5JDI image
Entry Detail
PDB ID:
5JDI
Keywords:
Title:
Trypanosoma brucei PTR1 in complex with cofactor and inhibitor NMT-H024 (compound 2)
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2016-04-16
Release Date:
2016-08-17
Method Details:
Experimental Method:
Resolution:
1.38 Å
R-Value Free:
0.15
R-Value Work:
0.11
R-Value Observed:
0.11
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Pteridine reductase
Chain IDs:A, B, D
Chain Length:288
Number of Molecules:3
Biological Source:Trypanosoma brucei brucei
Polymer Type:polypeptide(L)
Description:Pteridine reductase
Chain IDs:C
Chain Length:288
Number of Molecules:1
Biological Source:Trypanosoma brucei brucei
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CSX C CYS modified residue
Primary Citation

Abstact

Flavonoids represent a potential source of new antitrypanosomatidic leads. Starting from a library of natural products, we combined target-based screening on pteridine reductase 1 with phenotypic screening on Trypanosoma brucei for hit identification. Flavonols were identified as hits, and a library of 16 derivatives was synthesized. Twelve compounds showed EC50 values against T. brucei below 10 μM. Four X-ray crystal structures and docking studies explained the observed structure-activity relationships. Compound 2 (3,6-dihydroxy-2-(3-hydroxyphenyl)-4H-chromen-4-one) was selected for pharmacokinetic studies. Encapsulation of compound 2 in PLGA nanoparticles or cyclodextrins resulted in lower in vitro toxicity when compared to the free compound. Combination studies with methotrexate revealed that compound 13 (3-hydroxy-6-methoxy-2-(4-methoxyphenyl)-4H-chromen-4-one) has the highest synergistic effect at concentration of 1.3 μM, 11.7-fold dose reduction index and no toxicity toward host cells. Our results provide the basis for further chemical modifications aimed at identifying novel antitrypanosomatidic agents showing higher potency toward PTR1 and increased metabolic stability.

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Chemical

Disease

Primary Citation of related structures