6QM7

Leishmania tarentolae proteasome 20S subunit complexed with GSK3494245


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.USA 116: 9318-9323

  • DOI: 10.1073/pnas.1820175116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Visceral leishmaniasis (VL), caused by the protozoan parasites <i>Leishmania donovani </i> and <i>Leishmania infantum </i>, is one of the major parasitic diseases worldwide. There is an urgent need for new drugs to treat VL, because current therapi ...

    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

    Global Health R&D, GlaxoSmithKline, Tres Cantos, 28760, Spain.,David Jack Centre for R&D, GlaxoSmithKline, Ware SG12 0DP, United Kingdom.,Global Health R&D, GlaxoSmithKline, Tres Cantos, 28760, Spain; k.read@dundee.ac.uk maria.m.marco@gsk.com p.g.wyatt@dundee.ac.uk.,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.,Medicines Research Centre, Stevenage, Hertfordshire SG1 2NY, United Kingdom.,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; k.read@dundee.ac.uk maria.m.marco@gsk.com p.g.wyatt@dundee.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome alpha1 chain
A, O
250Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for Q7JMX2 (Leishmania infantum)
Go to UniProtKB:  Q7JMX2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome alpha2 chain
B, P
231Leishmania infantumMutation(s): 0 
Gene Names: 91E11
EC: 3.4.25.1
Find proteins for Q9GNZ8 (Leishmania infantum)
Go to UniProtKB:  Q9GNZ8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome alpha3 chain
C, Q
285Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4HVX3 (Leishmania infantum)
Go to UniProtKB:  A4HVX3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome alpha4 chain
D, R
248Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4HUT6 (Leishmania infantum)
Go to UniProtKB:  A4HUT6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome alpha5 chain
E, S
344Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4HZI9 (Leishmania infantum)
Go to UniProtKB:  A4HZI9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome alpha6 chain
F, T
428Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4IDD0 (Leishmania infantum)
Go to UniProtKB:  A4IDD0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome alpha7 chain
G, U
238Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4I357 (Leishmania infantum)
Go to UniProtKB:  A4I357
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome beta1 chain
H, V
283Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4HV47 (Leishmania infantum)
Go to UniProtKB:  A4HV47
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome beta2 chain
I, W
254Leishmania braziliensisMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4HN55 (Leishmania braziliensis)
Go to UniProtKB:  A4HN55
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome beta3 chain
J, X
205Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4I384 (Leishmania infantum)
Go to UniProtKB:  A4I384
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome beta4 chain
K, Y
206Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4ICV5 (Leishmania infantum)
Go to UniProtKB:  A4ICV5
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome beta5 chain
L, Z
302Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4IDD6 (Leishmania infantum)
Go to UniProtKB:  A4IDD6
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome beta6 chain
M, a
339Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A4HSQ5 (Leishmania infantum)
Go to UniProtKB:  A4HSQ5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome beta7 chain
N, b
220Leishmania infantumMutation(s): 0 
EC: 3.4.25.1
Find proteins for A0A381MU64 (Leishmania infantum)
Go to UniProtKB:  A0A381MU64
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J6E
Query on J6E

Download SDF File 
Download CCD File 
L, 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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-05-22
    Type: Data collection, Database references