5NFH

Trypanosoma brucei methionyl-tRNA synthetase in complex with a quinazolinone inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Chemical Validation of Methionyl-tRNA Synthetase as a Druggable Target in Leishmania donovani.

Torrie, L.S.Brand, S.Robinson, D.A.Ko, E.J.Stojanovski, L.Simeons, F.R.C.Wyllie, S.Thomas, J.Ellis, L.Osuna-Cabello, M.Epemolu, O.Nuhs, A.Riley, J.MacLean, L.Manthri, S.Read, K.D.Gilbert, I.H.Fairlamb, A.H.De Rycker, M.

(2017) ACS Infect Dis 3: 718-727

  • DOI: 10.1021/acsinfecdis.7b00047
  • Primary Citation of Related Structures:  
    5NFH

  • PubMed Abstract: 
  • Methionyl-tRNA synthetase (MetRS) has been chemically validated as a drug target in the kinetoplastid parasite Trypanosoma brucei. In the present study, we investigate the validity of this target in the related trypanosomatid Leishmania donovani. Following development of a robust high-throughput compatible biochemical assay, a compound screen identified DDD806905 as a highly potent inhibitor of LdMetRS (K i of 18 nM) ...

    Methionyl-tRNA synthetase (MetRS) has been chemically validated as a drug target in the kinetoplastid parasite Trypanosoma brucei. In the present study, we investigate the validity of this target in the related trypanosomatid Leishmania donovani. Following development of a robust high-throughput compatible biochemical assay, a compound screen identified DDD806905 as a highly potent inhibitor of LdMetRS (K i of 18 nM). Crystallography revealed this compound binds to the methionine pocket of MetRS with enzymatic studies confirming DDD806905 displays competitive inhibition with respect to methionine and mixed inhibition with respect to ATP binding. DDD806905 showed activity, albeit with different levels of potency, in various Leishmania cell-based viability assays, with on-target activity observed in both Leishmania promastigote cell assays and a Leishmania tarentolae in vitro translation assay. Unfortunately, this compound failed to show efficacy in an animal model of leishmaniasis. We investigated the potential causes for the discrepancies in activity observed in different Leishmania cell assays and the lack of efficacy in the animal model and found that high protein binding as well as sequestration of this dibasic compound into acidic compartments may play a role. Despite medicinal chemistry efforts to address the dibasic nature of DDD806905 and analogues, no progress could be achieved with the current chemical series. Although DDD806905 is not a developable antileishmanial compound, MetRS remains an attractive antileishmanial drug target.


    Organizational Affiliation

    Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dow Street, Dundee DD1 5EH, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionyl-tRNA synthetase, putativeA, B536Trypanosoma brucei brucei TREU927Mutation(s): 3 
Gene Names: Tb10.70.6470
EC: 6.1.1.10
UniProt
Find proteins for Q38C91 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q38C91 
Go to UniProtKB:  Q38C91
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8W2 (Subject of Investigation/LOI)
Query on 8W2

Download Ideal Coordinates CCD File 
L [auth B]2-[3-[[4,6-bis(chloranyl)-1~{H}-indol-2-yl]methylamino]propylamino]-3~{H}-quinazolin-4-one
C20 H19 Cl2 N5 O
NMEFYZKHRBDWLZ-UHFFFAOYSA-N
 Ligand Interaction
MET
Query on MET

Download Ideal Coordinates CCD File 
I [auth A]METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A], F [auth A], J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], K [auth B]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.09α = 90
b = 105.985β = 90
c = 207.071γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom092340
Wellcome TrustUnited Kingdom105021
Wellcome TrustUnited Kingdom100476

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references