6HCW

Crystal Structure of Lysyl-tRNA Synthetase from Cryptosporidium parvum complexed with L-lysine and a difluoro cyclohexyl chromone ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


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Literature

Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.

Baragana, B.Forte, B.Choi, R.Nakazawa Hewitt, S.Bueren-Calabuig, J.A.Pisco, J.P.Peet, C.Dranow, D.M.Robinson, D.A.Jansen, C.Norcross, N.R.Vinayak, S.Anderson, M.Brooks, C.F.Cooper, C.A.Damerow, S.Delves, M.Dowers, K.Duffy, J.Edwards, T.E.Hallyburton, I.Horst, B.G.Hulverson, M.A.Ferguson, L.Jimenez-Diaz, M.B.Jumani, R.S.Lorimer, D.D.Love, M.S.Maher, S.Matthews, H.McNamara, C.W.Miller, P.O'Neill, S.Ojo, K.K.Osuna-Cabello, M.Pinto, E.Post, J.Riley, J.Rottmann, M.Sanz, L.M.Scullion, P.Sharma, A.Shepherd, S.M.Shishikura, Y.Simeons, F.R.C.Stebbins, E.E.Stojanovski, L.Straschil, U.Tamaki, F.K.Tamjar, J.Torrie, L.S.Vantaux, A.Witkowski, B.Wittlin, S.Yogavel, M.Zuccotto, F.Angulo-Barturen, I.Sinden, R.Baum, J.Gamo, F.J.Maser, P.Kyle, D.E.Winzeler, E.A.Myler, P.J.Wyatt, P.G.Floyd, D.Matthews, D.Sharma, A.Striepen, B.Huston, C.D.Gray, D.W.Fairlamb, A.H.Pisliakov, A.V.Walpole, C.Read, K.D.Van Voorhis, W.C.Gilbert, I.H.

(2019) Proc Natl Acad Sci U S A 116: 7015-7020

  • DOI: 10.1073/pnas.1814685116
  • Primary Citation of Related Structures:  
    6HCV, 6HCU, 6HCW, 6AGT, 5ELO, 5ELN

  • PubMed Abstract: 
  • Malaria and cryptosporidiosis, caused by apicomplexan parasites, remain major drivers of global child mortality. New drugs for the treatment of malaria and cryptosporidiosis, in particular, are of high priority; however, there are few chemically validated targets ...

    Malaria and cryptosporidiosis, caused by apicomplexan parasites, remain major drivers of global child mortality. New drugs for the treatment of malaria and cryptosporidiosis, in particular, are of high priority; however, there are few chemically validated targets. The natural product cladosporin is active against blood- and liver-stage Plasmodium falciparum and Cryptosporidium parvum in cell-culture studies. Target deconvolution in P. falciparum has shown that cladosporin inhibits lysyl-tRNA synthetase ( Pf KRS1). Here, we report the identification of a series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small-molecule hit was identified and then optimized by using a structure-based approach, supported by structures of both Pf KRS1 and C. parvum KRS ( Cp KRS). In vivo proof of concept was established in an SCID mouse model of malaria, after oral administration (ED 90 = 1.5 mg/kg, once a day for 4 d). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between Pf KRS1 and Cp KRS. This series of compounds inhibit Cp KRS and C. parvum and Cryptosporidium hominis in culture, and our lead compound shows oral efficacy in two cryptosporidiosis mouse models. X-ray crystallography and molecular dynamics simulations have provided a model to rationalize the selectivity of our compounds for Pf KRS1 and Cp KRS vs. (human) Hs KRS. Our work validates apicomplexan KRSs as promising targets for the development of drugs for malaria and cryptosporidiosis.


    Organizational Affiliation

    Wellcome Centre for Anti-Infectives Research, Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, University of Dundee, DD1 5EH Dundee, United Kingdom; i.h.gilbert@dundee.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lysine--tRNA ligaseA, B535Cryptosporidium parvum Iowa IIMutation(s): 0 
Gene Names: cgd4_2370
EC: 6.1.1.6
UniProt
Find proteins for Q5CR27 (Cryptosporidium parvum (strain Iowa II))
Explore Q5CR27 
Go to UniProtKB:  Q5CR27
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FYB (Subject of Investigation/LOI)
Query on FYB

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide
C17 H16 F3 N O4
PJBRCGHQNUWERQ-UHFFFAOYSA-N
 Ligand Interaction
LYS
Query on LYS

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
G [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
FYB Binding MOAD:  6HCW IC50: 130 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.514α = 90
b = 142.65β = 90
c = 72.939γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
xia2data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1032548

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references