKJZJHI-GOSISDBHSA-N
SO4	F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.253 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.33	α = 90
b = 112.33	β = 90
c = 217.33	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-05 
Deposition Author(s): Mathews, I.I., Pokhrel, S., Wakatsuki, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133894
Department of Energy (DOE, United States)	United States	AC02-76SF00515

Revision History  

• Version 1.0: 2023-04-05
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary