1
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Woodland JG, Horatscheck A, Soares de Melo C, Dziwornu GA, Taylor D. Another decade of antimalarial drug discovery: New targets, tools and molecules. PROGRESS IN MEDICINAL CHEMISTRY 2024; 63:161-234. [PMID: 39370241 DOI: 10.1016/bs.pmch.2024.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
Abstract
Malaria remains a devastating but preventable infectious disease that disproportionately affects the African continent. Emerging resistance to current frontline therapies means that not only are new treatments urgently required, but also novel validated antimalarial targets to circumvent cross-resistance. Fortunately, tremendous efforts have been made by the global drug discovery community over the past decade. In this chapter, we will highlight some of the antimalarial drug discovery and development programmes currently underway across the globe, charting progress in the identification of new targets and the development of new classes of drugs to prosecute them. These efforts have been complemented by the development of valuable tools to accelerate target validation such as the NOD scid gamma (NSG) humanized mouse efficacy model and progress in predictive modelling and open-source software. Among the medicinal chemistry programmes that have been conducted over the past decade are those targeting Plasmodium falciparum ATPase4 (ATP4) and acetyl-CoA synthetase (AcAS) as well as proteins disrupting parasite protein translation such as the aminoacyl-tRNA synthetases (aaRSs) and eukaryotic elongation factor 2 (eEF2). The benefits and challenges of targeting Plasmodium kinases will be examined, with a focus on Plasmodium cyclic GMP-dependent protein kinase (PKG), cyclin-dependent-like protein kinase 3 (CLK3) and phosphatidylinositol 4-kinase (PI4K). The chapter concludes with a survey of incipient drug discovery centres in Africa and acknowledges the value of recent international meetings in galvanizing and uniting the antimalarial drug discovery community.
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Affiliation(s)
- John G Woodland
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa; South African Medical Research Council Drug Discovery and Development Research Unit, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - André Horatscheck
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
| | - Candice Soares de Melo
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
| | - Godwin A Dziwornu
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa
| | - Dale Taylor
- Holistic Drug Discovery and Development (H3D) Centre, University of Cape Town, Rondebosch, South Africa.
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2
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Pallabothula VSK, Abdalrahman NT, Mori M, Fekri AH, Janďourek O, Konečná K, Paterová P, Novák M, Dudášová-Hatoková P, Štěrbová-Kovaříková P, Castellano C, Meneghetti F, Villa S, Kuneš J, Juhás M, Zitko J. A hit expansion of 3-benzamidopyrazine-2-carboxamide: Toward inhibitors of prolyl-tRNA synthetase with antimycobacterial activity. Arch Pharm (Weinheim) 2024; 357:e2400171. [PMID: 38710636 DOI: 10.1002/ardp.202400171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/06/2024] [Accepted: 04/09/2024] [Indexed: 05/08/2024]
Abstract
This study presents an exploration of the chemical space around derivatives of 3-benzamidopyrazine-2-carboxamides, previously identified as potent antimycobacterial compounds with predicted binding to mycobacterial prolyl-transfer RNA synthetase. New urea derivatives (Series-1) were generally inactive, probably due to their preference for cis-trans conformation (confirmed by density functional theory calculations and experimentally by nuclear overhauser effect spectroscopy NMR). Series-2 (3-benzamidopyrazine-2-carboxamides with disubstituted benzene ring) demonstrated that substituents larger than fluorine are not tolerated in the ortho position of the benzene ring. This series brought two new compounds (21: R = 2-F, 4-Cl and 22: R = 2-F, 4-Br) with in vitro activity against Mycobacterium tuberculosis H37Rv as well as multidrug-resistant clinical isolates, with minimum inhibitory concentration ranging from 6.25 to 25 μg/mL. The lactone-type derivatives 4H-pyrazino[2,3-d][1,3]oxazin-4-ones (Series-3) were inactive, but solvent stability studies of compound 29 indicated that they might be developed to usable lactone prodrugs of inhibitors of mycobacterial aspartate decarboxylase (PanD).
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Affiliation(s)
| | | | - Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Amir Hossein Fekri
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Ondřej Janďourek
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Klára Konečná
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Pavla Paterová
- Department of Clinical Microbiology, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Martin Novák
- Biomedical Research Centre, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | | | | | | | | | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Jiří Kuneš
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Martin Juhás
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
- Faculty of Science, University of Hradec Králové, Hradec Králové, Czech Republic
| | - Jan Zitko
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
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3
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Mishra S, Malhotra N, Laleu B, Chakraborti S, Yogavel M, Sharma A. ATP mimetics targeting prolyl-tRNA synthetases as a new avenue for antimalarial drug development. iScience 2024; 27:110049. [PMID: 39104570 PMCID: PMC11298890 DOI: 10.1016/j.isci.2024.110049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/24/2023] [Accepted: 05/17/2024] [Indexed: 08/07/2024] Open
Abstract
The prolyl-tRNA synthetase (PRS) is an essential enzyme for protein translation and a validated target against malaria parasite. We describe five ATP mimetics (L95, L96, L97, L35, and L36) against PRS, exhibiting enhanced thermal stabilities in co-operativity with L-proline. L35 displays the highest thermal stability akin to halofuginone, an established inhibitor of Plasmodium falciparum PRS. Four compounds exhibit nanomolar inhibitory potency against PRS. L35 exhibits the highest potency of ∼1.6 nM against asexual-blood-stage (ABS) and ∼100-fold (effective concentration [EC50]) selectivity for the parasite. The macromolecular structures of PfPRS with L95 and L97 in complex with L-pro reveal their binding modes and catalytic site malleability. Arg401 of PfPRS oscillates between two rotameric configurations when in complex with L95, whereas it is locked in one of the configurations due to the larger size of L97. Harnessing such specific and selective chemical features holds significant promise for designing potential inhibitors and expediting drug development efforts.
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Affiliation(s)
- Siddhartha Mishra
- Molecular Medicine – Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
- ICMR-National Institute of Malaria Research (NIMR), Dwarka, New Delhi 110077, India
- Academy of Scientific and Innovative Research (AcSIR), UP, India
| | - Nipun Malhotra
- Molecular Medicine – Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Benoît Laleu
- Medicines for Malaria Venture (MMV), International Center Cointrin (ICC), Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Soumyananda Chakraborti
- ICMR-National Institute of Malaria Research (NIMR), Dwarka, New Delhi 110077, India
- Academy of Scientific and Innovative Research (AcSIR), UP, India
| | - Manickam Yogavel
- Molecular Medicine – Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Amit Sharma
- Molecular Medicine – Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
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4
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Khan D, Ramachandiran I, Vasu K, China A, Khan K, Cumbo F, Halawani D, Terenzi F, Zin I, Long B, Costain G, Blaser S, Carnevale A, Gogonea V, Dutta R, Blankenberg D, Yoon G, Fox PL. Homozygous EPRS1 missense variant causing hypomyelinating leukodystrophy-15 alters variant-distal mRNA m 6A site accessibility. Nat Commun 2024; 15:4284. [PMID: 38769304 PMCID: PMC11106242 DOI: 10.1038/s41467-024-48549-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Hypomyelinating leukodystrophy (HLD) is an autosomal recessive disorder characterized by defective central nervous system myelination. Exome sequencing of two siblings with severe cognitive and motor impairment and progressive hypomyelination characteristic of HLD revealed homozygosity for a missense single-nucleotide variant (SNV) in EPRS1 (c.4444 C > A; p.Pro1482Thr), encoding glutamyl-prolyl-tRNA synthetase, consistent with HLD15. Patient lymphoblastoid cell lines express markedly reduced EPRS1 protein due to dual defects in nuclear export and cytoplasmic translation of variant EPRS1 mRNA. Variant mRNA exhibits reduced METTL3 methyltransferase-mediated writing of N6-methyladenosine (m6A) and reduced reading by YTHDC1 and YTHDF1/3 required for efficient mRNA nuclear export and translation, respectively. In contrast to current models, the variant does not alter the sequence of m6A target sites, but instead reduces their accessibility for modification. The defect was rescued by antisense morpholinos predicted to expose m6A sites on target EPRS1 mRNA, or by m6A modification of the mRNA by METTL3-dCas13b, a targeted RNA methylation editor. Our bioinformatic analysis predicts widespread occurrence of SNVs associated with human health and disease that similarly alter accessibility of distal mRNA m6A sites. These results reveal a new RNA-dependent etiologic mechanism by which SNVs can influence gene expression and disease, consequently generating opportunities for personalized, RNA-based therapeutics targeting these disorders.
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Affiliation(s)
- Debjit Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Iyappan Ramachandiran
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Kommireddy Vasu
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Arnab China
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Krishnendu Khan
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fabio Cumbo
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Dalia Halawani
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Fulvia Terenzi
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Isaac Zin
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Briana Long
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Gregory Costain
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Susan Blaser
- Department of Diagnostic Imaging, Division of Neuroradiology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Amanda Carnevale
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH, USA
| | - Ranjan Dutta
- Department of Neuroscience, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Daniel Blankenberg
- Genomic Medicine Institute, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA
| | - Grace Yoon
- Department of Paediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
- Department of Paediatrics, Division of Neurology, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.
| | - Paul L Fox
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, USA.
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5
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Xie SC, Griffin MDW, Winzeler EA, Ribas de Pouplana L, Tilley L. Targeting Aminoacyl tRNA Synthetases for Antimalarial Drug Development. Annu Rev Microbiol 2023; 77:111-129. [PMID: 37018842 DOI: 10.1146/annurev-micro-032421-121210] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Infections caused by malaria parasites place an enormous burden on the world's poorest communities. Breakthrough drugs with novel mechanisms of action are urgently needed. As an organism that undergoes rapid growth and division, the malaria parasite Plasmodium falciparum is highly reliant on protein synthesis, which in turn requires aminoacyl-tRNA synthetases (aaRSs) to charge tRNAs with their corresponding amino acid. Protein translation is required at all stages of the parasite life cycle; thus, aaRS inhibitors have the potential for whole-of-life-cycle antimalarial activity. This review focuses on efforts to identify potent plasmodium-specific aaRS inhibitors using phenotypic screening, target validation, and structure-guided drug design. Recent work reveals that aaRSs are susceptible targets for a class of AMP-mimicking nucleoside sulfamates that target the enzymes via a novel reaction hijacking mechanism. This finding opens up the possibility of generating bespoke inhibitors of different aaRSs, providing new drug leads.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia; , ,
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia; , ,
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California, USA;
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Catalonia, Spain;
- Catalan Institution for Research and Advanced Studies, Barcelona, Catalonia, Spain
| | - Leann Tilley
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria, Australia; , ,
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6
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Yogavel M, Bougdour A, Mishra S, Malhotra N, Chhibber-Goel J, Bellini V, Harlos K, Laleu B, Hakimi MA, Sharma A. Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis. PLoS Pathog 2023; 19:e1011124. [PMID: 36854028 PMCID: PMC9974123 DOI: 10.1371/journal.ppat.1011124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/16/2023] [Indexed: 03/02/2023] Open
Abstract
The prolyl-tRNA synthetase (PRS) is a validated drug target for febrifugine and its synthetic analog halofuginone (HFG) against multiple apicomplexan parasites including Plasmodium falciparum and Toxoplasma gondii. Here, a novel ATP-mimetic centered on 1-(pyridin-4-yl) pyrrolidin-2-one (PPL) scaffold has been validated to bind to Toxoplasma gondii PRS and kill toxoplasma parasites. PPL series exhibited potent inhibition at the cellular (T. gondii parasites) and enzymatic (TgPRS) levels compared to the human counterparts. Cell-based chemical mutagenesis was employed to determine the mechanism of action via a forward genetic screen. Tg-resistant parasites were analyzed with wild-type strain by RNA-seq to identify mutations in the coding sequence conferring drug resistance by computational analysis of variants. DNA sequencing established two mutations, T477A and T592S, proximal to terminals of the PPL scaffold and not directly in the ATP, tRNA, or L-pro sites, as supported by the structural data from high-resolution crystal structures of drug-bound enzyme complexes. These data provide an avenue for structure-based activity enhancement of this chemical series as anti-infectives.
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Affiliation(s)
- Manickam Yogavel
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Alexandre Bougdour
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Siddhartha Mishra
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi, India
| | - Nipun Malhotra
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Jyoti Chhibber-Goel
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Valeria Bellini
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Benoît Laleu
- Medicines for Malaria Venture (MMV), International Center Cointrin (ICC), Geneva, Switzerland
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Amit Sharma
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi, India
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7
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Kurata K, James-Bott A, Tye MA, Yamamoto L, Samur MK, Tai YT, Dunford J, Johansson C, Senbabaoglu F, Philpott M, Palmer C, Ramasamy K, Gooding S, Smilova M, Gaeta G, Guo M, Christianson JC, Payne NC, Singh K, Karagoz K, Stokes ME, Ortiz M, Hagner P, Thakurta A, Cribbs A, Mazitschek R, Hideshima T, Anderson KC, Oppermann U. Prolyl-tRNA synthetase as a novel therapeutic target in multiple myeloma. Blood Cancer J 2023; 13:12. [PMID: 36631435 PMCID: PMC9834298 DOI: 10.1038/s41408-023-00787-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/23/2022] [Accepted: 01/05/2023] [Indexed: 01/13/2023] Open
Abstract
Multiple myeloma (MM) is a plasma cell malignancy characterised by aberrant production of immunoglobulins requiring survival mechanisms to adapt to proteotoxic stress. We here show that glutamyl-prolyl-tRNA synthetase (GluProRS) inhibition constitutes a novel therapeutic target. Genomic data suggest that GluProRS promotes disease progression and is associated with poor prognosis, while downregulation in MM cells triggers apoptosis. We developed NCP26, a novel ATP-competitive ProRS inhibitor that demonstrates significant anti-tumour activity in multiple in vitro and in vivo systems and overcomes metabolic adaptation observed with other inhibitor chemotypes. We demonstrate a complex phenotypic response involving protein quality control mechanisms that centers around the ribosome as an integrating hub. Using systems approaches, we identified multiple downregulated proline-rich motif-containing proteins as downstream effectors. These include CD138, transcription factors such as MYC, and transcription factor 3 (TCF3), which we establish as a novel determinant in MM pathobiology through functional and genomic validation. Our preclinical data therefore provide evidence that blockade of prolyl-aminoacylation evokes a complex pro-apoptotic response beyond the canonical integrated stress response and establish a framework for its evaluation in a clinical setting.
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Affiliation(s)
- Keiji Kurata
- grid.38142.3c000000041936754XJerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
| | - Anna James-Bott
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - Mark A. Tye
- grid.32224.350000 0004 0386 9924Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114 USA ,Harvard Graduate School of Arts and Sciences, Cambridge, MA 02138 USA ,grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA 02115 USA
| | - Leona Yamamoto
- grid.38142.3c000000041936754XJerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
| | - Mehmet K. Samur
- grid.38142.3c000000041936754XJerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA ,grid.38142.3c000000041936754XDepartment of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115 USA ,grid.65499.370000 0001 2106 9910Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Yu-Tzu Tai
- grid.38142.3c000000041936754XJerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
| | - James Dunford
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - Catrine Johansson
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - Filiz Senbabaoglu
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - Martin Philpott
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - Charlotte Palmer
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - Karthik Ramasamy
- grid.4991.50000 0004 1936 8948Oxford Centre for Translational Myeloma Research, Botnar Research Centre, University of Oxford, Oxford, OX3 7LD UK ,grid.4991.50000 0004 1936 8948Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7LD UK
| | - Sarah Gooding
- grid.4991.50000 0004 1936 8948Oxford Centre for Translational Myeloma Research, Botnar Research Centre, University of Oxford, Oxford, OX3 7LD UK ,grid.421962.a0000 0004 0641 4431Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 7LD UK
| | - Mihaela Smilova
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - Giorgia Gaeta
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - Manman Guo
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK
| | - John C. Christianson
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK ,grid.4991.50000 0004 1936 8948Oxford Centre for Translational Myeloma Research, Botnar Research Centre, University of Oxford, Oxford, OX3 7LD UK
| | - N. Connor Payne
- grid.32224.350000 0004 0386 9924Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114 USA ,grid.38142.3c000000041936754XDepartment of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138 USA
| | - Kritika Singh
- grid.32224.350000 0004 0386 9924Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114 USA ,grid.261112.70000 0001 2173 3359Department of Bioengineering, Northeastern University, Boston, MA 02115 USA
| | - Kubra Karagoz
- grid.419971.30000 0004 0374 8313Bristol Myers Squibb, Summit, NJ 07901 USA
| | - Matthew E. Stokes
- grid.419971.30000 0004 0374 8313Bristol Myers Squibb, Summit, NJ 07901 USA
| | - Maria Ortiz
- grid.419971.30000 0004 0374 8313Bristol Myers Squibb, Summit, NJ 07901 USA
| | - Patrick Hagner
- grid.419971.30000 0004 0374 8313Bristol Myers Squibb, Summit, NJ 07901 USA
| | - Anjan Thakurta
- grid.4991.50000 0004 1936 8948Oxford Centre for Translational Myeloma Research, Botnar Research Centre, University of Oxford, Oxford, OX3 7LD UK ,grid.419971.30000 0004 0374 8313Bristol Myers Squibb, Summit, NJ 07901 USA
| | - Adam Cribbs
- grid.4991.50000 0004 1936 8948Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD UK ,grid.4991.50000 0004 1936 8948Oxford Centre for Translational Myeloma Research, Botnar Research Centre, University of Oxford, Oxford, OX3 7LD UK
| | - Ralph Mazitschek
- grid.32224.350000 0004 0386 9924Center for Systems Biology, Massachusetts General Hospital, Boston, MA 02114 USA ,grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA 02115 USA ,grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Teru Hideshima
- Jerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA.
| | - Kenneth C. Anderson
- grid.38142.3c000000041936754XJerome Lipper Multiple Myeloma Center, LeBow Institute for Myeloma Therapeutics, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215 USA
| | - Udo Oppermann
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK. .,Oxford Centre for Translational Myeloma Research, Botnar Research Centre, University of Oxford, Oxford, OX3 7LD, UK.
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8
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Cheng B, Cai Z, Luo Z, Luo S, Luo Z, Cheng Y, Yu Y, Guo J, Ju Y, Gu Q, Xu J, Jiang X, Li G, Zhou H. Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase. J Med Chem 2022; 65:15840-15855. [PMID: 36394909 DOI: 10.1021/acs.jmedchem.2c01496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are promising antimicrobial targets due to their essential roles in protein translation, and expanding their inhibitory mechanisms will provide new opportunities for drug discovery. We report here that halofuginone (HF), an herb-derived medicine, moderately inhibits prolyl-tRNA synthetases (ProRSs) from various pathogenic bacteria. A cocrystal structure of Staphylococcus aureus ProRS (SaProRS) with HF and an ATP analog was determined, which guided the design of new HF analogs. Compound 3 potently inhibited SaProRS at IC50 = 0.18 μM and Kd = 30.3 nM and showed antibacterial activities with an MIC of 1-4 μg/mL in vitro. The bacterial drug resistance to 3 only developed at a rate similar to or slower than those of clinically used antibiotics in vitro. Our study indicates that the scaffold and ATP-aided inhibitory mechanism of HF could apply to bacterial ProRS and also provides a chemical validation for using bacterial ProRS as an antibacterial target.
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Affiliation(s)
- Bao Cheng
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Zhengjun Cai
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Ziqing Luo
- Animal Experiment Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Siting Luo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Zhiteng Luo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yanfang Cheng
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Ying Yu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Junsong Guo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Yingchen Ju
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Xianxing Jiang
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
| | - Geng Li
- Animal Experiment Center, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Huihao Zhou
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
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9
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Pallabothula VSK, Kerda M, Juhás M, Janďourek O, Konečná K, Bárta P, Paterová P, Zitko J. Adenosine-Mimicking Derivatives of 3-Aminopyrazine-2-Carboxamide: Towards Inhibitors of Prolyl-tRNA Synthetase with Antimycobacterial Activity. Biomolecules 2022; 12:1561. [PMID: 36358911 PMCID: PMC9687610 DOI: 10.3390/biom12111561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 08/16/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) poses a significant threat to mankind and as such earned its place on the WHO list of priority pathogens. New antimycobacterials with a mechanism of action different to currently used agents are highly required. This study presents the design, synthesis, and biological evaluation of 3-acylaminopyrazine-2-carboxamides derived from a previously reported inhibitor of human prolyl-tRNA synthetase. Compounds were evaluated in vitro against various strains of mycobacteria, pathogenic bacteria, and fungi of clinical significance. In general, high activity against mycobacteria was noted, while the antibacterial and antifungal activity was minimal. The most active compounds were 4'-substituted 3-(benzamido)pyrazine-2-carboxamides, exerting MIC (Minimum Inhibitory Concentration) from 1.95 to 31.25 µg/mL. Detailed structure-activity relationships were established and rationalized in silico with regard to mycobacterial ProRS as a probable target. The active compounds preserved their activity even against multidrug-resistant strains of Mycobacterium tuberculosis. At the same time, they were non-cytotoxic against HepG2 human hepatocellular carcinoma cells. This project is the first step in the successful repurposing of inhibitors of human ProRS to inhibitors of mycobacterial ProRS with antimycobacterial activity.
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Affiliation(s)
| | - Marek Kerda
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Martin Juhás
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Ondřej Janďourek
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Klára Konečná
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Pavel Bárta
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
| | - Pavla Paterová
- Department of Clinical Microbiology, University Hospital Hradec Králové, Sokolská 581, 500 05 Hradec Králové, Czech Republic
| | - Jan Zitko
- Faculty of Pharmacy in Hradec Králové, Charles University, Ak. Heyrovského 1203/8, 500 05 Hradec Králové, Czech Republic
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10
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Tye MA, Payne NC, Johansson C, Singh K, Santos SA, Fagbami L, Pant A, Sylvester K, Luth MR, Marques S, Whitman M, Mota MM, Winzeler EA, Lukens AK, Derbyshire ER, Oppermann U, Wirth DF, Mazitschek R. Elucidating the path to Plasmodium prolyl-tRNA synthetase inhibitors that overcome halofuginone resistance. Nat Commun 2022; 13:4976. [PMID: 36008486 PMCID: PMC9403976 DOI: 10.1038/s41467-022-32630-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 08/10/2022] [Indexed: 02/07/2023] Open
Abstract
The development of next-generation antimalarials that are efficacious against the human liver and asexual blood stages is recognized as one of the world's most pressing public health challenges. In recent years, aminoacyl-tRNA synthetases, including prolyl-tRNA synthetase, have emerged as attractive targets for malaria chemotherapy. We describe the development of a single-step biochemical assay for Plasmodium and human prolyl-tRNA synthetases that overcomes critical limitations of existing technologies and enables quantitative inhibitor profiling with high sensitivity and flexibility. Supported by this assay platform and co-crystal structures of representative inhibitor-target complexes, we develop a set of high-affinity prolyl-tRNA synthetase inhibitors, including previously elusive aminoacyl-tRNA synthetase triple-site ligands that simultaneously engage all three substrate-binding pockets. Several compounds exhibit potent dual-stage activity against Plasmodium parasites and display good cellular host selectivity. Our data inform the inhibitor requirements to overcome existing resistance mechanisms and establish a path for rational development of prolyl-tRNA synthetase-targeted anti-malarial therapies.
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Affiliation(s)
- Mark A Tye
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Graduate School of Arts and Sciences, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - N Connor Payne
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Catrine Johansson
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Kritika Singh
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Sofia A Santos
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Lọla Fagbami
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Graduate School of Arts and Sciences, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Akansha Pant
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Madeline R Luth
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Sofia Marques
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Maria M Mota
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Udo Oppermann
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Dyann F Wirth
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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Manickam Y, Malhotra N, Mishra S, Babbar P, Dusane A, Laleu B, Bellini V, Hakimi MA, Bougdour A, Sharma A. Double drugging of prolyl-tRNA synthetase provides a new paradigm for anti-infective drug development. PLoS Pathog 2022; 18:e1010363. [PMID: 35333915 PMCID: PMC9004777 DOI: 10.1371/journal.ppat.1010363] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/12/2022] [Accepted: 02/11/2022] [Indexed: 01/13/2023] Open
Abstract
Toxoplasmosis is caused by Toxoplasma gondii and in immunocompromised patients it may lead to seizures, encephalitis or death. The conserved enzyme prolyl-tRNA synthetase (PRS) is a validated druggable target in Toxoplasma gondii but the traditional ‘single target–single drug’ approach has its caveats. Here, we describe two potent inhibitors namely halofuginone (HFG) and a novel ATP mimetic (L95) that bind to Toxoplasma gondii PRS simultaneously at different neighbouring sites to cover all three of the enzyme substrate subsites. HFG and L95 act as one triple-site inhibitor in tandem and form an unusual ternary complex wherein HFG occupies the 3’-end of tRNA and the L-proline (L-pro) binding sites while L95 occupies the ATP pocket. These inhibitors exhibit nanomolar IC50 and EC50 values independently, and when given together reveal an additive mode of action in parasite inhibition assays. This work validates a novel approach and lays a structural framework for further drug development based on simultaneous targeting of multiple pockets to inhibit druggable proteins. Among infectious diseases, parasitic diseases are a major cause of death and morbidity. Toxoplasmosis is caused by an infection of the apicomplexan parasite Toxoplasma gondii. In immunocompromised patients Toxoplasmosis may lead to seizures, encephalitis or death. Novel therapeutics for human parasites are constantly needed. In recent years, the aminoacyl-tRNA synthetase (aaRS) enzyme family has been validated as a drug target for several parasitic infections. The Toxoplasma gondii prolyl-tRNA synthetase inhibitor halofuginone (HFG) has been validated earlier but here we show that an ATP-mimic called L95 is a potent inhibitor and can bind to the target enzyme in the presence of HFG. Thus, the two inhibitors described in this study simultaneously occupy all three natural substrate (ATP, L-amino acid and 3’-end of tRNA) binding pockets and thereby inhibit the enzyme leading to parasite death. This unprecedented double drugging of a pathogen enzyme may delay resistance mutation generation and this approach opens the path to multi-drugging of validated parasite proteins.
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Affiliation(s)
- Yogavel Manickam
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Nipun Malhotra
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Siddhartha Mishra
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- ICMR-National Institute of Malaria Research (NIMR), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Palak Babbar
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Abhishek Dusane
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Benoît Laleu
- Medicines for Malaria Venture (MMV), International Center Cointrin (ICC), Geneva, Switzerland
| | - Valeria Bellini
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Alexandre Bougdour
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
- * E-mail: (AB); (AS)
| | - Amit Sharma
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- ICMR-National Institute of Malaria Research (NIMR), New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- * E-mail: (AB); (AS)
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12
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Pang L, Weeks SD, Juhás M, Strelkov SV, Zitko J, Van Aerschot A. Towards Novel 3-Aminopyrazinamide-Based Prolyl-tRNA Synthetase Inhibitors: In Silico Modelling, Thermal Shift Assay and Structural Studies. Int J Mol Sci 2021; 22:ijms22157793. [PMID: 34360555 PMCID: PMC8346053 DOI: 10.3390/ijms22157793] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/08/2021] [Accepted: 07/17/2021] [Indexed: 11/16/2022] Open
Abstract
Human cytosolic prolyl-tRNA synthetase (HcProRS) catalyses the formation of the prolyl-tRNAPro, playing an important role in protein synthesis. Inhibition of HcProRS activity has been shown to have potential benefits in the treatment of fibrosis, autoimmune diseases and cancer. Recently, potent pyrazinamide-based inhibitors were identified by a high-throughput screening (HTS) method, but no further elaboration was reported. The pyrazinamide core is a bioactive fragment found in numerous clinically validated drugs and has been subjected to various modifications. Therefore, we applied a virtual screening protocol to our in-house library of pyrazinamide-containing small molecules, searching for potential novel HcProRS inhibitors. We identified a series of 3-benzylaminopyrazine-2-carboxamide derivatives as positive hits. Five of them were confirmed by a thermal shift assay (TSA) with the best compounds 3b and 3c showing EC50 values of 3.77 and 7.34 µM, respectively, in the presence of 1 mM of proline (Pro) and 3.45 µM enzyme concentration. Co-crystal structures of HcProRS in complex with these compounds and Pro confirmed the initial docking studies and show how the Pro facilitates binding of the ligands that compete with ATP substrate. Modelling 3b into other human class II aminoacyl-tRNA synthetases (aaRSs) indicated that the subtle differences in the ATP binding site of these enzymes likely contribute to its potential selective binding of HcProRS. Taken together, this study successfully identified novel HcProRS binders from our anti-tuberculosis in-house compound library, displaying opportunities for repurposing old drug candidates for new applications such as therapeutics in HcProRS-related diseases.
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Affiliation(s)
- Luping Pang
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49—Box 822, 3000 Leuven, Belgium; (L.P.); (S.D.W.); (S.V.S.)
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49—Box 1041, 3000 Leuven, Belgium
| | - Stephen D. Weeks
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49—Box 822, 3000 Leuven, Belgium; (L.P.); (S.D.W.); (S.V.S.)
- Pledge Therapeutics, Gaston Geenslaan 1, 3001 Leuven, Belgium
| | - Martin Juhás
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic;
| | - Sergei V. Strelkov
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49—Box 822, 3000 Leuven, Belgium; (L.P.); (S.D.W.); (S.V.S.)
| | - Jan Zitko
- Faculty of Pharmacy in Hradec Králové, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic;
- Correspondence: (J.Z.); (A.V.A.)
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49—Box 1041, 3000 Leuven, Belgium
- Correspondence: (J.Z.); (A.V.A.)
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13
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Okaniwa M, Shibata A, Ochida A, Akao Y, White KL, Shackleford DM, Duffy S, Lucantoni L, Dey S, Striepen J, Yeo T, Mok S, Aguiar ACC, Sturm A, Crespo B, Sanz LM, Churchyard A, Baum J, Pereira DB, Guido RVC, Dechering KJ, Wittlin S, Uhlemann AC, Fidock DA, Niles JC, Avery VM, Charman SA, Laleu B. Repositioning and Characterization of 1-(Pyridin-4-yl)pyrrolidin-2-one Derivatives as Plasmodium Cytoplasmic Prolyl-tRNA Synthetase Inhibitors. ACS Infect Dis 2021; 7:1680-1689. [PMID: 33929818 PMCID: PMC8204304 DOI: 10.1021/acsinfecdis.1c00020] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Prolyl-tRNA synthetase
(PRS) is a clinically validated antimalarial
target. Screening of a set of PRS ATP-site binders, initially designed
for human indications, led to identification of 1-(pyridin-4-yl)pyrrolidin-2-one
derivatives representing a novel antimalarial scaffold. Evidence designates
cytoplasmic PRS as the drug target. The frontrunner 1 and its active enantiomer 1-S exhibited low-double-digit nanomolar activity against resistant Plasmodium falciparum (Pf) laboratory strains
and development of liver schizonts. No cross-resistance with strains
resistant to other known antimalarials was noted. In addition, a similar
level of growth inhibition was observed against clinical field isolates
of Pf and P. vivax. The slow killing
profile and the relative high propensity to develop resistance in vitro (minimum inoculum resistance of 8 × 105 parasites at a selection pressure of 3 × IC50) constitute unfavorable features for treatment of malaria. However,
potent blood stage and antischizontal activity are compelling for
causal prophylaxis which does not require fast onset of action. Achieving
sufficient on-target selectivity appears to be particularly challenging
and should be the primary focus during the next steps of optimization
of this chemical series. Encouraging preliminary off-target profile
and oral efficacy in a humanized murine model of Pf malaria allowed us to conclude that 1-(pyridin-4-yl)pyrrolidin-2-one
derivatives represent a promising starting point for the identification
of novel antimalarial prophylactic agents that selectively target Plasmodium PRS.
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Affiliation(s)
- Masanori Okaniwa
- Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Akira Shibata
- Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Atsuko Ochida
- Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yuichiro Akao
- Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Karen L. White
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - David M. Shackleford
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Sandra Duffy
- Discovery Biology, Griffith University, Brisbane Innovation Park, Don Young Road, Nathan, Queensland 4111, Australia
| | - Leonardo Lucantoni
- Discovery Biology, Griffith University, Brisbane Innovation Park, Don Young Road, Nathan, Queensland 4111, Australia
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
| | - Josefine Striepen
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Tomas Yeo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sachel Mok
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Anna Caroline C. Aguiar
- Sao Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100, São Carlos, São Paulo 13563-120, Brazil
| | - Angelika Sturm
- TropIQ Health Sciences, Transistorweg 5-C02, 6534 AT Nijmegen, The Netherlands
| | - Benigno Crespo
- Global Health, GlaxoSmithKline R&D, Tres Cantos, Madrid 28760, Spain
| | - Laura M. Sanz
- Global Health, GlaxoSmithKline R&D, Tres Cantos, Madrid 28760, Spain
| | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Dhelio B. Pereira
- Tropical Medicine Research Center of Rondonia, Av. Guaporé, 215, Porto Velho, Rondonia 76812-329, Brazil
| | - Rafael V. C. Guido
- Sao Carlos Institute of Physics, University of São Paulo, Av. João Dagnone, 1100, São Carlos, São Paulo 13563-120, Brazil
| | - Koen J. Dechering
- TropIQ Health Sciences, Transistorweg 5-C02, 6534 AT Nijmegen, The Netherlands
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland
- University of Basel, 4002 Basel, Switzerland
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - David A. Fidock
- Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, New York 10032, United States
- Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, United States
| | - Vicky M. Avery
- Discovery Biology, Griffith University, Brisbane Innovation Park, Don Young Road, Nathan, Queensland 4111, Australia
| | - Susan A. Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Benoît Laleu
- Medicines for Malaria Venture, ICC, Route de Pré-Bois 20, 1215 Geneva, Switzerland
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14
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Sandoval DR, Clausen TM, Nora C, Cribbs AP, Denardo A, Clark AE, Garretson AF, Coker JKC, Narayanan A, Majowicz SA, Philpott M, Johansson C, Dunford JE, Spliid CB, Golden GJ, Payne NC, Tye MA, Nowell CJ, Griffis ER, Piermatteo A, Grunddal KV, Alle T, Magida JA, Hauser BM, Feldman J, Caradonna TM, Pu Y, Yin X, McVicar RN, Kwong EM, Weiss RJ, Downes M, Tsimikas S, Smidt AG, Ballatore C, Zengler K, Evans RM, Chanda SK, Croker BA, Leibel SL, Jose J, Mazitschek R, Oppermann U, Esko JD, Carlin AF, Gordts PLSM. The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33791697 PMCID: PMC8010724 DOI: 10.1101/2021.03.22.436522] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We identify the prolyl-tRNA synthetase (PRS) inhibitor halofuginone 1 , a compound in clinical trials for anti-fibrotic and anti-inflammatory applications 2 , as a potent inhibitor of SARS-CoV-2 infection and replication. The interaction of SARS-CoV-2 spike protein with cell surface heparan sulfate (HS) promotes viral entry 3 . We find that halofuginone reduces HS biosynthesis, thereby reducing spike protein binding, SARS-CoV-2 pseudotyped virus, and authentic SARS-CoV-2 infection. Halofuginone also potently suppresses SARS-CoV-2 replication post-entry and is 1,000-fold more potent than Remdesivir 4 . Inhibition of HS biosynthesis and SARS-CoV-2 infection depends on specific inhibition of PRS, possibly due to translational suppression of proline-rich proteins. We find that pp1a and pp1ab polyproteins of SARS-CoV-2, as well as several HS proteoglycans, are proline-rich, which may make them particularly vulnerable to halofuginone's translational suppression. Halofuginone is orally bioavailable, has been evaluated in a phase I clinical trial in humans and distributes to SARS-CoV-2 target organs, including the lung, making it a near-term clinical trial candidate for the treatment of COVID-19.
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15
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Pang L, Weeks SD, Van Aerschot A. Aminoacyl-tRNA Synthetases as Valuable Targets for Antimicrobial Drug Discovery. Int J Mol Sci 2021; 22:1750. [PMID: 33578647 PMCID: PMC7916415 DOI: 10.3390/ijms22041750] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 12/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze the esterification of tRNA with a cognate amino acid and are essential enzymes in all three kingdoms of life. Due to their important role in the translation of the genetic code, aaRSs have been recognized as suitable targets for the development of small molecule anti-infectives. In this review, following a concise discussion of aaRS catalytic and proof-reading activities, the various inhibitory mechanisms of reported natural and synthetic aaRS inhibitors are discussed. Using the expanding repository of ligand-bound X-ray crystal structures, we classified these compounds based on their binding sites, focusing on their ability to compete with the association of one, or more of the canonical aaRS substrates. In parallel, we examined the determinants of species-selectivity and discuss potential resistance mechanisms of some of the inhibitor classes. Combined, this structural perspective highlights the opportunities for further exploration of the aaRS enzyme family as antimicrobial targets.
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Affiliation(s)
- Luping Pang
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
- KU Leuven, Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Herestraat 49–box 822, 3000 Leuven, Belgium
| | | | - Arthur Van Aerschot
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49–box 1041, 3000 Leuven, Belgium;
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16
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Doshi K, Pandya N, Datt M. In silico assessment of natural products and approved drugs as potential inhibitory scaffolds targeting aminoacyl-tRNA synthetases from Plasmodium. 3 Biotech 2020; 10:470. [PMID: 33088666 DOI: 10.1007/s13205-020-02460-6] [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: 06/18/2020] [Accepted: 09/30/2020] [Indexed: 10/23/2022] Open
Abstract
Malaria remains the leading cause of deaths globally, despite significant advancement towards understanding its epidemiology and availability of multiple therapeutic interventions. Poor efficacy of the approved vaccine, and the rapid emergence of antimalarial drug resistance, warrants an urgent need to expedite the process of development of new lead molecules targeting malaria. Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes crucial for ribosomal protein synthesis and are valid antimalarial targets. This study explores the prospects of (re-)positioning the repertoire of approved drugs and natural products as potential malarial aaRS inhibitors. Molecular docking of these two sets of small-molecules to lysyl-, prolyl-, and tyrosyl- synthetases from Plasmodium followed by a comparison of the top-ranking docked compounds against human homologs facilitated identification of promising molecular scaffolds. Raltitrexed and Cefprozil, an anticancer drug and an antibiotic, respectively, showed stronger binding to Plasmodium aaRSs compared to human homologs with > 4 kcal/mol difference in the docking scores. Similarly, a difference of ~ 3 kcal/mol in Glide scores was observed for docked Calcipotriol, a drug used for psoriasis treatment, against the two lysyl-tRNA synthetases. Natural products such as Dihydroxanthohumol and Betmidin, having aromatic rings as a substructure, showed preferential docking to the purine binding pocket in Plasmodium tyrosyl-tRNA synthetase as evident from the calculated change in binding free energies. We present detailed analyses of the calculated intermolecular interaction for all top-scoring docked poses. Overall, this study provides a compelling foundation to design and develop specific antimalarials.
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Affiliation(s)
- Ketki Doshi
- Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat 380009 India
| | - Niyati Pandya
- Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat 380009 India
| | - Manish Datt
- Biological and Life Sciences Division, School of Arts and Sciences, Ahmedabad University, Ahmedabad, Gujarat 380009 India
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17
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Nawrot D, Suchánková E, Janďourek O, Konečná K, Bárta P, Doležal M, Zitko J. N-pyridinylbenzamides: an isosteric approach towards new antimycobacterial compounds. Chem Biol Drug Des 2020; 97:686-700. [PMID: 33068457 DOI: 10.1111/cbdd.13804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/02/2020] [Accepted: 10/11/2020] [Indexed: 11/27/2022]
Abstract
A series of N-pyridinylbenzamides was designed and prepared to investigate the influence of isosterism and positional isomerism on antimycobacterial activity. Comparison to previously published isosteric N-pyrazinylbenzamides was made as an attempt to draw structure-activity relationships in such type of compounds. In total, we prepared 44 different compounds, out of which fourteen had minimum inhibitory concentration (MIC) values against Mycobacterium tuberculosis H37Ra below 31.25 µg/ml, most promising being N-(5-chloropyridin-2-yl)-3-(trifluoromethyl)benzamide (23) and N-(6-chloropyridin-2-yl)-3-(trifluoromethyl)benzamide (24) with MIC = 7.81 µg/ml (26 µm). Five compounds showed broad-spectrum antimycobacterial activity against M. tuberculosis H37Ra, M. smegmatis and M. aurum. N-(pyridin-2-yl)benzamides were generally more active than N-(pyridin-3-yl)benzamides, indicating that N-1 in the parental structure of N-pyrazinylbenzamides might be more important for antimycobacterial activity than N-4. Marginal antibacterial and antifungal activity was observed for title compounds. The hepatotoxicity of title compounds was assessed in vitro on hepatocellular carcinoma cell line HepG2, and they may be considered non-toxic (22 compounds with IC50 over 200 µm).
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Affiliation(s)
- Daria Nawrot
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Eliška Suchánková
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Ondřej Janďourek
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Klára Konečná
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Pavel Bárta
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Martin Doležal
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
| | - Jan Zitko
- Faculty of Pharmacy in Hradec Králové, Charles University, Hradec Králové, Czech Republic
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18
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Abstract
Pyrazine-based compounds are of great importance in medicinal chemistry. Due to their heteroaromatic nature, they uniquely combine properties of heteroatoms (polar interactions) with the properties of aromatic moieties (nonpolar interactions). This review summarizes results of a systematic analysis of RCSB PDB database focused on important binding interactions of pyrazine-based ligands cocrystallized in protein targets. The most frequent interaction of pyrazine was hydrogen bond to pyrazine nitrogen atom as an acceptor, followed by weak hydrogen bond with pyrazine hydrogen as donor. We also identified intramolecular hydrogen bonds within pyrazine ligands, π-interactions, coordination to metal ions, and few halogen bonds in chloropyrazines. In many cases the binding mode of the pyrazine fragment was complex, involving a combination of several interactions. We conclude that pyrazine as a molecular fragment should not be perceived as a simple aromatic isostere but rather as a readily interacting moiety of drug-like molecules with high potential for interactions to proteins.
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Affiliation(s)
- Martin Juhás
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Jan Zitko
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Králové, Charles University, Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
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19
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Roles of aminoacyl-tRNA synthetases in immune regulation and immune diseases. Cell Death Dis 2019; 10:901. [PMID: 31780718 PMCID: PMC6883034 DOI: 10.1038/s41419-019-2145-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022]
Abstract
Aminoacyl-tRNA synthetases (ARSs) play a vital role in protein synthesis by linking amino acids to their cognate transfer RNAs (tRNAs). This typical function has been well recognized over the past few decades. However, accumulating evidence reveals that ARSs are involved in a wide range of physiological and pathological processes apart from translation. Strikingly, certain ARSs are closely related to different types of immune responses. In this review, we address the infection and immune responses induced by pathogen ARSs, as well as the potential anti-infective compounds that target pathogen ARSs. Meanwhile, we describe the functional mechanisms of ARSs in the development of immune cells. In addition, we focus on the roles of ARSs in certain immune diseases, such as autoimmune diseases, infectious diseases, and tumor immunity. Although our knowledge of ARSs in the immunological context is still in its infancy, research in this field may provide new ideas for the treatment of immune-related diseases.
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20
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Yam M, Engel AL, Wang Y, Zhu S, Hauer A, Zhang R, Lohner D, Huang J, Dinterman M, Zhao C, Chao JR, Du J. Proline mediates metabolic communication between retinal pigment epithelial cells and the retina. J Biol Chem 2019; 294:10278-10289. [PMID: 31110046 PMCID: PMC6664195 DOI: 10.1074/jbc.ra119.007983] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/16/2019] [Indexed: 01/16/2023] Open
Abstract
The retinal pigment epithelium (RPE) is a monolayer of pigmented cells between the choroid and the retina. RPE dysfunction underlies many retinal degenerative diseases, including age-related macular degeneration, the leading cause of age-related blindness. To perform its various functions in nutrient transport, phagocytosis of the outer segment, and cytokine secretion, the RPE relies on an active energy metabolism. We previously reported that human RPE cells prefer proline as a nutrient and transport proline-derived metabolites to the apical, or retinal, side. In this study, we investigated how RPE utilizes proline in vivo and why proline is a preferred substrate. By using [13C]proline labeling both ex vivo and in vivo, we found that the retina rarely uses proline directly, whereas the RPE utilizes it at a high rate, exporting proline-derived mitochondrial intermediates for use by the retina. We observed that in primary human RPE cell culture, proline is the only amino acid whose uptake increases with cellular maturity. In human RPE, proline was sufficient to stimulate de novo serine synthesis, increase reductive carboxylation, and protect against oxidative damage. Blocking proline catabolism in RPE impaired glucose metabolism and GSH production. Notably, in an acute model of RPE-induced retinal degeneration, dietary proline improved visual function. In conclusion, proline is an important nutrient that supports RPE metabolism and the metabolic demand of the retina.
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Affiliation(s)
- Michelle Yam
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Abbi L Engel
- the Department of Ophthalmology, University of Washington, Seattle, Washington 98109
| | - Yekai Wang
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Siyan Zhu
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Allison Hauer
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Rui Zhang
- From the Departments of Ophthalmology and
- the Save Sight Institute, University of Sydney, 8 Macquarie Street, Sydney, New South Wales 2000, Australia
| | - Daniel Lohner
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Jiancheng Huang
- From the Departments of Ophthalmology and
- the Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200031, China, and
- the Department of Ophthalmology, State Key Laboratory of Reproductive Medicine, First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Marlee Dinterman
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
| | - Chen Zhao
- the Eye Institute, Eye and ENT Hospital, Shanghai Medical College, Fudan University, Shanghai 200031, China, and
| | - Jennifer R Chao
- the Department of Ophthalmology, University of Washington, Seattle, Washington 98109,
| | - Jianhai Du
- From the Departments of Ophthalmology and
- Biochemistry, West Virginia University, Morgantown, West Virginia 26506
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21
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Shibata A, Kuno M, Adachi R, Sato Y, Hattori H, Matsuda A, Okuzono Y, Igaki K, Tominari Y, Takagi T, Yabuki M, Okaniwa M. Discovery and pharmacological characterization of a new class of prolyl-tRNA synthetase inhibitor for anti-fibrosis therapy. PLoS One 2017; 12:e0186587. [PMID: 29065190 PMCID: PMC5655428 DOI: 10.1371/journal.pone.0186587] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/03/2017] [Indexed: 11/19/2022] Open
Abstract
Scleroderma has clinical characteristics including skin and other tissue fibrosis, but there is an unmet need for anti-fibrotic therapy. Halofuginone (HF) is a well-known anti-fibrosis agent in preclinical and clinical studies which exerts its effect via inhibition of TGF-β/Smad3 signaling pathway. Recently, prolyl-tRNA synthetase (PRS) was elucidated as a target protein for HF that binds to the proline binding site of the catalytic domain of PRS. Here, we characterized a new class of PRS inhibitor (T-3833261) that is carefully designed in a way that binds to the ATP site of the catalytic domain and does not disrupt binding of proline. The anti-fibrotic activity and the mechanism of action for T-3833261 on TGF-β-induced fibrotic assay were compared with those of HF in primary human skin fibroblast. We evaluated in vivo effect of topical application of T-3833261 and HF on TGF-β-induced fibrotic genes expression in mice. We found that T-3833261 suppressed TGF-β-induced α-smooth muscle actin (α-SMA) and type I collagen α1 (COL1A1) expression through the Smad3 axis in a similar fashion to HF. In vivo topical application of T-3833261 reduced the increase of fibrotic genes expression such as α-Sma, Col1a1 and Col1a2 by TGF-β intradermal injection to the ear of a mouse. We revealed that T-3833261 is more effective than HF under the conditions of high proline concentration, as reported in fibrotic tissues. These results suggest the potential of ATP competitive PRS inhibitors for the treatment of fibrotic diseases such as scleroderma.
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Affiliation(s)
- Akira Shibata
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
- * E-mail: (AS); (MO)
| | - Masako Kuno
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Ryutaro Adachi
- Biomolecular Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Yosuke Sato
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Harumi Hattori
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Atsushi Matsuda
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Yuumi Okuzono
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Keiko Igaki
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Yusuke Tominari
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Terufumi Takagi
- Medicinal Chemistry Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Masato Yabuki
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Masanori Okaniwa
- Immunology Unit, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
- * E-mail: (AS); (MO)
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