5FMG

Structure and function based design of Plasmodium-selective proteasome inhibitors


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 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

Structure and Function Based Design of Plasmodium-Selective Proteasome Inhibitors

Li, H.O'Donoghue, A.J.Van Der Linden, W.A.Xie, S.C.Yoo, E.Foe, I.T.Tilley, L.Craik, C.S.Da Fonseca, P.C.A.Bogyo, M.

(2016) Nature 530: 233

  • DOI: 10.1038/nature16936

  • PubMed Abstract: 
  • The proteasome is a multi-component protease complex responsible for regulating key processes such as the cell cycle and antigen presentation. Compounds that target the proteasome are potentially valuable tools for the treatment of pathogens that dep ...

    The proteasome is a multi-component protease complex responsible for regulating key processes such as the cell cycle and antigen presentation. Compounds that target the proteasome are potentially valuable tools for the treatment of pathogens that depend on proteasome function for survival and replication. In particular, proteasome inhibitors have been shown to be toxic for the malaria parasite Plasmodium falciparum at all stages of its life cycle. Most compounds that have been tested against the parasite also inhibit the mammalian proteasome, resulting in toxicity that precludes their use as therapeutic agents. Therefore, better definition of the substrate specificity and structural properties of the Plasmodium proteasome could enable the development of compounds with sufficient selectivity to allow their use as anti-malarial agents. To accomplish this goal, here we use a substrate profiling method to uncover differences in the specificities of the human and P. falciparum proteasome. We design inhibitors based on amino-acid preferences specific to the parasite proteasome, and find that they preferentially inhibit the β2-subunit. We determine the structure of the P. falciparum 20S proteasome bound to the inhibitor using cryo-electron microscopy and single-particle analysis, to a resolution of 3.6 Å. These data reveal the unusually open P. falciparum β2 active site and provide valuable information about active-site architecture that can be used to further refine inhibitor design. Furthermore, consistent with the recent finding that the proteasome is important for stress pathways associated with resistance of artemisinin family anti-malarials, we observe growth inhibition synergism with low doses of this β2-selective inhibitor in artemisinin-sensitive and -resistant parasites. Finally, we demonstrate that a parasite-selective inhibitor could be used to attenuate parasite growth in vivo without appreciable toxicity to the host. Thus, the Plasmodium proteasome is a chemically tractable target that could be exploited by next-generation anti-malarial agents.


    Organizational Affiliation

    Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA, PUTATIVE
A, O
260Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IAR3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IAR3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE 2, PUTATIVE
B, P
235Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for C6KST3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C6KST3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE
C, Q
246Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IDG3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IDG3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE
D, R
241Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IDG2 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IDG2
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE
E, S
256Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IBI3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IBI3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PROTEOSOME SUBUNIT ALPHA TYPE 1, PUTATIVE
F, T
254Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IK90 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IK90
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME COMPONENT C8, PUTATIVE
G, U
252Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for O77396 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  O77396
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME, PUTATIVE
H, V
252Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8I0U7 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I0U7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE
I, W
229Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8I6T3 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I6T3
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
BETA3 PROTEASOME SUBUNIT, PUTATIVE
J, X
218Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8I261 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8I261
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE
K, Y
195Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IKC9 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IKC9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE
L, Z
211Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q8IJT1 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q8IJT1
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE
M, a
240Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for C0H4E8 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  C0H4E8
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE
N, b
265Plasmodium falciparum (isolate 3D7)Mutation(s): 0 
EC: 3.4.25.1
Find proteins for Q7K6A9 (Plasmodium falciparum (isolate 3D7))
Go to UniProtKB:  Q7K6A9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7F1
Query on 7F1

Download SDF File 
Download CCD File 
I, W
(2S)-N-[(E,2S)-1-(1H-indol-3-yl)-4-methylsulfonyl-but-3-en-2-yl]-2-[[(2S)-3-(1H-indol-3-yl)-2-(2-morpholin-4-ylethanoylamino)propanoyl]amino]-4-methyl-pentanamide
C36 H46 N6 O6 S
AZZZSQJQBKRGDX-LGBXHZPNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Data collection