7TQ7

Structure of MERS 3CL protease in complex with the cyclopropane based inhibitor 13c


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.

Dampalla, C.S.Nguyen, H.N.Rathnayake, A.D.Kim, Y.Perera, K.D.Madden, T.K.Thurman, H.A.Machen, A.J.Kashipathy, M.M.Liu, L.Battaile, K.P.Lovell, S.Chang, K.O.Groutas, W.C.

(2023) Acs Pharmacol Transl Sci 6: 181-194

  • DOI: https://doi.org/10.1021/acsptsci.2c00206
  • Primary Citation of Related Structures:  
    7TQ2, 7TQ3, 7TQ4, 7TQ5, 7TQ6, 7TQ7, 7TQ8, 8CZT, 8CZU, 8CZV, 8CZW, 8CZX, 8DGY

  • PubMed Abstract: 

    The advent of SARS-CoV-2, the causative agent of COVID-19, and its worldwide impact on global health, have provided the impetus for the development of effective countermeasures that can be deployed against the virus, including vaccines, monoclonal antibodies, and direct-acting antivirals (DAAs). Despite these efforts, the current paucity of DAAs has created an urgent need for the creation of an enhanced and diversified portfolio of broadly acting agents with different mechanisms of action that can effectively abrogate viral infection. SARS-CoV-2 3C-like protease (3CL pro ), an enzyme essential for viral replication, is a validated target for the discovery of SARS-CoV-2 therapeutics. In this report, we describe the structure-guided utilization of the cyclopropane moiety in the design of highly potent inhibitors of SARS-CoV-2 3CL pro , SARS-CoV-1 3CL pro , and MERS-CoV 3CL pro . High-resolution cocrystal structures were used to identify the structural determinants associated with the binding of the inhibitors to the active site of the enzyme and unravel the mechanism of action. Aldehydes 5c and 11c inhibited SARS-CoV-2 replication with EC 50 values of 12 and 11 nM, respectively. Furthermore, the corresponding aldehyde bisulfite adducts 5d and 11d were equipotent with EC 50 values of 13 and 12 nM, respectively. The safety index (SI) values for compounds 5c / 11c and 5d / 11d ranged between 7692 and 9090. Importantly, aldehydes 5c / 11c and bisulfite adducts 5d / 11d potently inhibited MERS-CoV 3CL pro with IC 50 values of 80 and 120 nM, and 70 and 70 nM, respectively. Likewise, compounds 5c / 11c and 5d / 11d inhibited SARS-CoV-1 with IC 50 values of 960 and 350 nM and 790 and 240 nM, respectively. Taken together, these studies suggest that the inhibitors described herein have low cytotoxicity and high potency and are promising candidates for further development as broad-spectrum direct-acting antivirals against highly pathogenic coronaviruses.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Wichita State University, Wichita, Kansas 67260, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Orf1a protein313Middle East respiratory syndrome-related coronavirusMutation(s): 0 
Gene Names: orf1a
UniProt
Find proteins for K9N7C7 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N7C7 
Go to UniProtKB:  K9N7C7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9N7C7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IRR (Subject of Investigation/LOI)
Query on IRR

Download Ideal Coordinates CCD File 
B [auth A]N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-N~2~-({[(1R,2R)-2-propylcyclopropyl]methoxy}carbonyl)-L-leucinamide
C21 H35 N3 O5
JXXLXBAHHCCJDG-FPSMNIFISA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
C [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.437α = 90
b = 57.94β = 112.37
c = 49.852γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI161085

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-08-03
    Changes: Database references, Structure summary
  • Version 1.2: 2023-01-11
    Changes: Database references
  • Version 1.3: 2023-02-01
    Changes: Database references
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description