6HCU

Crystal Structure of Lysyl-tRNA Synthetase from Plasmodium falciparum bound to a difluoro cyclohexyl chromone ligand

Summary for 6HCU

• Entry DOI: 10.2210/pdb6hcu/pdb
• Descriptor: Lysine--tRNA ligase, ~{N}-[[4,4-bis(fluoranyl)-1-oxidanyl-cyclohexyl]methyl]-6-fluoranyl-4-oxidanylidene-chromene-2-carboxamide, LYSINE, ... (7 entities in total)
• Functional Keywords: adenylyltransferase activity, trna binding, ligase, transferase
• Biological source: Plasmodium falciparum 3D7
• Total number of polymer chains: 2
• Total formula weight: 119022.53

Authors

Tamjar, J.,Robinson, D.A.,Baragana, B.,Norcross, N.,Forte, B.,Walpole, C.,Gilbert, I.H. (deposition date: 2018-08-16, release date: 2019-04-03, Last modification date: 2024-10-23)

Primary citation

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.
Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis.
Proc.Natl.Acad.Sci.USA, 116:7015-7020, 2019

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. The natural product cladosporin is active against blood- and liver-stage and in cell-culture studies. Target deconvolution in has shown that cladosporin inhibits lysyl-tRNA synthetase (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 KRS1 and KRS (KRS). In vivo proof of concept was established in an SCID mouse model of malaria, after oral administration (ED = 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 KRS1 and KRS. This series of compounds inhibit KRS and and 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 KRS1 and KRS vs. (human) KRS. Our work validates apicomplexan KRSs as promising targets for the development of drugs for malaria and cryptosporidiosis.

PubMed: 30894487
DOI: 10.1073/pnas.1814685116

Experimental method

X-RAY DIFFRACTION (1.62 Å)