1
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Wirjanata G, Lin J, Dziekan JM, El Sahili A, Chung Z, Tjia S, Binte Zulkifli NE, Boentoro J, Tham R, Jia LS, Go KD, Yu H, Partridge A, Olsen D, Prabhu N, Sobota RM, Nordlund P, Lescar J, Bozdech Z. Identification of an inhibitory pocket in falcilysin provides a new avenue for malaria drug development. Cell Chem Biol 2024; 31:743-759.e8. [PMID: 38593807 DOI: 10.1016/j.chembiol.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/02/2023] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Identification of new druggable protein targets remains the key challenge in the current antimalarial development efforts. Here we used mass-spectrometry-based cellular thermal shift assay (MS-CETSA) to identify potential targets of several antimalarials and drug candidates. We found that falcilysin (FLN) is a common binding partner for several drug candidates such as MK-4815, MMV000848, and MMV665806 but also interacts with quinoline drugs such as chloroquine and mefloquine. Enzymatic assays showed that these compounds can inhibit FLN proteolytic activity. Their interaction with FLN was explored systematically by isothermal titration calorimetry and X-ray crystallography, revealing a shared hydrophobic pocket in the catalytic chamber of the enzyme. Characterization of transgenic cell lines with lowered FLN expression demonstrated statistically significant increases in susceptibility toward MK-4815, MMV000848, and several quinolines. Importantly, the hydrophobic pocket of FLN appears amenable to inhibition and the structures reported here can guide the development of novel drugs against malaria.
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Affiliation(s)
- Grennady Wirjanata
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Jianqing Lin
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Infectious Diseases Labs & Singapore Immunology Network, Agency for Science, Technology and Research, 138648 Singapore, Singapore
| | - Jerzy Michal Dziekan
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Abbas El Sahili
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore
| | - Zara Chung
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Seth Tjia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - Josephine Boentoro
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Roy Tham
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Lai Si Jia
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Ka Diam Go
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Han Yu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | | | - David Olsen
- Merck & Co., Inc., West Point, PA 19486, USA
| | - Nayana Prabhu
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Functional Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore
| | - Pär Nordlund
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A∗STAR), Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technology University, Singapore 637551, Singapore; Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 637551, Singapore.
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technology University, Singapore 637551, Singapore.
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2
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Lindblom JR, Zhang X, Lehane AM. A pH Fingerprint Assay to Identify Inhibitors of Multiple Validated and Potential Antimalarial Drug Targets. ACS Infect Dis 2024; 10:1185-1200. [PMID: 38499199 PMCID: PMC11019546 DOI: 10.1021/acsinfecdis.3c00588] [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: 10/31/2023] [Revised: 01/22/2024] [Accepted: 02/09/2024] [Indexed: 03/20/2024]
Abstract
New drugs with novel modes of action are needed to safeguard malaria treatment. In recent years, millions of compounds have been tested for their ability to inhibit the growth of asexual blood-stage Plasmodium falciparum parasites, resulting in the identification of thousands of compounds with antiplasmodial activity. Determining the mechanisms of action of antiplasmodial compounds informs their further development, but remains challenging. A relatively high proportion of compounds identified as killing asexual blood-stage parasites show evidence of targeting the parasite's plasma membrane Na+-extruding, H+-importing pump, PfATP4. Inhibitors of PfATP4 give rise to characteristic changes in the parasite's internal [Na+] and pH. Here, we designed a "pH fingerprint" assay that robustly identifies PfATP4 inhibitors while simultaneously allowing the detection of (and discrimination between) inhibitors of the lactate:H+ transporter PfFNT, which is a validated antimalarial drug target, and the V-type H+ ATPase, which was suggested as a possible target of the clinical candidate ZY19489. In our pH fingerprint assays and subsequent secondary assays, ZY19489 did not show evidence for the inhibition of pH regulation by the V-type H+ ATPase, suggesting that it has a different mode of action in the parasite. The pH fingerprint assay also has the potential to identify protonophores, inhibitors of the acid-loading Cl- transporter(s) (for which the molecular identity(ies) remain elusive), and compounds that act through inhibition of either the glucose transporter PfHT or glycolysis. The pH fingerprint assay therefore provides an efficient starting point to match a proportion of antiplasmodial compounds with their mechanisms of action.
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Affiliation(s)
| | | | - Adele M. Lehane
- Research School of Biology, Australian National University, Canberra, Australian Capital
Territory 2600, Australia
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3
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Redway A, Spry C, Brown A, Wiedemann U, Fathoni I, Garnie LF, Qiu D, Egan TJ, Lehane AM, Jackson Y, Saliba KJ, Downer-Riley N. Discovery of antiplasmodial pyridine carboxamides and thiocarboxamides. Int J Parasitol Drugs Drug Resist 2024; 25:100536. [PMID: 38663046 PMCID: PMC11068522 DOI: 10.1016/j.ijpddr.2024.100536] [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: 06/01/2023] [Revised: 03/30/2024] [Accepted: 04/01/2024] [Indexed: 05/07/2024]
Abstract
Malaria continues to be a significant burden, particularly in Africa, which accounts for 95% of malaria deaths worldwide. Despite advances in malaria treatments, malaria eradication is hampered by insecticide and antimalarial drug resistance. Consequently, the need to discover new antimalarial lead compounds remains urgent. To help address this need, we evaluated the antiplasmodial activity of twenty-two amides and thioamides with pyridine cores and their non-pyridine analogues. Twelve of these compounds showed in vitro anti-proliferative activity against the intraerythrocytic stage of Plasmodium falciparum, the most virulent species of Plasmodium infecting humans. Thiopicolinamide 13i was found to possess submicromolar activity (IC50 = 142 nM) and was >88-fold less active against a human cell line. The compound was equally effective against chloroquine-sensitive and -resistant parasites and did not inhibit β-hematin formation, pH regulation or PfATP4. Compound 13i may therefore possess a novel mechanism of action.
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Affiliation(s)
- Alexa Redway
- Department of Chemistry, The University of the West Indies, Mona, Kingston 7, Jamaica; Chemistry Divison, University of Technology, 237 Old Hope Road, Kingston 6, Jamaica
| | - Christina Spry
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Ainka Brown
- Department of Chemistry, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - Ursula Wiedemann
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Imam Fathoni
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Larnelle F Garnie
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Deyun Qiu
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Timothy J Egan
- Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa; Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, 7925, South Africa
| | - Adele M Lehane
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Yvette Jackson
- Department of Chemistry, The University of the West Indies, Mona, Kingston 7, Jamaica
| | - Kevin J Saliba
- Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Nadale Downer-Riley
- Department of Chemistry, The University of the West Indies, Mona, Kingston 7, Jamaica.
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4
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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: 5] [Impact Index Per Article: 5.0] [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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5
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Gharibi Z, Shahbazi B, Gouklani H, Nassira H, Rezaei Z, Ahmadi K. Computational screening of FDA-approved drugs to identify potential TgDHFR, TgPRS, and TgCDPK1 proteins inhibitors against Toxoplasma gondii. Sci Rep 2023; 13:5396. [PMID: 37012275 PMCID: PMC10070243 DOI: 10.1038/s41598-023-32388-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
Toxoplasma gondii (T. gondii) is one of the most successful parasites in the world, because about a third of the world's population is seropositive for toxoplasmosis. Treatment regimens for toxoplasmosis have remained unchanged for the past 20 years, and no new drugs have been introduced to the market recently. This study, performed molecular docking to identify interactions of FDA-approved drugs with essential residues in the active site of proteins of T. gondii Dihydrofolate Reductase (TgDHFR), Prolyl-tRNA Synthetase (TgPRS), and Calcium-Dependent Protein Kinase 1 (TgCDPK1). Each protein was docked with 2100 FDA-approved drugs using AutoDock Vina. Also, the Pharmit software was used to generate pharmacophore models based on the TgDHFR complexed with TRC-2533, TgPRS in complex with halofuginone, and TgCDPK1 in complex with a bumped kinase inhibitor, RM-1-132. Molecular dynamics (MD) simulation was also performed for 100 ns to verify the stability of interaction in drug-protein complexes. Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) analysis evaluated the binding energy of selected complexes. Ezetimibe, Raloxifene, Sulfasalazine, Triamterene, and Zafirlukast drugs against the TgDHFR protein, Cromolyn, Cefexim, and Lactulose drugs against the TgPRS protein, and Pentaprazole, Betamethasone, and Bromocriptine drugs against TgCDPK1 protein showed the best results. These drugs had the lowest energy-based docking scores and also stable interactions based on MD analyses with TgDHFR, TgPRS, and TgCDPK1 drug targets that can be introduced as possible drugs for laboratory investigations to treat T. gondii parasite infection.
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Affiliation(s)
- Zahra Gharibi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Behzad Shahbazi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hoda Nassira
- Polymer Division, Department of Chemistry, Faculty of Science, University of Zanjan, Zanjan, Iran
| | - Zahra Rezaei
- Professor Alborzi Clinical Microbiology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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6
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Sun P, Wang C, Zhang Y, Tang X, Hu D, Xie F, Hao Z, Suo J, Yu Y, Suo X, Liu X. Transcriptome profile of halofuginone resistant and sensitive strains of Eimeria tenella. Front Microbiol 2023; 14:1141952. [PMID: 37065111 PMCID: PMC10098198 DOI: 10.3389/fmicb.2023.1141952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/10/2023] [Indexed: 04/03/2023] Open
Abstract
The antiparasitic drug halofuginone is important for controlling apicomplexan parasites. However, the occurrence of halofuginone resistance is a major obstacle for it to the treatment of apicomplexan parasites. Current studies have identified the molecular marker and drug resistance mechanisms of halofuginone in Plasmodium falciparum. In this study, we tried to use transcriptomic data to explore resistance mechanisms of halofuginone in apicomplexan parasites of the genus Eimeria (Apicomplexa: Eimeriidae). After halofuginone treatment of E. tenella parasites, transcriptome analysis was performed using samples derived from both resistant and sensitive strains. In the sensitive group, DEGs associated with enzymes were significantly downregulated, whereas the DNA damaging process was upregulated after halofuginone treatment, revealing the mechanism of halofuginone-induced parasite death. In addition, 1,325 differentially expressed genes (DEGs) were detected between halofuginone resistant and sensitive strains, and the DEGs related to translation were significantly downregulated after halofuginone induction. Overall, our results provide a gene expression profile for further studies on the mechanism of halofuginone resistance in E. tenella.
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Affiliation(s)
- Pei Sun
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chaoyue Wang
- Department of Pathogen Biology, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuanyuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture and Beijing Key Laboratory of Animal Genetic Improvement, China Agricultural University, Beijing, China
| | - Xinming Tang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dandan Hu
- School of Animal Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Fujie Xie
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhenkai Hao
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jingxia Suo
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yonglan Yu
- Department of Clinic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xun Suo
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
- *Correspondence: Xun Suo,
| | - Xianyong Liu
- National Key Laboratory of Veterinary Public Health Security, Key Laboratory of Animal Epidemiology and Zoonosis of Ministry of Agriculture, National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing, China
- Xianyong Liu,
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7
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Bisbenzylisoquinolines from Cissampelos pareira L. as antimalarial agents: Molecular docking, pharmacokinetics analysis, and molecular dynamic simulation studies. Comput Biol Chem 2023; 104:107826. [PMID: 36848855 DOI: 10.1016/j.compbiolchem.2023.107826] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/14/2023]
Abstract
Malaria is a major global health issue due to the emergence of resistance to most of the available antimalarial drugs. There is an urgent need to discover new antimalarials to tackle the resistance issue. The present study aims to explore the antimalarial potential of chemical constituents reported from Cissampelos pareira L., a medicinal plant traditionally known for treating malaria. Phytochemically, benzylisoquinolines and bisbenzylisoquinolines are the major classes of alkaloids reported from this plant. In silico molecular docking revealed prominent interactions of bisbenzylisoquinolines such as hayatinine and curine with Pfdihydrofolate reductase (-6.983 Kcal/mol and -6.237 Kcal/mol), PfcGMP-dependent protein kinase (-6.652 Kcal/mol and -7.158 Kcal/mol), and Pfprolyl-tRNA synthetase (-7.569 Kcal/mol and -7.122 Kcal/mol). The binding affinity of hayatinine and curine with identified antimalarial targets was further evaluated using MD-simulation analysis. Among the identified antimalarial targets, the RMSD, RMSF, the radius of gyration, and PCA indicated the formation of stable complexes of hayatinine and curine with Pfprolyl-tRNA synthetase. The outcomes of in silico investigation putatively suggested that bisbenzylisoquinolines may act on the translation of the Plasmodium parasite to exhibit antimalarial potency.
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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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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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10
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Qiu D, Pei JV, Rosling JEO, Thathy V, Li D, Xue Y, Tanner JD, Penington JS, Aw YTV, Aw JYH, Xu G, Tripathi AK, Gnadig NF, Yeo T, Fairhurst KJ, Stokes BH, Murithi JM, Kümpornsin K, Hasemer H, Dennis ASM, Ridgway MC, Schmitt EK, Straimer J, Papenfuss AT, Lee MCS, Corry B, Sinnis P, Fidock DA, van Dooren GG, Kirk K, Lehane AM. A G358S mutation in the Plasmodium falciparum Na + pump PfATP4 confers clinically-relevant resistance to cipargamin. Nat Commun 2022; 13:5746. [PMID: 36180431 PMCID: PMC9525273 DOI: 10.1038/s41467-022-33403-9] [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: 06/26/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Diverse compounds target the Plasmodium falciparum Na+ pump PfATP4, with cipargamin and (+)-SJ733 the most clinically-advanced. In a recent clinical trial for cipargamin, recrudescent parasites emerged, with most having a G358S mutation in PfATP4. Here, we show that PfATP4G358S parasites can withstand micromolar concentrations of cipargamin and (+)-SJ733, while remaining susceptible to antimalarials that do not target PfATP4. The G358S mutation in PfATP4, and the equivalent mutation in Toxoplasma gondii ATP4, decrease the sensitivity of ATP4 to inhibition by cipargamin and (+)-SJ733, thereby protecting parasites from disruption of Na+ regulation. The G358S mutation reduces the affinity of PfATP4 for Na+ and is associated with an increase in the parasite's resting cytosolic [Na+]. However, no defect in parasite growth or transmissibility is observed. Our findings suggest that PfATP4 inhibitors in clinical development should be tested against PfATP4G358S parasites, and that their combination with unrelated antimalarials may mitigate against resistance development.
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Affiliation(s)
- Deyun Qiu
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Jinxin V Pei
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - James E O Rosling
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Vandana Thathy
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Dongdi Li
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Yi Xue
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - John D Tanner
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Jocelyn Sietsma Penington
- Bioinformatic Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Yi Tong Vincent Aw
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Jessica Yi Han Aw
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Guoyue Xu
- Department of Molecular Microbiology & Immunology and Johns Hopkins Malaria Institute, Johns Hopkins School of Public Health, Baltimore, MD, 21205, USA
| | - Abhai K Tripathi
- Department of Molecular Microbiology & Immunology and Johns Hopkins Malaria Institute, Johns Hopkins School of Public Health, Baltimore, MD, 21205, USA
| | - Nina F Gnadig
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Tomas Yeo
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Kate J Fairhurst
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Barbara H Stokes
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - James M Murithi
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | | | - Heath Hasemer
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Adelaide S M Dennis
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Melanie C Ridgway
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | | | - Judith Straimer
- Novartis Institute for Tropical Diseases, Emeryville, CA, 94608, USA
| | - Anthony T Papenfuss
- Bioinformatic Division, The Walter & Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Marcus C S Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Ben Corry
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Photini Sinnis
- Department of Molecular Microbiology & Immunology and Johns Hopkins Malaria Institute, Johns Hopkins School of Public Health, Baltimore, MD, 21205, USA
| | - David A Fidock
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
- Center for Malaria Therapeutics and Antimicrobial Resistance, Division of Infectious Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Giel G van Dooren
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Kiaran Kirk
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia
| | - Adele M Lehane
- Research School of Biology, Australian National University, Canberra, ACT, 2600, Australia.
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11
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Wang H, Chen S. A streamlined process for discovery and characterization of inhibitors against phenylalanyl-tRNA synthetase of Mycobacterium tuberculosis. Methods Enzymol 2022; 679:275-293. [PMID: 36682865 DOI: 10.1016/bs.mie.2022.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) catalyze aminoacylation of tRNAs to produce aminoacyl-tRNAs for protein synthesis. Bacterial aaRSs have distinctive features, play an essential role in channeling amino acids into biomolecular assembly, and are vulnerable to inhibition by small molecules. The aaRSs continue to be targets for potential antibacterial drug development. The first step of aaRS reaction is the activation of amino acid by hydrolyzing ATP to form an acyladenylate intermediate with the concomitant release of pyrophosphate. None-radioactive assays usually measure the rate of ATP consumption or phosphate generation, offering advantages in high-throughput drug screening. These simple aaRS enzyme assays can be adapted to study the mode of inhibition of natural or synthetic aaRS inhibitors. Taking phenylalanyl-tRNA synthetase (PheRS) of Mycobacterium tuberculosis (Mtb) as an example, we describe a process for identification and characterization of Mtb PheRS inhibitor.
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Affiliation(s)
- Heng Wang
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Shawn Chen
- Global Health Drug Discovery Institute, Haidian, Beijing, China.
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12
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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: 7] [Impact Index Per Article: 3.5] [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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13
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Gill J, Sharma A. Prospects of halofuginone as an antiprotozoal drug scaffold. Drug Discov Today 2022; 27:2586-2592. [DOI: 10.1016/j.drudis.2022.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/05/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022]
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14
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Yi J, Cai Z, Qiu H, Lu F, Luo Z, Chen B, Gu Q, Xu J, Zhou H. Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase. Nucleic Acids Res 2022; 50:4755-4768. [PMID: 35474479 PMCID: PMC9071491 DOI: 10.1093/nar/gkac285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/05/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022] Open
Abstract
Methionyl-tRNA synthetase (MetRS) charges tRNAMet with l-methionine (L-Met) to decode the ATG codon for protein translation, making it indispensable for all cellular lives. Many gram-positive bacteria use a type 1 MetRS (MetRS1), which is considered a promising antimicrobial drug target due to its low sequence identity with human cytosolic MetRS (HcMetRS, which belongs to MetRS2). Here, we report crystal structures of a representative MetRS1 from Staphylococcus aureus (SaMetRS) in its apo and substrate-binding forms. The connecting peptide (CP) domain of SaMetRS differs from HcMetRS in structural organization and dynamic movement. We screened 1049 chemical fragments against SaMetRS preincubated with or without substrate ATP, and ten hits were identified. Four cocrystal structures revealed that the fragments bound to either the L-Met binding site or an auxiliary pocket near the tRNA CCA end binding site of SaMetRS. Interestingly, fragment binding was enhanced by ATP in most cases, suggesting a potential ATP-assisted ligand binding mechanism in MetRS1. Moreover, co-binding with ATP was also observed in our cocrystal structure of SaMetRS with a class of newly reported inhibitors that simultaneously occupied the auxiliary pocket, tRNA site and L-Met site. Our findings will inspire the development of new MetRS1 inhibitors for fighting microbial infections.
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Affiliation(s)
| | | | - Haipeng Qiu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Feihu Lu
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiteng Luo
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Bingyi Chen
- Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China,Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huihao Zhou
- To whom correspondence should be addressed. Tel: +86 20 39943350;
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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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16
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Li H, Zhang Y, Lan X, Yu J, Yang C, Sun Z, Kang P, Han Y, Yu D. Halofuginone Sensitizes Lung Cancer Organoids to Cisplatin via Suppressing PI3K/AKT and MAPK Signaling Pathways. Front Cell Dev Biol 2021; 9:773048. [PMID: 34901018 PMCID: PMC8652204 DOI: 10.3389/fcell.2021.773048] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/04/2021] [Indexed: 01/23/2023] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide. Cisplatin is the major DNA-damaging anticancer drug that cross-links the DNA in cancer cells, but many patients inevitably develop resistance with treatment. Identification of a cisplatin sensitizer might postpone or even reverse the development of cisplatin resistance. Halofuginone (HF), a natural small molecule isolated from Dichroa febrifuga, has been found to play an antitumor role. In this study, we found that HF inhibited the proliferation, induced G0/G1 phase arrest, and promoted apoptosis in lung cancer cells in a dose-dependent manner. To explore the underlying mechanism of this antitumor effect of halofuginone, we performed RNA sequencing to profile transcriptomes of NSCLC cells treated with or without halofuginone. Gene expression profiling and KEGG analysis indicated that PI3K/AKT and MAPK signaling pathways were top-ranked pathways affected by halofuginone. Moreover, combination of cisplatin and HF revealed that HF could sensitize the cisplatin-resistant patient-derived lung cancer organoids and lung cancer cells to cisplatin treatment. Taken together, this study identified HF as a cisplatin sensitizer and a dual pathway inhibitor, which might provide a new strategy to improve prognosis of patients with cisplatin-resistant lung cancer.
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Affiliation(s)
- Hefei Li
- Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Yushan Zhang
- Department of Thoracic Surgery, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, China
| | | | - Jianhua Yu
- Oncology Department, Wang Jing Hospital of China Academy of Chinese Medical Sciences, Beijing, China
| | | | | | - Ping Kang
- K2 Oncology Co. Ltd., Beijing, China
| | - Yi Han
- Department of Thoracic Surgery, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, China
| | - Daping Yu
- Department of Thoracic Surgery, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, China
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17
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Patriarca EJ, Cermola F, D’Aniello C, Fico A, Guardiola O, De Cesare D, Minchiotti G. The Multifaceted Roles of Proline in Cell Behavior. Front Cell Dev Biol 2021; 9:728576. [PMID: 34458276 PMCID: PMC8397452 DOI: 10.3389/fcell.2021.728576] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Herein, we review the multifaceted roles of proline in cell biology. This peculiar cyclic imino acid is: (i) A main precursor of extracellular collagens (the most abundant human proteins), antimicrobial peptides (involved in innate immunity), salivary proteins (astringency, teeth health) and cornifins (skin permeability); (ii) an energy source for pathogenic bacteria, protozoan parasites, and metastatic cancer cells, which engage in extracellular-protein degradation to invade their host; (iii) an antistress molecule (an osmolyte and chemical chaperone) helpful against various potential harms (UV radiation, drought/salinity, heavy metals, reactive oxygen species); (iv) a neural metabotoxin associated with schizophrenia; (v) a modulator of cell signaling pathways such as the amino acid stress response and extracellular signal-related kinase pathway; (vi) an epigenetic modifier able to promote DNA and histone hypermethylation; (vii) an inducer of proliferation of stem and tumor cells; and (viii) a modulator of cell morphology and migration/invasiveness. We highlight how proline metabolism impacts beneficial tissue regeneration, but also contributes to the progression of devastating pathologies such as fibrosis and metastatic cancer.
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Affiliation(s)
| | | | | | | | | | | | - Gabriella Minchiotti
- Stem Cell Fate Laboratory, Institute of Genetics and Biophysics “A. Buzzati Traverso”, Consiglio Nazionale delle Ricerche, Naples, Italy
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18
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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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Mahapatra AD, Shaik A, Thiruvenkatam V, Datta B. Supramolecular architecture in sulfonylurea, sulfonyldiurea and sulfonyltriurea drugs: Synthesis, X-ray structure and Hirshfeld surface analysis. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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20
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Naegleria fowleri: Protein structures to facilitate drug discovery for the deadly, pathogenic free-living amoeba. PLoS One 2021; 16:e0241738. [PMID: 33760815 PMCID: PMC7990177 DOI: 10.1371/journal.pone.0241738] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 12/19/2022] Open
Abstract
Naegleria fowleri is a pathogenic, thermophilic, free-living amoeba which causes primary amebic meningoencephalitis (PAM). Penetrating the olfactory mucosa, the brain-eating amoeba travels along the olfactory nerves, burrowing through the cribriform plate to its destination: the brain’s frontal lobes. The amoeba thrives in warm, freshwater environments, with peak infection rates in the summer months and has a mortality rate of approximately 97%. A major contributor to the pathogen’s high mortality is the lack of sensitivity of N. fowleri to current drug therapies, even in the face of combination-drug therapy. To enable rational drug discovery and design efforts we have pursued protein production and crystallography-based structure determination efforts for likely drug targets from N. fowleri. The genes were selected if they had homology to drug targets listed in Drug Bank or were nominated by primary investigators engaged in N. fowleri research. In 2017, 178 N. fowleri protein targets were queued to the Seattle Structural Genomics Center of Infectious Disease (SSGCID) pipeline, and to date 89 soluble recombinant proteins and 19 unique target structures have been produced. Many of the new protein structures are potential drug targets and contain structural differences compared to their human homologs, which could allow for the development of pathogen-specific inhibitors. Five of the structures were analyzed in more detail, and four of five show promise that selective inhibitors of the active site could be found. The 19 solved crystal structures build a foundation for future work in combating this devastating disease by encouraging further investigation to stimulate drug discovery for this neglected pathogen.
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21
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Bouz G, Zitko J. Inhibitors of aminoacyl-tRNA synthetases as antimycobacterial compounds: An up-to-date review. Bioorg Chem 2021; 110:104806. [PMID: 33799176 DOI: 10.1016/j.bioorg.2021.104806] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 11/26/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are crucial for the correct assembly of amino acids to cognate tRNA to maintain the fidelity of proteosynthesis. AaRSs have become a hot target in antimicrobial research. Three aaRS inhibitors are already in clinical practice; antibacterial mupirocin inhibits the synthetic site of isoleucyl-tRNA synthetase, antifungal tavaborole inhibits the editing site of leucyl-tRNA synthetase, and antiprotozoal halofuginone inhibits proline-tRNA synthetase. According to the World Health Organization, tuberculosis globally remains the leading cause of death from a single infectious agent. The rising incidence of multidrug-resistant tuberculosis is alarming and urges the search for new antimycobacterial compounds, preferably with yet unexploited mechanism of action. In this literature review, we have covered the up-to-date state in the field of inhibitors of mycobacterial aaRSs. The most studied aaRS in mycobacteria is LeuRS with at least four structural types of inhibitors, followed by TyrRS and AspRS. Inhibitors of MetRS, LysRS, and PheRS were addressed in a single significant study each. In many cases, the enzyme inhibition activity translated into micromolar or submicromolar inhibition of growth of mycobacteria. The most promising aaRS inhibitor as an antimycobacterial compound is GSK656 (compound 8), the only aaRS inhibitor in clinical trials (Phase IIa) for systemic use against tuberculosis. GSK656 is orally available and shares the oxaborole tRNA-trapping mechanism of action with antifungal tavaborole.
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Affiliation(s)
- Ghada Bouz
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy, Charles University
| | - Jan Zitko
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy, Charles University.
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22
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SSnet: A Deep Learning Approach for Protein-Ligand Interaction Prediction. Int J Mol Sci 2021; 22:ijms22031392. [PMID: 33573266 PMCID: PMC7869013 DOI: 10.3390/ijms22031392] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 12/15/2022] Open
Abstract
Computational prediction of Protein-Ligand Interaction (PLI) is an important step in the modern drug discovery pipeline as it mitigates the cost, time, and resources required to screen novel therapeutics. Deep Neural Networks (DNN) have recently shown excellent performance in PLI prediction. However, the performance is highly dependent on protein and ligand features utilized for the DNN model. Moreover, in current models, the deciphering of how protein features determine the underlying principles that govern PLI is not trivial. In this work, we developed a DNN framework named SSnet that utilizes secondary structure information of proteins extracted as the curvature and torsion of the protein backbone to predict PLI. We demonstrate the performance of SSnet by comparing against a variety of currently popular machine and non-Machine Learning (ML) models using various metrics. We visualize the intermediate layers of SSnet to show a potential latent space for proteins, in particular to extract structural elements in a protein that the model finds influential for ligand binding, which is one of the key features of SSnet. We observed in our study that SSnet learns information about locations in a protein where a ligand can bind, including binding sites, allosteric sites and cryptic sites, regardless of the conformation used. We further observed that SSnet is not biased to any specific molecular interaction and extracts the protein fold information critical for PLI prediction. Our work forms an important gateway to the general exploration of secondary structure-based Deep Learning (DL), which is not just confined to protein-ligand interactions, and as such will have a large impact on protein research, while being readily accessible for de novo drug designers as a standalone package.
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Wang H, Xu M, Engelhart CA, Zhang X, Yan B, Pan M, Xu Y, Fan S, Liu R, Xu L, Hua L, Schnappinger D, Chen S. Rediscovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis. J Biol Chem 2021; 296:100257. [PMID: 33837735 PMCID: PMC7948948 DOI: 10.1016/j.jbc.2021.100257] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/24/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) remains the deadliest pathogenic bacteria worldwide. The search for new antibiotics to treat drug-sensitive as well as drug-resistant tuberculosis has become a priority. The essential enzyme phenylalanyl-tRNA synthetase (PheRS) is an antibacterial drug target because of the large differences between bacterial and human PheRS counterparts. In a high-throughput screening of 2148 bioactive compounds, PF-3845, which is a known inhibitor of human fatty acid amide hydrolase, was identified inhibiting Mtb PheRS at Ki ∼ 0.73 ± 0.06 μM. The inhibition mechanism was studied with enzyme kinetics, protein structural modeling, and crystallography, in comparison to a PheRS inhibitor of the noted phenyl–thiazolylurea–sulfonamide class. The 2.3-Å crystal structure of Mtb PheRS in complex with PF-3845 revealed its novel binding mode, in which a trifluoromethyl–pyridinylphenyl group occupies the phenylalanine pocket, whereas a piperidine–piperazine urea group binds into the ATP pocket through an interaction network enforced by a sulfate ion. It represents the first non-nucleoside bisubstrate competitive inhibitor of bacterial PheRS. PF-3845 inhibits the in vitro growth of Mtb H37Rv at ∼24 μM, and the potency of PF-3845 increased against an engineered strain Mtb pheS–FDAS, suggesting on target activity in mycobacterial whole cells. PF-3845 does not inhibit human cytoplasmic or mitochondrial PheRS in biochemical assay, which can be explained from the crystal structures. Further medicinal chemistry efforts focused on the piperidine–piperazine urea moiety may result in the identification of a selective antibacterial lead compound.
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Affiliation(s)
- Heng Wang
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Min Xu
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Xi Zhang
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Baohua Yan
- Center of Protein Science Facility, Tsinghua University, Beijing, China
| | - Miaomiao Pan
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Yuanyuan Xu
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Shilong Fan
- Center of Protein Science Facility, Tsinghua University, Beijing, China
| | - Renhe Liu
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Lan Xu
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Lan Hua
- Global Health Drug Discovery Institute, Haidian, Beijing, China
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Shawn Chen
- Global Health Drug Discovery Institute, Haidian, Beijing, China.
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24
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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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25
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Brullo C, Rapetti F, Bruno O. Pyrazolyl-Ureas as Interesting Scaffold in Medicinal Chemistry. Molecules 2020; 25:molecules25153457. [PMID: 32751358 PMCID: PMC7435939 DOI: 10.3390/molecules25153457] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/19/2022] Open
Abstract
The pyrazole nucleus has long been known as a privileged scaffold in the synthesis of biologically active compounds. Within the numerous pyrazole derivatives developed as potential drugs, this review is focused on molecules characterized by a urea function directly linked to the pyrazole nucleus in a different position. In the last 20 years, the interest of numerous researchers has been especially attracted by pyrazolyl-ureas showing a wide spectrum of biological activities, ranging from the antipathogenic activities (bacteria, plasmodium, toxoplasma, and others) to the anticarcinogenic activities. In particular, in the anticancer field, pyrazolyl-ureas have been shown to interact at the intracellular level on many pathways, in particular on different kinases such as Src, p38-MAPK, TrKa, and others. In addition, some of them evidenced an antiangiogenic potential that deserves to be explored. This review therefore summarizes all these biological data (from 2000 to date), including patented compounds.
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26
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Nyamai DW, Tastan Bishop Ö. Identification of Selective Novel Hits against Plasmodium falciparum Prolyl tRNA Synthetase Active Site and a Predicted Allosteric Site Using in silico Approaches. Int J Mol Sci 2020; 21:E3803. [PMID: 32471245 PMCID: PMC7312540 DOI: 10.3390/ijms21113803] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/10/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
Abstract
Recently, there has been increased interest in aminoacyl tRNA synthetases (aaRSs) as potential malarial drug targets. These enzymes play a key role in protein translation by the addition of amino acids to their cognate tRNA. The aaRSs are present in all Plasmodium life cycle stages, and thus present an attractive malarial drug target. Prolyl tRNA synthetase is a class II aaRS that functions in charging tRNA with proline. Various inhibitors against Plasmodium falciparum ProRS (PfProRS) active site have been designed. However, none have gone through clinical trials as they have been found to be highly toxic to human cells. Recently, a possible allosteric site was reported in PfProRS with two possible allosteric modulators: glyburide and TCMDC-124506. In this study, we sought to identify novel selective inhibitors targeting PfProRS active site and possible novel allosteric modulators of this enzyme. To achieve this, virtual screening of South African natural compounds against PfProRS and the human homologue was carried out using AutoDock Vina. The modulation of protein motions by ligand binding was studied by molecular dynamics (MD) using the GROningen MAchine for Chemical Simulations (GROMACS) tool. To further analyse the protein global motions and energetic changes upon ligand binding, principal component analysis (PCA), and free energy landscape (FEL) calculations were performed. Further, to understand the effect of ligand binding on the protein communication, dynamic residue network (DRN) analysis of the MD trajectories was carried out using the MD-TASK tool. A total of ten potential natural hit compounds were identified with strong binding energy scores. Binding of ligands to the protein caused observable global and residue level changes. Dynamic residue network calculations showed increase in betweenness centrality (BC) metric of residues at the allosteric site implying these residues are important in protein communication. A loop region at the catalytic domain between residues 300 and 350 and the anticodon binding domain showed significant contributions to both PC1 and PC2. Large motions were observed at a loop in the Z-domain between residues 697 and 710 which was also in agreement with RMSF calculations that showed increase in flexibility of residues in this region. Residues in this loop region are implicated in ATP binding and thus a change in dynamics may affect ATP binding affinity. Free energy landscape (FEL) calculations showed that the holo protein (protein-ADN complex) and PfProRS-SANC184 complexes were stable, as shown by the low energy with very few intermediates and hardly distinguishable low energy barriers. In addition, FEL results agreed with backbone RMSD distribution plots where stable complexes showed a normal RMSD distribution while unstable complexes had multimodal RMSD distribution. The betweenness centrality metric showed a loss of functional importance of key ATP binding site residues upon allosteric ligand binding. The deep basins in average L observed at the allosteric region imply that there is high accessibility of residues at this region. To further analyse BC and average L metrics data, we calculated the ΔBC and ΔL values by taking each value in the holo protein BC or L matrix less the corresponding value in the ligand-bound complex BC or L matrix. Interestingly, in allosteric complexes, residues located in a loop region implicated in ATP binding had negative ΔL values while in orthosteric complexes these residues had positive ΔL values. An increase in contact frequency between residues Ser263, Thr267, Tyr285, and Leu707 at the allosteric site and residues Thr397, Pro398, Thr402, and Gln395 at the ATP binding TXE loop was observed. In summary, this study identified five potential orthosteric inhibitors and five allosteric modulators against PfProRS. Allosteric modulators changed ATP binding site dynamics, as shown by RMSF, PCA, and DRN calculations. Changes in dynamics of the ATP binding site and increased contact frequency between residues at the proposed allosteric site and the ATP binding site may explain how allosteric modulators distort the ATP binding site and thus might inhibit PfProRS. The scaffolds of the identified hits in the study can be used as a starting point for antimalarial inhibitor development with low human cytotoxicity.
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Affiliation(s)
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa;
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27
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Affiliation(s)
- Matthew D. Lloyd
- Drug & Target Development, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, U.K
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28
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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: 49] [Impact Index Per Article: 9.8] [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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29
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Wang JS, Huang KS, Han WY, Cui BD, Wan NW, Chen YZ. Ex Situ Generation of Difluorodiazoethane (CF 2HCHN 2): Application in the Regioselective Synthesis of CF 2H-Containing Pyrazoles. Org Lett 2019; 21:8751-8755. [PMID: 31642680 DOI: 10.1021/acs.orglett.9b03371] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A new method for the ex situ generation of difluorodiazoethane (CF2HCHN2) and a procedure for its efficient use in [3 + 2] cycloaddition with nitroolefins by the AcOH/O2 catalyst system were developed by using a simple two-chamber system. The method provides a facile and straightforward access to a series of 4-substituted 5-difluoromethyl-3-nitro-1H-pyrazoles that are of interest in medicinal chemistry. Interestingly, the key factor for the success of this method is the efficient preparation of CF2HCHN2 by an ex situ process.
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Affiliation(s)
- Jian-Shu Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy , Zunyi Medical University , Zunyi 563006 , P. R. China
| | - Kai-Shun Huang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy , Zunyi Medical University , Zunyi 563006 , P. R. China
| | - Wen-Yong Han
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy , Zunyi Medical University , Zunyi 563006 , P. R. China
| | - Bao-Dong Cui
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy , Zunyi Medical University , Zunyi 563006 , P. R. China
| | - Nan-Wei Wan
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy , Zunyi Medical University , Zunyi 563006 , P. R. China
| | - Yong-Zheng Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy , Zunyi Medical University , Zunyi 563006 , P. R. China
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30
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Cabrera AC. Collaborative drug discovery and the Tres Cantos Antimalarial Set (TCAMS). Drug Discov Today 2019; 24:1304-1310. [PMID: 30980903 DOI: 10.1016/j.drudis.2019.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/18/2019] [Accepted: 04/04/2019] [Indexed: 12/01/2022]
Abstract
Malaria affects a population of over 200 million people worldwide. New drugs are needed because of widespread resistance, and the hunt for such drugs involves a coordinated research effort from the scientific community. The release of the Tres Cantos Antimalarial Set (TCAMS) in 2010 represented a landmark in the field of collaborative drug discovery for malaria. This set of >13 000 molecules with confirmed activity against several strains of Plasmodium falciparum was publicly released with the goal of fostering additional research beyond the GlaxoSmithKline (GSK) network of collaborators. Here, we examine the outcomes realized from TCAMS over the past 8 years and whether the expectations surrounding this initiative have become a reality.
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Affiliation(s)
- Alvaro Cortes Cabrera
- Department of Pharmacology, Universidad de Alcalá, Crta Madrid-Zaragoza Km 33.6, Alcalá de Henares, Spain.
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31
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Nyamai DW, Tastan Bishop Ö. Aminoacyl tRNA synthetases as malarial drug targets: a comparative bioinformatics study. Malar J 2019; 18:34. [PMID: 30728021 PMCID: PMC6366043 DOI: 10.1186/s12936-019-2665-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/27/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Treatment of parasitic diseases has been challenging due to evolution of drug resistant parasites, and thus there is need to identify new class of drugs and drug targets. Protein translation is important for survival of malarial parasite, Plasmodium, and the pathway is present in all of its life cycle stages. Aminoacyl tRNA synthetases are primary enzymes in protein translation as they catalyse amino acid addition to the cognate tRNA. This study sought to understand differences between Plasmodium and human aminoacyl tRNA synthetases through bioinformatics analysis. METHODS Plasmodium berghei, Plasmodium falciparum, Plasmodium fragile, Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale, Plasmodium vivax, Plasmodium yoelii and human aminoacyl tRNA synthetase sequences were retrieved from UniProt database and grouped into 20 families based on amino acid specificity. These families were further divided into two classes. Both families and classes were analysed. Motif discovery was carried out using the MEME software, sequence identity calculation was done using an in-house Python script, multiple sequence alignments were performed using PROMALS3D and TCOFFEE tools, and phylogenetic tree calculations were performed using MEGA vs 7.0 tool. Possible alternative binding sites were predicted using FTMap webserver and SiteMap tool. RESULTS Motif discovery revealed Plasmodium-specific motifs while phylogenetic tree calculations showed that Plasmodium proteins have different evolutionary history to the human homologues. Human aaRSs sequences showed low sequence identity (below 40%) compared to Plasmodium sequences. Prediction of alternative binding sites revealed potential druggable sites in PfArgRS, PfMetRS and PfProRS at regions that are weakly conserved when compared to the human homologues. Multiple sequence analysis, motif discovery, pairwise sequence identity calculations and phylogenetic tree analysis showed significant differences between parasite and human aaRSs proteins despite functional and structural conservation. These differences may provide a basis for further exploration of Plasmodium aminoacyl tRNA synthetases as potential drug targets. CONCLUSION This study showed that, despite, functional and structural conservation, Plasmodium aaRSs have key differences from the human homologues. These differences in Plasmodium aaRSs can be targeted to develop anti-malarial drugs with less toxicity to the host.
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Affiliation(s)
- Dorothy Wavinya Nyamai
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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32
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Lehane AM, Dennis ASM, Bray KO, Li D, Rajendran E, McCoy JM, McArthur HM, Winterberg M, Rahimi F, Tonkin CJ, Kirk K, van Dooren GG. Characterization of the ATP4 ion pump in Toxoplasma gondii. J Biol Chem 2019; 294:5720-5734. [PMID: 30723156 DOI: 10.1074/jbc.ra118.006706] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
The Plasmodium falciparum ATPase PfATP4 is the target of a diverse range of antimalarial compounds, including the clinical drug candidate cipargamin. PfATP4 was originally annotated as a Ca2+ transporter, but recent evidence suggests that it is a Na+ efflux pump, extruding Na+ in exchange for H+ Here we demonstrate that ATP4 proteins belong to a clade of P-type ATPases that are restricted to apicomplexans and their closest relatives. We employed a variety of genetic and physiological approaches to investigate the ATP4 protein of the apicomplexan Toxoplasma gondii, TgATP4. We show that TgATP4 is a plasma membrane protein. Knockdown of TgATP4 had no effect on resting pH or Ca2+ but rendered parasites unable to regulate their cytosolic Na+ concentration ([Na+]cyt). PfATP4 inhibitors caused an increase in [Na+]cyt and a cytosolic alkalinization in WT but not TgATP4 knockdown parasites. Parasites in which TgATP4 was knocked down or disrupted exhibited a growth defect, attributable to reduced viability of extracellular parasites. Parasites in which TgATP4 had been disrupted showed reduced virulence in mice. These results provide evidence for ATP4 proteins playing a key conserved role in Na+ regulation in apicomplexan parasites.
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Affiliation(s)
- Adele M Lehane
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia,
| | - Adelaide S M Dennis
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Katherine O Bray
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Dongdi Li
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Esther Rajendran
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - James M McCoy
- the Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia, and.,the Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hillary M McArthur
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Markus Winterberg
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Farid Rahimi
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Christopher J Tonkin
- the Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia, and.,the Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kiaran Kirk
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia,
| | - Giel G van Dooren
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia,
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33
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Pant A, Kumar R, Wani NA, Verma S, Sharma R, Pande V, Saxena AK, Dixit R, Rai R, Pandey KC. Allosteric Site Inhibitor Disrupting Auto-Processing of Malarial Cysteine Proteases. Sci Rep 2018; 8:16193. [PMID: 30385827 PMCID: PMC6212536 DOI: 10.1038/s41598-018-34564-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 10/16/2018] [Indexed: 02/08/2023] Open
Abstract
Falcipains are major haemoglobinases of Plasmodium falciparum required for parasite growth and development. They consist of pro- and mature domains that interact via 'hot-spot' interactions and maintain the structural integrity of enzyme in zymogen state. Upon sensing the acidic environment, these interactions dissociate and active enzyme is released. For inhibiting falcipains, several active site inhibitors exist, however, compounds that target via allosteric mechanism remains uncharacterized. Therefore, we designed and synthesized six azapeptide compounds, among which, NA-01 & NA-03 arrested parasite growth by specifically blocking the auto-processing of falcipains. Inhibitors showed high affinity for enzymes in presence of the prodomain without affecting the secondary structure. Binding of NA-03 at the interface induced rigidity in the prodomain preventing structural reorganization. We further reported a histidine-dependent activation of falcipain. Collectively, for the first time we provide a framework for blocking the allosteric site of crucial haemoglobinases of the human malaria parasite. Targeting the allosteric site could provide high selectivity and less vulnerable to drug resistance.
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Affiliation(s)
- A Pant
- ICMR-National Institute of Malaria Research, Dwarka Sector 8, New Delhi, India
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - R Kumar
- Integrated Science Lab, Umeå University, Umeå, Sweden
| | - N A Wani
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - S Verma
- ICMR-National Institute of Malaria Research, Dwarka Sector 8, New Delhi, India
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - R Sharma
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - V Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - A K Saxena
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - R Dixit
- ICMR-National Institute of Malaria Research, Dwarka Sector 8, New Delhi, India
| | - R Rai
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - K C Pandey
- ICMR-National Institute of Malaria Research, Dwarka Sector 8, New Delhi, India.
- Department of Biochemistry, ICMR-National Institute for Research in Environmental Health, Bhopal, MP - 462001, India.
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34
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Rosling JEO, Ridgway MC, Summers RL, Kirk K, Lehane AM. Biochemical characterization and chemical inhibition of PfATP4-associated Na +-ATPase activity in Plasmodium falciparum membranes. J Biol Chem 2018; 293:13327-13337. [PMID: 29986883 DOI: 10.1074/jbc.ra118.003640] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/26/2018] [Indexed: 11/06/2022] Open
Abstract
The antimalarial activity of chemically diverse compounds, including the clinical candidate cipargamin, has been linked to the ATPase PfATP4 in the malaria-causing parasite Plasmodium falciparum The characterization of PfATP4 has been hampered by the inability thus far to achieve its functional expression in a heterologous system. Here, we optimized a membrane ATPase assay to probe the function of PfATP4 and its chemical sensitivity. We found that cipargamin inhibited the Na+-dependent ATPase activity present in P. falciparum membranes from WT parasites and that its potency was reduced in cipargamin-resistant PfATP4-mutant parasites. The cipargamin-sensitive fraction of membrane ATPase activity was inhibited by all 28 of the compounds in the "Malaria Box" shown previously to disrupt ion regulation in P. falciparum in a cipargamin-like manner. This is consistent with PfATP4 being the direct target of these compounds. Characterization of the cipargamin-sensitive ATPase activity yielded data consistent with PfATP4 being a Na+ transporter that is sensitive to physiologically relevant perturbations of pH, but not of [K+] or [Ca2+]. With an apparent Km for ATP of 0.2 mm and an apparent Km for Na+ of 16-17 mm, the protein is predicted to operate at below its half-maximal rate under normal physiological conditions, allowing the rate of Na+ efflux to increase in response to an increase in cytosolic [Na+]. In membranes from a cipargamin-resistant PfATP4-mutant line, the apparent Km for Na+ is slightly elevated. Our study provides new insights into the biochemical properties and chemical sensitivity of an important new antimalarial drug target.
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Affiliation(s)
- James E O Rosling
- From the Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Melanie C Ridgway
- From the Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Robert L Summers
- From the Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Kiaran Kirk
- From the Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Adele M Lehane
- From the Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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35
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Cell Swelling Induced by the Antimalarial KAE609 (Cipargamin) and Other PfATP4-Associated Antimalarials. Antimicrob Agents Chemother 2018; 62:AAC.00087-18. [PMID: 29555632 DOI: 10.1128/aac.00087-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/18/2018] [Indexed: 12/15/2022] Open
Abstract
For an increasing number of antimalarial agents identified in high-throughput phenotypic screens, there is evidence that they target PfATP4, a putative Na+ efflux transporter on the plasma membrane of the human malaria parasite Plasmodium falciparum For several such "PfATP4-associated" compounds, it has been noted that their addition to parasitized erythrocytes results in cell swelling. Here we show that six structurally diverse PfATP4-associated compounds, including the clinical candidate KAE609 (cipargamin), induce swelling of both isolated blood-stage parasites and intact parasitized erythrocytes. The swelling of isolated parasites is dependent on the presence of Na+ in the external environment and may be attributed to the osmotic consequences of Na+ uptake. The swelling of the parasitized erythrocyte results in an increase in its osmotic fragility. Countering cell swelling by increasing the osmolarity of the extracellular medium reduces the antiplasmodial efficacy of PfATP4-associated compounds, consistent with cell swelling playing a role in the antimalarial activity of this class of compounds.
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36
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Antimalarial agents against both sexual and asexual parasites stages: structure-activity relationships and biological studies of the Malaria Box compound 1-[5-(4-bromo-2-chlorophenyl)furan-2-yl]-N-[(piperidin-4-yl)methyl]methanamine (MMV019918) and analogues. Eur J Med Chem 2018; 150:698-718. [PMID: 29571157 DOI: 10.1016/j.ejmech.2018.03.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 01/31/2023]
Abstract
Therapies addressing multiple stages of Plasmodium falciparum life cycle are highly desirable for implementing malaria elimination strategies. MMV019918 (1, 1-[5-(4-bromo-2-chlorophenyl)furan-2-yl]-N-[(piperidin-4-yl)methyl]methanamine) was selected from the MMV Malaria Box for its dual activity against both asexual stages and gametocytes. In-depth structure-activity relationship studies and cytotoxicity evaluation led to the selection of 25 for further biological investigation. The potential transmission blocking activity of 25 versus P. falciparum was confirmed through the standard membrane-feeding assay. Both 1 and 25 significantly prolonged atrioventricular conduction time in Langendorff-isolated rat hearts, and showed inhibitory activity of Ba2+ current through Cav1.2 channels. An in silico target-fishing study suggested the enzyme phosphoethanolamine methyltransferase (PfPMT) as a potential target. However, compound activity against PfPMT did not track with the antiplasmodial activity, suggesting the latter activity relies on a different molecular target. Nevertheless, 25 showed interesting activity against PfPMT, which could be an important starting point for the identification of more potent inhibitors active against both sexual and asexual stages of the parasite.
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37
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Manickam Y, Chaturvedi R, Babbar P, Malhotra N, Jain V, Sharma A. Drug targeting of one or more aminoacyl-tRNA synthetase in the malaria parasite Plasmodium falciparum. Drug Discov Today 2018; 23:1233-1240. [PMID: 29408369 DOI: 10.1016/j.drudis.2018.01.050] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/02/2018] [Accepted: 01/29/2018] [Indexed: 11/28/2022]
Abstract
Malaria remains a major infectious disease and, despite incidence reduction, it threatens resurgence in drug-resistant forms. Antimalarial drugs remain the mainstay of therapeutic options and hence there is a constant need to identify and validate new druggable targets. Plasmodium falciparum aminoacyl-tRNA synthetases (Pf-aaRSs) drive protein translation and are potent targets for development of next-generation antimalarials. Here, we detail advances made in structural-biology-based investigations in Pf-aaRSs and discuss their distribution of druggable pockets. This review establishes a platform for systematic experimental dissection of malarial parasite aaRSs as a new focus for sustained drug development efforts against malaria.
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Affiliation(s)
- Yogavel Manickam
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Rini Chaturvedi
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Palak Babbar
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Nipun Malhotra
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India
| | - Vitul Jain
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India; Present address: Division of Structural Biology, Wellcome Trust Centre for Human Genetics, The Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi 110067, India.
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38
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Alencar N, Sola I, Linares M, Juárez-Jiménez J, Pont C, Viayna A, Vílchez D, Sampedro C, Abad P, Pérez-Benavente S, Lameira J, Bautista JM, Muñoz-Torrero D, Luque FJ. First homology model of Plasmodium falciparum glucose-6-phosphate dehydrogenase: Discovery of selective substrate analog-based inhibitors as novel antimalarial agents. Eur J Med Chem 2018; 146:108-122. [PMID: 29407943 DOI: 10.1016/j.ejmech.2018.01.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/27/2017] [Accepted: 01/15/2018] [Indexed: 01/07/2023]
Abstract
In Plasmodium falciparum the bifunctional enzyme glucose-6-phosphate dehydrogenase‒6-phosphogluconolactonase (PfG6PD‒6PGL) is involved in the catalysis of the first reaction of the pentose phosphate pathway. Since this enzyme has a key role in parasite development, its unique structure represents a potential target for the discovery of antimalarial drugs. Here we describe the first 3D structural model of the G6PD domain of PfG6PD‒6PGL. Compared to the human enzyme (hG6PD), the 3D model has enabled the identification of a key difference in the substrate-binding site, which involves the replacement of Arg365 in hG6PD by Asp750 in PfG6PD. In a prospective validation of the model, this critical change has been exploited to rationally design a novel family of substrate analog-based inhibitors that can display the necessary selectivity towards PfG6PD. A series of glucose derivatives featuring an α-methoxy group at the anomeric position and different side chains at position 6 bearing distinct basic functionalities has been synthesized, and their PfG6PD and hG6PD inhibitory activities and their toxicity against parasite and mammalian cells have been assessed. Several compounds displayed micromolar affinity (Ki up to 23 μM), favorable selectivity (up to > 26-fold), and low cytotoxicity. Phenotypic assays with P. falciparum cultures revealed high micromolar IC50 values, likely as a result of poor internalization of the compounds in the parasite cell. Overall, these results endorse confidence to the 3D model of PfG6PD, paving the way for the use of target-based drug design approaches in antimalarial drug discovery studies around this promising target.
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Affiliation(s)
- Nelson Alencar
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain
| | - Irene Sola
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences and IBUB, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - María Linares
- Research Institute Hospital 12 de Octubre, Avda. de Cordoba s/n, 28041 Madrid, Spain
| | - Jordi Juárez-Jiménez
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain
| | - Caterina Pont
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences and IBUB, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Antonio Viayna
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain
| | - David Vílchez
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain
| | - Cristina Sampedro
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences and IBUB, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
| | - Paloma Abad
- Research Institute Hospital 12 de Octubre, Avda. de Cordoba s/n, 28041 Madrid, Spain; Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Facultad de Veterinaria, Ciudad Universitaria, 28040 Madrid, Spain
| | - Susana Pérez-Benavente
- Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Facultad de Veterinaria, Ciudad Universitaria, 28040 Madrid, Spain
| | - Jerónimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos-LPDF, Instituto de Ciências Exatas e Naturais- ICEN, Universidade Federal do Pará - UFPA, Av. Augusto Correa, Nº 1- Bairro: Guamá, Cep: 66.075-900 Belém-Pará, Brazil
| | - José M Bautista
- Research Institute Hospital 12 de Octubre, Avda. de Cordoba s/n, 28041 Madrid, Spain; Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Facultad de Veterinaria, Ciudad Universitaria, 28040 Madrid, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences and IBUB, University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain.
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Prat de la Riba 171, E-08921 Santa Coloma de Gramenet, Spain.
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39
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Moen SO, Edwards TE, Dranow DM, Clifton MC, Sankaran B, Van Voorhis WC, Sharma A, Manoil C, Staker BL, Myler PJ, Lorimer DD. Ligand co-crystallization of aminoacyl-tRNA synthetases from infectious disease organisms. Sci Rep 2017; 7:223. [PMID: 28303005 PMCID: PMC5428304 DOI: 10.1038/s41598-017-00367-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/20/2017] [Indexed: 12/15/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) charge tRNAs with their cognate amino acid, an essential precursor step to loading of charged tRNAs onto the ribosome and addition of the amino acid to the growing polypeptide chain during protein synthesis. Because of this important biological function, aminoacyl-tRNA synthetases have been the focus of anti-infective drug development efforts and two aaRS inhibitors have been approved as drugs. Several researchers in the scientific community requested aminoacyl-tRNA synthetases to be targeted in the Seattle Structural Genomics Center for Infectious Disease (SSGCID) structure determination pipeline. Here we investigate thirty-one aminoacyl-tRNA synthetases from infectious disease organisms by co-crystallization in the presence of their cognate amino acid, ATP, and/or inhibitors. Crystal structures were determined for a CysRS from Borrelia burgdorferi bound to AMP, GluRS from Borrelia burgdorferi and Burkholderia thailandensis bound to glutamic acid, a TrpRS from the eukaryotic pathogen Encephalitozoon cuniculi bound to tryptophan, a HisRS from Burkholderia thailandensis bound to histidine, and a LysRS from Burkholderia thailandensis bound to lysine. Thus, the presence of ligands may promote aaRS crystallization and structure determination. Comparison with homologous structures shows conformational flexibility that appears to be a recurring theme with this enzyme class.
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Affiliation(s)
- Spencer O Moen
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA. .,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA.
| | - David M Dranow
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Matthew C Clifton
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Berkeley, CA, 94720, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,University of Washington, Seattle, WA, 98195-6423, USA
| | - Amit Sharma
- International Center for Genetic Engineering and Biotechnology, New Delhi, 110 067, India
| | - Colin Manoil
- University of Washington, Department of Genome Sciences, Seattle, WA, 98195-5065, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, 98109, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, WA, 98109, USA.,University of Washington, Department of Medical Education and Biomedical Informatics & Department of Global Health, Seattle, WA, 98195, USA
| | - Donald D Lorimer
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), Bethesda, MD, USA.,Beryllium Discovery Corp, Bainbridge Island, WA, 98110, USA
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