6QM7

Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Preclinical candidate for the treatment of visceral leishmaniasis that acts through proteasome inhibition.

Wyllie, S.Brand, S.Thomas, M.De Rycker, M.Chung, C.W.Pena, I.Bingham, R.P.Bueren-Calabuig, J.A.Cantizani, J.Cebrian, D.Craggs, P.D.Ferguson, L.Goswami, P.Hobrath, J.Howe, J.Jeacock, L.Ko, E.J.Korczynska, J.MacLean, L.Manthri, S.Martinez, M.S.Mata-Cantero, L.Moniz, S.Nuhs, A.Osuna-Cabello, M.Pinto, E.Riley, J.Robinson, S.Rowland, P.Simeons, F.R.C.Shishikura, Y.Spinks, D.Stojanovski, L.Thomas, J.Thompson, S.Viayna Gaza, E.Wall, R.J.Zuccotto, F.Horn, D.Ferguson, M.A.J.Fairlamb, A.H.Fiandor, J.M.Martin, J.Gray, D.W.Miles, T.J.Gilbert, I.H.Read, K.D.Marco, M.Wyatt, P.G.

(2019) Proc Natl Acad Sci U S A 116: 9318-9323

  • DOI: https://doi.org/10.1073/pnas.1820175116
  • Primary Citation of Related Structures:  
    6QM7, 6QM8

  • PubMed Abstract: 

    Visceral leishmaniasis (VL), caused by the protozoan parasites Leishmania donovani and Leishmania infantum , is one of the major parasitic diseases worldwide. There is an urgent need for new drugs to treat VL, because current therapies are unfit for purpose in a resource-poor setting. Here, we describe the development of a preclinical drug candidate, GSK3494245/DDD01305143/compound 8, with potential to treat this neglected tropical disease. The compound series was discovered by repurposing hits from a screen against the related parasite Trypanosoma cruzi Subsequent optimization of the chemical series resulted in the development of a potent cidal compound with activity against a range of clinically relevant L. donovani and L. infantum isolates. Compound 8 demonstrates promising pharmacokinetic properties and impressive in vivo efficacy in our mouse model of infection comparable with those of the current oral antileishmanial miltefosine. Detailed mode of action studies confirm that this compound acts principally by inhibition of the chymotrypsin-like activity catalyzed by the β5 subunit of the L. donovani proteasome. High-resolution cryo-EM structures of apo and compound 8-bound Leishmania tarentolae 20S proteasome reveal a previously undiscovered inhibitor site that lies between the β4 and β5 proteasome subunits. This induced pocket exploits β4 residues that are divergent between humans and kinetoplastid parasites and is consistent with all of our experimental and mutagenesis data. As a result of these comprehensive studies and due to a favorable developability and safety profile, compound 8 is being advanced toward human clinical trials.


  • Organizational Affiliation

    Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha1 chain
A, O
250Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A6L0XSJ0 (Leishmania infantum)
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UniProt GroupA0A6L0XSJ0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha2 chain
B, P
231Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q9GNZ8 (Leishmania infantum)
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UniProt GroupQ9GNZ8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha3 chain
C, Q
285Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4HVX3 (Leishmania infantum)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha4 chain
D, R
248Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4HUT6 (Leishmania infantum)
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UniProt GroupA4HUT6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha5 chain
E, S
344Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4HZI9 (Leishmania infantum)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha6 chain
F, T
428Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4IDD0 (Leishmania infantum)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome alpha7 chain
G, U
238Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4I357 (Leishmania infantum)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome beta1 chain
H, V
283Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4HV47 (Leishmania infantum)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome beta2 chain
I, W
254Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4HN55 (Leishmania braziliensis)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome beta3 chain
J, X
205Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4I384 (Leishmania infantum)
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UniProt GroupA4I384
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome beta4 chain
K, Y
206Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4ICV5 (Leishmania infantum)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome beta5 chain
L, Z
302Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4IDD6 (Leishmania infantum)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome beta6 chainAA [auth a],
M
339Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4HSQ5 (Leishmania infantum)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome beta7 chainBA [auth b],
N
220Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A0A381MU64 (Leishmania infantum)
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J6E (Subject of Investigation/LOI)
Query on J6E

Download Ideal Coordinates CCD File 
CA [auth L],
DA [auth Z]
~{N}-[4-fluoranyl-3-(3-morpholin-4-ylimidazo[1,2-a]pyrimidin-7-yl)phenyl]pyrrolidine-1-carboxamide
C21 H23 F N6 O2
SAJUCKZZYFFICP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Other