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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Ligand Structure Quality Assessment 


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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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
A1LZS (Subject of Investigation/LOI)
Query on A1LZS

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
4-[4-[4-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]oxybutoxy]phenyl]benzoic acid
C23 H26 N4 O4
BZWMZSPIVLREMK-UHFFFAOYSA-N
UMP
Query on UMP

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
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