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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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2
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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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3
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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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5
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Rybak MY, Balanda AO, Yatsyshyna AP, Kotey IM, Starosyla SA, Bdzhola VG, Lukash LL, Yarmoluk SM, Tukalo MA, Volynets GP. Discovery of novel antituberculosis agents among 3-phenyl-5-(1-phenyl-1H-[1,2,3]triazol-4-yl)-[1,2,4]oxadiazole derivatives targeting aminoacyl-tRNA synthetases. Sci Rep 2021; 11:7162. [PMID: 33785838 PMCID: PMC8010095 DOI: 10.1038/s41598-021-86562-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/17/2021] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance is a major problem of tuberculosis treatment. This provides the stimulus for the search of novel molecular targets and approaches to reduce or forestall resistance emergence in Mycobacterium tuberculosis. Earlier, we discovered a novel small-molecular inhibitor among 3-phenyl-5-(1-phenyl-1H-[1,2,3]triazol-4-yl)-[1,2,4]oxadiazoles targeting simultaneously two enzymes—mycobacterial leucyl-tRNA synthetase (LeuRS) and methionyl-tRNA synthetase (MetRS), which are promising molecular targets for antibiotic development. Unfortunately, the identified inhibitor does not reveal antibacterial activity toward M. tuberculosis. This study aims to develop novel aminoacyl-tRNA synthetase inhibitors among this chemical class with antibacterial activity toward resistant strains of M. tuberculosis. We performed molecular docking of the library of 3-phenyl-5-(1-phenyl-1H-[1,2,3]triazol-4-yl)-[1,2,4]oxadiazole derivatives and selected 41 compounds for investigation of their inhibitory activity toward MetRS and LeuRS in aminoacylation assay and antibacterial activity toward M. tuberculosis strains using microdilution assay. In vitro screening resulted in 10 compounds active against MetRS and 3 compounds active against LeuRS. Structure-related relationships (SAR) were established. The antibacterial screening revealed 4 compounds active toward M. tuberculosis mono-resistant strains in the range of concentrations 2–20 mg/L. Among these compounds, only one compound 27 has significant enzyme inhibitory activity toward mycobacterial MetRS (IC50 = 148.5 µM). The MIC for this compound toward M. tuberculosis H37Rv strain is 12.5 µM. This compound is not cytotoxic to human HEK293 and HepG2 cell lines. Therefore, 3-phenyl-5-(1-phenyl-1H-[1,2,3]triazol-4-yl)-[1,2,4]oxadiazole derivatives can be used for further chemical optimization and biological research to find non-toxic antituberculosis agents with a novel mechanism of action.
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Affiliation(s)
- Mariia Yu Rybak
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine.
| | - Anatoliy O Balanda
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Anna P Yatsyshyna
- Department of Human Genetics, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Igor M Kotey
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy A Starosyla
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Volodymyr G Bdzhola
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Lubov L Lukash
- Department of Human Genetics, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
| | - Galyna P Volynets
- Department of Medicinal Chemistry, Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kyiv, Ukraine
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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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7
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Abstract
Aminoacyl-tRNA synthetases (AARSs) have been considered very attractive drug-targets for decades. This interest probably emerged with the identification of differences in AARSs between prokaryotic and eukaryotic species, which provided a rationale for the development of antimicrobials targeting bacterial AARSs with minimal effect on the homologous human AARSs. Today we know that AARSs are not only attractive, but also valid drug targets as they are housekeeping proteins that: (i) play a fundamental role in protein translation by charging the corresponding amino acid to its cognate tRNA and preventing mistranslation mistakes [1], a critical process during fast growing conditions of microbes; and (ii) present significant differences between microbes and humans that can be used for drug development [2]. Together with the vast amount of available data on both pathogenic and mammalian AARSs, it is expected that, in the future, the numerous reported inhibitors of AARSs will provide the basis to develop new therapeutics for the treatment of human diseases. In this chapter, a detailed summary on the state-of-the-art in drug discovery and drug development for each aminoacyl-tRNA synthetase will be presented.
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Affiliation(s)
- Maria Lukarska
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences (IAB), Structural Biology of Novel Drug Targets in Human Diseases, INSERM U1209, CNRS UMR 5309, University Grenoble Alpes, Grenoble, France.
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8
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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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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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Kelly P, Hadi-Nezhad F, Liu DY, Lawrence TJ, Linington RG, Ibba M, Ardell DH. Targeting tRNA-synthetase interactions towards novel therapeutic discovery against eukaryotic pathogens. PLoS Negl Trop Dis 2020; 14:e0007983. [PMID: 32106219 PMCID: PMC7046186 DOI: 10.1371/journal.pntd.0007983] [Citation(s) in RCA: 9] [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: 07/22/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022] Open
Abstract
The development of chemotherapies against eukaryotic pathogens is especially challenging because of both the evolutionary conservation of drug targets between host and parasite, and the evolution of strain-dependent drug resistance. There is a strong need for new nontoxic drugs with broad-spectrum activity against trypanosome parasites such as Leishmania and Trypanosoma. A relatively untested approach is to target macromolecular interactions in parasites rather than small molecular interactions, under the hypothesis that the features specifying macromolecular interactions diverge more rapidly through coevolution. We computed tRNA Class-Informative Features in humans and independently in eight distinct clades of trypanosomes, identifying parasite-specific informative features, including base pairs and base mis-pairs, that are broadly conserved over approximately 250 million years of trypanosome evolution. Validating these observations, we demonstrated biochemically that tRNA:aminoacyl-tRNA synthetase (aaRS) interactions are a promising target for anti-trypanosomal drug discovery. From a marine natural products extract library, we identified several fractions with inhibitory activity toward Leishmania major alanyl-tRNA synthetase (AlaRS) but no activity against the human homolog. These marine natural products extracts showed cross-reactivity towards Trypanosoma cruzi AlaRS indicating the broad-spectrum potential of our network predictions. We also identified Leishmania major threonyl-tRNA synthetase (ThrRS) inhibitors from the same library. We discuss why chemotherapies targeting multiple aaRSs should be less prone to the evolution of resistance than monotherapeutic or synergistic combination chemotherapies targeting only one aaRS. Trypanosome parasites pose a significant health risk worldwide. Conventional drug development strategies have proven challenging given the high conservation between humans and pathogens, with off-target toxicity being a common problem. Protein synthesis inhibitors have historically been an attractive target for antimicrobial discovery against bacteria, and more recently for eukaryotic pathogens. Here we propose that exploiting pathogen-specific tRNA-synthetase interactions offers the potential for highly targeted drug discovery. To this end, we improved tRNA gene annotations in trypanosome genomes, identified functionally informative trypanosome-specific tRNA features, and showed that these features are highly conserved over approximately 250 million years of trypanosome evolution. Highlighting the species-specific and broad-spectrum potential of our approach, we identified natural product inhibitors against the parasite translational machinery that have no effect on the homologous human enzyme.
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Affiliation(s)
- Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
| | - Fatemeh Hadi-Nezhad
- Quantitative and Systems Biology Program, University of California, Merced, California, United States of America
| | - Dennis Y. Liu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Travis J. Lawrence
- Quantitative and Systems Biology Program, University of California, Merced, California, United States of America
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee, United States of America
| | - Roger G. Linington
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Michael Ibba
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, Ohio, United States of America
- Center for RNA Biology, The Ohio State University, Ohio, United States of America
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (MI); (DHA)
| | - David H. Ardell
- Quantitative and Systems Biology Program, University of California, Merced, California, United States of America
- Department of Molecular & Cell Biology, University of California, Merced, California, United States of America
- * E-mail: (MI); (DHA)
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11
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Kovalenko OP, Volynets GP, Rybak MY, Starosyla SA, Gudzera OI, Lukashov SS, Bdzhola VG, Yarmoluk SM, Boshoff HI, Tukalo MA. Dual-target inhibitors of mycobacterial aminoacyl-tRNA synthetases among N-benzylidene- N'-thiazol-2-yl-hydrazines. MEDCHEMCOMM 2019; 10:2161-2169. [PMID: 32206244 PMCID: PMC7069510 DOI: 10.1039/c9md00347a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/09/2019] [Indexed: 12/19/2022]
Abstract
Effective treatment of tuberculosis is challenged by the rapid development of Mycobacterium tuberculosis (Mtb) multidrug resistance that presumably could be overcome with novel multi-target drugs. Aminoacyl-tRNA synthetases (AARSs) are an essential part of protein biosynthesis machinery and attractive targets for drug discovery. Here, we experimentally verify a hypothesis of simultaneous targeting of structurally related AARSs by a single inhibitor. We previously identified a new class of mycobacterial leucyl-tRNA synthetase inhibitors, N-benzylidene-N'-thiazol-2-yl-hydrazines. Molecular docking of a library of novel N-benzylidene-N'-thiazol-2-yl-hydrazine derivatives into active sites of M. tuberculosis LeuRS (MtbLeuRS) and MetRS (MtbMetRS) resulted in a panel of the best ranking compounds, which were then evaluated for enzymatic potency. Screening data revealed 11 compounds active against MtbLeuRS and 28 compounds active against MtbMetRS. The hit compounds display dual inhibitory potency as demonstrated by IC50 values for both enzymes. Compound 3 is active against Mtb H37Rv cells in in vitro bioassays.
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Affiliation(s)
- Oksana P Kovalenko
- Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine . ; ; ; Tel: +38 044 5265589
| | - Galyna P Volynets
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Mariia Yu Rybak
- Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine . ; ; ; Tel: +38 044 5265589
| | - Sergiy A Starosyla
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Olga I Gudzera
- Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine . ; ; ; Tel: +38 044 5265589
| | - Sergiy S Lukashov
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Volodymyr G Bdzhola
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Sergiy M Yarmoluk
- Department of Medicinal Chemistry , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology , National Institute of Allergy and Infectious Disease , National Institute of Health , 5601 Fishers Lane, MSC 9806 , Bethesda , MD 20892-9806 , Maryland , USA
| | - Michael A Tukalo
- Department of Protein Synthesis Enzymology , Institute of Molecular Biology and Genetics , The NAS of Ukraine , 150 Zabolotnogo St , 03143 Kyiv , Ukraine . ; ; ; Tel: +38 044 5265589
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Dual-targeted hit identification using pharmacophore screening. J Comput Aided Mol Des 2019; 33:955-964. [PMID: 31691918 DOI: 10.1007/s10822-019-00245-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/30/2019] [Indexed: 12/20/2022]
Abstract
Mycobacterium tuberculosis infection remains a major cause of global morbidity and mortality due to the increase of antibiotics resistance. Dual/multi-target drug discovery is a promising approach to overcome bacterial resistance. In this study, we built ligand-based pharmacophore models and performed pharmacophore screening in order to identify hit compounds targeting simultaneously two enzymes-M. tuberculosis leucyl-tRNA synthetase (LeuRS) and methionyl-tRNA synthetase (MetRS). In vitro aminoacylation assay revealed five compounds from different chemical classes inhibiting both enzymes. Among them the most active compound-3-(3-chloro-4-methoxy-phenyl)-5-[3-(4-fluoro-phenyl)-[1,2,4]oxadiazol-5-yl]-3H-[1,2,3]triazol-4-ylamine (1) inhibits mycobacterial LeuRS and MetRS with IC50 values of 13 µM and 13.8 µM, respectively. Molecular modeling study indicated that compound 1 has similar binding mode with the active sites of both aminoacyl-tRNA synthetases and can be valuable compound for further chemical optimization in order to find promising antituberculosis agents.
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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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