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Dobrescu I, Hammam E, Dziekan JM, Claës A, Halby L, Preiser P, Bozdech Z, Arimondo PB, Scherf A, Nardella F. Plasmodium falciparum Eukaryotic Translation Initiation Factor 3 is Stabilized by Quinazoline-Quinoline Bisubstrate Inhibitors. ACS Infect Dis 2023; 9:1257-1266. [PMID: 37216290 PMCID: PMC10262199 DOI: 10.1021/acsinfecdis.3c00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Indexed: 05/24/2023]
Abstract
Malaria drug resistance is hampering the fight against the deadliest parasitic disease affecting over 200 million people worldwide. We recently developed quinoline-quinazoline-based inhibitors (as compound 70) as promising new antimalarials. Here, we aimed to investigate their mode of action by using thermal proteome profiling (TPP). The eukaryotic translation initiation factor 3 (EIF3i) subunit I was identified as the main target protein stabilized by compound 70 in Plasmodium falciparum. This protein has never been characterized in malaria parasites. P. falciparum parasite lines were generated expressing either a HA tag or an inducible knockdown of the PfEIF3i gene to further characterize the target protein. PfEIF3i was stabilized in the presence of compound 70 in a cellular thermal shift Western blot assay, pointing that PfEIF3i indeed interacts with quinoline-quinazoline-based inhibitors. In addition, PfEIF3i-inducible knockdown blocks intra-erythrocytic development in the trophozoite stage, indicating that it has a vital function. We show that PfEIF3i is mostly expressed in late intra-erythrocytic stages and localizes in the cytoplasm. Previous mass spectrometry reports show that PfEIF3i is expressed in all parasite life cycle stages. Further studies will explore the potential of PfEIF3i as a target for the design of new antimalarial drugs active all along the life cycle of the parasite.
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Affiliation(s)
- Irina Dobrescu
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Elie Hammam
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Jerzy M. Dziekan
- School
of Biological Sciences, Nanyang Technological
University, Singapore 639798, Singapore
| | - Aurélie Claës
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Ludovic Halby
- Epigenetic
Chemical Biology, Department of Structural Biology and Chemistry,
Institut Pasteur, Université de Paris-Cité,
UMR n3523 Chem4Life, CNRS, 28 Rue Du Dr Roux, Paris 75015, France
| | - Peter Preiser
- School
of Biological Sciences, Nanyang Technological
University, Singapore 639798, Singapore
| | - Zbynek Bozdech
- School
of Biological Sciences, Nanyang Technological
University, Singapore 639798, Singapore
| | - Paola B. Arimondo
- Epigenetic
Chemical Biology, Department of Structural Biology and Chemistry,
Institut Pasteur, Université de Paris-Cité,
UMR n3523 Chem4Life, CNRS, 28 Rue Du Dr Roux, Paris 75015, France
| | - Artur Scherf
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
| | - Flore Nardella
- Unité
Biology of Host-Parasite Interactions, Department of Parasites and
Insect Vectors, Institut Pasteur, Université
de Paris-Cité, CNRS EMR 9195, INSERM Unit U1201, 25-28 Rue Du Dr Roux, Paris 75015, France
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Schlott AC, Mayclin S, Reers AR, Coburn-Flynn O, Bell AS, Green J, Knuepfer E, Charter D, Bonnert R, Campo B, Burrows J, Lyons-Abbott S, Staker BL, Chung CW, Myler PJ, Fidock DA, Tate EW, Holder AA. Structure-Guided Identification of Resistance Breaking Antimalarial N‑Myristoyltransferase Inhibitors. Cell Chem Biol 2019; 26:991-1000.e7. [PMID: 31080074 PMCID: PMC6658617 DOI: 10.1016/j.chembiol.2019.03.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/25/2019] [Accepted: 03/25/2019] [Indexed: 01/26/2023]
Abstract
The attachment of myristate to the N-terminal glycine of certain proteins is largely a co-translational modification catalyzed by N-myristoyltransferase (NMT), and involved in protein membrane-localization. Pathogen NMT is a validated therapeutic target in numerous infectious diseases including malaria. In Plasmodium falciparum, NMT substrates are important in essential processes including parasite gliding motility and host cell invasion. Here, we generated parasites resistant to a particular NMT inhibitor series and show that resistance in an in vitro parasite growth assay is mediated by a single amino acid substitution in the NMT substrate-binding pocket. The basis of resistance was validated and analyzed with a structure-guided approach using crystallography, in combination with enzyme activity, stability, and surface plasmon resonance assays, allowing identification of another inhibitor series unaffected by this substitution. We suggest that resistance studies incorporated early in the drug development process help selection of drug combinations to impede rapid evolution of parasite resistance.
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Affiliation(s)
- Anja C Schlott
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK.
| | - Stephen Mayclin
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; UCB Pharma, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
| | - Alexandra R Reers
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Olivia Coburn-Flynn
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Andrew S Bell
- Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK
| | - Judith Green
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Ellen Knuepfer
- Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David Charter
- Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Roger Bonnert
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Brice Campo
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Jeremy Burrows
- Medicines for Malaria Venture, Route de Pré-Bois 20, Post Box 1826, 1215 Geneva 15, Switzerland
| | - Sally Lyons-Abbott
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA
| | - Chun-Wa Chung
- Structural and Biophysical Sciences, GlaxoSmithKline, Stevenage, Hertfordshire, UK; Crick-GSK Biomedical LinkLabs, GSK Medicines Research Centre, Stevenage, UK
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle, WA 98109, USA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue North, Suite 500, Seattle, USA; Department of Biomedical Informatics & Medical Education, University of Washington, Seattle, USA; Department of Global Health, University of Washington, Seattle, USA
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Edward W Tate
- Molecular Sciences Research Hub, Imperial College, White City Campus Wood Lane, London W12 0BZ, UK.
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Chitnumsub P, Ittarat W, Jaruwat A, Noytanom K, Amornwatcharapong W, Pornthanakasem W, Chaiyen P, Yuthavong Y, Leartsakulpanich U. The structure of Plasmodium falciparum serine hydroxymethyltransferase reveals a novel redox switch that regulates its activities. Acta Crystallogr D Biol Crystallogr 2014; 70:1517-27. [PMID: 24914963 PMCID: PMC4051499 DOI: 10.1107/s1399004714005598] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/11/2014] [Indexed: 11/10/2022]
Abstract
Plasmodium falciparum serine hydroxymethyltransferase (PfSHMT), an enzyme in the dTMP synthesis cycle, is an antimalarial target because inhibition of its expression or function has been shown to be lethal to the parasite. As the wild-type enzyme could not be crystallized, protein engineering of residues on the surface was carried out. The surface-engineered mutant PfSHMT-F292E was successfully crystallized and its structure was determined at 3 Å resolution. The PfSHMT-F292E structure is a good representation of PfSHMT as this variant revealed biochemical properties similar to those of the wild type. Although the overall structure of PfSHMT is similar to those of other SHMTs, unique features including the presence of two loops and a distinctive cysteine pair formed by Cys125 and Cys364 in the tetrahydrofolate (THF) substrate binding pocket were identified. These structural characteristics have never been reported in other SHMTs. Biochemical characterization and mutation analysis of these two residues confirm that they act as a disulfide/sulfhydryl switch to regulate the THF-dependent catalytic function of the enzyme. This redox switch is not present in the human enzyme, in which the cysteine pair is absent. The data reported here can be further exploited as a new strategy to specifically disrupt the activity of the parasite enzyme without interfering with the function of the human enzyme.
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Affiliation(s)
- Penchit Chitnumsub
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Wanwipa Ittarat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Aritsara Jaruwat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Krittikar Noytanom
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Watcharee Amornwatcharapong
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Wichai Pornthanakasem
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein Structure and Function, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Yongyuth Yuthavong
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Ubolsree Leartsakulpanich
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
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