7TZJ

SARS CoV-2 PLpro in complex with inhibitor 3k


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Insights Into Drug Repurposing, as Well as Specificity and Compound Properties of Piperidine-Based SARS-CoV-2 PLpro Inhibitors.

Calleja, D.J.Kuchel, N.Lu, B.G.C.Birkinshaw, R.W.Klemm, T.Doerflinger, M.Cooney, J.P.Mackiewicz, L.Au, A.E.Yap, Y.Q.Blackmore, T.R.Katneni, K.Crighton, E.Newman, J.Jarman, K.E.Call, M.J.Lechtenberg, B.C.Czabotar, P.E.Pellegrini, M.Charman, S.A.Lowes, K.N.Mitchell, J.P.Nachbur, U.Lessene, G.Komander, D.

(2022) Front Chem 10: 861209-861209

  • DOI: https://doi.org/10.3389/fchem.2022.861209
  • Primary Citation of Related Structures:  
    7TZJ

  • PubMed Abstract: 

    The COVID-19 pandemic continues unabated, emphasizing the need for additional antiviral treatment options to prevent hospitalization and death of patients infected with SARS-CoV-2. The papain-like protease (PLpro) domain is part of the SARS-CoV-2 non-structural protein (nsp)-3, and represents an essential protease and validated drug target for preventing viral replication. PLpro moonlights as a deubiquitinating (DUB) and deISGylating enzyme, enabling adaptation of a DUB high throughput (HTS) screen to identify PLpro inhibitors. Drug repurposing has been a major focus through the COVID-19 pandemic as it may provide a fast and efficient route for identifying clinic-ready, safe-in-human antivirals. We here report our effort to identify PLpro inhibitors by screening the ReFRAME library of 11,804 compounds, showing that none inhibit PLpro with any reasonable activity or specificity to justify further progression towards the clinic. We also report our latest efforts to improve piperidine-scaffold inhibitors, 5c and 3k , originally developed for SARS-CoV PLpro. We report molecular details of binding and selectivity, as well as in vitro absorption, distribution, metabolism and excretion (ADME) studies of this scaffold. A co-crystal structure of SARS-CoV-2 PLpro bound to inhibitor 3k guides medicinal chemistry efforts to improve binding and ADME characteristics. We arrive at compounds with improved and favorable solubility and stability characteristics that are tested for inhibiting viral replication. Whilst still requiring significant improvement, our optimized small molecule inhibitors of PLpro display decent antiviral activity in an in vitro SARS-CoV-2 infection model, justifying further optimization.


  • Organizational Affiliation

    Department of Medical Biology, Walter and Eliza Hall Institute, University of Melbourne, Melbourne, VIC, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Papain-like protease
A, B
318Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
EC: 3.4.19.12
UniProt
Find proteins for P0DTC1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC1 
Go to UniProtKB:  P0DTC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S88 (Subject of Investigation/LOI)
Query on S88

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
N-[(3-fluorophenyl)methyl]-1-[(1R)-1-naphthalen-1-ylethyl]piperidine-4-carboxamide
C25 H27 F N2 O
XJTWGMHOQKGBDO-GOSISDBHSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
H [auth A],
O [auth B]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
J [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.951α = 90
b = 90.632β = 90
c = 99.766γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1178122
Wellcome TrustUnited KingdomWT222698/Z/21/Z
National Health and Medical Research Council (NHMRC, Australia)AustraliaMRF2002119
National Health and Medical Research Council (NHMRC, Australia)AustraliaGNT1117089

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-02
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description