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

Beatriz Baragaña; Barbara Forte; Ryan Choi; Stephen Nakazawa Hewitt; Juan A. Bueren-Calabuig; João Pedro Pisco; Caroline Peet; David M. Dranow; David A. Robinson; Chimed Jansen; Neil R. Norcross; Sumiti Vinayak; Mark Anderson; Carrie F. Brooks; Caitlin A. Cooper; Sebastian Damerow; Michael Delves; Karen Dowers; James Duffy; Thomas E. Edwards; Irene Hallyburton; Benjamin G. Horst; Matthew A. Hulverson; Liam Ferguson; María Belén Jiménez-Díaz; Rajiv S. Jumani; Donald D. Lorimer; Melissa S. Love; Steven Maher; Holly Matthews; Case W. McNamara; Peter Miller; Sandra O'Neill; Kayode K. Ojo; Maria Osuna-Cabello; Erika Pinto; John Post; Jennifer Riley; Matthias Rottmann; Laura M. Sanz; Paul Scullion; Arvind Sharma; Sharon M. Shepherd; Yoko Shishikura; Frederick R. C. Simeons; Erin E. Stebbins; Laste Stojanovski; Ursula Straschil; Fabio K. Tamaki; Jevgenia Tamjar; Leah S. Torrie; Amélie Vantaux; Benoît Witkowski; Sergio Wittlin; Manickam Yogavel; Fabio Zuccotto; Iñigo Angulo-Barturen; Robert Sinden; Jake Baum; Francisco-Javier Gamo; Pascal Mäser; Dennis E. Kyle; Elizabeth A. Winzeler; Peter J. Myler; Paul G. Wyatt; David Floyd; David Matthews; Amit Sharma; Boris Striepen; Christopher D. Huston; David W. Gray; Alan H. Fairlamb; Andrei V. Pisliakov; Chris Walpole; Kevin D. Read; Wesley C. Van Voorhis; Ian H. Gilbert

doi:10.1073/pnas.1814685116

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

Beatriz Baragaña, Barbara Forte, Ryan Choi, Stephen Nakazawa Hewitt, Juan A. Bueren-Calabuig, João Pedro Pisco, Caroline Peet, David M. Dranow, David A. Robinson, Chimed Jansen, Neil R. Norcross, Sumiti Vinayak, Mark Anderson, Carrie F. Brooks, Caitlin A. Cooper, Sebastian Damerow, Michael Delves, Karen Dowers, James Duffy, Thomas E. EdwardsIrene Hallyburton, Benjamin G. Horst, Matthew A. Hulverson, Liam Ferguson, María Belén Jiménez-Díaz, Rajiv S. Jumani, Donald D. Lorimer, Melissa S. Love, Steven Maher, Holly Matthews, Case W. McNamara, Peter Miller, Sandra O'Neill, Kayode K. Ojo, Maria Osuna-Cabello, Erika Pinto, John Post, Jennifer Riley, Matthias Rottmann, Laura M. Sanz, Paul Scullion, Arvind Sharma, Sharon M. Shepherd, Yoko Shishikura, Frederick R. C. Simeons, Erin E. Stebbins, Laste Stojanovski, Ursula Straschil, Fabio K. Tamaki, Jevgenia Tamjar, Leah S. Torrie, Amélie Vantaux, Benoît Witkowski, Sergio Wittlin, Manickam Yogavel, Fabio Zuccotto, Iñigo Angulo-Barturen, Robert Sinden, Jake Baum, Francisco-Javier Gamo, Pascal Mäser, Dennis E. Kyle, Elizabeth A. Winzeler, Peter J. Myler, Paul G. Wyatt, David Floyd, David Matthews, Amit Sharma, Boris Striepen, Christopher D. Huston, David W. Gray, Alan H. Fairlamb, Andrei V. Pisliakov, Chris Walpole, Kevin D. Read, Wesley C. Van Voorhis, Ian H. Gilbert (Lead / Corresponding author)

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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 Plasmodium falciparum and Cryptosporidium parvum in cell culture studies. Target deconvolution in P. falciparum has shown that cladosporin inhibits lysyl-tRNA synthetase (PfKRS1). Here, we report the identification of a novel series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small molecule hit was identified and then optimized using a structurebased approach, supported by structures of both PfKRS1 and C. parvum lysyl-tRNA synthetase (CpKRS). In vivo proof of concept was established in a SCID mouse model of malaria, after oral administration (ED90 = 1.5 mg/kg, once a day for 4 days). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between PfKRS1 and CpKRS. This series of compounds inhibit CpKRS and C. parvum and C. hominis in culture and our optimized lead 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 PfKRS1 and CpKRS versus human HsKRS. Our work validates apicomplexan lysyl-tRNA synthetases as promising targets for the development of new drugs for malaria and cryptosporidiosis.

Original language	English
Pages (from-to)	7015-7020
Number of pages	6
Journal	Proceedings of the National Academy of Sciences
Volume	116
Issue number	14
Early online date	20 Mar 2019
DOIs	https://doi.org/10.1073/pnas.1814685116
Publication status	Published - 2 Apr 2019

Keywords

Cryptosporidiosis
Malaria
TRNA synthetase

ASJC Scopus subject areas

General

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1073/pnas.1814685116Licence: CC BY

Final Published VersionFinal published version, 1.38 MBLicence: CC BY
Supplementary InformationOther version, 4.05 MB

Institutional Strategic Support Fund (2016)
Cantrell, D. (Investigator), Dinkova-Kostova, A. (Investigator), Kang, L. (Investigator), Murray, P. (Investigator) & Pearson, E. (Investigator)
1/10/16 → 31/05/23
Project: Research
Chemical Biology: Leveraging Phenotypic Hits Against Kinetoplastids (Strategic Grant)
Fairlamb, A. (Investigator), Field, M. (Investigator), Gilbert, I. (Investigator), Gray, D. (Investigator), Horn, D. (Investigator) & Wyatt, P. (Investigator)
1/01/15 → 31/12/20
Project: Research
State-of-the-Art Facilities for Structural Biology at the University of Dundee
Hunter, B. (Investigator), Lilley, D. (Investigator), Owen-Hughes, T. (Investigator), Wyatt, P. (Investigator) & van Aalten, D. (Investigator)
1/03/12 → 28/02/17
Project: Research

Gilbert, Ian
- Drug Discovery Unit - Professor/Head of the Drug Discovery Unit & Roscoe Chair in Drug Discovery
Person: Academic
Pisliakov, Andrei
- Physics - Senior Lecturer (Teaching and Research)
Person: Academic

Cite this

Baragaña, 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., ... Gilbert, I. H. (2019). Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis. Proceedings of the National Academy of Sciences, 116(14), 7015-7020. https://doi.org/10.1073/pnas.1814685116

@article{9b5ac0cd63f44f0a9ae80407b3f36dda,

title = "Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis",

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 Plasmodium falciparum and Cryptosporidium parvum in cell culture studies. Target deconvolution in P. falciparum has shown that cladosporin inhibits lysyl-tRNA synthetase (PfKRS1). Here, we report the identification of a novel series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small molecule hit was identified and then optimized using a structurebased approach, supported by structures of both PfKRS1 and C. parvum lysyl-tRNA synthetase (CpKRS). In vivo proof of concept was established in a SCID mouse model of malaria, after oral administration (ED90 = 1.5 mg/kg, once a day for 4 days). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between PfKRS1 and CpKRS. This series of compounds inhibit CpKRS and C. parvum and C. hominis in culture and our optimized lead 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 PfKRS1 and CpKRS versus human HsKRS. Our work validates apicomplexan lysyl-tRNA synthetases as promising targets for the development of new drugs for malaria and cryptosporidiosis.",

keywords = "Cryptosporidiosis, Malaria, TRNA synthetase",

author = "Beatriz Baraga{\~n}a and Barbara Forte and Ryan Choi and {Nakazawa Hewitt}, Stephen and Bueren-Calabuig, {Juan A.} and Pisco, {Jo{\~a}o Pedro} and Caroline Peet and Dranow, {David M.} and Robinson, {David A.} and Chimed Jansen and Norcross, {Neil R.} and Sumiti Vinayak and Mark Anderson and Brooks, {Carrie F.} and Cooper, {Caitlin A.} and Sebastian Damerow and Michael Delves and Karen Dowers and James Duffy and Edwards, {Thomas E.} and Irene Hallyburton and Horst, {Benjamin G.} and Hulverson, {Matthew A.} and Liam Ferguson and Jim{\'e}nez-D{\'i}az, {Mar{\'i}a Bel{\'e}n} and Jumani, {Rajiv S.} and Lorimer, {Donald D.} and Love, {Melissa S.} and Steven Maher and Holly Matthews and McNamara, {Case W.} and Peter Miller and Sandra O'Neill and Ojo, {Kayode K.} and Maria Osuna-Cabello and Erika Pinto and John Post and Jennifer Riley and Matthias Rottmann and Sanz, {Laura M.} and Paul Scullion and Arvind Sharma and Shepherd, {Sharon M.} and Yoko Shishikura and Simeons, {Frederick R. C.} and Stebbins, {Erin E.} and Laste Stojanovski and Ursula Straschil and Tamaki, {Fabio K.} and Jevgenia Tamjar and Torrie, {Leah S.} and Am{\'e}lie Vantaux and Beno{\^i}t Witkowski and Sergio Wittlin and Manickam Yogavel and Fabio Zuccotto and I{\~n}igo Angulo-Barturen and Robert Sinden and Jake Baum and Francisco-Javier Gamo and Pascal M{\"a}ser and Kyle, {Dennis E.} and Winzeler, {Elizabeth A.} and Myler, {Peter J.} and Wyatt, {Paul G.} and David Floyd and David Matthews and Amit Sharma and Boris Striepen and Huston, {Christopher D.} and Gray, {David W.} and Fairlamb, {Alan H.} and Pisliakov, {Andrei V.} and Chris Walpole and Read, {Kevin D.} and {Van Voorhis}, {Wesley C.} and Gilbert, {Ian H.}",

note = "Funding Information: This work was supported by the Bill and Melinda Gates Foundation through Grant OPP1032548 to the Structure-Guided Drug Discovery Coalition and OPP1134302 (to B.S.). This work was also supported in part from federal funds, from the NIH/National Institute of Allergy and Infectious Diseases Grant R21AI123690 (to K.K.O.) and Contracts HHSN272201200025C and HHSN272201700059C (to P.J.M.); Medicines for Malaria Venture (through access to assays to I.H.G. and through RD/08/2800 to J.B.); Wellcome Trust for support of the X-ray Crystallography Facility 094090, IT support Grant 105021 (to I.H.G.), and Institutional Strategic Support Fund 204816 (to A.V.P.), all at the University of Dundee and for Investigator Award 100993 (to J.B.). Copyright: {\textcopyright} 2019 the Author(s). Published by PNAS.",

year = "2019",

month = apr,

day = "2",

doi = "10.1073/pnas.1814685116",

language = "English",

volume = "116",

pages = "7015--7020",

journal = "Proceedings of the National Academy of Sciences",

issn = "0027-8424",

publisher = "National Academy of Sciences",

number = "14",

}

Baragaña, B , Forte, B, Choi, R, Nakazawa Hewitt, S, Bueren-Calabuig, JA, Pisco, JP, Peet, C, Dranow, DM, Robinson, DA, Jansen, C, Norcross, NR, Vinayak, S, Anderson, M, Brooks, CF, Cooper, CA, Damerow, S, Delves, M, Dowers, K, Duffy, J, Edwards, TE, Hallyburton, I, Horst, BG, Hulverson, MA, Ferguson, L, Jiménez-Díaz, MB, Jumani, RS, Lorimer, DD, Love, MS, Maher, S, Matthews, H, McNamara, CW, Miller, P, O'Neill, S, Ojo, KK, Osuna-Cabello, M, Pinto, E, Post, J, Riley, J, Rottmann, M, Sanz, LM, Scullion, P, Sharma, A, Shepherd, SM, Shishikura, Y , Simeons, FRC, Stebbins, EE, Stojanovski, L, Straschil, U, Tamaki, FK, Tamjar, J, Torrie, LS, Vantaux, A, Witkowski, B, Wittlin, S, Yogavel, M, Zuccotto, F, Angulo-Barturen, I, Sinden, R, Baum, J, Gamo, F-J, Mäser, P, Kyle, DE, Winzeler, EA, Myler, PJ, Wyatt, PG, Floyd, D, Matthews, D, Sharma, A, Striepen, B, Huston, CD, Gray, DW , Fairlamb, AH , Pisliakov, AV, Walpole, C, Read, KD, Van Voorhis, WC & Gilbert, IH 2019, 'Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis', Proceedings of the National Academy of Sciences, vol. 116, no. 14, pp. 7015-7020. https://doi.org/10.1073/pnas.1814685116

TY - JOUR

T1 - Lysyl-tRNA synthetase as a drug target in malaria and cryptosporidiosis

AU - Baragaña, Beatriz

AU - Forte, Barbara

AU - Choi, Ryan

AU - Nakazawa Hewitt, Stephen

AU - Bueren-Calabuig, Juan A.

AU - Pisco, João Pedro

AU - Peet, Caroline

AU - Dranow, David M.

AU - Robinson, David A.

AU - Jansen, Chimed

AU - Norcross, Neil R.

AU - Vinayak, Sumiti

AU - Anderson, Mark

AU - Brooks, Carrie F.

AU - Cooper, Caitlin A.

AU - Damerow, Sebastian

AU - Delves, Michael

AU - Dowers, Karen

AU - Duffy, James

AU - Edwards, Thomas E.

AU - Hallyburton, Irene

AU - Horst, Benjamin G.

AU - Hulverson, Matthew A.

AU - Ferguson, Liam

AU - Jiménez-Díaz, María Belén

AU - Jumani, Rajiv S.

AU - Lorimer, Donald D.

AU - Love, Melissa S.

AU - Maher, Steven

AU - Matthews, Holly

AU - McNamara, Case W.

AU - Miller, Peter

AU - O'Neill, Sandra

AU - Ojo, Kayode K.

AU - Osuna-Cabello, Maria

AU - Pinto, Erika

AU - Post, John

AU - Riley, Jennifer

AU - Rottmann, Matthias

AU - Sanz, Laura M.

AU - Scullion, Paul

AU - Sharma, Arvind

AU - Shepherd, Sharon M.

AU - Shishikura, Yoko

AU - Simeons, Frederick R. C.

AU - Stebbins, Erin E.

AU - Stojanovski, Laste

AU - Straschil, Ursula

AU - Tamaki, Fabio K.

AU - Tamjar, Jevgenia

AU - Torrie, Leah S.

AU - Vantaux, Amélie

AU - Witkowski, Benoît

AU - Wittlin, Sergio

AU - Yogavel, Manickam

AU - Zuccotto, Fabio

AU - Angulo-Barturen, Iñigo

AU - Sinden, Robert

AU - Baum, Jake

AU - Gamo, Francisco-Javier

AU - Mäser, Pascal

AU - Kyle, Dennis E.

AU - Winzeler, Elizabeth A.

AU - Myler, Peter J.

AU - Wyatt, Paul G.

AU - Floyd, David

AU - Matthews, David

AU - Sharma, Amit

AU - Striepen, Boris

AU - Huston, Christopher D.

AU - Gray, David W.

AU - Fairlamb, Alan H.

AU - Pisliakov, Andrei V.

AU - Walpole, Chris

AU - Read, Kevin D.

AU - Van Voorhis, Wesley C.

AU - Gilbert, Ian H.

N1 - Funding Information: This work was supported by the Bill and Melinda Gates Foundation through Grant OPP1032548 to the Structure-Guided Drug Discovery Coalition and OPP1134302 (to B.S.). This work was also supported in part from federal funds, from the NIH/National Institute of Allergy and Infectious Diseases Grant R21AI123690 (to K.K.O.) and Contracts HHSN272201200025C and HHSN272201700059C (to P.J.M.); Medicines for Malaria Venture (through access to assays to I.H.G. and through RD/08/2800 to J.B.); Wellcome Trust for support of the X-ray Crystallography Facility 094090, IT support Grant 105021 (to I.H.G.), and Institutional Strategic Support Fund 204816 (to A.V.P.), all at the University of Dundee and for Investigator Award 100993 (to J.B.). Copyright: © 2019 the Author(s). Published by PNAS.

PY - 2019/4/2

Y1 - 2019/4/2

N2 - 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 (PfKRS1). Here, we report the identification of a novel series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small molecule hit was identified and then optimized using a structurebased approach, supported by structures of both PfKRS1 and C. parvum lysyl-tRNA synthetase (CpKRS). In vivo proof of concept was established in a SCID mouse model of malaria, after oral administration (ED90 = 1.5 mg/kg, once a day for 4 days). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between PfKRS1 and CpKRS. This series of compounds inhibit CpKRS and C. parvum and C. hominis in culture and our optimized lead 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 PfKRS1 and CpKRS versus human HsKRS. Our work validates apicomplexan lysyl-tRNA synthetases as promising targets for the development of new drugs for malaria and cryptosporidiosis.

AB - 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 (PfKRS1). Here, we report the identification of a novel series of selective inhibitors of apicomplexan KRSs. Following a biochemical screen, a small molecule hit was identified and then optimized using a structurebased approach, supported by structures of both PfKRS1 and C. parvum lysyl-tRNA synthetase (CpKRS). In vivo proof of concept was established in a SCID mouse model of malaria, after oral administration (ED90 = 1.5 mg/kg, once a day for 4 days). Furthermore, we successfully identified an opportunity for pathogen hopping based on the structural homology between PfKRS1 and CpKRS. This series of compounds inhibit CpKRS and C. parvum and C. hominis in culture and our optimized lead 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 PfKRS1 and CpKRS versus human HsKRS. Our work validates apicomplexan lysyl-tRNA synthetases as promising targets for the development of new drugs for malaria and cryptosporidiosis.

KW - Cryptosporidiosis

KW - Malaria

KW - TRNA synthetase

U2 - 10.1073/pnas.1814685116

DO - 10.1073/pnas.1814685116

M3 - Article

C2 - 30894487

SN - 0027-8424

VL - 116

SP - 7015

EP - 7020

JO - Proceedings of the National Academy of Sciences

JF - Proceedings of the National Academy of Sciences

IS - 14

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

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Projects

Institutional Strategic Support Fund (2016)

Chemical Biology: Leveraging Phenotypic Hits Against Kinetoplastids (Strategic Grant)

State-of-the-Art Facilities for Structural Biology at the University of Dundee

Profiles

Gilbert, Ian

Pisliakov, Andrei

Cite this