7P2G | pdb_00007p2g

Identification of low micromolar SARS-CoV-2 Mpro inhibitors from hits identified by in silico screens

• PDB DOI: https://doi.org/10.2210/pdb7P2G/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-05 Released: 2022-05-04 
• Deposition Author(s): Rempel, S., Halazonetis, T.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.277 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

Non-covalent SARS-CoV-2 M pro inhibitors developed from in silico screen hits.

Rossetti, G.G., Ossorio, M.A., Rempel, S., Kratzel, A., Dionellis, V.S., Barriot, S., Tropia, L., Gorgulla, C., Arthanari, H., Thiel, V., Mohr, P., Gamboni, R., Halazonetis, T.D.

(2022) Sci Rep 12: 2505-2505

• PubMed: 35169179 
• DOI: https://doi.org/10.1038/s41598-022-06306-4
• Primary Citation Related Structures: 
  7P2G


• PubMed Abstract: 
  

  M ^pro , the main protease of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is essential for the viral life cycle. Accordingly, several groups have performed in silico screens to identify M ^pro inhibitors that might be used to treat SARS-CoV-2 infections. We selected more than five hundred compounds from the top-ranking hits of two very large in silico screens for on-demand synthesis. We then examined whether these compounds could bind to M ^pro and inhibit its protease activity. Two interesting chemotypes were identified, which were further evaluated by characterizing an additional five hundred synthesis on-demand analogues. The compounds of the first chemotype denatured M ^pro and were considered not useful for further development. The compounds of the second chemotype bound to and enhanced the melting temperature of M ^pro . The most active compound from this chemotype inhibited M ^pro in vitro with an IC ₅₀ value of 1 μM and suppressed replication of the SARS-CoV-2 virus in tissue culture cells. Its mode of binding to M ^pro was determined by X-ray crystallography, revealing that it is a non-covalent inhibitor. We propose that the inhibitors described here could form the basis for medicinal chemistry efforts that could lead to the development of clinically relevant inhibitors.

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Organizational Affiliation: 
• Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland.
FoRx Therapeutics AG, 4056, Basel, Switzerland.
Institute of Virology and Immunology, University of Bern, 3012, Bern, Switzerland.
Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012, Bern, Switzerland.
Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA, 02115, USA.
Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, 02138, USA.
Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.
NANDASI Pharma Advisors, 4123, Allschwil, Switzerland.
Department of Molecular Biology, University of Geneva, 1205, Geneva, Switzerland. [e-mail].
FoRx Therapeutics AG, 4056, Basel, Switzerland. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.22 kDa 
• Atom Count: 2,383 
• Modeled Residue Count: 305 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  Gene Names: ORF1ab EC: 2.7.7.48 (PDB Primary Data), 3.4.19.12 (PDB Primary Data), 3.4.22.69 (PDB Primary Data), 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4N0 (Subject of Investigation/LOI)	B [auth A]	(4~{R})-~{N}-(4-iodophenyl)-2-oxidanylidene-3,4-dihydro-1~{H}-quinoline-4-carboxamide C16 H13 I N2 O2 DDBKMCQLKKZOJH-CYBMUJFWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.277 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.61	α = 90
b = 53.79	β = 100.976
c = 45.44	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-05-04 
Deposition Author(s): Rempel, S., Halazonetis, T.D.

Revision History  

• Version 1.0: 2022-05-04
  Type: Initial release
  
• Version 1.1: 2022-05-11
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description