8RHX

Crystal Structure of Trypanosoma brucei PTR1 in complex with the cofactor and inhibitor P32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 ?
  • R-Value Free: 0.186 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Identification of Innovative Folate Inhibitors Leveraging the Amino Dihydrotriazine Motif from Cycloguanil for Their Potential as Anti- Trypanosoma brucei Agents.

Francesconi, V.Rizzo, M.Pozzi, C.Tagliazucchi, L.Konchie Simo, C.U.Saporito, G.Landi, G.Mangani, S.Carbone, A.Schenone, S.Santarem, N.Tavares, J.Cordeiro-da-Silva, A.Costi, M.P.Tonelli, M.

(2024) ACS Infect Dis 10: 2755-2774

  • DOI: https://doi.org/10.1021/acsinfecdis.4c00113
  • Primary Citation of Related Structures:  
    8RHT, 8RHU, 8RHV, 8RHW, 8RHX, 8RHY

  • PubMed Abstract: 

    Folate enzymes, namely, dihydrofolate reductase (DHFR) and pteridine reductase (PTR1) are acknowledged targets for the development of antiparasitic agents against Trypanosomiasis and Leishmaniasis. Based on the amino dihydrotriazine motif of the drug Cycloguanil (Cyc), a known inhibitor of both folate enzymes, we have identified two novel series of inhibitors, the 2-amino triazino benzimidazoles ( 1 ) and 2-guanidino benzimidazoles ( 2 ), as their open ring analogues. Enzymatic screening was carried out against PTR1, DHFR, and thymidylate synthase (TS). The crystal structures of Tb DHFR and Tb PTR1 in complex with selected compounds experienced in both cases a substrate-like binding mode and allowed the rationalization of the main chemical features supporting the inhibitor ability to target folate enzymes. Biological evaluation of both series was performed against T. brucei and L. infantum and the toxicity against THP-1 human macrophages. Notably, the 5,6-dimethyl-2-guanidinobenzimidazole 2g resulted to be the most potent ( K i = 9 nM) and highly selective Tb DHFR inhibitor, 6000-fold over Tb PTR1 and 394-fold over h DHFR. The 5,6-dimethyl tricyclic analogue 1g , despite showing a lower potency and selectivity profile than 2g , shared a comparable antiparasitic activity against T. brucei in the low micromolar domain. The dichloro-substituted 2-guanidino benzimidazoles 2c and 2d revealed their potent and broad-spectrum antitrypanosomatid activity affecting the growth of T. brucei and L. infantum parasites. Therefore, both chemotypes could represent promising templates that could be valorized for further drug development.


  • Organizational Affiliation

    Department of Pharmacy, University of Genoa, viale Benedetto XV n.3, Genoa 16132, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pteridine reductase
A, B, C, D
289Trypanosoma brucei bruceiMutation(s): 0 
Gene Names: PTR1
UniProt
Find proteins for O76290 (Trypanosoma brucei brucei)
Explore O76290 
Go to UniProtKB:  O76290
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76290
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B],
K [auth C],
N [auth D]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
A1H0T (Subject of Investigation/LOI)
Query on A1H0T

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B],
L [auth C],
O [auth D]
1-[4,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]guanidine
C8 H7 Cl2 N5
OGKMGWPIDIMCSH-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
M [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 ?
  • R-Value Free: 0.186 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( ? )Angle ( ? )
a = 74.097¦Á = 90
b = 89.431¦Â = 115.95
c = 84.074¦Ă = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionCA21111

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
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