8OLU | pdb_00008olu

Leishmania tarentolae proteasome 20S subunit in complex with 1-Benzyl-N-(3-(cyclopropylcarbamoyl)phenyl)-6-oxo-1,6-dihydropyridazine-3-carboxamide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structure-Guided Design and Synthesis of a Pyridazinone Series of Trypanosoma cruzi Proteasome Inhibitors.

Thomas, M.G.McGonagle, K.Rowland, P.Robinson, D.A.Dodd, P.G.Camino-Diaz, I.Campbell, L.Cantizani, J.Castaneda, P.Conn, D.Craggs, P.D.Edwards, D.Ferguson, L.Fosberry, A.Frame, L.Goswami, P.Hu, X.Korczynska, J.MacLean, L.Martin, J.Mutter, N.Osuna-Cabello, M.Paterson, C.Pena, I.Pinto, E.G.Pont, C.Riley, J.Shishikura, Y.Simeons, F.R.C.Stojanovski, L.Thomas, J.Wrobel, K.Young, R.J.Zmuda, F.Zuccotto, F.Read, K.D.Gilbert, I.H.Marco, M.Miles, T.J.Manzano, P.De Rycker, M.

(2023) J Med Chem 66: 10413-10431

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00582
  • Primary Citation Related Structures: 
    8OLU

  • PubMed Abstract: 

    There is an urgent need for new treatments for Chagas disease, a parasitic infection which mostly impacts South and Central America. We previously reported on the discovery of GSK3494245/DDD01305143, a preclinical candidate for visceral leishmaniasis which acted through inhibition of the Leishmania proteasome. A related analogue, active against Trypanosoma cruzi , showed suboptimal efficacy in an animal model of Chagas disease, so alternative proteasome inhibitors were investigated. Screening a library of phenotypically active analogues against the T. cruzi proteasome identified an active, selective pyridazinone, the development of which is described herein. We obtained a cryo-EM co-structure of proteasome and a key inhibitor and used this to drive optimization of the compounds. Alongside this, optimization of the absorption, distribution, metabolism, and excretion (ADME) properties afforded a suitable compound for mouse efficacy studies. The outcome of these studies is discussed, alongside future plans to further understand the series and its potential to deliver a new treatment for Chagas disease.


  • Organizational Affiliation
    • Drug Discovery Unit, University of Dundee, School of Life Sciences, Dow Street, Dundee, U.K., DD1 5EH.

Macromolecule Content 

  • Total Structure Weight: 848.37 kDa 
  • Atom Count: 48,930 
  • Modeled Residue Count: 6,316 
  • Deposited Residue Count: 7,664 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
A, O
250Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KZP5 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
B, P
231Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KGL4 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
C, Q
285Leishmania tarentolaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type
D, R
248Leishmania tarentolaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome alpha 5 subunit, putative
E, S
344Leishmania tarentolaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome alpha 1 subunit, putative
F, T
428Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640L0A1 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome alpha 7 subunit, putative
G, U
238Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KJI7 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta
H, V
283Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KBR2 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta
I, W
254Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KUX2 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta
J, X
205Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KQX8 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta
K, Y
206Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KTY7 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta
L, Z
301Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KW57 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome beta 6 subunit, putativeAA [auth a],
M
339Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640K9U9 (Leishmania tarentolae)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth b],
N
220Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A640KSC5 (Leishmania tarentolae)
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VYW

Query on VYW



Download:Ideal Coordinates CCD File
CA [auth L],
DA [auth Z]
~{N}-[3-(cyclopropylcarbamoyl)phenyl]-6-oxidanylidene-1-(phenylmethyl)pyridazine-3-carboxamide
C22 H20 N4 O3
WTFTYKWBWNYQKS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0349
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2023-08-09 
  • Deposition Author(s): Rowland, P.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Data collection, Database references