8YQ8

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS V1/S) complexed with FB8, NADPH and dUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 

Starting Model: experimental
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Literature

Novel flexible biphenyl Pf DHFR inhibitors with improved antimalarial activity.

Decharuangsilp, S.Arwon, U.Sooksai, N.Rattanajak, R.Saeyang, T.Vitsupakorn, D.Vanichtanankul, J.Yuthavong, Y.Kamchonwongpaisan, S.Hoarau, M.

(2024) RSC Med Chem 15: 2496-2507

  • DOI: https://doi.org/10.1039/d4md00197d
  • Primary Citation of Related Structures:  
    8YQ8, 8YQ9

  • PubMed Abstract: 

    As pregnant women and young children remain the first victims of malaria worldwide, the search for new antimalarials has been focusing on compounds with a high safety profile and extended efficacy. In a previous study, a rigid biphenyl Pf DHFR inhibitor was developed by fragment-based screening, displaying sub nM enzyme inhibition but poor antiparasitic activity, presumably due to its low flexibility. Here, we report a new series of compounds that combines the biphenyl fragment with a flexible linker. Interestingly, their mode of binding differs from previously reported compounds, taking advantage of strong hydrophobic interaction. The new flexible biphenyl compounds show overall improved antiparasitic activity compared to rigid ones, with the best compound displaying a 2 nM antiplasmodial IC 50 and suitable drug-like properties. This confirms the importance of compound flexibility for antimalarial activity and opens the way to new opportunities for antimalarial drug design.


  • Organizational Affiliation

    National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency Pathum Thani 12120 Thailand marie.hoa@biotec.or.th.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthase
A, B
608Plasmodium falciparum VS/1Mutation(s): 0 
Gene Names: DHFR-TSV1/S
UniProt
Find proteins for D9N170 (Plasmodium falciparum)
Explore D9N170 
Go to UniProtKB:  D9N170
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD9N170
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.763α = 90
b = 156.41β = 90
c = 165.065γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata collection
Cootmodel building
PHASERphasing
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Center for Genetic Engineering and Biotechnology (Thailand)ThailandP1850116

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release