8DSR

Structure of Plasmepsin X (PM10, PMX) from Plasmodium falciparum 3D7 in complex with UCB7362


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Discovery and Characterization of Potent, Efficacious, Orally Available Antimalarial Plasmepsin X Inhibitors and Preclinical Safety Assessment of UCB7362 .

Lowe, M.A.Cardenas, A.Valentin, J.P.Zhu, Z.Abendroth, J.Castro, J.L.Class, R.Delaunois, A.Fleurance, R.Gerets, H.Gryshkova, V.King, L.Lorimer, D.D.MacCoss, M.Rowley, J.H.Rosseels, M.L.Royer, L.Taylor, R.D.Wong, M.Zaccheo, O.Chavan, V.P.Ghule, G.A.Tapkir, B.K.Burrows, J.N.Duffey, M.Rottmann, M.Wittlin, S.Angulo-Barturen, I.Jimenez-Diaz, M.B.Striepen, J.Fairhurst, K.J.Yeo, T.Fidock, D.A.Cowman, A.F.Favuzza, P.Crespo-Fernandez, B.Gamo, F.J.Goldberg, D.E.Soldati-Favre, D.Laleu, B.de Haro, T.

(2022) J Med Chem 65: 14121-14143

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01336
  • Primary Citation of Related Structures:  
    8DSR

  • PubMed Abstract: 

    Plasmepsin X (PMX) is an essential aspartyl protease controlling malaria parasite egress and invasion of erythrocytes, development of functional liver merozoites (prophylactic activity), and blocking transmission to mosquitoes, making it a potential multistage drug target. We report the optimization of an aspartyl protease binding scaffold and the discovery of potent, orally active PMX inhibitors with in vivo antimalarial efficacy. Incorporation of safety evaluation early in the characterization of PMX inhibitors precluded compounds with a long human half-life ( t 1/2 ) to be developed. Optimization focused on improving the off-target safety profile led to the identification of UCB7362 that had an improved in vitro and in vivo safety profile but a shorter predicted human t 1/2 . UCB7362 is estimated to achieve 9 log 10 unit reduction in asexual blood-stage parasites with once-daily dosing of 50 mg for 7 days. This work demonstrates the potential to deliver PMX inhibitors with in vivo efficacy to treat malaria.


  • Organizational Affiliation

    UCB, 216 Bath Road, Slough SL1 3WE, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plasmepsin X
A, B
465Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PMXPF3D7_0808200
EC: 3.4.23
UniProt
Find proteins for Q8IAS0 (Plasmodium falciparum (isolate 3D7))
Explore Q8IAS0 
Go to UniProtKB:  Q8IAS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IAS0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TWU (Subject of Investigation/LOI)
Query on TWU

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2E,6S)-6-{2-chloro-3-[(2-cyclopropylpyrimidin-5-yl)amino]phenyl}-2-imino-6-methyl-3-[(2S,4S)-2-methyloxan-4-yl]-1,3-diazinan-4-one
C24 H29 Cl N6 O2
RUZADINCVKIRSK-NPALWHDTSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TWU BindingDB:  8DSR IC50: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.71α = 90
b = 61.43β = 90.769
c = 143.98γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2023-01-25
    Changes: Other, Structure summary
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary