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Duffy S, Sleebs BE, Avery VM. An adaptable, fit-for-purpose screening approach with high-throughput capability to determine speed of action and stage specificity of anti-malarial compounds. Antimicrob Agents Chemother 2024; 68:e0074624. [PMID: 39264187 PMCID: PMC11459970 DOI: 10.1128/aac.00746-24] [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: 05/18/2024] [Accepted: 08/09/2024] [Indexed: 09/13/2024] Open
Abstract
A revamped in vitro compound identification and activity profiling approach is required to meet the large unmet need for new anti-malarial drugs to combat parasite drug resistance. Although compound hit identification utilizing high-throughput screening of large compound libraries is well established, the ability to rapidly prioritize such large numbers for further development is limited. Determining the speed of action of anti-malarial drug candidates is a vital component of malaria drug discovery, which currently occurs predominantly in lead optimization and development. This is due in part to the capacity of current methods which have low throughput due to the complexity and labor intensity of the approaches. Here, we provide an adaptable screening paradigm utilizing automated high content imaging, including the development of an automated schizont maturation assay, which collectively can identify anti-malarial compounds, classify activity into fast and slow acting, and provide an indication of the parasite stage specificity, with high-throughput capability. By frontloading these critical biological parameters much earlier in the drug discovery pipeline, it has the potential to reduce lead compound attrition rates later in the development process. The capability of the approach in its alternative formats is demonstrated using three Medicines for Malaria Venture open access compound "boxes," namely Pathogen Box (malaria set-125 compounds), Global Health Priority Box [Malaria Box 2 (80 compounds) and zoonotic neglected diseases (80 compounds)], and the Pandemic Response Box (400 compounds). From a total of 685 compounds tested, 79 were identified as having fast ring-stage-specific activity comparable to that of artemisinin and therefore of high priority for further consideration and development.
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Affiliation(s)
- Sandra Duffy
- Discovery Biology, School of Environment and Science, Griffith University, Griffith, Australia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical Research, The University of Melbourne, Parkville, Australia
- Department of Medical Biology, The Walter and Eliza Hall Institute of Medical Research, The University of Melbourne, Parkville, Australia
| | - Vicky M. Avery
- Discovery Biology, School of Environment and Science, Griffith University, Griffith, Australia
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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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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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Cheuka PM, Njaria P, Mayoka G, Funjika E. Emerging Drug Targets for Antimalarial Drug Discovery: Validation and Insights into Molecular Mechanisms of Function. J Med Chem 2024; 67:838-863. [PMID: 38198596 DOI: 10.1021/acs.jmedchem.3c01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Approximately 619,000 malaria deaths were reported in 2021, and resistance to recommended drugs, including artemisinin-combination therapies (ACTs), threatens malaria control. Treatment failure with ACTs has been found to be as high as 93% in northeastern Thailand, and parasite mutations responsible for artemisinin resistance have already been reported in some African countries. Therefore, there is an urgent need to identify alternative treatments with novel targets. In this Perspective, we discuss some promising antimalarial drug targets, including enzymes involved in proteolysis, DNA and RNA metabolism, protein synthesis, and isoprenoid metabolism. Other targets discussed are transporters, Plasmodium falciparum acetyl-coenzyme A synthetase, N-myristoyltransferase, and the cyclic guanosine monophosphate-dependent protein kinase G. We have outlined mechanistic details, where these are understood, underpinning the biological roles and hence druggability of such targets. We believe that having a clear understanding of the underlying chemical interactions is valuable to medicinal chemists in their quest to design appropriate inhibitors.
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Affiliation(s)
- Peter Mubanga Cheuka
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
| | - Paul Njaria
- Department of Pharmacognosy and Pharmaceutical Chemistry, Kenyatta University, P.O. Box 14548-00400, Nairobi 00100, Kenya
| | - Godfrey Mayoka
- Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi 00100, Kenya
| | - Evelyn Funjika
- Department of Chemistry, School of Natural Sciences, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia
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5
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Luo AP, Giannangelo C, Siddiqui G, Creek DJ. Promising antimalarial hits from phenotypic screens: a review of recently-described multi-stage actives and their modes of action. Front Cell Infect Microbiol 2023; 13:1308193. [PMID: 38162576 PMCID: PMC10757594 DOI: 10.3389/fcimb.2023.1308193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Over the last two decades, global malaria cases caused by Plasmodium falciparum have declined due to the implementation of effective treatments and the use of insecticides. However, the COVID-19 pandemic caused major disruption in the timely delivery of medical goods and diverted public health resources, impairing malaria control. The emergence of resistance to all existing frontline antimalarials underpins an urgent need for new antimalarials with novel mechanisms of action. Furthermore, the need to reduce malaria transmission and/or prevent malaria infection has shifted the focus of antimalarial research towards the discovery of compounds that act beyond the symptomatic blood stage and also impact other parasite life cycle stages. Phenotypic screening has been responsible for the majority of new antimalarial lead compounds discovered over the past 10 years. This review describes recently reported novel antimalarial hits that target multiple parasite stages and were discovered by phenotypic screening during the COVID-19 pandemic. Their modes of action and targets in blood stage parasites are also discussed.
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Affiliation(s)
| | | | - Ghizal Siddiqui
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Darren J. Creek
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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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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de Carvalho LP, Niepoth E, Mavraj-Husejni A, Kreidenweiss A, Herrmann J, Müller R, Knaab T, Burckhardt BB, Kurz T, Held J. Quantification of Plasmodium falciparum HRP-2 as an alternative method to [ 3H]hypoxanthine incorporation to measure the parasite reduction ratio in vitro. Int J Antimicrob Agents 2023; 62:106894. [PMID: 37348620 DOI: 10.1016/j.ijantimicag.2023.106894] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/24/2023]
Abstract
In the absence of a highly efficacious vaccine, chemotherapy remains the cornerstone to control malaria morbidity and mortality. The threat of the emergence of parasites resistant to artemisinin-based combination therapies highlights the need for new antimalarial drugs ideally with superior properties. The killing rate reflects the speed of action of antimalarial drugs, which can be measured in vitro through the parasite reduction ratio (PRR) assay to shortlist interesting candidates. As a standard, the in vitro PRR assay is performed by measuring [3H]hypoxanthine incorporation of Plasmodium falciparum. This methodology is restricted to specialised laboratories owing to the handling of radioactive material. In this work, we describe a sandwich enzyme-linked immunosorbent assay to detect P. falciparum histidine-rich protein 2 (HRP-2) as an alternative methodology to assess the PRR. We first validated the methodology with established antimalarial drugs (artesunate, chloroquine, pyrimethamine and atovaquone) by comparing our results with previous results of the [3H]hypoxanthine incorporation readout provided by an expert laboratory, and subsequently assessed the speed of action of four new antimalarial candidates (compound 22, chlorotonil A, boromycin and ivermectin). The HRP-2 PRR assay achieved comparable results to the [3H]hypoxanthine incorporation readout in terms of parasite growth rate over time, lag phase and parasite clearance time. In addition, parasite growth following drug exposure was quantified after 7, 14, 21 and 28 days of recovery time. In conclusion, the PRR assay based on HRP-2 is similar to [3H]hypoxanthine in determining a drug's parasite killing rate and can be widely used in all research laboratories.
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Affiliation(s)
| | - Elena Niepoth
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; German Center for Infection Research (DZIF), Braunschweig, Germany
| | - Jennifer Herrmann
- German Center for Infection Research (DZIF), Braunschweig, Germany; Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Rolf Müller
- German Center for Infection Research (DZIF), Braunschweig, Germany; Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany
| | - Tanja Knaab
- Institute of Pharmaceutics and Biopharmaceutics, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Bjoern B Burckhardt
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | - Thomas Kurz
- Institute of Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany; Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon; German Center for Infection Research (DZIF), Braunschweig, Germany.
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8
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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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Gill J, Sharma A. Exploration of aminoacyl-tRNA synthetases from eukaryotic parasites for drug development. J Biol Chem 2022; 299:102860. [PMID: 36596362 PMCID: PMC9978631 DOI: 10.1016/j.jbc.2022.102860] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
Parasitic diseases result in considerable human morbidity and mortality. The continuous emergence and spread of new drug-resistant parasite strains is an obstacle to controlling and eliminating many parasitic diseases. Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous enzymes essential for protein synthesis. The design and development of diverse small molecule, drug-like inhibitors against parasite-encoded and expressed aaRSs have validated this enzyme family as druggable. In this work, we have compiled the progress to date towards establishing the druggability of aaRSs in terms of their biochemical characterization, validation as targets, inhibitor development, and structural interpretation from parasites responsible for malaria (Plasmodium), lymphatic filariasis (Brugia,Wuchereria bancrofti), giardiasis (Giardia), toxoplasmosis (Toxoplasma gondii), leishmaniasis (Leishmania), cryptosporidiosis (Cryptosporidium), and trypanosomiasis (Trypanosoma). This work thus provides a robust framework for the systematic dissection of aaRSs from these pathogens and will facilitate the cross-usage of potential inhibitors to jump-start anti-parasite drug development.
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Affiliation(s)
- Jasmita Gill
- ICMR-National Institute of Malaria Research, New Delhi, India
| | - Amit Sharma
- ICMR-National Institute of Malaria Research, New Delhi, India; Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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10
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Guerra F, Winzeler EA. New targets for antimalarial drug discovery. Curr Opin Microbiol 2022; 70:102220. [PMID: 36228458 PMCID: PMC9934905 DOI: 10.1016/j.mib.2022.102220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/22/2022] [Accepted: 09/10/2022] [Indexed: 01/25/2023]
Abstract
Phenotypic screening methods have placed numerous preclinical candidates into the antimalarial drug-discovery pipeline. As more chemically validated targets become available, efforts are shifting to target-based drug discovery. Here, we briefly review some of the most attractive targets that have been identified in recent years.
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Affiliation(s)
- Francisco Guerra
- Department of Pediatrics MC 0760, School of Medicine, University of California, La Jolla, San Diego, CA 92093, USA
| | - Elizabeth A Winzeler
- Department of Pediatrics MC 0760, School of Medicine, University of California, La Jolla, San Diego, CA 92093, USA.
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11
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Cheng P, Wang C, Zhang L, Fei C, Liu Y, Wang M, Zhang K, Wang X, Gu F, Xue F. Label-free quantitative proteomic analysis of ethanamizuril-resistant versus -sensitive strains of Eimeria tenella. Parasit Vectors 2022; 15:319. [PMID: 36076292 PMCID: PMC9454127 DOI: 10.1186/s13071-022-05412-6] [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: 04/28/2022] [Accepted: 07/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background Avian coccidiosis is an important parasitic disease that has serious adverse effects on the global poultry industry. The extensive use of anticoccidial drugs has resulted in an increase in drug resistance. Ethanamizuril (EZL) is a novel triazine with high anticoccidial activity. Methods We compared oocyst production and sporulation between EZL-sensitive (S) and EZL-resistant Eimeria tenella strains (R10 and R200) and used label-free quantitative proteomics to identify differentially expressed proteins (DEPs) between these strains. Results We generated two EZL-resistant E. tenella strains: strain R10, which was induced using a constant dose of 10 mg EZL/kg poultry feed, and strain R200, which was generated by gradually increasing the EZL dosage to 200 mg EZL/kg poultry feed. With an increase in resistance, the total oocyst output decreased, but the percentage of sporulation did not change significantly. We identified a total of 7511 peptides and 1282 proteins, and found 152 DEPs in the R10 strain versus the S strain, 426 DEPs in the R200 strain versus the S strain and 494 DEPs in the R200 strain versus the R10 strain. When compared with the S strain, 86 DEPs were found to have consistent trends in both resistant strains. The DEPs were primarily involved in ATP and GTP binding, invasion, and membrane components. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses of the DEPs suggested that they are involved in transcription and translation processes. Protein–protein interaction network analysis of the 86 DEPs showed that 10 proteins were hubs in the functional interaction network (≥ 8 edges) and five of them were ribosomal proteins. Conclusions The results of the present study indicate that the resistance mechanisms of E. tenella against EZL might be related to the transcriptional and translational processes, especially in the factors that inhibit the growth of parasites. The DEPs found in this study provide new insights into the resistance mechanisms of E. tenella against EZL. Further research on these potential targets holds promise for new chemotherapeutic approaches for controlling E. tenella infections. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05412-6.
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Affiliation(s)
- Peipei Cheng
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Chunmei Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China.
| | - Lifang Zhang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Chenzhong Fei
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Yingchun Liu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Mi Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Keyu Zhang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Xiaoyang Wang
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Feng Gu
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China
| | - Feiqun Xue
- Key Laboratory of Veterinary Chemical Drugs and Pharmaceutics, Ministry of Agriculture and Rural Affairs/Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, 518 Ziyue Road, Minhang District, Shanghai, 200241, China.
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12
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The Antiarrhythmic and Hypotensive Effects of S-61 and S-73, the Pyrrolidin-2-one Derivatives with α1-Adrenolytic Properties. Int J Mol Sci 2022; 23:ijms231810381. [PMID: 36142287 PMCID: PMC9499458 DOI: 10.3390/ijms231810381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Heart rhythm abnormalities are a cause of many deaths worldwide. Unfortunately, the available antiarrhythmic drugs show limited efficacy and proarrhythmic potential. Thus, efforts should be made to search for new, more effective, and safer pharmacotherapies. Several studies suggested that blocking the α1-adrenoceptors could restore normal heart rhythm in arrhythmia. In this study, we aimed to assess the antiarrhythmic potential of S-61 and S-73, two novel pyrrolidin-2-one derivatives with high affinity for α1-adrenergic receptors. First, using radioligand binding studies, we demonstrated that S-61 and S-73 did not bind with β1-adrenoceptors. Next, we assessed whether S-61 and S-73 could protect rats against arrhythmia in adrenaline-, calcium chloride- and aconitine-induced arrhythmia models. Both compounds showed potent prophylactic antiarrhythmic properties in the adrenaline-induced arrhythmia model, but the effect of S-61 was more pronounced. None of the compounds displayed antiarrhythmic effects in calcium chloride- or aconitine-induced arrhythmia models. Interestingly, both derivatives revealed therapeutic antiarrhythmic activity in the adrenaline-induced arrhythmia, diminishing heart rhythm irregularities. Neither S-61 nor S-73 showed proarrhythmic potential in rats. Finally, the compounds decreased blood pressure in rodents. The hypotensive effects were not observed after coadministration with methoxamine, which suggests the α1-adrenolytic properties of both compounds. Our results confirm that pyrrolidin-2-one derivatives possess potent antiarrhythmic properties. Given the promising results of our experiments, further studies on pyrrolidin-2-one derivatives might result in the development of a new class of antiarrhythmic drugs.
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13
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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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14
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Bernard MM, Mohanty A, Rajendran V. Title: A Comprehensive Review on Classifying Fast-acting and Slow-acting Antimalarial Agents Based on Time of Action and Target Organelle of Plasmodium sp. Pathog Dis 2022; 80:6589403. [PMID: 35588061 DOI: 10.1093/femspd/ftac015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/20/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The clinical resistance towards malarial parasites has rendered many antimalarials ineffective, likely due to a lack of understanding of time of action and stage specificity of all life stages. Therefore, to tackle this problem a more incisive comprehensive analysis of the fast and slow-acting profile of antimalarial agents relating to parasite time-kill kinetics and the target organelle on the progression of blood-stage parasites was carried out. It is evident from numerous findings that drugs targeting food vacuole, nuclear components, and endoplasmic reticulum mainly exhibit a fast-killing phenotype within 24h affecting first-cycle activity. Whereas drugs targeting mitochondria, apicoplast, microtubules, parasite invasion and egress exhibit a largely slow-killing phenotype within 96-120h, affecting second-cycle activity with few exemptions as moderately fast-killing. It is essential to understand the susceptibility of drugs on rings, trophozoites, schizonts, merozoites, and the appearance of organelle at each stage of 48h intraerythrocytic parasite cycle. Therefore, these parameters may facilitate the paradigm for understanding the timing of antimalarials action in deciphering its precise mechanism linked with time. Thus, classifying drugs based on the time of killing may promote designing new combination regimens against varied strains of P. falciparum and evaluating potential clinical resistance.
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Affiliation(s)
- Monika Marie Bernard
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Abhinab Mohanty
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Vinoth Rajendran
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
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15
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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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