6QM8

Leishmania tarentolae proteasome 20S subunit apo structure


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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: 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 ...

    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; k.read@dundee.ac.uk maria.m.marco@gsk.com p.g.wyatt@dundee.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome alpha1 chainA, O250Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q7JMX2 (Leishmania infantum)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome alpha2 chainB, P231Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for Q9GNZ8 (Leishmania infantum)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome alpha3 chainC, Q285Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4HVX3 (Leishmania infantum)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome alpha4 chainD, R248Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4HUT6 (Leishmania infantum)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome alpha5 chainE, S344Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4HZI9 (Leishmania infantum)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome alpha6 chainF, T428Leishmania tarentolaeMutation(s): 0 
UniProt
Find proteins for A4IDD0 (Leishmania infantum)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome alpha7 chainG, U238Leishmania tarentolaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for A4I357 (Leishmania infantum)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome beta1 chainH, V283Leishmania tarentolaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for A4HV47 (Leishmania infantum)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome beta2 chainI, W254Leishmania tarentolaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for A4IBS2 (Leishmania infantum)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome beta3 chainJ, X205Leishmania tarentolaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for A4I384 (Leishmania infantum)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome beta4 chainK, Y206Leishmania tarentolaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for A4ICV5 (Leishmania infantum)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome beta5 chainL, Z302Leishmania tarentolaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for A4IDD6 (Leishmania infantum)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome beta6 chainM, AA [auth a]339Leishmania tarentolaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for A4HSQ5 (Leishmania infantum)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome beta7 chainN, BA [auth b]220Leishmania tarentolaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for A0A381MU64 (Leishmania infantum)
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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