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Mishra S, Malhotra N, Laleu B, Chakraborti S, Yogavel M, Sharma A. ATP mimetics targeting prolyl-tRNA synthetases as a new avenue for antimalarial drug development. iScience 2024; 27:110049. [PMID: 39104570 PMCID: PMC11298890 DOI: 10.1016/j.isci.2024.110049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 09/24/2023] [Accepted: 05/17/2024] [Indexed: 08/07/2024] Open
Abstract
The prolyl-tRNA synthetase (PRS) is an essential enzyme for protein translation and a validated target against malaria parasite. We describe five ATP mimetics (L95, L96, L97, L35, and L36) against PRS, exhibiting enhanced thermal stabilities in co-operativity with L-proline. L35 displays the highest thermal stability akin to halofuginone, an established inhibitor of Plasmodium falciparum PRS. Four compounds exhibit nanomolar inhibitory potency against PRS. L35 exhibits the highest potency of ∼1.6 nM against asexual-blood-stage (ABS) and ∼100-fold (effective concentration [EC50]) selectivity for the parasite. The macromolecular structures of PfPRS with L95 and L97 in complex with L-pro reveal their binding modes and catalytic site malleability. Arg401 of PfPRS oscillates between two rotameric configurations when in complex with L95, whereas it is locked in one of the configurations due to the larger size of L97. Harnessing such specific and selective chemical features holds significant promise for designing potential inhibitors and expediting drug development efforts.
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Affiliation(s)
- Siddhartha Mishra
- Molecular Medicine – Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
- ICMR-National Institute of Malaria Research (NIMR), Dwarka, New Delhi 110077, India
- Academy of Scientific and Innovative Research (AcSIR), UP, India
| | - Nipun Malhotra
- Molecular Medicine – Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Benoît Laleu
- Medicines for Malaria Venture (MMV), International Center Cointrin (ICC), Route de Pré-Bois 20, 1215 Geneva, Switzerland
| | - Soumyananda Chakraborti
- ICMR-National Institute of Malaria Research (NIMR), Dwarka, New Delhi 110077, India
- Academy of Scientific and Innovative Research (AcSIR), UP, India
| | - Manickam Yogavel
- Molecular Medicine – Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Amit Sharma
- Molecular Medicine – Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
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Lu F, Xia K, Su J, Yi J, Luo Z, Xu J, Gu Q, Chen B, Zhou H. Biochemical and structural characterization of chlorhexidine as an ATP-assisted inhibitor against type 1 methionyl-tRNA synthetase from Gram-positive bacteria. Eur J Med Chem 2024; 268:116303. [PMID: 38458107 DOI: 10.1016/j.ejmech.2024.116303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/27/2024] [Accepted: 03/02/2024] [Indexed: 03/10/2024]
Abstract
Methionyl-tRNA synthetase (MetRS) catalyzes the attachment of l-methionine (l-Met) to tRNAMet to generate methionyl-tRNAMet, an essential substrate for protein translation within ribosome. Owing to its indispensable biological function and the structural discrepancies with human counterpart, bacterial MetRS is considered an ideal target for developing antibacterials. Herein, chlorhexidine (CHX) was identified as a potent binder of Staphylococcus aureus MetRS (SaMetRS) through an ATP-aided affinity screening. The co-crystal structure showed that CHX simultaneously occupies the enlarged l-Met pocket (EMP) and the auxiliary pocket (AP) of SaMetRS with its two chlorophenyl groups, while its central hexyl linker swings upwards to interact with some conserved hydrophobic residues. ATP adopts alternative conformations in the active site cavity, and forms ionic bonds and water-mediated hydrogen bonds with CHX. Consistent with this synergistic binding mode, ATP concentration-dependently enhanced the binding affinity of CHX to SaMetRS from 10.2 μM (no ATP) to 0.45 μM (1 mM ATP). While it selectively inhibited two representative type 1 MetRSs from S. aureus and Enterococcus faecalis, CHX did not show significant interactions with three tested type 2 MetRSs, including human cytoplasmic MetRS, in the enzyme inhibition and biophysical binding assays, probably due to the conformational differences between two types of MetRSs at their EMP and AP. Our findings on CHX may inspire the design of MetRS-directed antimicrobials in future.
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Affiliation(s)
- 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
| | - Kaijiang Xia
- 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
| | - Jingtian Su
- 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
| | - Jia Yi
- 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
| | - Jun Xu
- 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
| | - 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.
| | - Huihao Zhou
- 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.
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Elbaramawi SS, Eissa AG, Noureldin NA, Simons C. Exploring Proteus mirabilis Methionine tRNA Synthetase Active Site: Homology Model Construction, Molecular Dynamics, Pharmacophore and Docking Validation. Pharmaceuticals (Basel) 2023; 16:1263. [PMID: 37765071 PMCID: PMC10535265 DOI: 10.3390/ph16091263] [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: 07/24/2023] [Revised: 08/23/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Currently, the treatment of Proteus mirabilis infections is considered to be complicated as the organism has become resistant to numerous antibiotic classes. Therefore, new inhibitors should be developed, targeting bacterial molecular functions. Methionine tRNA synthetase (MetRS), a member of the aminoacyl-tRNA synthetase family, is essential for protein biosynthesis offering a promising target for novel antibiotics discovery. In the context of computer-aided drug design (CADD), the current research presents the construction and analysis of a comparative homology model for P. mirabilis MetRS, enabling development of novel inhibitors with greater selectivity. Molecular Operating Environment (MOE) software was used to build a homology model for P. mirabilis MetRS using Escherichia coli MetRS as a template. The model was evaluated, and the active site of the target protein predicted from its sequence using conservation analysis. Molecular dynamic simulations were performed to evaluate the stability of the modeled protein structure. In order to evaluate the predicted active site interactions, methionine (the natural substrate of MetRS) and several inhibitors of bacterial MetRS were docked into the constructed model using MOE. After validation of the model, pharmacophore-based virtual screening for a systemically prepared dataset of compounds was performed to prove the feasibility of the proposed model, identifying possible parent compounds for further development of MetRS inhibitors against P. mirabilis.
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Affiliation(s)
- Samar S. Elbaramawi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (S.S.E.); (A.G.E.); (N.A.N.)
| | - Ahmed G. Eissa
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (S.S.E.); (A.G.E.); (N.A.N.)
| | - Nada A. Noureldin
- Department of Medicinal Chemistry, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt; (S.S.E.); (A.G.E.); (N.A.N.)
| | - Claire Simons
- School of Pharmacy & Pharmaceutical Sciences, Cardiff University, King Edward VII Avenue, Cardiff CF10 3NB, UK
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Nasim F, Qureshi IA. Aminoacyl tRNA Synthetases: Implications of Structural Biology in Drug Development against Trypanosomatid Parasites. ACS OMEGA 2023; 8:14884-14899. [PMID: 37151504 PMCID: PMC10157851 DOI: 10.1021/acsomega.3c00826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
The ensemble of aminoacyl tRNA synthetases is regarded as a key component of the protein translation machinery. With the progressive increase in structure-based studies on tRNA synthetase-ligand complexes, the detailed picture of these enzymes is becoming clear. Having known their critical role in deciphering the genetic code in a living system, they have always been chosen as one of the important targets for development of antimicrobial drugs. Later on, the role of aminoacyl tRNA synthetases (aaRSs) on the survivability of trypanosomatids has also been validated. It became evident through several gene knockout studies that targeting even one of these enzymes affected parasitic growth drastically. Such successful studies have inspired researchers to search for inhibitors that could specifically target trypanosomal aaRSs, and their never-ending efforts have provided fruitful results. Taking all such studies into consideration, these macromolecules of prime importance deserve further investigation for the development of drugs that cure spectrum of infections caused by trypanosomatids. In this review, we have compiled advancements of over a decade that have taken place in the pursuit of devising drugs by using trypanosomatid aaRSs as a major target of interest. Several of these inhibitors work on an exemplary low concentration range without posing any threat to the mammalian cells which is a very critical aspect of the drug discovery process. Advancements have been made in terms of using structural biology as an important tool to analyze the architecture of the trypanosomatids aaRSs and concoction of inhibitors with augmented specificities toward their targets. Some of the inhibitors that have been tested on other parasites successfully but their efficacy has so far not been validated against these trypanosomatids have also been appended.
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Sharma VK, Chhibber-Goel J, Yogavel M, Sharma A. Structural characterization of glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum. Mol Biochem Parasitol 2023; 253:111530. [PMID: 36370911 DOI: 10.1016/j.molbiopara.2022.111530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/05/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes in protein translation machinery that provide the charged tRNAs needed for protein synthesis. Over the past decades, aaRSs have been studied as anti-parasitic, anti-bacterial, and anti-fungal drug targets. This study focused on the cytoplasmic glutamyl-tRNA synthetase (GluRS) from Plasmodium falciparum, which belongs to class Ib in aaRSs. GluRS unlike most other aaRSs requires tRNA to activate its cognate amino acid substrate L-Glutamate (L-Glu), and fails to form an intermediate adenylate complex in the absence of tRNA. The crystal structures of the Apo, ATP, and ADP-bound forms of Plasmodium falciparum glutamyl-tRNA synthetase (PfGluRS) were solved at 2.1 Å, 2.2 Å, and 2.8 Å respectively. The structural comparison of the Apo- and ATP-bound holo-forms of PfGluRS showed considerable conformational changes in the loop regions around the ATP-binding pocket of the enzyme. Biophysical characterization of the PfGluRS showed binding of the enzyme substrates L-Gluand ATP.. The sequence and structural conservation were evident across GluRS compared to other species. The structural dissection of the PfGluRS gives insight into the critical residues involved in the binding of ATP substrate, which can be harvested to develop new antimalarial drugs.
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Affiliation(s)
- Vivek Kumar Sharma
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Jyoti Chhibber-Goel
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Manickam Yogavel
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Amit Sharma
- Molecular Medicine - Structural Parasitology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India.
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Yogavel M, Bougdour A, Mishra S, Malhotra N, Chhibber-Goel J, Bellini V, Harlos K, Laleu B, Hakimi MA, Sharma A. Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis. PLoS Pathog 2023; 19:e1011124. [PMID: 36854028 PMCID: PMC9974123 DOI: 10.1371/journal.ppat.1011124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/16/2023] [Indexed: 03/02/2023] Open
Abstract
The prolyl-tRNA synthetase (PRS) is a validated drug target for febrifugine and its synthetic analog halofuginone (HFG) against multiple apicomplexan parasites including Plasmodium falciparum and Toxoplasma gondii. Here, a novel ATP-mimetic centered on 1-(pyridin-4-yl) pyrrolidin-2-one (PPL) scaffold has been validated to bind to Toxoplasma gondii PRS and kill toxoplasma parasites. PPL series exhibited potent inhibition at the cellular (T. gondii parasites) and enzymatic (TgPRS) levels compared to the human counterparts. Cell-based chemical mutagenesis was employed to determine the mechanism of action via a forward genetic screen. Tg-resistant parasites were analyzed with wild-type strain by RNA-seq to identify mutations in the coding sequence conferring drug resistance by computational analysis of variants. DNA sequencing established two mutations, T477A and T592S, proximal to terminals of the PPL scaffold and not directly in the ATP, tRNA, or L-pro sites, as supported by the structural data from high-resolution crystal structures of drug-bound enzyme complexes. These data provide an avenue for structure-based activity enhancement of this chemical series as anti-infectives.
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Affiliation(s)
- Manickam Yogavel
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Alexandre Bougdour
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Siddhartha Mishra
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi, India
| | - Nipun Malhotra
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Jyoti Chhibber-Goel
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
| | - Valeria Bellini
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Benoît Laleu
- Medicines for Malaria Venture (MMV), International Center Cointrin (ICC), Geneva, Switzerland
| | - Mohamed-Ali Hakimi
- Institute for Advanced Biosciences (IAB), Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Amit Sharma
- Molecular Medicine–Structural Parasitology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- ICMR-National Institute of Malaria Research, Dwarka, New Delhi, India
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Gill J, Sharma A. Exploration of aminoacyl-tRNA synthetases from eukaryotic parasites for drug development. J Biol Chem 2022; 299:102860. [PMID: 36596362 PMCID: PMC9978631 DOI: 10.1016/j.jbc.2022.102860] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 01/01/2023] Open
Abstract
Parasitic diseases result in considerable human morbidity and mortality. The continuous emergence and spread of new drug-resistant parasite strains is an obstacle to controlling and eliminating many parasitic diseases. Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous enzymes essential for protein synthesis. The design and development of diverse small molecule, drug-like inhibitors against parasite-encoded and expressed aaRSs have validated this enzyme family as druggable. In this work, we have compiled the progress to date towards establishing the druggability of aaRSs in terms of their biochemical characterization, validation as targets, inhibitor development, and structural interpretation from parasites responsible for malaria (Plasmodium), lymphatic filariasis (Brugia,Wuchereria bancrofti), giardiasis (Giardia), toxoplasmosis (Toxoplasma gondii), leishmaniasis (Leishmania), cryptosporidiosis (Cryptosporidium), and trypanosomiasis (Trypanosoma). This work thus provides a robust framework for the systematic dissection of aaRSs from these pathogens and will facilitate the cross-usage of potential inhibitors to jump-start anti-parasite drug development.
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Affiliation(s)
- Jasmita Gill
- ICMR-National Institute of Malaria Research, New Delhi, India
| | - Amit Sharma
- ICMR-National Institute of Malaria Research, New Delhi, India; Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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8
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Teles HR, Valli M, Ferreira LLG, Andricopulo AD. Molecular Modeling, Virtual Screening, and Molecular Dynamics for Leishmania infantum Methionyl-tRNA Synthetase. J Phys Chem B 2022; 126:10834-10843. [PMID: 36534784 DOI: 10.1021/acs.jpcb.2c05427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Visceral leishmaniasis is a neglected tropical disease (NTD) caused by Leishmania infantum and L. donovani that is lethal in cases of nontreatment. The treatments are limited by serious drawbacks involving safety, resistance, stability, and high costs. In this work, we aimed to identify inhibitors of Leishmania infantum methionyl-tRNA synthetase (LiMetRS), a validated molecular target for leishmaniasis drug discovery, using a combination of strategies. A virtual database of compounds was organized by filtering compounds from the ZINC15 database. Homology modeling was used to obtain the structure of LiMetRS based on the crystal coordinates of the enzyme from Trypanosoma brucei (TbMetRS). A virtual screening using molecular docking identified 10 candidate compounds from among more than 5 million that were included in the initial database. The selected hits were further evaluated using a script created in this work to select only the ligands that interacted with specific amino acids in the catalytic site of the enzyme. Furthermore, suitable pharmacokinetic profiles were predicted for the selected compounds, especially a good balance between aqueous solubility and lipophilic character, no ability to cross the blood-brain barrier, good oral absorption, and no liability toward P-gp efflux for most compounds. Six compounds were then subjected to all-atom molecular dynamics. Two compounds showed good stability when bound to the leishmanial enzyme, which provided a deeper understanding of the structural differences between TbMetRS and LiMetRS that can guide further drug discovery efforts for visceral leishmaniasis.
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Affiliation(s)
- Henrique R Teles
- Laboratory of Medicinal and Computational Chemistry (LQMC), Center for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), Institute of Physics of São Carlos, University of São Paulo (USP), Av. João Dagnone, no. 1100, São Carlos, SP 13563-120, Brazil
| | - Marilia Valli
- Laboratory of Medicinal and Computational Chemistry (LQMC), Center for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), Institute of Physics of São Carlos, University of São Paulo (USP), Av. João Dagnone, no. 1100, São Carlos, SP 13563-120, Brazil
| | - Leonardo L G Ferreira
- Laboratory of Medicinal and Computational Chemistry (LQMC), Center for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), Institute of Physics of São Carlos, University of São Paulo (USP), Av. João Dagnone, no. 1100, São Carlos, SP 13563-120, Brazil
| | - Adriano D Andricopulo
- Laboratory of Medicinal and Computational Chemistry (LQMC), Center for Research and Innovation in Biodiversity and Drug Discovery (CIBFar), Institute of Physics of São Carlos, University of São Paulo (USP), Av. João Dagnone, no. 1100, São Carlos, SP 13563-120, Brazil
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Volynets GP, Gudzera OI, Usenko MO, Gorbatiuk OB, Yarmoluk SM, Tukalo MA. Probing interactions of aminoacyl-adenylate with Mycobacterium tuberculosis methionyl-tRNA synthetase through in silico site-directed mutagenesis and free energy calculation. J Biomol Struct Dyn 2022:1-9. [PMID: 35930324 DOI: 10.1080/07391102.2022.2107574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
Methionyl-tRNA synthetase (MetRS) is an attractive molecular target for antibiotic discovery. Recently, we have developed several classes of small-molecular inhibitors of Mycobacterium tuberculosis MetRS possessing antibacterial activity. In this article, we performed in silico site-directed mutagenesis of aminoacyl-adenylate binding site of M. tuberculosis MetRS in order to identify crucial amino acid residues for substrate interaction. The umbrella sampling algorithm was used to calculate the binding free energy (ΔG) of these mutated forms with methionyl-adenylate analogue. According to the obtained results, the replacement of Glu24 and Leu293 by alanine leads to the most significant decrease in the binding free energy (ΔG) for adenylate analogue with methionyl-tRNA synthetase indicating increasing of the affinity, which in turn causes the loss of compounds inhibitory activity. Therefore, these amino acid residues can be proposed for further experimental site-directed mutagenesis to confirm binding mode of inhibitors and should be taken into account during chemical optimization to overcome resistance due to mutations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Galyna P Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Olga I Gudzera
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Mariia O Usenko
- Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Oksana B Gorbatiuk
- Department of Cell Regulatory Mechanisms, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics, the NAS of Ukraine, Kyiv, Ukraine
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Spontaneous Selection of Cryptosporidium Drug Resistance in a Calf Model of Infection. Antimicrob Agents Chemother 2021; 65:AAC.00023-21. [PMID: 33753338 DOI: 10.1128/aac.00023-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/17/2021] [Indexed: 01/20/2023] Open
Abstract
The intestinal protozoan Cryptosporidium is a leading cause of diarrheal disease and mortality in young children. There is currently no fully effective treatment for cryptosporidiosis, which has stimulated interest in anticryptosporidial development over the last ∼10 years, with numerous lead compounds identified, including several tRNA synthetase inhibitors. Here, we report the results of a dairy calf efficacy trial of the methionyl-tRNA (Cryptosporidium parvum MetRS [CpMetRS]) synthetase inhibitor 2093 and the spontaneous emergence of drug resistance. Dairy calves experimentally infected with Cryptosporidium parvum initially improved with 2093 treatment, but parasite shedding resumed in two of three calves on treatment day 5. Parasites shed by each recrudescent calf had different amino acid-altering mutations in the gene encoding CpMetRS (CpMetRS), yielding either an aspartate 243-to-glutamate (D243E) or a threonine 246-to-isoleucine (T246I) mutation. Transgenic parasites engineered to have either the D243E or T246I CpMetRS mutation using CRISPR/Cas9 grew normally but were highly 2093 resistant; the D243E and T246I mutant-expressing parasites, respectively, had 2093 half-maximal effective concentrations (EC50s) that were 613- and 128-fold that of transgenic parasites with wild-type CpMetRS. In studies using recombinant enzymes, the D243E and T246I mutations shifted the 2093 IC50 >170-fold. Structural modeling of CpMetRS based on an inhibitor-bound Trypanosoma brucei MetRS crystal structure suggested that the resistance mutations reposition nearby hydrophobic residues, interfering with compound binding while minimally impacting substrate binding. This is the first report of naturally emerging Cryptosporidium drug resistance, highlighting the need to address the potential for anticryptosporidial resistance and establish strategies to limit its occurrence.
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Mercaldi GF, Andrade MDO, Zanella JDL, Cordeiro AT, Benedetti CE. Molecular basis for diaryldiamine selectivity and competition with tRNA in a type 2 methionyl-tRNA synthetase from a Gram-negative bacterium. J Biol Chem 2021; 296:100658. [PMID: 33857480 PMCID: PMC8165550 DOI: 10.1016/j.jbc.2021.100658] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/20/2022] Open
Abstract
Gram-negative bacteria are responsible for a variety of human, animal, and plant diseases. The spread of multidrug-resistant Gram-negative bacteria poses a challenge to disease control and highlights the need for novel antimicrobials. Owing to their critical role in protein synthesis, aminoacyl-tRNA synthetases, including the methionyl-tRNA synthetases MetRS1 and MetRS2, are attractive drug targets. MetRS1 has long been exploited as a drug target in Gram-positive bacteria and protozoan parasites. However, MetRS1 inhibitors have limited action upon Gram-negative pathogens or on Gram-positive bacteria that produce MetRS2 enzymes. The underlying mechanism by which MetRS2 enzymes are insensitive to MetRS1 inhibitors is presently unknown. Herein, we report the first structures of MetRS2 from a multidrug-resistant Gram-negative bacterium in its ligand-free state and bound to its substrate or MetRS1 inhibitors. The structures reveal the binding mode of two diaryldiamine MetRS1 inhibitors that occupy the amino acid-binding site and a surrounding auxiliary pocket implicated in tRNA acceptor arm binding. The structural features associated with amino acid polymorphisms found in the methionine and auxiliary pockets reveal the molecular basis for diaryldiamine binding and selectivity between MetRS1 and MetRS2 enzymes. Moreover, we show that mutations in key polymorphic residues in the methionine and auxiliary pockets not only altered inhibitor binding affinity but also significantly reduced enzyme function. Our findings thus reinforce the tRNA acceptor arm binding site as a druggable pocket in class I aminoacyl-tRNA synthetases and provide a structural basis for optimization of MetRS2 inhibitors for the development of new antimicrobials against Gram-negative pathogens.
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Affiliation(s)
- Gustavo Fernando Mercaldi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.
| | - Maxuel de Oliveira Andrade
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Jackeline de Lima Zanella
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Artur Torres Cordeiro
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Celso Eduardo Benedetti
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.
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12
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Zhang Z, Barros-Álvarez X, Gillespie JR, Ranade RM, Huang W, Shibata S, Molasky NMR, Faghih O, Mushtaq A, Choy RKM, de Hostos E, Hol WGJ, Verlinde CLMJ, Buckner FS, Fan E. Structure-guided discovery of selective methionyl-tRNA synthetase inhibitors with potent activity against Trypanosoma brucei. RSC Med Chem 2020; 11:885-895. [PMID: 33479683 PMCID: PMC7649832 DOI: 10.1039/d0md00057d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 04/21/2020] [Indexed: 12/25/2022] Open
Abstract
Based on crystal structures of Trypanosoma brucei methionyl-tRNA synthetase (TbMetRS) bound to inhibitors, we designed, synthesized, and evaluated two series of novel TbMetRS inhibitors targeting this parasite enzyme. One series has a 1,3-dihydro-imidazol-2-one containing linker, the other has a rigid fused aromatic ring in the linker. For both series of compounds, potent inhibition of parasite growth was achieved with EC50 < 10 nM and most compounds exhibited low general toxicity to mammalian cells with CC50s > 20 000 nM. Selectivity over human mitochondrial methionyl tRNA synthetase was also evaluated, using a cell-based mitochondrial protein synthesis assay, and selectivity in a range of 20-200-fold was achieved. The inhibitors exhibited poor permeability across the blood brain barrier, necessitating future efforts to optimize the compounds for use in late stage human African trypanosomiasis.
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Affiliation(s)
- Zhongsheng Zhang
- Department of Biochemistry , University of Washington , Seattle , WA 98195 , USA .
| | | | - J Robert Gillespie
- Department of Medicine , Division of Allergy & Infectious Disease , Center for Emerging & Re-emerging Infectious Disease (CERID) , University of Washington , Seattle , WA 98109 , USA .
| | - Ranae M Ranade
- Department of Medicine , Division of Allergy & Infectious Disease , Center for Emerging & Re-emerging Infectious Disease (CERID) , University of Washington , Seattle , WA 98109 , USA .
| | - Wenlin Huang
- Department of Biochemistry , University of Washington , Seattle , WA 98195 , USA .
| | - Sayaka Shibata
- Department of Biochemistry , University of Washington , Seattle , WA 98195 , USA .
| | - Nora M R Molasky
- Department of Medicine , Division of Allergy & Infectious Disease , Center for Emerging & Re-emerging Infectious Disease (CERID) , University of Washington , Seattle , WA 98109 , USA .
| | - Omeed Faghih
- Department of Medicine , Division of Allergy & Infectious Disease , Center for Emerging & Re-emerging Infectious Disease (CERID) , University of Washington , Seattle , WA 98109 , USA .
| | - Aisha Mushtaq
- Department of Medicine , Division of Allergy & Infectious Disease , Center for Emerging & Re-emerging Infectious Disease (CERID) , University of Washington , Seattle , WA 98109 , USA .
| | | | | | - Wim G J Hol
- Department of Biochemistry , University of Washington , Seattle , WA 98195 , USA .
| | | | - Frederick S Buckner
- Department of Medicine , Division of Allergy & Infectious Disease , Center for Emerging & Re-emerging Infectious Disease (CERID) , University of Washington , Seattle , WA 98109 , USA .
| | - Erkang Fan
- Department of Biochemistry , University of Washington , Seattle , WA 98195 , USA .
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13
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Torrie LS, Robinson DA, Thomas MG, Hobrath JV, Shepherd SM, Post JM, Ko EJ, Ferreira RA, Mackenzie CJ, Wrobel K, Edwards DP, Gilbert IH, Gray DW, Fairlamb AH, De Rycker M. Discovery of an Allosteric Binding Site in Kinetoplastid Methionyl-tRNA Synthetase. ACS Infect Dis 2020; 6:1044-1057. [PMID: 32275825 PMCID: PMC7294809 DOI: 10.1021/acsinfecdis.9b00453] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Methionyl-tRNA
synthetase (MetRS) is a chemically validated drug target in kinetoplastid
parasites Trypanosoma brucei and Leishmania
donovani. To date, all kinetoplastid MetRS inhibitors described
bind in a similar way to an expanded methionine pocket and an adjacent,
auxiliary pocket. In the current study, we have identified a structurally
novel class of inhibitors containing a 4,6-diamino-substituted pyrazolopyrimidine
core (the MetRS02 series). Crystallographic studies revealed that
MetRS02 compounds bind to an allosteric pocket in L. major MetRS not previously described, and enzymatic studies demonstrated
a noncompetitive mode of inhibition. Homology modeling of the Trypanosoma cruzi MetRS enzyme revealed key differences
in the allosteric pocket between the T. cruzi and Leishmania enzymes. These provide a likely explanation for
the lower MetRS02 potencies that we observed for the T. cruzi enzyme compared to the Leishmania enzyme. The identification
of a new series of MetRS inhibitors and the discovery of a new binding
site in kinetoplastid MetRS enzymes provide a novel strategy in the
search for new therapeutics for kinetoplastid diseases.
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Affiliation(s)
- Leah S. Torrie
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - David A. Robinson
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Michael G. Thomas
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Judith V. Hobrath
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Sharon M. Shepherd
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - John M. Post
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Eun-Jung Ko
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Rafael Alves Ferreira
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Claire J. Mackenzie
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Karolina Wrobel
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Darren P. Edwards
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Ian H. Gilbert
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - David W. Gray
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Alan H. Fairlamb
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Manu De Rycker
- Drug Discovery Unit, Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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14
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Altamura F, Rajesh R, Catta-Preta CMC, Moretti NS, Cestari I. The current drug discovery landscape for trypanosomiasis and leishmaniasis: Challenges and strategies to identify drug targets. Drug Dev Res 2020; 83:225-252. [PMID: 32249457 DOI: 10.1002/ddr.21664] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 02/05/2020] [Accepted: 03/13/2020] [Indexed: 12/11/2022]
Abstract
Human trypanosomiasis and leishmaniasis are vector-borne neglected tropical diseases caused by infection with the protozoan parasites Trypanosoma spp. and Leishmania spp., respectively. Once restricted to endemic areas, these diseases are now distributed worldwide due to human migration, climate change, and anthropogenic disturbance, causing significant health and economic burden globally. The current chemotherapy used to treat these diseases has limited efficacy, and drug resistance is spreading. Hence, new drugs are urgently needed. Phenotypic compound screenings have prevailed as the leading method to discover new drug candidates against these diseases. However, the publication of the complete genome sequences of multiple strains, advances in the application of CRISPR/Cas9 technology, and in vivo bioluminescence-based imaging have set the stage for advancing target-based drug discovery. This review analyses the limitations of the narrow pool of available drugs presently used for treating these diseases. It describes the current drug-based clinical trials highlighting the most promising leads. Furthermore, the review presents a focused discussion on the most important biological and pharmacological challenges that target-based drug discovery programs must overcome to advance drug candidates. Finally, it examines the advantages and limitations of modern research tools designed to identify and validate essential genes as drug targets, including genomic editing applications and in vivo imaging.
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Affiliation(s)
- Fernando Altamura
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | - Rishi Rajesh
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
| | | | - Nilmar S Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Igor Cestari
- Institute of Parasitology, McGill University, Ste Anne de Bellevue, Quebec, Canada
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15
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Abstract
Human African trypanosomiasis (HAT) is a deadly neglected tropical disease caused by the protozoan parasite Trypanosoma brucei. During the course of screening a collection of diverse nitrogenous heterocycles, we discovered two novel compounds that contain the tetracyclic core of the Yohimbine and Corynanthe alkaloids, were potent inhibitors of T. brucei proliferation and T. brucei methionyl-tRNA synthetase (TbMetRS) activity. Inspired by these key findings, we prepared several novel series of hydroxyalkyl δ-lactam, δ-lactam, and piperidine analogs and tested their anti-trypanosomal activity. A number of inhibitors are more potent against T. brucei than these initial hits with one hydroxyalkyl δ-lactam derivative being 25-fold more effective in our assay. Surprisingly, most of these active compounds failed to inhibit TbMetRS. This work underscores the importance of verifying, irrespective of close structural similarities, that new compounds designed from a lead with a known biological target engage the putative binding site.
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16
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Buckner FS, Ranade RM, Gillespie JR, Shibata S, Hulverson MA, Zhang Z, Huang W, Choi R, Verlinde CLMJ, Hol WGJ, Ochida A, Akao Y, Choy RKM, Van Voorhis WC, Arnold SLM, Jumani RS, Huston CD, Fan E. Optimization of Methionyl tRNA-Synthetase Inhibitors for Treatment of Cryptosporidium Infection. Antimicrob Agents Chemother 2019; 63:e02061-18. [PMID: 30745384 PMCID: PMC6437504 DOI: 10.1128/aac.02061-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/01/2019] [Indexed: 02/07/2023] Open
Abstract
Cryptosporidiosis is one of the leading causes of moderate to severe diarrhea in children in low-resource settings. The therapeutic options for cryptosporidiosis are limited to one drug, nitazoxanide, which unfortunately has poor activity in the most needy populations of malnourished children and HIV-infected persons. We describe here the discovery and early optimization of a class of imidazopyridine-containing compounds with potential for treating Cryptosporidium infections. The compounds target the Cryptosporidium methionyl-tRNA synthetase (MetRS), an enzyme that is essential for protein synthesis. The most potent compounds inhibited the enzyme with Ki values in the low picomolar range. Cryptosporidium cells in culture were potently inhibited with 50% effective concentrations as low as 7 nM and >1,000-fold selectivity over mammalian cells. A parasite persistence assay indicates that the compounds act by a parasiticidal mechanism. Several compounds were demonstrated to control infection in two murine models of cryptosporidiosis without evidence of toxicity. Pharmacological and physicochemical characteristics of compounds were investigated to determine properties that were associated with higher efficacy. The results indicate that MetRS inhibitors are excellent candidates for development for anticryptosporidiosis therapy.
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Affiliation(s)
| | - Ranae M Ranade
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - J Robert Gillespie
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Sayaka Shibata
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Wenlin Huang
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Ryan Choi
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Wim G J Hol
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | | | - Robert K M Choy
- Drug Development Program, PATH, San Francisco, California, USA
| | | | - Sam L M Arnold
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Rajiv S Jumani
- Department of Medicine, University of Vermont, Burlington, Vermont, USA
| | | | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
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17
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Yi H, Lee H, Cho KH, Kim HS. Mutations in MetG (methionyl-tRNA synthetase) and TrmD [tRNA (guanine-N1)-methyltransferase] conferring meropenem tolerance in Burkholderia thailandensis. J Antimicrob Chemother 2019; 73:332-338. [PMID: 29136176 DOI: 10.1093/jac/dkx378] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/19/2017] [Indexed: 01/08/2023] Open
Abstract
Objectives Although meropenem is widely used to treat Burkholderia infections, the response of Burkholderia pathogens to this antibiotic is largely unexplored. Methods Burkholderia thailandensis, a model for Burkholderia spp., particularly Burkholderia mallei and Burkholderia pseudomallei, was challenged with a lethal level of meropenem and survivors were isolated. The genomes of two of the isolates were analysed to identify mutated genes and these genes were then specifically examined in more isolates to profile mutation diversity. Mutants were characterized to investigate the biological basis underlying survival against meropenem. Results One of two genes associated with tRNA metabolism [metG or trmD, encoding methionyl-tRNA synthetase or tRNA (guanine-N1)-methyltransferase, respectively] was found to be mutated in the two survivors. A single nucleotide substitution and a frameshift mutation were found in metG and trmD, respectively. Five different substitution mutations affecting methionine- or tRNA-binding sites were found in metG during further screening. The mutants exhibited slowed growth and increased tolerance not only to meropenem but also various other antibiotics. This tolerance required intact RelA, a key stringent response. Conclusions Specific mutations affecting the tRNA pool, particularly those in metG, play a pivotal role in the B. thailandensis response to meropenem challenge. This mechanism of antibiotic tolerance is important because it can reduce the effectiveness of meropenem and thereby facilitate chronic infection by Burkholderia pathogens. In addition, specific mutations found in MetG will prove useful in the effort to develop new drugs to completely inhibit this essential enzyme, while preventing stringent-response-mediated antibiotic tolerance in pathogens.
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Affiliation(s)
- Hyojeong Yi
- Department of Biomedical Sciences, College of Medicine, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-705, Korea
| | - Hyeri Lee
- Department of Biomedical Sciences, College of Medicine, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-705, Korea
| | - Kwang-Hwi Cho
- School of Systems Biomedical Science and Research Center for Integrative Basic Science, Soongsil University, Seoul 156-743, Korea
| | - Heenam Stanley Kim
- Department of Biomedical Sciences, College of Medicine, Korea University, Anam-Dong, Seongbuk-Gu, Seoul 136-705, Korea
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18
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Barros-Álvarez X, Turley S, Ranade RM, Gillespie JR, Duster NA, Verlinde CLMJ, Fan E, Buckner FS, Hol WGJ. The crystal structure of the drug target Mycobacterium tuberculosis methionyl-tRNA synthetase in complex with a catalytic intermediate. Acta Crystallogr F Struct Biol Commun 2018; 74:245-254. [PMID: 29633973 PMCID: PMC5893993 DOI: 10.1107/s2053230x18003151] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 02/23/2018] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis is a pathogenic bacterial infectious agent that is responsible for approximately 1.5 million human deaths annually. Current treatment requires the long-term administration of multiple medicines with substantial side effects. Lack of compliance, together with other factors, has resulted in a worrisome increase in resistance. New treatment options are therefore urgently needed. Here, the crystal structure of methionyl-tRNA synthetase (MetRS), an enzyme critical for protein biosynthesis and therefore a drug target, in complex with its catalytic intermediate methionyl adenylate is reported. Phenylalanine 292 of the M. tuberculosis enzyme is in an `out' conformation and barely contacts the adenine ring, in contrast to other MetRS structures where ring stacking occurs between the adenine and a protein side-chain ring in the `in' conformation. A comparison with human cytosolic MetRS reveals substantial differences in the active site as well as regarding the position of the connective peptide subdomain 1 (CP1) near the active site, which bodes well for arriving at selective inhibitors. Comparison with the human mitochondrial enzyme at the amino-acid sequence level suggests that arriving at inhibitors with higher affinity for the mycobacterial enzyme than for the mitochondrial enzyme might be achievable.
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Affiliation(s)
- Ximena Barros-Álvarez
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de los Andes, Mérida, Venezuela
| | - Stewart Turley
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Ranae M. Ranade
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, Washington, USA
| | - J. Robert Gillespie
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Nicole A. Duster
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Frederick S. Buckner
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Wim G. J. Hol
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
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19
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Abbott JA, Meyer-Schuman R, Lupo V, Feely S, Mademan I, Oprescu SN, Griffin LB, Alberti MA, Casasnovas C, Aharoni S, Basel-Vanagaite L, Züchner S, De Jonghe P, Baets J, Shy ME, Espinós C, Demeler B, Antonellis A, Francklyn C. Substrate interaction defects in histidyl-tRNA synthetase linked to dominant axonal peripheral neuropathy. Hum Mutat 2018; 39:415-432. [PMID: 29235198 PMCID: PMC5983030 DOI: 10.1002/humu.23380] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/01/2017] [Accepted: 12/07/2017] [Indexed: 11/09/2022]
Abstract
Histidyl-tRNA synthetase (HARS) ligates histidine to cognate tRNA molecules, which is required for protein translation. Mutations in HARS cause the dominant axonal peripheral neuropathy Charcot-Marie-Tooth disease type 2W (CMT2W); however, the precise molecular mechanism remains undefined. Here, we investigated three HARS missense mutations associated with CMT2W (p.Tyr330Cys, p.Ser356Asn, and p.Val155Gly). The three mutations localize to the HARS catalytic domain and failed to complement deletion of the yeast ortholog (HTS1). Enzyme kinetics, differential scanning fluorimetry (DSF), and analytical ultracentrifugation (AUC) were employed to assess the effect of these substitutions on primary aminoacylation function and overall dimeric structure. Notably, the p.Tyr330Cys, p.Ser356Asn, and p.Val155Gly HARS substitutions all led to reduced aminoacylation, providing a direct connection between CMT2W-linked HARS mutations and loss of canonical ARS function. While DSF assays revealed that only one of the variants (p.Val155Gly) was less thermally stable relative to wild-type, all three HARS mutants formed stable dimers, as measured by AUC. Our work represents the first biochemical analysis of CMT-associated HARS mutations and underscores how loss of the primary aminoacylation function can contribute to disease pathology.
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Affiliation(s)
- Jamie A. Abbott
- Department of Biochemistry, University of Vermont, College of Medicine, Burlington, Vermont
| | - Rebecca Meyer-Schuman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Vincenzo Lupo
- Unit of Genetics and Genomics of Neuromuscular Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Shawna Feely
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Inès Mademan
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
| | - Stephanie N. Oprescu
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Laurie B. Griffin
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, Michigan
| | - M. Antonia Alberti
- Department of Neurology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Carlos Casasnovas
- Department of Neurology, Hospital Universitario de Bellvitge, Barcelona, Spain
| | - Sharon Aharoni
- Institute of Child Neurology, Schneider Children’s Medical Center of Israel, Petah Tikva, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lina Basel-Vanagaite
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Raphael Recanati Genetic Institute, Rabin Medical Center, Beilinson Campus, Petah Tikva, Israel
- Pediatric Genetics Unit, Schneider Children’s Medical Center, Petah Tikva, Israel
- Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Stephan Züchner
- Dr John T McDonald Foundation Department of Human Genetics & John P Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Peter De Jonghe
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerpen, Belgium
| | - Jonathan Baets
- Neurogenetics Group, Center for Molecular Neurology, VIB, Antwerp, Belgium
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium
- Department of Neurology, Antwerp University Hospital, Antwerpen, Belgium
| | - Michael E. Shy
- Department of Neurology, University of Iowa Hospitals and Clinics, Iowa City, Iowa
| | - Carmen Espinós
- Unit of Genetics and Genomics of Neuromuscular Disorders, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Borries Demeler
- Department of Biochemistry, The University of Texas Health Sciences at San Antonio, San Antonio, Texas
| | - Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan
| | - Christopher Francklyn
- Department of Biochemistry, University of Vermont, College of Medicine, Burlington, Vermont
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20
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Borsari C, Quotadamo A, Ferrari S, Venturelli A, Cordeiro-da-Silva A, Santarem N, Costi MP. Scaffolds and Biological Targets Avenue to Fight Against Drug Resistance in Leishmaniasis. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2018. [DOI: 10.1016/bs.armc.2018.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Development of Methionyl-tRNA Synthetase Inhibitors as Antibiotics for Gram-Positive Bacterial Infections. Antimicrob Agents Chemother 2017; 61:AAC.00999-17. [PMID: 28848016 DOI: 10.1128/aac.00999-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/22/2017] [Indexed: 01/17/2023] Open
Abstract
Antibiotic-resistant bacteria are widespread and pose a growing threat to human health. New antibiotics acting by novel mechanisms of action are needed to address this challenge. The bacterial methionyl-tRNA synthetase (MetRS) enzyme is essential for protein synthesis, and the type found in Gram-positive bacteria is substantially different from its counterpart found in the mammalian cytoplasm. Both previously published and new selective inhibitors were shown to be highly active against Gram-positive bacteria with MICs of ≤1.3 μg/ml against Staphylococcus, Enterococcus, and Streptococcus strains. Incorporation of radioactive precursors demonstrated that the mechanism of activity was due to the inhibition of protein synthesis. Little activity against Gram-negative bacteria was observed, consistent with the fact that Gram-negative bacterial species contain a different type of MetRS enzyme. The ratio of the MIC to the minimum bactericidal concentration (MBC) was consistent with a bacteriostatic mechanism. The level of protein binding of the compounds was high (>95%), and this translated to a substantial increase in MICs when the compounds were tested in the presence of serum. Despite this, the compounds were very active when they were tested in a Staphylococcus aureus murine thigh infection model. Compounds 1717 and 2144, given by oral gavage, resulted in 3- to 4-log decreases in the bacterial load compared to that in vehicle-treated mice, which was comparable to the results observed with the comparator drugs, vancomycin and linezolid. In summary, the research describes MetRS inhibitors with oral bioavailability that represent a class of compounds acting by a novel mechanism with excellent potential for clinical development.
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22
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Torrie LS, Brand S, Robinson DA, Ko EJ, Stojanovski L, Simeons FRC, Wyllie S, Thomas J, Ellis L, Osuna-Cabello M, Epemolu O, Nühs A, Riley J, MacLean L, Manthri S, Read KD, Gilbert IH, Fairlamb AH, De Rycker M. Chemical Validation of Methionyl-tRNA Synthetase as a Druggable Target in Leishmania donovani. ACS Infect Dis 2017; 3:718-727. [PMID: 28967262 PMCID: PMC5663395 DOI: 10.1021/acsinfecdis.7b00047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Methionyl-tRNA synthetase
(MetRS) has been chemically validated as a drug target in the kinetoplastid
parasite Trypanosoma brucei. In the present study,
we investigate the validity of this target in the related trypanosomatid Leishmania donovani. Following development of a robust high-throughput
compatible biochemical assay, a compound screen identified DDD806905
as a highly potent inhibitor of LdMetRS (Ki of 18 nM). Crystallography revealed this compound
binds to the methionine pocket of MetRS with enzymatic studies confirming
DDD806905 displays competitive inhibition with respect to methionine
and mixed inhibition with respect to ATP binding. DDD806905 showed
activity, albeit with different levels of potency, in various Leishmania cell-based viability assays, with on-target activity
observed in both Leishmania promastigote cell assays
and a Leishmania tarentolae in vitro translation
assay. Unfortunately, this compound failed to show efficacy in an
animal model of leishmaniasis. We investigated the potential causes
for the discrepancies in activity observed in different Leishmania cell assays and the lack of efficacy in the animal model and found
that high protein binding as well as sequestration of this dibasic
compound into acidic compartments may play a role. Despite medicinal
chemistry efforts to address the dibasic nature of DDD806905 and analogues,
no progress could be achieved with the current chemical series. Although
DDD806905 is not a developable antileishmanial compound, MetRS remains
an attractive antileishmanial drug target.
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Affiliation(s)
- Leah S. Torrie
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Stephen Brand
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - David A. Robinson
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Eun Jung Ko
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Laste Stojanovski
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Frederick R. C. Simeons
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Susan Wyllie
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - John Thomas
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Lucy Ellis
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Maria Osuna-Cabello
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Ola Epemolu
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Andrea Nühs
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Jennifer Riley
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Lorna MacLean
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Sujatha Manthri
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Kevin D. Read
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Ian H. Gilbert
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Alan H. Fairlamb
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
| | - Manu De Rycker
- Drug Discovery Unit, Division of Biological
Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
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23
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Polyamine-based analogs and conjugates as antikinetoplastid agents. Eur J Med Chem 2017; 139:982-1015. [DOI: 10.1016/j.ejmech.2017.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/24/2017] [Accepted: 08/04/2017] [Indexed: 12/12/2022]
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24
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Berninger M, Schmidt I, Ponte-Sucre A, Holzgrabe U. Novel lead compounds in pre-clinical development against African sleeping sickness. MEDCHEMCOMM 2017; 8:1872-1890. [PMID: 30108710 PMCID: PMC6072528 DOI: 10.1039/c7md00280g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/29/2017] [Indexed: 01/21/2023]
Abstract
Human African trypanosomiasis (HAT), also known as African sleeping sickness, is caused by parasitic protozoa of the genus Trypanosoma. As the disease progresses, the parasites cross the blood brain barrier and are lethal for the patients if the disease is left untreated. Current therapies suffer from several drawbacks due to e.g. toxicity of the respective compounds or resistance to approved antitrypanosomal drugs. In this review, the different strategies of drug development against HAT are considered, namely the target-based approach, the phenotypic high throughput screening and the drug repurposing strategy. The most promising compounds emerging from these approaches entering an in vivo evaluation are mentioned herein. Of note, it may turn out to be difficult to confirm in vitro activity in an animal model of infection; however, possible reasons for the missing efficacy in unsuccessful in vivo studies are discussed.
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Affiliation(s)
- Michael Berninger
- Institute of Pharmacy and Food Chemistry , University of Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Ines Schmidt
- Institute of Pharmacy and Food Chemistry , University of Würzburg , Am Hubland , 97074 Würzburg , Germany .
| | - Alicia Ponte-Sucre
- Laboratory of Molecular Physiology , Institute of Experimental Medicine , Luis Razetti School of Medicine , Faculty of Medicine , Universidad Central de Venezuela Caracas , Venezuela . Tel: +0931 31 85461
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry , University of Würzburg , Am Hubland , 97074 Würzburg , Germany .
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25
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Barros-Álvarez X, Kerchner KM, Koh CY, Turley S, Pardon E, Steyaert J, Ranade RM, Gillespie JR, Zhang Z, Verlinde CLMJ, Fan E, Buckner FS, Hol WGJ. Leishmania donovani tyrosyl-tRNA synthetase structure in complex with a tyrosyl adenylate analog and comparisons with human and protozoan counterparts. Biochimie 2017; 138:124-136. [PMID: 28427904 PMCID: PMC5484532 DOI: 10.1016/j.biochi.2017.04.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 04/12/2017] [Indexed: 02/06/2023]
Abstract
The crystal structure of Leishmania donovani tyrosyl-tRNA synthetase (LdTyrRS) in complex with a nanobody and the tyrosyl adenylate analog TyrSA was determined at 2.75 Å resolution. Nanobodies are the variable domains of camelid heavy chain-only antibodies. The nanobody makes numerous crystal contacts and in addition reduces the flexibility of a loop of LdTyrRS. TyrSA is engaged in many interactions with active site residues occupying the tyrosine and adenine binding pockets. The LdTyrRS polypeptide chain consists of two pseudo-monomers, each consisting of two domains. Comparing the two independent chains in the asymmetric unit reveals that the two pseudo-monomers of LdTyrRS can bend with respect to each other essentially as rigid bodies. This flexibility might be useful in the positioning of tRNA for catalysis since both pseudo-monomers in the LdTyrRS chain are needed for charging tRNATyr. An "extra pocket" (EP) appears to be present near the adenine binding region of LdTyrRS. Since this pocket is absent in the two human homologous enzymes, the EP provides interesting opportunities for obtaining selective drugs for treating infections caused by L. donovani, a unicellular parasite causing visceral leishmaniasis, or kala azar, which claims 20,000 to 30,000 deaths per year. Sequence and structural comparisons indicate that the EP is a characteristic which also occurs in the active site of several other important pathogenic protozoa. Therefore, the structure of LdTyrRS could inspire the design of compounds useful for treating several different parasitic diseases.
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Affiliation(s)
- Ximena Barros-Álvarez
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de los Andes, Mérida, Venezuela
| | - Keshia M Kerchner
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Cho Yeow Koh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Stewart Turley
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussel, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Ranae M Ranade
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA, USA
| | - J Robert Gillespie
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA, USA
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Frederick S Buckner
- Division of Allergy and Infectious Diseases, School of Medicine, University of Washington, Seattle, WA, USA
| | - Wim G J Hol
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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26
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Devine WG, Diaz-Gonzalez R, Ceballos-Perez G, Rojas D, Satoh T, Tear W, Ranade RM, Barros-Álvarez X, Hol WGJ, Buckner FS, Navarro M, Pollastri MP. From Cells to Mice to Target: Characterization of NEU-1053 (SB-443342) and Its Analogues for Treatment of Human African Trypanosomiasis. ACS Infect Dis 2017; 3:225-236. [PMID: 28110521 DOI: 10.1021/acsinfecdis.6b00202] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Human African trypanosomiasis is a neglected tropical disease that is lethal if left untreated. Existing therapeutics have limited efficacy and severe associated toxicities. 2-(2-(((3-((1H-Benzo[d]imidazol-2-yl)amino)propyl)amino)methyl)-4,6-dichloro-1H-indol-1-yl)ethan-1-ol (NEU-1053) has recently been identified from a high-throughput screen of >42,000 compounds as a highly potent and fast-acting trypanocidal agent capable of curing a bloodstream infection of Trypanosoma brucei in mice. We have designed a library of analogues to probe the structure-activity relationship and improve the predicted central nervous system (CNS) exposure of NEU-1053. We report the activity of these inhibitors of T. brucei, the efficacy of NEU-1053 in a murine CNS model of infection, and identification of the target of NEU-1053 via X-ray crystallography.
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Affiliation(s)
- William G. Devine
- Department of Chemistry & Chemical Biology, Northeastern University 360 Huntington Avenue, Boston, Massachusetts, United States
| | - Rosario Diaz-Gonzalez
- Instituto de Parasitologia y Biomedicina “Lopez-Neyra”, Consejo Superior de Investigaciones Cientificas (CSIC), Granada 18100, Spain
| | - Gloria Ceballos-Perez
- Instituto de Parasitologia y Biomedicina “Lopez-Neyra”, Consejo Superior de Investigaciones Cientificas (CSIC), Granada 18100, Spain
| | - Domingo Rojas
- Instituto de Parasitologia y Biomedicina “Lopez-Neyra”, Consejo Superior de Investigaciones Cientificas (CSIC), Granada 18100, Spain
| | - Takashi Satoh
- Department of Chemistry & Chemical Biology, Northeastern University 360 Huntington Avenue, Boston, Massachusetts, United States
| | - Westley Tear
- Department of Chemistry & Chemical Biology, Northeastern University 360 Huntington Avenue, Boston, Massachusetts, United States
| | | | - Ximena Barros-Álvarez
- Laboratorio de Enzimología de Parásitos, Facultad de
Ciencias, Universidad de los Andes, Mérida, Venezuela
| | | | | | - Miguel Navarro
- Instituto de Parasitologia y Biomedicina “Lopez-Neyra”, Consejo Superior de Investigaciones Cientificas (CSIC), Granada 18100, Spain
| | - Michael P. Pollastri
- Department of Chemistry & Chemical Biology, Northeastern University 360 Huntington Avenue, Boston, Massachusetts, United States
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27
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The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol 2017; 1607:77-115. [PMID: 28573570 DOI: 10.1007/978-1-4939-7000-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.
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28
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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29
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Ojo KK, Ranade RM, Zhang Z, Dranow DM, Myers JB, Choi R, Nakazawa Hewitt S, Edwards TE, Davies DR, Lorimer D, Boyle SM, Barrett LK, Buckner FS, Fan E, Van Voorhis WC. Brucella melitensis Methionyl-tRNA-Synthetase (MetRS), a Potential Drug Target for Brucellosis. PLoS One 2016; 11:e0160350. [PMID: 27500735 PMCID: PMC4976878 DOI: 10.1371/journal.pone.0160350] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/18/2016] [Indexed: 12/22/2022] Open
Abstract
We investigated Brucella melitensis methionyl-tRNA-synthetase (BmMetRS) with molecular, structural and phenotypic methods to learn if BmMetRS is a promising target for brucellosis drug development. Recombinant BmMetRS was expressed, purified from wild type Brucella melitensis biovar Abortus 2308 strain ATCC/CRP #DD-156 and screened by a thermal melt assay against a focused library of one hundred previously classified methionyl-tRNA-synthetase inhibitors of the blood stage form of Trypanosoma brucei. Three compounds showed appreciable shift of denaturation temperature and were selected for further studies on inhibition of the recombinant enzyme activity and cell viability against wild type B. melitensis strain 16M. BmMetRS protein complexed with these three inhibitors resolved into three-dimensional crystal structures and was analyzed. All three selected methionyl-tRNA-synthetase compounds inhibit recombinant BmMetRS enzymatic functions in an aminoacylation assay at varying concentrations. Furthermore, growth inhibition of B. melitensis strain 16M by the compounds was shown. Inhibitor-BmMetRS crystal structure models were used to illustrate the molecular basis of the enzyme inhibition. Our current data suggests that BmMetRS is a promising target for brucellosis drug development. However, further studies are needed to optimize lead compound potency, efficacy and safety as well as determine the pharmacokinetics, optimal dosage, and duration for effective treatment.
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Affiliation(s)
- Kayode K. Ojo
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Ranae M. Ranade
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - David M. Dranow
- Beryllium, Bainbridge Island, Washington, United States of America
| | - Janette B. Myers
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Ryan Choi
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Steve Nakazawa Hewitt
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | | | | | - Donald Lorimer
- Beryllium, Bainbridge Island, Washington, United States of America
| | - Stephen M. Boyle
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Lynn K. Barrett
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Frederick S. Buckner
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Wesley C. Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases (CERID), Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
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30
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Zhang Z, Koh CY, Ranade RM, Shibata S, Gillespie JR, Hulverson MA, Huang W, Nguyen J, Pendem N, Gelb MH, Verlinde CLMJ, Hol WGJ, Buckner FS, Fan E. 5-Fluoroimidazo[4,5-b]pyridine Is a Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-tRNA Synthetase Inhibitors. ACS Infect Dis 2016; 2:399-404. [PMID: 27627628 PMCID: PMC5108244 DOI: 10.1021/acsinfecdis.6b00036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Fluorination
is a well-known strategy for improving the bioavailability of drug
molecules. However, its impact on efficacy is not easily predicted.
On the basis of inhibitor-bound protein crystal structures, we found
a beneficial fluorination spot for inhibitors targeting methionyl-tRNA
synthetase of Trypanosoma brucei. In
particular, incorporating 5-fluoroimidazo[4,5-b]pyridine
into inhibitors leads to central nervous system bioavailability and
maintained or even improved efficacy.
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Affiliation(s)
- Zhongsheng Zhang
- Department of Biochemistry, University of Washington, 1705 N.E. Pacific Street, Seattle, Washington 98195, United States
| | - Cho Yeow Koh
- Department of Biochemistry, University of Washington, 1705 N.E. Pacific Street, Seattle, Washington 98195, United States
| | - Ranae M. Ranade
- Department of Medicine, Division of Allergy
and Infectious Diseases, and the Center for Emerging and Re-emerging
Infectious Diseases (CERID), University of Washington, 750 Republican
Street, Seattle, Washington 98109, United States
| | - Sayaka Shibata
- Department of Biochemistry, University of Washington, 1705 N.E. Pacific Street, Seattle, Washington 98195, United States
| | - J. Robert Gillespie
- Department of Medicine, Division of Allergy
and Infectious Diseases, and the Center for Emerging and Re-emerging
Infectious Diseases (CERID), University of Washington, 750 Republican
Street, Seattle, Washington 98109, United States
| | - Matthew A. Hulverson
- Department of Medicine, Division of Allergy
and Infectious Diseases, and the Center for Emerging and Re-emerging
Infectious Diseases (CERID), University of Washington, 750 Republican
Street, Seattle, Washington 98109, United States
| | - Wenlin Huang
- Department of Biochemistry, University of Washington, 1705 N.E. Pacific Street, Seattle, Washington 98195, United States
| | - Jasmine Nguyen
- Department of Biochemistry, University of Washington, 1705 N.E. Pacific Street, Seattle, Washington 98195, United States
| | - Nagendar Pendem
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, Washington 98195, United States
| | - Michael H. Gelb
- Department of Chemistry, Bagley Hall, University of Washington, Seattle, Washington 98195, United States
| | - Christophe L. M. J. Verlinde
- Department of Biochemistry, University of Washington, 1705 N.E. Pacific Street, Seattle, Washington 98195, United States
| | - Wim G. J. Hol
- Department of Biochemistry, University of Washington, 1705 N.E. Pacific Street, Seattle, Washington 98195, United States
| | - Frederick S. Buckner
- Department of Medicine, Division of Allergy
and Infectious Diseases, and the Center for Emerging and Re-emerging
Infectious Diseases (CERID), University of Washington, 750 Republican
Street, Seattle, Washington 98109, United States
| | - Erkang Fan
- Department of Biochemistry, University of Washington, 1705 N.E. Pacific Street, Seattle, Washington 98195, United States
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31
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Fang P, Guo M. Evolutionary Limitation and Opportunities for Developing tRNA Synthetase Inhibitors with 5-Binding-Mode Classification. Life (Basel) 2015; 5:1703-25. [PMID: 26670257 PMCID: PMC4695845 DOI: 10.3390/life5041703] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 12/30/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are enzymes that catalyze the transfer of amino acids to their cognate tRNAs as building blocks for translation. Each of the aaRS families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. In addition, aaRSs in higher species have evolved important non-translational functions. These translational and non-translational functions of aaRS are attractive for developing antibacterial, antifungal, and antiparasitic agents and for treating other human diseases. The interplay between amino acids, tRNA, ATP, EF-Tu and non-canonical binding partners, had shaped each family with distinct pattern of key sites for regulation, with characters varying among species across the path of evolution. These sporadic variations in the aaRSs offer great opportunity to target these essential enzymes for therapy. Up to this day, growing numbers of aaRS inhibitors have been discovered and developed. Here, we summarize the latest developments and structural studies of aaRS inhibitors, and classify them with distinct binding modes into five categories.
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Affiliation(s)
- Pengfei Fang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
| | - Min Guo
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
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32
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Koh CY, Kallur Siddaramaiah L, Ranade RM, Nguyen J, Jian T, Zhang Z, Gillespie JR, Buckner FS, Verlinde CLMJ, Fan E, Hol WGJ. A binding hotspot in Trypanosoma cruzi histidyl-tRNA synthetase revealed by fragment-based crystallographic cocktail screens. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:1684-98. [PMID: 26249349 PMCID: PMC4528801 DOI: 10.1107/s1399004715007683] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/18/2015] [Indexed: 01/04/2023]
Abstract
American trypanosomiasis, commonly known as Chagas disease, is a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi. The chronic form of the infection often causes debilitating morbidity and mortality. However, the current treatment for the disease is typically inadequate owing to drug toxicity and poor efficacy, necessitating a continual effort to discover and develop new antiparasitic therapeutic agents. The structure of T. cruzi histidyl-tRNA synthetase (HisRS), a validated drug target, has previously been reported. Based on this structure and those of human cytosolic HisRS, opportunities for the development of specific inhibitors were identified. Here, efforts are reported to identify small molecules that bind to T. cruzi HisRS through fragment-based crystallographic screening in order to arrive at chemical starting points for the development of specific inhibitors. T. cruzi HisRS was soaked into 68 different cocktails from the Medical Structural Genomics of Pathogenic Protozoa (MSGPP) fragment library and diffraction data were collected to identify bound fragments after soaking. A total of 15 fragments were identified, all bound to the same site on the protein, revealing a fragment-binding hotspot adjacent to the ATP-binding pocket. On the basis of the initial hits, the design of reactive fragments targeting the hotspot which would be simultaneously covalently linked to a cysteine residue present only in trypanosomatid HisRS was initiated. Inhibition of T. cruzi HisRS was observed with the resultant reactive fragments and the anticipated binding mode was confirmed crystallographically. These results form a platform for the development of future generations of selective inhibitors for trypanosomatid HisRS.
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Affiliation(s)
- Cho Yeow Koh
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Ranae M. Ranade
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jasmine Nguyen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Tengyue Jian
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | | | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Wim G. J. Hol
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Hol WGJ. Three-dimensional structures in the design of therapeutics targeting parasitic protozoa: reflections on the past, present and future. Acta Crystallogr F Struct Biol Commun 2015; 71:485-99. [PMID: 25945701 PMCID: PMC4427157 DOI: 10.1107/s2053230x15004987] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/11/2015] [Indexed: 11/10/2022] Open
Abstract
Parasitic protozoa cause a range of diseases which threaten billions of human beings. They are responsible for tremendous mortality and morbidity in the least-developed areas of the world. Presented here is an overview of the evolution over the last three to four decades of structure-guided design of inhibitors, leads and drug candidates aiming at targets from parasitic protozoa. Target selection is a crucial and multi-faceted aspect of structure-guided drug design. The major impact of advances in molecular biology, genome sequencing and high-throughput screening is touched upon. The most advanced crystallographic techniques, including XFEL, have already been applied to structure determinations of drug targets from parasitic protozoa. Even cryo-electron microscopy is contributing to our understanding of the mode of binding of inhibitors to parasite ribosomes. A number of projects have been selected to illustrate how structural information has assisted in arriving at promising compounds that are currently being evaluated by pharmacological, pharmacodynamic and safety tests to assess their suitability as pharmaceutical agents. Structure-guided approaches are also applied to incorporate properties into compounds such that they are less likely to become the victim of resistance mechanisms. A great increase in the number of novel antiparasitic compounds will be needed in the future. These should then be combined into various multi-compound therapeutics to circumvent the diverse resistance mechanisms that render single-compound, or even multi-compound, drugs ineffective. The future should also see (i) an increase in the number of projects with a tight integration of structural biology, medicinal chemistry, parasitology and pharmaceutical sciences; (ii) the education of more `medicinal structural biologists' who are familiar with the properties that compounds need to have for a high probability of success in the later steps of the drug-development process; and (iii) the expansion of drug-development capabilities in middle- and low-income countries.
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Affiliation(s)
- Wim G. J. Hol
- Department of Biochemistry and Biomolecular Structure Center, University of Washington, Seattle, WA 98195, USA
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Gadakh B, Smaers S, Rozenski J, Froeyen M, Van Aerschot A. 5'-(N-aminoacyl)-sulfonamido-5'-deoxyadenosine: attempts for a stable alternative for aminoacyl-sulfamoyl adenosines as aaRS inhibitors. Eur J Med Chem 2015; 93:227-36. [PMID: 25686591 DOI: 10.1016/j.ejmech.2015.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/04/2015] [Accepted: 02/07/2015] [Indexed: 10/24/2022]
Abstract
Synthesis of aminoacyl-sulfamoyl adenosines (aaSAs) and their peptidyl conjugates as aminoacyl tRNA synthetase (aaRS) inhibitors remains problematic due to the low yield of the aminoacylation and the subsequent conjugation reaction causing concomitant formation of a cyclic adenosine derivative. In an effort to reduce this undesirable side reaction, we aimed to prepare the corresponding aminoacyl sulfonamide (aaSoA) analogues as more stable alternatives for aaSA derivatives. Deletion of the 5'-oxygen in aaSA analogues should render the C-5' less electrophilic and therefore improve the stability of the aminoacyl sulfamate analogues. We therefore synthesized six sulfonamides and compared their activity against the respective aaSA analogues. However, except for the aspartyl derivative, the new compounds are not able to inhibit the corresponding aaRS. Possible reasons for this loss of activity are discussed by modeling and comparison of the newly synthesized aaSoA derivatives with their parent aaSA analogues.
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Affiliation(s)
- Bharat Gadakh
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Simon Smaers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium.
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Pedró-Rosa L, Buckner FS, Ranade RM, Eberhart C, Madoux F, Gillespie JR, Koh CY, Brown S, Lohse J, Verlinde CLM, Fan E, Bannister T, Scampavia L, Hol WGJ, Spicer T, Hodder P. Identification of potent inhibitors of the Trypanosoma brucei methionyl-tRNA synthetase via high-throughput orthogonal screening. JOURNAL OF BIOMOLECULAR SCREENING 2015; 20:122-30. [PMID: 25163684 PMCID: PMC4378865 DOI: 10.1177/1087057114548832] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Improved therapies for the treatment of Trypanosoma brucei, the etiological agent of the neglected tropical disease human African trypanosomiasis, are urgently needed. We targeted T. brucei methionyl-tRNA synthetase (MetRS), an aminoacyl-tRNA synthase (aaRS), which is considered an important drug target due to its role in protein synthesis, cell survival, and its significant differences in structure from its mammalian ortholog. Previous work using RNA interference of MetRS demonstrated growth inhibition of T. brucei, further validating it as an attractive target. We report the development and implementation of two orthogonal high-throughput screening assays to identify inhibitors of T. brucei MetRS. First, a chemiluminescence assay was implemented in a 1536-well plate format and used to monitor adenosine triphosphate depletion during the aminoacylation reaction. Hit confirmation then used a counterscreen in which adenosine monophosphate production was assessed using fluorescence polarization technology. In addition, a miniaturized cell viability assay was used to triage cytotoxic compounds. Finally, lower throughput assays involving whole parasite growth inhibition of both human and parasite MetRS were used to analyze compound selectivity and efficacy. The outcome of this high-throughput screening campaign has led to the discovery of 19 potent and selective T. brucei MetRS inhibitors.
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Affiliation(s)
- Laura Pedró-Rosa
- The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | | | - Ranae M Ranade
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Christina Eberhart
- The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | - Franck Madoux
- The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | | | - Cho Yeow Koh
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Steven Brown
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jacqueline Lohse
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Erkang Fan
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Thomas Bannister
- The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | - Louis Scampavia
- The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | - Wim G J Hol
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Timothy Spicer
- The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA
| | - Peter Hodder
- The Scripps Research Institute Molecular Screening Center, Scripps Florida, Jupiter, FL, USA Amgen, Inc., Thousand Oaks, CA
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Koh CY, Wetzel AB, de van der Schueren WJ, Hol WGJ. Comparison of histidine recognition in human and trypanosomatid histidyl-tRNA synthetases. Biochimie 2014; 106:111-20. [PMID: 25151410 DOI: 10.1016/j.biochi.2014.08.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 08/12/2014] [Indexed: 02/05/2023]
Abstract
As part of a project aimed at obtaining selective inhibitors and drug-like compounds targeting tRNA synthetases from trypanosomatids, we have elucidated the crystal structure of human cytosolic histidyl-tRNA synthetase (Hs-cHisRS) in complex with histidine in order to be able to compare human and parasite enzymes. The resultant structure of Hs-cHisRS•His represents the substrate-bound state (H-state) of the enzyme. It provides an interesting opportunity to compare with ligand-free and imidazole-bound structures Hs-cHisRS published recently, both of which represent the ligand-free state (F-state) of the enzyme. The H-state Hs-cHisRS undergoes conformational changes in active site residues and several conserved motif of HisRS, compared to F-state structures. The histidine forms eight hydrogen bonds with HisRS of which six engage the amino and carboxylate groups of this amino acid. The availability of published imidazole-bound structure provides a unique opportunity to dissect the structural roles of individual chemical groups of histidine. The analysis revealed the importance of the amino and carboxylate groups, of the histidine in leading to these dramatic conformational changes of the H-state. Further, comparison with previously published trypanosomatid HisRS structures reveals a pocket in the F-state of the parasite enzyme that may provide opportunities for developing specific inhibitors of Trypanosoma brucei HisRS.
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Affiliation(s)
- Cho Yeow Koh
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Allan B Wetzel
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Wim G J Hol
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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