8PF4

Crystal structure of Trypanosoma brucei trypanothione reductase in complex with 4-(((5-((4-fluorophenethyl)carbamoyl)furan-2-yl)methyl)(4-fluorophenyl)carbamoyl)-1-methyl-1-(3-phenylpropyl)piperazin-1-ium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Fragment Merging, Growing, and Linking Identify New Trypanothione Reductase Inhibitors for Leishmaniasis.

Exertier, C.Salerno, A.Antonelli, L.Fiorillo, A.Ocello, R.Seghetti, F.Caciolla, J.Uliassi, E.Masetti, M.Fiorentino, E.Orsini, S.Di Muccio, T.Ilari, A.Bolognesi, M.L.

(2024) J Med Chem 67: 402-419

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c01439
  • Primary Citation of Related Structures:  
    8PF3, 8PF4, 8PF5

  • PubMed Abstract: 

    Trypanothione reductase (TR) is a suitable target for drug discovery approaches against leishmaniasis, although the identification of potent inhibitors is still challenging. Herein, we harnessed a fragment-based drug discovery (FBDD) strategy to develop new TR inhibitors. Previous crystallographic screening identified fragments 1 - 3 , which provided ideal starting points for a medicinal chemistry campaign. In silico investigations revealed critical hotspots in the TR binding site, guiding our structure- and ligand-based structure-actvity relationship (SAR) exploration that yielded fragment-derived compounds 4 - 14 . A trend of improvement in Leishmania infantum TR inhibition was detected along the optimization and confirmed by the crystal structures of 9 , 10 , and 14 in complex with Trypanosoma brucei TR. Compound 10 showed the best TR inhibitory profile ( K i = 0.2 μM), whereas 9 was the best one in terms of in vitro and ex vivo activity. Although further fine-tuning is needed to improve selectivity, we demonstrated the potentiality of FBDD on a classic but difficult target for leishmaniasis.


  • Organizational Affiliation

    Institute of Molecular Biology and Pathology (IBPM) of the National Research Council of Italy (CNR), c/o Department of Biochemical Sciences, Sapienza University of Rome, Piazzale A. Moro 5, Roma 00185, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Trypanothione reductase
A, B, C, D
495Trypanosoma bruceiMutation(s): 0 
Gene Names: DPX39_100110900
EC: 1.8.1.12
UniProt
Find proteins for Q389T8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q389T8 
Go to UniProtKB:  Q389T8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ389T8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A],
EA [auth C],
O [auth B],
QA [auth D]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
YIA (Subject of Investigation/LOI)
Query on YIA

Download Ideal Coordinates CCD File 
F [auth A],
N [auth A],
PA [auth D],
RA [auth D]
~{N}-(4-fluorophenyl)-~{N}-[[5-[2-(4-fluorophenyl)ethylcarbamoyl]furan-2-yl]methyl]-4-methyl-4-(3-phenylpropyl)-1,4$l^{4}-diazinane-1-carboxamide
C35 H39 F2 N4 O3
XIDHOMHZHFMUIP-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
FA [auth C]
G [auth A]
GA [auth C]
H [auth A]
HA [auth C]
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
NA [auth C],
OA [auth C],
Q [auth B],
R [auth B],
S [auth B],
SA [auth D],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
Z [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth D]
BA [auth B]
CA [auth B]
DA [auth B]
AA [auth B],
AB [auth D],
BA [auth B],
CA [auth B],
DA [auth B],
M [auth A],
YA [auth D],
ZA [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
IMD
Query on IMD

Download Ideal Coordinates CCD File 
J [auth A],
MA [auth C],
P [auth B],
T [auth B]
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.922α = 90
b = 63.635β = 97.29
c = 169.104γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministero dell Universita e della RicercaItalyFISR2019_03796

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release