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Olotu F, Tali MBT, Chepsiror C, Sheik Amamuddy O, Boyom FF, Tastan Bishop Ö. Repurposing DrugBank compounds as potential Plasmodium falciparum class 1a aminoacyl tRNA synthetase multi-stage pan-inhibitors with a specific focus on mitomycin. Int J Parasitol Drugs Drug Resist 2024; 25:100548. [PMID: 38805932 PMCID: PMC11152978 DOI: 10.1016/j.ijpddr.2024.100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/11/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
Plasmodium falciparum aminoacyl tRNA synthetases (PfaaRSs) are potent antimalarial targets essential for proteome fidelity and overall parasite survival in every stage of the parasite's life cycle. So far, some of these proteins have been singly targeted yielding inhibitor compounds that have been limited by incidences of resistance which can be overcome via pan-inhibition strategies. Hence, herein, for the first time, we report the identification and in vitro antiplasmodial validation of Mitomycin (MMC) as a probable pan-inhibitor of class 1a (arginyl(A)-, cysteinyl(C), isoleucyl(I)-, leucyl(L), methionyl(M), and valyl(V)-) PfaaRSs which hypothetically may underlie its previously reported activity on the ribosomal RNA to inhibit protein translation and biosynthesis. We combined multiple in silico structure-based discovery strategies that first helped identify functional and druggable sites that were preferentially targeted by the compound in each of the plasmodial proteins: Ins1-Ins2 domain in Pf-ARS; anticodon binding domain in Pf-CRS; CP1-editing domain in Pf-IRS and Pf-MRS; C-terminal domain in Pf-LRS; and CP-core region in Pf-VRS. Molecular dynamics studies further revealed that MMC allosterically induced changes in the global structures of each protein. Likewise, prominent structural perturbations were caused by the compound across the functional domains of the proteins. More so, MMC induced systematic alterations in the binding of the catalytic nucleotide and amino acid substrates which culminated in the loss of key interactions with key active site residues and ultimate reduction in the nucleotide-binding affinities across all proteins, as deduced from the binding energy calculations. These altogether confirmed that MMC uniformly disrupted the structure of the target proteins and essential substrates. Further, MMC demonstrated IC50 < 5 μM against the Dd2 and 3D7 strains of parasite making it a good starting point for malarial drug development. We believe that findings from our study will be important in the current search for highly effective multi-stage antimalarial drugs.
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Affiliation(s)
- Fisayo Olotu
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, 6139, South Africa
| | - Mariscal Brice Tchatat Tali
- Antimicrobial & Biocontrol Agents Unit, Laboratory for Phytobiochemistry & Medicinal Plants Studies, Department of Biochemistry, Faculty of Science-University of Yaounde 1, P.O. Box 812, Yaounde, Cameroon; Advanced Research and Health Innovation Hub (ARHIH), Magzi Street, P.O. Box 812, Yaounde, Cameroon
| | - Curtis Chepsiror
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, 6139, South Africa
| | - Olivier Sheik Amamuddy
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, 6139, South Africa
| | - Fabrice Fekam Boyom
- Antimicrobial & Biocontrol Agents Unit, Laboratory for Phytobiochemistry & Medicinal Plants Studies, Department of Biochemistry, Faculty of Science-University of Yaounde 1, P.O. Box 812, Yaounde, Cameroon; Advanced Research and Health Innovation Hub (ARHIH), Magzi Street, P.O. Box 812, Yaounde, Cameroon
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry, Microbiology and Bioinformatics, Rhodes University, Makhanda, 6139, South Africa.
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2
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Nasim F, Kumar MS, Alvala M, Qureshi IA. Unraveling the peculiarities and development of novel inhibitors of leishmanial arginyl-tRNA synthetase. FEBS J 2024; 291:2955-2979. [PMID: 38525644 DOI: 10.1111/febs.17122] [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: 12/17/2023] [Revised: 02/22/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
Aminoacylation by tRNA synthetase is a crucial part of protein synthesis and is widely recognized as a therapeutic target for drug development. Unlike the arginyl-tRNA synthetases (ArgRSs) reported previously, here, we report an ArgRS of Leishmania donovani (LdArgRS) that can follow the canonical two-step aminoacylation process. Since a previously uncharacterized insertion region is present within its catalytic domain, we implemented the splicing by overlap extension PCR (SOE-PCR) method to create a deletion mutant (ΔIns-LdArgRS) devoid of this region to investigate its function. Notably, the purified LdArgRS and ΔIns-LdArgRS exhibited different oligomeric states along with variations in their enzymatic activity. The full-length protein showed better catalytic efficiency than ΔIns-LdArgRS, and the insertion region was identified as the tRNA binding domain. In addition, a benzothiazolo-coumarin derivative (Comp-7j) possessing high pharmacokinetic properties was recognized as a competitive and more specific inhibitor of LdArgRS than its human counterpart. Removal of the insertion region altered the mode of inhibition for ΔIns-LdArgRS and caused a reduction in the inhibitor's binding affinity. Both purified proteins depicted variances in the secondary structural content upon ligand binding and thus, thermostability. Apart from the trypanosomatid-specific insertion and Rossmann fold motif, LdArgRS revealed typical structural characteristics of ArgRSs, and Comp-7j was found to bind within the ATP binding pocket. Furthermore, the placement of tRNAArg near the insertion region enhanced the stability and compactness of LdArgRS compared to other ligands. This study thus reports a unique ArgRS with respect to catalytic as well as structural properties, which can be considered a plausible drug target for the derivation of novel anti-leishmanial agents.
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Affiliation(s)
- Fouzia Nasim
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Muppidi Shravan Kumar
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | - Mallika Alvala
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Hyderabad, India
| | - Insaf Ahmed Qureshi
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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3
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McLellan JL, Sausman W, Reers AB, Bunnik EM, Hanson KK. Single-cell quantitative bioimaging of P. berghei liver stage translation. mSphere 2023; 8:e0054423. [PMID: 37909773 PMCID: PMC10732057 DOI: 10.1128/msphere.00544-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Plasmodium parasites cause malaria in humans. New multistage active antimalarial drugs are needed, and a promising class of drugs targets the core cellular process of translation, which has many potential molecular targets. During the obligate liver stage, Plasmodium parasites grow in metabolically active hepatocytes, making it challenging to study core cellular processes common to both host cells and parasites, as the signal from the host typically overwhelms that of the parasite. Here, we present and validate a flexible assay to quantify Plasmodium liver stage translation using a technique to fluorescently label the newly synthesized proteins of both host and parasite followed by computational separation of their respective nascent proteomes in confocal image sets. We use the assay to determine whether a test set of known compounds are direct or indirect liver stage translation inhibitors and show that the assay can also predict the mode of action for novel antimalarial compounds.
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Affiliation(s)
- James L. McLellan
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
| | - William Sausman
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
| | - Ashley B. Reers
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, Texas, USA
| | - Kirsten K. Hanson
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, Texas, USA
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Siqueira-Neto JL, Wicht KJ, Chibale K, Burrows JN, Fidock DA, Winzeler EA. Antimalarial drug discovery: progress and approaches. Nat Rev Drug Discov 2023; 22:807-826. [PMID: 37652975 PMCID: PMC10543600 DOI: 10.1038/s41573-023-00772-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 09/02/2023]
Abstract
Recent antimalarial drug discovery has been a race to produce new medicines that overcome emerging drug resistance, whilst considering safety and improving dosing convenience. Discovery efforts have yielded a variety of new molecules, many with novel modes of action, and the most advanced are in late-stage clinical development. These discoveries have led to a deeper understanding of how antimalarial drugs act, the identification of a new generation of drug targets, and multiple structure-based chemistry initiatives. The limited pool of funding means it is vital to prioritize new drug candidates. They should exhibit high potency, a low propensity for resistance, a pharmacokinetic profile that favours infrequent dosing, low cost, preclinical results that demonstrate safety and tolerability in women and infants, and preferably the ability to block Plasmodium transmission to Anopheles mosquito vectors. In this Review, we describe the approaches that have been successful, progress in preclinical and clinical development, and existing challenges. We illustrate how antimalarial drug discovery can serve as a model for drug discovery in diseases of poverty.
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Affiliation(s)
| | - Kathryn J Wicht
- 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, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | - Kelly Chibale
- 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, Department of Chemistry and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
| | | | - David A Fidock
- Department of Microbiology and Immunology and Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
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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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Simmons C, Gibbons J, Wang C, Pires CV, Zhang M, Siddiqui F, Oberstaller J, Casandra D, Seyfang A, Cui L, Otto TD, Adams JH. A novel Modulator of Ring Stage Translation (MRST) gene alters artemisinin sensitivity in Plasmodium falciparum. mSphere 2023; 8:e0015223. [PMID: 37219373 PMCID: PMC10449512 DOI: 10.1128/msphere.00152-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/18/2023] [Indexed: 05/24/2023] Open
Abstract
The implementation of artemisinin (ART) combination therapies (ACTs) has greatly decreased deaths caused by Plasmodium falciparum malaria, but increasing ACT resistance in Southeast Asia and Africa could reverse this progress. Parasite population genetic studies have identified numerous genes, single-nucleotide polymorphisms (SNPs), and transcriptional signatures associated with altered artemisinin activity with SNPs in the Kelch13 (K13) gene being the most well-characterized artemisinin resistance marker. However, there is an increasing evidence that resistance to artemisinin in P. falciparum is not related only to K13 SNPs, prompting the need to characterize other novel genes that can alter ART responses in P. falciparum. In our previous analyses of P. falciparum piggyBac mutants, several genes of unknown function exhibited increased sensitivity to artemisinin that was similar to a mutant of K13. Further analysis of these genes and their gene co-expression networks indicated that the ART sensitivity cluster was functionally linked to DNA replication and repair, stress responses, and maintenance of homeostatic nuclear activity. In this study, we have characterized PF3D7_1136600, another member of the ART sensitivity cluster. Previously annotated as a conserved Plasmodium gene of unknown function, we now provide putative annotation of this gene as a Modulator of Ring Stage Translation (MRST). Our findings reveal that the mutagenesis of MRST affects gene expression of multiple translation-associated pathways during the early ring stage of asexual development via putative ribosome assembly and maturation activity, suggesting an essential role of MRST in protein biosynthesis and another novel mechanism of altering the parasite's ART drug response.IMPORTANCEPlasmodium falciparum malaria killed more than 600,000 people in 2021, though ACTs have been critical in reducing malaria mortality as a first-line treatment for infection. However, ACT resistance in Southeast Asia and emerging resistance in Africa are detrimental to this progress. Mutations to Kelch13 (K13) have been identified to confer increased artemisinin tolerance in field isolates, however, genes other than K13 are implicated in altering how the parasite responds to artemisinin prompts additional analysis. Therefore, in this study we have characterized a P. falciparum mutant clone with altered sensitivity to artemisinin and identified a novel gene (PF3D7_1136600) that is associated with alterations to parasite translational metabolism during critical timepoints for artemisinin drug response. Many genes of the P. falciparum genome remain unannotated, posing a challenge for drug-gene characterizations in the parasite. Therefore, through this study, we have putatively annotated PF3D7_1136600 as a novel MRST gene and have identified a potential link between MRST and parasite stress response mechanisms.
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Affiliation(s)
- Caroline Simmons
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Justin Gibbons
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Chengqi Wang
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Camilla Valente Pires
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Min Zhang
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Faiza Siddiqui
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Jenna Oberstaller
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Debora Casandra
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
| | - Andreas Seyfang
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Liwang Cui
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Thomas D. Otto
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - John H. Adams
- Center for Global Health and Infectious Diseases Research and USF Genomics Program, College of Public Health, University of South Florida, Tampa, Florida, USA
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7
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McLellan JL, Sausman W, Reers AB, Bunnik EM, Hanson KK. Single-cell quantitative bioimaging of P. berghei liver stage translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547872. [PMID: 37461595 PMCID: PMC10350035 DOI: 10.1101/2023.07.05.547872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
Plasmodium parasite resistance to existing antimalarial drugs poses a devastating threat to the lives of many who depend on their efficacy. New antimalarial drugs and novel drug targets are in critical need, along with novel assays to accelerate their identification. Given the essentiality of protein synthesis throughout the complex parasite lifecycle, translation inhibitors are a promising drug class, capable of targeting the disease-causing blood stage of infection, as well as the asymptomatic liver stage, a crucial target for prophylaxis. To identify compounds capable of inhibiting liver stage parasite translation, we developed an assay to visualize and quantify translation in the P. berghei-HepG2 infection model. After labeling infected monolayers with o-propargyl puromycin (OPP), a functionalized analog of puromycin permitting subsequent bioorthogonal addition of a fluorophore to each OPP-terminated nascent polypetide, we use automated confocal feedback microscopy followed by batch image segmentation and feature extraction to visualize and quantify the nascent proteome in individual P. berghei liver stage parasites and host cells simultaneously. After validation, we demonstrate specific, concentration-dependent liver stage translation inhibition by both parasite-selective and pan-eukaryotic active compounds, and further show that acute pre-treatment and competition modes of the OPP assay can distinguish between direct and indirect translation inhibitors. We identify a Malaria Box compound, MMV019266, as a direct translation inhibitor in P. berghei liver stages and confirm this potential mode of action in P. falciparum asexual blood stages.
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Affiliation(s)
- James L McLellan
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| | - William Sausman
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
| | - Ashley B Reers
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Evelien M Bunnik
- Department of Microbiology, Immunology, and Molecular Genetics, Long School of Medicine, University of Texas Health Science Center, San Antonio, TX, USA
| | - Kirsten K Hanson
- Department of Molecular Microbiology and Immunology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, USA
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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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9
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Gill J, Sharma A. Genomic analysis of single nucleotide polymorphisms in malaria parasite drug targets. Parasit Vectors 2022; 15:309. [PMID: 36042490 PMCID: PMC9425944 DOI: 10.1186/s13071-022-05422-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/22/2022] [Indexed: 12/02/2022] Open
Abstract
Malaria is a life-threatening parasitic disease caused by members of the genus Plasmodium. The development and spread of drug-resistant strains of Plasmodium parasites represent a major challenge to malaria control and elimination programmes. Evaluating genetic polymorphism in a drug target improves our understanding of drug resistance and facilitates drug design. Approximately 450 and 19 whole-genome assemblies of Plasmodium falciparum and Plasmodium vivax, respectively, are currently available, and numerous sequence variations have been found due to the presence of single nucleotide polymorphism (SNP). In the study reported here, we analysed global SNPs in the malaria parasite aminoacyl-tRNA synthetases (aaRSs). Our analysis revealed 3182 unique SNPs in the 20 cytoplasmic P. falciparum aaRSs. Structural mapping of SNPs onto the three-dimensional inhibitor-bound complexes of the three advanced drug targets within aaRSs revealed a remarkably low mutation frequency in the crucial aminoacylation domains, low overall occurrence of mutations across samples and high conservation in drug/substrate binding regions. In contrast to aaRSs, dihydropteroate synthase (DHPS), also a malaria drug target, showed high occurrences of drug resistance-causing mutations. Our results show that it is pivotal to screen potent malaria drug targets against global SNP profiles to assess genetic variances to ensure success in designing drugs against validated targets and tackle drug resistance early on.
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Affiliation(s)
- Jasmita Gill
- ICMR-National Institute of Malaria Research, Sector 8, Dwarka, 110077, New Delhi, India
| | - Amit Sharma
- ICMR-National Institute of Malaria Research, Sector 8, Dwarka, 110077, New Delhi, India. .,International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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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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11
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Chhibber-Goel J, Yogavel M, Sharma A. Structural analyses of the malaria parasite aminoacyl-tRNA synthetases provide new avenues for antimalarial drug discovery. Protein Sci 2021; 30:1793-1803. [PMID: 34184352 DOI: 10.1002/pro.4148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/12/2021] [Accepted: 06/22/2021] [Indexed: 11/10/2022]
Abstract
Malaria is a parasitic illness caused by the genus Plasmodium from the apicomplexan phylum. Five plasmodial species of P. falciparum (Pf), P. knowlesi, P. malariae, P. ovale, and P. vivax (Pv) are responsible for causing malaria in humans. According to the World Malaria Report 2020, there were 229 million cases and ~ 0.04 million deaths of which 67% were in children below 5 years of age. While more than 3 billion people are at risk of malaria infection globally, antimalarial drugs are their only option for treatment. Antimalarial drug resistance keeps arising periodically and thus threatens the main line of malaria treatment, emphasizing the need to find new alternatives. The availability of whole genomes of P. falciparum and P. vivax has allowed targeting their unexplored plasmodial enzymes for inhibitor development with a focus on multistage targets that are crucial for parasite viability in both the blood and liver stages. Over the past decades, aminoacyl-tRNA synthetases (aaRSs) have been explored as anti-bacterial and anti-fungal drug targets, and more recently (since 2009) aaRSs are also the focus of antimalarial drug targeting. Here, we dissect the structure-based knowledge of the most advanced three aaRSs-lysyl- (KRS), prolyl- (PRS), and phenylalanyl- (FRS) synthetases in terms of development of antimalarial drugs. These examples showcase the promising potential of this family of enzymes to provide druggable targets that stall protein synthesis upon inhibition and thereby kill malaria parasites selectively.
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Affiliation(s)
- Jyoti Chhibber-Goel
- Structural Parasitology Group, Molecular Medicine, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Manickam Yogavel
- Structural Parasitology Group, Molecular Medicine, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Amit Sharma
- Structural Parasitology Group, Molecular Medicine, International Center for Genetic Engineering and Biotechnology, New Delhi, India.,ICMR-National Institute of Malaria Research, New Delhi, India
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