8W2F

Plasmodium falciparum 20S proteasome bound to an inhibitor


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Identification of potent and reversible piperidine carboxamides that are species-selective orally active proteasome inhibitors to treat malaria.

Lawong, A.Gahalawat, S.Ray, S.Ho, N.Han, Y.Ward, K.E.Deng, X.Chen, Z.Kumar, A.Xing, C.Hosangadi, V.Fairhurst, K.J.Tashiro, K.Liszczak, G.Shackleford, D.M.Katneni, K.Chen, G.Saunders, J.Crighton, E.Casas, A.Robinson, J.J.Imlay, L.S.Zhang, X.Lemoff, A.Zhao, Z.Angulo-Barturen, I.Jimenez-Diaz, M.B.Wittlin, S.Campbell, S.F.Fidock, D.A.Laleu, B.Charman, S.A.Ready, J.M.Phillips, M.A.

(2024) Cell Chem Biol 31: 1503

  • DOI: https://doi.org/10.1016/j.chembiol.2024.07.001
  • Primary Citation of Related Structures:  
    8W2F

  • PubMed Abstract: 

    Malaria remains a global health concern as drug resistance threatens treatment programs. We identified a piperidine carboxamide (SW042) with anti-malarial activity by phenotypic screening. Selection of SW042-resistant Plasmodium falciparum (Pf) parasites revealed point mutations in the Pf_proteasome β5 active-site (Pfβ5). A potent analog (SW584) showed efficacy in a mouse model of human malaria after oral dosing. SW584 had a low propensity to generate resistance (minimum inoculum for resistance [MIR] >10 9 ) and was synergistic with dihydroartemisinin. Pf_proteasome purification was facilitated by His 8 -tag introduction onto β7. Inhibition of Pfβ5 correlated with parasite killing, without inhibiting human proteasome isoforms or showing cytotoxicity. The Pf_proteasome_SW584 cryoelectron microscopy (cryo-EM) structure showed that SW584 bound non-covalently distal from the catalytic threonine, in an unexplored pocket at the β5/β6/β3 subunit interface that has species differences between Pf and human proteasomes. Identification of a reversible, species selective, orally active series with low resistance propensity provides a path for drugging this essential target.


  • Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexA,
N [auth O]
260Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for Q8IAR3 (Plasmodium falciparum (isolate 3D7))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexB,
O [auth P]
235Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeC,
P [auth Q]
242Plasmodium falciparum 3D7Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeD,
Q [auth R]
241Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha typeE,
R [auth S]
256Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome endopeptidase complexF,
S [auth T]
254Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3, putativeG,
T [auth U]
252Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6, putativeH,
U [auth V]
252Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaAA [auth W],
I
229Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaJ,
V [auth X]
218Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaK,
W [auth Y]
195Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta typeL,
X [auth Z]
211Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaBA [auth b],
M [auth N]
284Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0803800
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit betaY [auth M],
Z [auth a]
240Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.25.1
UniProt
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AE6 (Subject of Investigation/LOI)
Query on A1AE6

Download Ideal Coordinates CCD File 
CA [auth M],
DA [auth a]
(3S)-1-[(2-fluoroethoxy)acetyl]-N-{[(4P)-4-(6-methylpyridin-3-yl)-1,3-thiazol-2-yl]methyl}piperidine-3-carboxamide
C20 H25 F N4 O3 S
BAIMYTMUAKNCDJ-INIZCTEOSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI103947
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI155784
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM007062
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP220582

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-14
    Changes: Data collection, Database references
  • Version 1.2: 2024-08-28
    Changes: Data collection, Database references
  • Version 1.3: 2024-09-04
    Changes: Data collection, Database references