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Ence CC, Uddin T, Borrel J, Mittal P, Xie H, Zoller J, Sharma A, Comer E, Schreiber SL, Melillo B, Sibley LD, Chatterjee AK. Bicyclic Pyrrolidine Inhibitors of Toxoplasma gondii Phenylalanine t-RNA Synthetase with Antiparasitic Potency In Vitro and Brain Exposure. ACS Infect Dis 2024; 10:2212-2221. [PMID: 38743643 DOI: 10.1021/acsinfecdis.4c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Previous studies have shown that bicyclic azetidines are potent and selective inhibitors of apicomplexan phenylalanine tRNA synthetase (PheRS), leading to parasite growth inhibition in vitro and in vivo, including in models of Toxoplasma infection. Despite these useful properties, additional optimization is required for the development of efficacious treatments of toxoplasmosis from this inhibitor series, in particular, to achieve optimal exposure in the brain. Here, we describe a series of PheRS inhibitors built on a new bicyclic pyrrolidine core scaffold designed to retain the exit-vector geometry of the isomeric bicyclic azetidine core scaffold while offering avenues to sample diverse chemical space. Relative to the parent series, bicyclic pyrrolidines retain reasonable potency and target selectivity for parasite PheRS vs host. Further structure-activity relationship studies revealed that the introduction of aliphatic groups improved potency and ADME and PK properties, including brain exposure. The identification of this new scaffold provides potential opportunities to extend the analogue series to further improve selectivity and potency and ultimately deliver a novel, efficacious treatment of toxoplasmosis.
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Affiliation(s)
- Chloe C Ence
- Calibr at Scripps Research, La Jolla, California 92037, United States
| | - Taher Uddin
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63130, United States
| | - Julien Borrel
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Payal Mittal
- Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
- ICMR-NIMR, Sector-8, Dwarka, New Delhi 110077, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Han Xie
- Calibr at Scripps Research, La Jolla, California 92037, United States
| | - Jochen Zoller
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Amit Sharma
- Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Eamon Comer
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, Massachusetts 02142, United States
| | - Stuart L Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, Massachusetts 02142, United States
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Bruno Melillo
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, Massachusetts 02142, United States
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri 63130, United States
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Wirjanata G, Lin J, Dziekan JM, El Sahili A, Chung Z, Tjia S, Binte Zulkifli NE, Boentoro J, Tham R, Jia LS, Go KD, Yu H, Partridge A, Olsen D, Prabhu N, Sobota RM, Nordlund P, Lescar J, Bozdech Z. Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development. Cell Chem Biol 2024; 31:743-759.e8. [PMID: 38593807 DOI: 10.1016/j.chembiol.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/02/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Identification of new druggable protein targets remains the key challenge in the current antimalarial development efforts. Here we used mass-spectrometry-based cellular thermal shift assay (MS-CETSA) to identify potential targets of several antimalarials and drug candidates. We found that falcilysin (FLN) is a common binding partner for several drug candidates such as MK-4815, MMV000848, and MMV665806 but also interacts with quinoline drugs such as chloroquine and mefloquine. Enzymatic assays showed that these compounds can inhibit FLN proteolytic activity. Their interaction with FLN was explored systematically by isothermal titration calorimetry and X-ray crystallography, revealing a shared hydrophobic pocket in the catalytic chamber of the enzyme. Characterization of transgenic cell lines with lowered FLN expression demonstrated statistically significant increases in susceptibility toward MK-4815, MMV000848, and several quinolines. Importantly, the hydrophobic pocket of FLN appears amenable to inhibition and the structures reported here can guide the development of novel drugs against malaria.
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Affiliation(s)
- Grennady Wirjanata
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Infectious Diseases Labs & Singapore Immunology Network, Agency for Science, Technology and Research, 138648 Singapore, Singapore
| | - Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore
| | - Zara Chung
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Seth Tjia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - Josephine Boentoro
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Roy Tham
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Lai Si Jia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - David Olsen
- Merck & Co., Inc., West Point, PA 19486, USA
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 637551, Singapore.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore.
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Ence CC, Uddin T, Borrel J, Mittal P, Xie H, Zoller J, Sharma A, Comer E, Schreiber SL, Melillo B, Sibley LD, Chatterjee AK. Bicyclic pyrrolidine inhibitors of Toxoplasma gondii phenylalanine t-RNA synthetase with antiparasitic potency in vitro and brain exposure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582607. [PMID: 38464220 PMCID: PMC10925249 DOI: 10.1101/2024.02.28.582607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Previous studies have shown that bicyclic azetidines are potent and selective inhibitors of apicomplexan phenylalanine tRNA synthetase (PheRS), leading to parasite growth inhibition in vitro and in vivo, including in models of Toxoplasma infection. Despite these useful properties, additional optimization is required for the development of efficacious treatments of toxoplasmosis from this inhibitor series, in particular to achieve sufficient exposure in the brain. Here, we describe a series of PheRS inhibitors built on a new bicyclic pyrrolidine core scaffold designed to retain the exit-vector geometry of the isomeric bicyclic azetidine core scaffold while offering avenues to sample diverse chemical space. Relative to the parent series, bicyclic pyrrolidines retain reasonable potency and target selectivity for parasite PheRS vs. host. Further structure-activity relationship studies revealed that the introduction of aliphatic groups improved potency, ADME and PK properties, including brain exposure. The identification of this new scaffold provides potential opportunities to extend the analog series to further improve selectivity and potency and ultimately deliver a novel, efficacious treatment of toxoplasmosis.
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Affiliation(s)
| | - Taher Uddin
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Julien Borrel
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
| | - Payal Mittal
- Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
- ICMR-NIMR, Sector-8, Dwarka, New Delhi-110077, India, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Han Xie
- Calibr at Scripps Research, La Jolla, CA 92037, USA
| | - Jochen Zoller
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
| | - Amit Sharma
- Molecular Medicine-Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Eamon Comer
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
| | - Stuart L. Schreiber
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Bruno Melillo
- Chemical Biology and Therapeutics Science Program, Broad Institute, Cambridge, MA 02142, USA
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - L. David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63130, USA
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Sharma VK, Chhibber-Goel J, Yogavel M, Sharma A. Structural characterization of glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum. Mol Biochem Parasitol 2023; 253:111530. [PMID: 36370911 DOI: 10.1016/j.molbiopara.2022.111530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes in protein translation machinery that provide the charged tRNAs needed for protein synthesis. Over the past decades, aaRSs have been studied as anti-parasitic, anti-bacterial, and anti-fungal drug targets. This study focused on the cytoplasmic glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum, which belongs to class Ib in aaRSs. GluRS unlike most other aaRSs requires tRNA to activate its cognate amino acid substrate L-Glutamate (L-Glu), and fails to form an intermediate adenylate complex in the absence of tRNA. The crystal structures of the Apo, ATP, and ADP-bound forms of Plasmodium falciparum glutamyl-tRNA synthetase (PfGluRS) were solved at 2.1 Å, 2.2 Å, and 2.8 Å respectively. The structural comparison of the Apo- and ATP-bound holo-forms of PfGluRS showed considerable conformational changes in the loop regions around the ATP-binding pocket of the enzyme. Biophysical characterization of the PfGluRS showed binding of the enzyme substrates L-Gluand ATP.. The sequence and structural conservation were evident across GluRS compared to other species. The structural dissection of the PfGluRS gives insight into the critical residues involved in the binding of ATP substrate, which can be harvested to develop new antimalarial drugs.
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Affiliation(s)
- Vivek Kumar Sharma
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Jyoti Chhibber-Goel
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Manickam Yogavel
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Amit Sharma
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.
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Mee-udorn P, Nutho B, Chootrakool R, Maenpuen S, Leartsakulpanich U, Chitnumsub P, Rungrotmongkol T. Structural dynamics and in silico design of pyrazolopyran-based inhibitors against Plasmodium serine hydroxymethyltransferases. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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