7RNW | pdb_00007rnw

SARS-CoV-2 Main Protease in complex with a cyclic peptide inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7RNW/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Severe acute respiratory syndrome coronavirus 2, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-30 Released: 2022-03-16 
• Deposition Author(s): Frkic, R.L., Jackson, C.J.
• Funding Organization(s): Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.231 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.171 (Depositor) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Antiviral cyclic peptides targeting the main protease of SARS-CoV-2.

Johansen-Leete, J., Ullrich, S., Fry, S.E., Frkic, R., Bedding, M.J., Aggarwal, A., Ashhurst, A.S., Ekanayake, K.B., Mahawaththa, M.C., Sasi, V.M., Luedtke, S., Ford, D.J., O'Donoghue, A.J., Passioura, T., Larance, M., Otting, G., Turville, S., Jackson, C.J., Nitsche, C., Payne, R.J.

(2022) Chem Sci 13: 3826-3836

• PubMed: 35432913 
• DOI: https://doi.org/10.1039/d1sc06750h
• Primary Citation Related Structures: 
  7RNW


• PubMed Abstract: 
  

  Antivirals that specifically target SARS-CoV-2 are needed to control the COVID-19 pandemic. The main protease (M ^pro ) is essential for SARS-CoV-2 replication and is an attractive target for antiviral development. Here we report the use of the Random nonstandard Peptide Integrated Discovery (RaPID) mRNA display on a chemically cross-linked SARS-CoV-2 M ^pro dimer, which yielded several high-affinity thioether-linked cyclic peptide inhibitors of the protease. Structural analysis of M ^pro complexed with a selenoether analogue of the highest-affinity peptide revealed key binding interactions, including glutamine and leucine residues in sites S1 and S2, respectively, and a binding epitope straddling both protein chains in the physiological dimer. Several of these M ^pro peptide inhibitors possessed antiviral activity against SARS-CoV-2 in vitro with EC ₅₀ values in the low micromolar range. These cyclic peptides serve as a foundation for the development of much needed antivirals that specifically target SARS-CoV-2.

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Organizational Affiliation: 
• School of Chemistry, The University of Sydney Sydney NSW 2006 Australia [e-mail].
Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney Sydney NSW 2006 Australia.
Research School of Chemistry, Australian National University Canberra ACT 2601 Australia [e-mail].
Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University Canberra ACT 2601 Australia.
Kirby Institute Sydney NSW 2052 Australia.
School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney Sydney NSW 2006 Australia.
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Dr. La Jolla CA 92093 USA.
School of Life and Environmental Sciences, The University of Sydney Sydney NSW 2006 Australia.
Sydney Analytical, The University of Sydney Sydney NSW 2006 Australia.
Charles Perkins Centre, The University of Sydney Sydney NSW 2006 Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 142.95 kDa 
• Atom Count: 9,819 
• Modeled Residue Count: 1,259 
• Deposited Residue Count: 1,284 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A, B, C, D	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-DTY-LEU-GLN-TYR-ALA-VAL-LEU-ARG-HIS-LYS-ARG-ARG-GLU-SEC	E [auth X], F [auth Y], G [auth Z], H [auth W]	15	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.231 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.171 (Depositor) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.36	α = 90
b = 201.726	β = 113.49
c = 60.543	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-16 
Deposition Author(s): Frkic, R.L., Jackson, C.J.

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Funding Organization	Location	Grant Number
Australian Research Council (ARC)	Australia	CE200100012

Revision History  

• Version 1.0: 2022-03-16
  Type: Initial release
  
• Version 1.1: 2022-05-04
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description