8ACL | pdb_00008acl

Crystal structure of SARS-CoV-2 main protease (MPro) in complex with the non-covalent inhibitor GC-14

• PDB DOI: https://doi.org/10.2210/pdb8ACL/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-05 Released: 2022-09-28 
• Deposition Author(s): Strater, N., Muller, C., Sylvester, K., Claff, T., Weisse, R.H., Gao, S., Tollefson, A.E., Liu, X., Zhan, P.
• Funding Organization(s): Volkswagen Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: experimental

Literature

Discovery and Crystallographic Studies of Trisubstituted Piperazine Derivatives as Non-Covalent SARS-CoV-2 Main Protease Inhibitors with High Target Specificity and Low Toxicity.

Gao, S., Sylvester, K., Song, L., Claff, T., Jing, L., Woodson, M., Weisse, R.H., Cheng, Y., Schakel, L., Petry, M., Gutschow, M., Schiedel, A.C., Strater, N., Kang, D., Xu, S., Toth, K., Tavis, J., Tollefson, A.E., Muller, C.E., Liu, X., Zhan, P.

(2022) J Med Chem 65: 13343-13364

• PubMed: 36107752 
• DOI: https://doi.org/10.1021/acs.jmedchem.2c01146
• Primary Citation Related Structures: 
  8ACD, 8ACL


• PubMed Abstract: 
  

  The continuous spread of SARS-CoV-2 calls for more direct-acting antiviral agents to combat the highly infectious variants. The main protease (M ^pro ) is an promising target for anti-SARS-CoV-2 drug design. Here, we report the discovery of potent non-covalent non-peptide M ^pro inhibitors featuring a 1,2,4-trisubstituted piperazine scaffold. We systematically modified the non-covalent hit MCULE-5948770040 by structure-based rational design combined with multi-site binding and privileged structure assembly strategies. The optimized compound GC-14 inhibits M ^pro with high potency (IC ₅₀ = 0.40 μM) and displays excellent antiviral activity (EC ₅₀ = 1.1 μM), being more potent than Remdesivir. Notably, GC-14 exhibits low cytotoxicity (CC ₅₀ > 100 μM) and excellent target selectivity for SARS-CoV-2 M ^pro (IC ₅₀ > 50 μM for cathepsins B, F, K, L, and caspase 3). X-ray co-crystal structures prove that the inhibitors occupy multiple subpockets by critical non-covalent interactions. These studies may provide a basis for developing a more efficient and safer therapy for COVID-19.

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Organizational Affiliation: 
• Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China.
Shenzhen Research Institute of Shandong University, A301 Virtual University Park in South District of Shenzhen, Guangdong 518057, P. R. China.
PharmaCenter Bonn & Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn 53113, Germany.
Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri 63103, United States.
Saint Louis University Institute for Drug and Biotherapeutic Innovation, St. Louis, Missouri 63103, United States.
Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Deutscher Platz 5, Leipzig 04103, Germany.

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: 34.3 kDa 
• Atom Count: 2,792 
• Modeled Residue Count: 301 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LQL (Subject of Investigation/LOI)	B [auth A]	(2~{S})-1-(3,4-dichlorophenyl)-4-pyridin-3-ylcarbonyl-~{N}-(thiophen-2-ylmethyl)piperazine-2-carboxamide C22 H20 Cl2 N4 O2 S XEFYJHCPILXFKJ-FQEVSTJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.138 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.671	α = 90
b = 81.185	β = 114.52
c = 51.658	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
STARANISO	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-28 
Deposition Author(s): Strater, N., Muller, C., Sylvester, K., Claff, T., Weisse, R.H., Gao, S., Tollefson, A.E., Liu, X., Zhan, P.

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Funding Organization	Location	Grant Number
Volkswagen Foundation	Germany	--

Revision History  

• Version 1.0: 2022-09-28
  Type: Initial release
  
• Version 1.1: 2022-10-26
  Changes: Database references
• Version 1.2: 2023-08-30
  Changes: Data collection, Source and taxonomy, Structure summary
• Version 1.3: 2024-01-31
  Changes: Refinement description, Structure summary