7LDL

Improved Feline Drugs as SARS-CoV-2 Mpro Inhibitors: Structure-Activity Studies & Micellar Solubilization for Enhanced Bioavailability


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Improved SARS-CoV-2 M pro inhibitors based on feline antiviral drug GC376: Structural enhancements, increased solubility, and micellar studies.

Vuong, W.Fischer, C.Khan, M.B.van Belkum, M.J.Lamer, T.Willoughby, K.D.Lu, J.Arutyunova, E.Joyce, M.A.Saffran, H.A.Shields, J.A.Young, H.S.Nieman, J.A.Tyrrell, D.L.Lemieux, M.J.Vederas, J.C.

(2021) Eur J Med Chem 222: 113584-113584

  • DOI: 10.1016/j.ejmech.2021.113584
  • Primary Citation of Related Structures:  
    7LDL, 7LCO, 7LCT, 7LCS

  • PubMed Abstract: 
  • Replication of SARS-CoV-2, the coronavirus causing COVID-19, requires a main protease (M pro ) to cleave viral proteins. Consequently, M pro is a target for antiviral agents. We and others previously demonstrated that GC376, a bisulfite prodrug with efficacy as an anti-coronaviral agent in animals, is an effective inhibitor of M pro in SARS-CoV-2 ...

    Replication of SARS-CoV-2, the coronavirus causing COVID-19, requires a main protease (M pro ) to cleave viral proteins. Consequently, M pro is a target for antiviral agents. We and others previously demonstrated that GC376, a bisulfite prodrug with efficacy as an anti-coronaviral agent in animals, is an effective inhibitor of M pro in SARS-CoV-2. Here, we report structure-activity studies of improved GC376 derivatives with nanomolar affinities and therapeutic indices >200. Crystallographic structures of inhibitor-M pro complexes reveal that an alternative binding pocket in M pro , S4, accommodates the P3 position. Alternative binding is induced by polar P3 groups or a nearby methyl. NMR and solubility studies with GC376 show that it exists as a mixture of stereoisomers and forms colloids in aqueous media at higher concentrations, a property not previously reported. Replacement of its Na + counter ion with choline greatly increases solubility. The physical, biochemical, crystallographic, and cellular data reveal new avenues for M pro inhibitor design.


    Organizational Affiliation

    Department of Chemistry, University of Alberta, Edmonton AB, T6G 2G2, Canada. Electronic address: john.vederas@ualberta.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA, B306Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 3.1 (UniProt), 2.1.1 (UniProt)
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XV4 (Subject of Investigation/LOI)
Query on XV4

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]N-[(2S)-1-({(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide
C23 H32 N4 O5
WHTWOUANZWYZGR-MPGHIAIKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.07α = 79.846
b = 60.86β = 68.236
c = 63.67γ = 70.402
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada549297-2019

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release