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Thakur S, Mehra R. Computational Insight into Substrate-Induced Conformational Changes in Methionyl-tRNA Synthetase of Mycobacterium Tuberculosis. Protein J 2023; 42:533-546. [PMID: 37402109 DOI: 10.1007/s10930-023-10135-3] [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] [Accepted: 06/26/2023] [Indexed: 07/05/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (M.tb) has killed millions worldwide. Antibiotic resistance leads to the ineffectiveness of the current therapies. Aminoacyl tRNA synthetase (aaRS) class of proteins involved in protein synthesis are promising bacterial targets for developing new therapies. Here, we carried out a systematic comparative study on the aaRS sequences from M.tb and human. We listed important M.tb aaRS that could be explored as potential M.tb targets alongside the detailed conformational space analysis of methionyl-tRNA synthetase (MetRS) in apo- and substrate-bound form, which is among the proposed targets. Understanding the conformational dynamics is central to the mechanistic understanding of MetRS, as the substrate binding leads to the conformational changes causing the reaction to proceed. We performed the most complete simulation study of M.tb MetRS for 6 microseconds (2 systems × 3 runs × 1 microsecond) in the apo and substrate-bound states. Interestingly, we observed differential features, showing comparatively large dynamics for the holo simulations, whereas the apo structures became slightly compact with reduced solvent exposed area. In contrast, the ligand size decreased significantly in holo structures possibly to relax ligand conformation. Our findings correlate with experimental studies, thus validating our protocol. Adenosine monophosphate moiety of the substrate exhibited quite higher fluctuations than the methionine. His21 and Lys54 were found to be the important residues forming prominent hydrogen bond and salt-bridge interactions with the ligand. The ligand-protein affinity decreased during simulations as computed by MMGBSA analysis over the last 500 ns trajectories, which indicates the conformational changes upon ligand binding. These differential features could be further explored for designing new M.tb inhibitors.
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Affiliation(s)
- Shivani Thakur
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India
| | - Rukmankesh Mehra
- Department of Chemistry, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
- Department of Bioscience and Biomedical Engineering, Indian Institute of Technology Bhilai, Sejbahar, Raipur, Chhattisgarh, 492015, India.
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Tsui CKM, Sorrentino F, Narula G, Mendoza-Losana A, del Rio RG, Herrán EP, Lopez A, Bojang A, Zheng X, Remuiñán-Blanco MJ, Av-Gay Y. Hit Compounds and Associated Targets in Intracellular Mycobacterium tuberculosis. Molecules 2022; 27:molecules27144446. [PMID: 35889319 PMCID: PMC9324642 DOI: 10.3390/molecules27144446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 02/04/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, is one of the most devastating infectious agents in the world. Chemical-genetic characterization through in vitro evolution combined with whole genome sequencing analysis was used identify novel drug targets and drug resistance genes in Mtb associated with its intracellular growth in human macrophages. We performed a genome analysis of 53 Mtb mutants resistant to 15 different hit compounds. We found nonsynonymous mutations/indels in 30 genes that may be associated with drug resistance acquisitions. Beyond confirming previously identified drug resistance mechanisms such as rpoB and lead targets reported in novel anti-tuberculosis drug screenings such as mmpL3, ethA, and mbtA, we have discovered several unrecognized candidate drug targets including prrB. The exploration of the Mtb chemical mutant genomes could help novel drug discovery and the structural biology of compounds and associated mechanisms of action relevant to tuberculosis treatment.
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Affiliation(s)
- Clement K. M. Tsui
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore 308442, Singapore
| | - Flavia Sorrentino
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Gagandeep Narula
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
| | - Alfonso Mendoza-Losana
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
- Department of Bioengineering and Aerospace Engineering, Carlos III University of Madrid, 28040 Madrid, Spain
| | - Ruben Gonzalez del Rio
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Esther Pérez Herrán
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Abraham Lopez
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Adama Bojang
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
| | - Xingji Zheng
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
| | - Modesto Jesus Remuiñán-Blanco
- GSK, Global Health Medicines R&D, PTM, Tres Cantos, 28760 Madrid, Spain; (A.M.-L.); (R.G.d.R.); (E.P.H.); (M.J.R.-B.)
| | - Yossef Av-Gay
- Department of Medicine and Microbiology and Immunology, Life Science Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (C.K.M.T.); (F.S.); (G.N.); (A.L.); (A.B.); (X.Z.)
- Correspondence: ; Tel.: +1-604-822-3432
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Antitubercular, Cytotoxicity, and Computational Target Validation of Dihydroquinazolinone Derivatives. Antibiotics (Basel) 2022; 11:antibiotics11070831. [PMID: 35884084 PMCID: PMC9311641 DOI: 10.3390/antibiotics11070831] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 02/04/2023] Open
Abstract
A series of 2,3-dihydroquinazolin-4(1H)-one derivatives (3a–3m) was screened for in vitro whole-cell antitubercular activity against the tubercular strain H37Rv and multidrug-resistant (MDR) Mycobacterium tuberculosis (MTB) strains. Compounds 3l and 3m with di-substituted aryl moiety (halogens) attached to the 2-position of the scaffold showed a minimum inhibitory concentration (MIC) of 2 µg/mL against the MTB strain H37Rv. Compound 3k with an imidazole ring at the 2-position of the dihydroquinazolin-4(1H)-one also showed significant inhibitory action against both the susceptible strain H37Rv and MDR strains with MIC values of 4 and 16 µg/mL, respectively. The computational results revealed the mycobacterial pyridoxal-5′-phosphate (PLP)-dependent aminotransferase (BioA) enzyme as the potential target for the tested compounds. In vitro, ADMET calculations and cytotoxicity studies against the normal human dermal fibroblast cells indicated the safety and tolerability of the test compounds 3k–3m. Thus, compounds 3k–3m warrant further optimization to develop novel BioA inhibitors for the treatment of drug-sensitive H37Rv and drug-resistant MTB.
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Mandelic acid-based spirothiazolidinones targeting M. tuberculosis: Synthesis, in vitro and in silico investigations. Bioorg Chem 2022; 121:105688. [DOI: 10.1016/j.bioorg.2022.105688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/09/2022] [Accepted: 02/13/2022] [Indexed: 01/01/2023]
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Habjan E, Ho VQT, Gallant J, Van Stempvoort G, Jim KK, Kuijl C, Geerke DP, Bitter W, Speer A. Anti-tuberculosis Compound Screen using a Zebrafish Infection Model identifies an Aspartyl-tRNA Synthetase Inhibitor. Dis Model Mech 2021; 14:273850. [PMID: 34643222 PMCID: PMC8713996 DOI: 10.1242/dmm.049145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/03/2021] [Indexed: 11/20/2022] Open
Abstract
Finding new anti-tuberculosis compounds with convincing in vivo activity is an ongoing global challenge to fight the emergence of multidrug-resistant Mycobacterium tuberculosis isolates. In this study, we exploited the medium-throughput capabilities of the zebrafish embryo infection model with Mycobacterium marinum as a surrogate for M. tuberculosis. Using a representative set of clinically established drugs, we demonstrate that this model could be predictive and selective for antibiotics that can be administered orally. We further used the zebrafish infection model to screen 240 compounds from an anti-tuberculosis hit library for their in vivo activity and identified 14 highly active compounds. One of the most active compounds was the tetracyclic compound TBA161, which was studied in more detail. Analysis of resistant mutants revealed point mutations in aspS (rv2572c), encoding an aspartyl-tRNA synthetase. The target was genetically confirmed, and molecular docking studies propose the possible binding of TBA161 in a pocket adjacent to the catalytic site. This study shows that the zebrafish infection model is suitable for rapidly identifying promising scaffolds with in vivo activity. Summary: Exploitation of the medium-throughput capabilities of a zebrafish embryo infection model of tuberculosis to screen compounds for their in vivo activity, one of which was characterized as an aspartyl-tRNA synthetase inhibitor.
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Affiliation(s)
- Eva Habjan
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.,Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Vien Q T Ho
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - James Gallant
- Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Gunny Van Stempvoort
- Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Kin Ki Jim
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Coen Kuijl
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Daan P Geerke
- Department of Molecular Toxicology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Wilbert Bitter
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands.,Section Molecular Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Alexander Speer
- Department of Medical Microbiology and Infection Control, Amsterdam UMC, Location VU Medical Center, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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6
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Abstract
Most bacteria employ a two-step indirect tRNA aminoacylation pathway for the synthesis of aminoacylated tRNAGln and tRNAAsn. The heterotrimeric enzyme GatCAB performs a critical amidotransferase reaction in the second step of this pathway. We have previously demonstrated in mycobacteria that this two-step pathway is error prone and translational errors contribute to adaptive phenotypes such as antibiotic tolerance. Furthermore, we identified clinical isolates of the globally important pathogen Mycobacterium tuberculosis with partial loss-of-function mutations in gatA, and demonstrated that these mutations result in high, specific rates of translational error and increased rifampin tolerance. However, the mechanisms by which these clinically derived mutations in gatA impact GatCAB function were unknown. Here, we describe biochemical and biophysical characterization of M. tuberculosis GatCAB, containing either wild-type gatA or one of two gatA mutants from clinical strains. We show that these mutations have minimal impact on enzymatic activity of GatCAB; however, they result in destabilization of the GatCAB complex as well as that of the ternary asparaginyl-transamidosome. Stabilizing complex formation with the solute trehalose increases specific translational fidelity of not only the mutant strains but also of wild-type mycobacteria. Therefore, our data suggest that alteration of GatCAB stability may be a mechanism for modulation of translational fidelity. IMPORTANCE Most bacteria use a two-step indirect pathway to aminoacylate tRNAGln and tRNAAsn, despite the fact that the indirect pathway consumes more energy and is error prone. We have previously shown that the higher protein synthesis errors from this indirect pathway in mycobacteria allow adaptation to hostile environments such as antibiotic treatment through generation of novel alternate proteins not coded by the genome. However, the precise mechanisms of how translational fidelity is tuned were not known. Here, we biochemically and biophysically characterize the critical enzyme of the Mycobacterium tuberculosis indirect pathway, GatCAB, as well as two mutant enzymes previously identified from clinical isolates that were associated with increased mistranslation. We show that the mutants dysregulate the pathway via destabilizing the enzyme complex. Importantly, increasing stability improves translational fidelity in both wild-type and mutant bacteria, demonstrating a mechanism by which mycobacteria may tune mistranslation rates.
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Deb PK, Al-Shar'i NA, Venugopala KN, Pillay M, Borah P. In vitro anti-TB properties, in silico target validation, molecular docking and dynamics studies of substituted 1,2,4-oxadiazole analogues against Mycobacterium tuberculosis. J Enzyme Inhib Med Chem 2021; 36:869-884. [PMID: 34060396 PMCID: PMC8172222 DOI: 10.1080/14756366.2021.1900162] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The alarming increase in multi- and extensively drug-resistant (MDR and XDR) strains of Mycobacterium tuberculosis (MTB) has triggered the scientific community to search for novel, effective, and safer therapeutics. To this end, a series of 3,5-disubstituted-1,2,4-oxadiazole derivatives (3a–3i) were tested against H37Rv, MDR and XDR strains of MTB. Of which, compound 3a with para-trifluorophenyl substituted oxadiazole showed excellent activity against the susceptible H37Rv and MDR-MTB strain with a MIC values of 8 and 16 µg/ml, respectively. To understand the mechanism of action of these compounds (3a–3i) and identify their putative drug target, molecular docking and dynamics studies were employed against a panel of 20 mycobacterial enzymes reported to be essential for mycobacterial growth and survival. These computational studies revealed polyketide synthase (Pks13) enzyme as the putative target. Moreover, in silico ADMET predictions showed satisfactory properties for these compounds, collectively, making them, particularly compound 3a, promising leads worthy of further optimisation.
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Affiliation(s)
- Pran Kishore Deb
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Philadelphia University, Amman, Jordan
| | - Nizar A Al-Shar'i
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa, Kingdom of Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban, South Africa
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Pobitra Borah
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, India
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8
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Abstract
Mycobacterium tuberculosis is the causative pathogen of the pulmonary disease tuberculosis. Despite the availability of effective treatment programs, there is a global pursuit of new anti-tubercular agents to respond to the developing threat of drug resistance, in addition to reducing the extensive duration of chemotherapy and any associated toxicity. The route to mycobacterial drug discovery can be considered from two directions: target-to-drug and drug-to-target. The former approach uses conventional methods including biochemical assays along with innovative computational screens, but is yet to yield any drug candidates to the clinic, with a high attrition rate owing to lack of whole cell activity. In the latter approach, compound libraries are screened for efficacy against the bacilli or model organisms, ensuring whole cell activity, but here subsequent target identification is the rate-limiting step. Advances in a variety of scientific fields have enabled the amalgamation of aspects of both approaches in the development of novel drug discovery tools, which are now primed to accelerate the discovery of novel hits and leads with known targets and whole cell activity. This review discusses these traditional and innovative techniques, which are widely used in the quest for new anti-tubercular compounds. Innovations in mycobacterial drug discovery to accelerate the identification of new drug candidates with confirmed targets and whole cell activity.![]()
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Affiliation(s)
- Katherine A Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK +44 (0)121 41 45925 +44 (0)121 41 58125
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham Edgbaston Birmingham B15 2TT UK +44 (0)121 41 45925 +44 (0)121 41 58125
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9
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Burke C, Jankute M, Moynihan P, Gonzalez Del Rio R, Li X, Esquivias J, Lelièvre J, Cox JAG, Sacchettini J, Besra GS. Development of a novel secondary phenotypic screen to identify hits within the mycobacterial protein synthesis pipeline. FASEB Bioadv 2020; 2:600-612. [PMID: 33089076 PMCID: PMC7566049 DOI: 10.1096/fba.2020-00022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/17/2020] [Accepted: 07/31/2020] [Indexed: 12/03/2022] Open
Abstract
Background Whole‐cell phenotypic screening is the driving force behind modern anti‐tubercular drug discovery efforts. Focus has shifted from screening for bactericidal scaffolds to screens incorporating target deconvolution. Target‐based screening aims to direct drug discovery toward known effective targets and avoid investing resources into unproductive lines of enquiry. The protein synthesis pipeline, including RNA polymerase and the ribosome, is a clinically proven target in Mycobacterium tuberculosis. Screening for new hits of this effective target pathway is an invaluable tool in the drug discovery arsenal. Methods Using M. tuberculosis H37Rv augmented with anhydrotetracycline‐inducible expression of mCherry, a phenotypic screen was developed for the identification of protein synthesis inhibitors in a medium throughput screening format. Results The assay was validated using known inhibitors of protein synthesis to show a dose‐dependent reduction in mCherry fluorescence. This was expanded to a proprietary screen of hypothetical protein synthesis hits and modified to include quantitative viability measurement of cells using resazurin. Conclusion Following the success of the proprietary screen, a larger scale screen of the GlaxoSmithKline anti‐tubercular library containing 2799 compounds was conducted. Combined single shot and dose‐response screening yielded 18 hits, 0.64% of all screened compounds.
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Affiliation(s)
- Christopher Burke
- Institute of Microbiology and Infection School of Biosciences University of Birmingham Birmingham UK
| | - Monika Jankute
- Institute of Microbiology and Infection School of Biosciences University of Birmingham Birmingham UK
| | - Patrick Moynihan
- Institute of Microbiology and Infection School of Biosciences University of Birmingham Birmingham UK
| | | | - Xiaojun Li
- Department of Biochemistry and Biophysics Texas A&M University College Station Texas United States
| | - Jorge Esquivias
- Diseases of the Developing World GlaxoSmithKline Tres Cantos Madrid Spain
| | - Joël Lelièvre
- Diseases of the Developing World GlaxoSmithKline Tres Cantos Madrid Spain
| | | | - James Sacchettini
- Department of Biochemistry and Biophysics Texas A&M University College Station Texas United States
| | - Gurdyal S Besra
- Institute of Microbiology and Infection School of Biosciences University of Birmingham Birmingham UK
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Abrahams KA, Hu W, Li G, Lu Y, Richardson EJ, Loman NJ, Huang H, Besra GS. Anti-tubercular derivatives of rhein require activation by the monoglyceride lipase Rv0183. ACTA ACUST UNITED AC 2020; 6:100040. [PMID: 32743152 PMCID: PMC7389528 DOI: 10.1016/j.tcsw.2020.100040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/17/2020] [Accepted: 04/17/2020] [Indexed: 02/01/2023]
Abstract
The emergence and perseverance of drug resistant strains of Mycobacterium tuberculosis (Mtb) ensures that drug discovery efforts remain at the forefront of tuberculosis research. There are numerous different approaches that can be employed to lead to the discovery of anti-tubercular agents. In this work, we endeavored to optimize the anthraquinone chemical scaffold of a known drug, rhein, converting it from a compound with negligible activity against Mtb, to a series of compounds with potent activity. Two compounds exhibited low toxicity and good liver microsome stability and were further progressed in attempts to identify the biological target. Whole genome sequencing of resistant isolates revealed inactivating mutations in a monoglyceride lipase. Over-expression trials and an enzyme assay confirmed that the designed compounds are prodrugs, activated by the monoglyceride lipase. We propose that rhein is the active moiety of the novel compounds, which requires chemical modifications to enable access to the cell through the extensive cell wall structure. This work demonstrates that re-engineering of existing antimicrobial agents is a valid method in the development of new anti-tubercular compounds.
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Affiliation(s)
- Katherine A Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Wei Hu
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Gang Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Yu Lu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Department of Pharmacology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, 97 Ma Chang Street, Beijing 101149, China
| | - Emily J Richardson
- MicrobesNG, Units 1-2 First Floor, The BioHub, Birmingham Research Park, 97 Vincent Drive, Birmingham B15 2SQ, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Haihong Huang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences, 1 Xian Nong Tan Street, Beijing 100050, China
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Behra PRK, Pettersson BMF, Das S, Dasgupta S, Kirsebom LA. Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA. BMC Evol Biol 2019; 19:124. [PMID: 31215393 PMCID: PMC6582537 DOI: 10.1186/s12862-019-1447-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 05/27/2019] [Indexed: 02/07/2023] Open
Abstract
Background Mycobacteria occupy various ecological niches and can be isolated from soil, tap water and ground water. Several cause diseases in humans and animals. To get deeper insight into our understanding of mycobacterial evolution focusing on tRNA and non-coding (nc)RNA, we conducted a comparative genome analysis of Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clade members. Results Genome sizes for Mmuc- and Mneo-clade members vary between 5.4 and 6.5 Mbps with the complete MmucT (type strain) genome encompassing 6.1 Mbp. The number of tRNA genes range between 46 and 79 (including one pseudo tRNA gene) with 39 tRNA genes common among the members of these clades, while additional tRNA genes were probably acquired through horizontal gene transfer. Selected tRNAs and ncRNAs (RNase P RNA, tmRNA, 4.5S RNA, Ms1 RNA and 6C RNA) are expressed, and the levels for several of these are higher in stationary phase compared to exponentially growing cells. The rare tRNAIleTAT isoacceptor and two for mycobacteria novel ncRNAs: the Lactobacillales-derived GOLLD RNA and a homolog to the antisense Salmonella typhimurium phage Sar RNA, were shown to be present and expressed in certain Mmuc-clade members. Conclusions Phages, IS elements, horizontally transferred tRNA gene clusters, and phage-derived ncRNAs appears to have influenced the evolution of the Mmuc- and Mneo-clades. While the number of predicted coding sequences correlates with genome size, the number of tRNA coding genes does not. The majority of the tRNA genes in mycobacteria are transcribed mainly from single genes and the levels of certain ncRNAs, including RNase P RNA (essential for the processing of tRNAs), are higher at stationary phase compared to exponentially growing cells. We provide supporting evidence that Ms1 RNA represents a mycobacterial 6S RNA variant. The evolutionary routes for the ncRNAs RNase P RNA, tmRNA and Ms1 RNA are different from that of the core genes. Electronic supplementary material The online version of this article (10.1186/s12862-019-1447-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - B M Fredrik Pettersson
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Sarbashis Das
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Biomedical Centre, Box 596, SE-751 24, Uppsala, Sweden.
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12
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Burke C, Abrahams KA, Richardson EJ, Loman NJ, Alemparte C, Lelievre J, Besra GS. Development of a whole-cell high-throughput phenotypic screen to identify inhibitors of mycobacterial amino acid biosynthesis. FASEB Bioadv 2019; 1:246-254. [PMID: 32123830 PMCID: PMC6996392 DOI: 10.1096/fba.2018-00048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/17/2018] [Accepted: 12/20/2018] [Indexed: 01/08/2023] Open
Abstract
Anti-tubercular drug discovery continues to be dominated by whole-cell high-throughput screening campaigns, enabling the rapid discovery of new inhibitory chemical scaffolds. Target-based screening is a popular approach to direct inhibitor discovery with a specified mode of action, eliminating the discovery of anti-tubercular agents against unsuitable targets. Herein, a screening method has been developed using Mycobacterium bovis BCG to identify inhibitors of amino acid biosynthesis. The methodology was initially optimized using the known branched-chain amino acid biosynthetic inhibitors metsulfuron-methyl (MSM) and sulfometuron-methyl (SMM), and subsequently, whole genome sequencing of resistant mutants and the use of over-expressor strains confirming their mode of action. The GlaxoSmithKline compound library of small molecule inhibitors with known activity against Mycobacterium tuberculosis was then used to validate the screen. In this paper, we have shown that media supplementation with amino acids can rescue M bovis BCG from known amino acid synthesis inhibitors, MSM and SMM, in a pathway specific manner. The therapeutic potential of amino acid biosynthesis inhibitors emphasizes the importance of this innovative screen, enabling the discovery of compounds targeting a multitude of related essential biochemical pathways, without limiting drug discovery toward a single target.
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Affiliation(s)
| | | | | | | | | | - Joel Lelievre
- Diseases of the Developing World, GlaxoSmithKlineMadridSpain
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Kanvatirth P, Jeeves RE, Bacon J, Besra GS, Alderwick LJ. Utilisation of the Prestwick Chemical Library to identify drugs that inhibit the growth of mycobacteria. PLoS One 2019; 14:e0213713. [PMID: 30861059 PMCID: PMC6414029 DOI: 10.1371/journal.pone.0213713] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/27/2019] [Indexed: 11/19/2022] Open
Abstract
Tuberculosis (TB) is an infectious bacterial disease that kills approximately 1.3 million people every year. Despite global efforts to reduce both the incidence and mortality associated with TB, the emergence of drug resistant strains has slowed any progress made towards combating the spread of this deadly disease. The current TB drug regimen is inadequate, takes months to complete and poses significant challenges when administering to patients suffering from drug resistant TB. New treatments that are faster, simpler and more affordable are urgently required. Arguably, a good strategy to discover new drugs is to start with an old drug. Here, we have screened a library of 1200 FDA approved drugs from the Prestwick Chemical library using a GFP microplate assay. Drugs were screened against GFP expressing strains of Mycobacterium smegmatis and Mycobacterium bovis BCG as surrogates for Mycobacterium tuberculosis, the causative agent of TB in humans. We identified several classes of drugs that displayed antimycobacterial activity against both M. smegmatis and BCG, however each organism also displayed some selectivity towards certain drug classes. Variant analysis of whole genomes sequenced for resistant mutants raised to florfenicol, vanoxerine and pentamidine highlight new pathways that could be exploited in drug repurposing programmes.
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Affiliation(s)
- Panchali Kanvatirth
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rose E. Jeeves
- TB Research Group, National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Joanna Bacon
- TB Research Group, National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Luke J. Alderwick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail:
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14
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Identification and characterization of aspartyl-tRNA synthetase inhibitors against Mycobacterium tuberculosis by an integrated whole-cell target-based approach. Sci Rep 2018; 8:12664. [PMID: 30140040 PMCID: PMC6107548 DOI: 10.1038/s41598-018-31157-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/13/2018] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, has surpassed HIV as the leading cause of death due to an infectious disease worldwide, being responsible for more than 1.5 million deaths in low-income countries. In response to a pandemic threat by drug resistant strains, the tuberculosis research community is searching for new chemical entities with novel mechanisms of action to avoid drug resistance and shorten treatment regimens using combinatorial chemotherapy. Herein, we have identified several novel chemical scaffolds, GSK97C (spiro-oxazolidin-2-one), GSK93A (2-amino-1,3-thiazole, GSK85A and GSK92A (enamides), which target M. tuberculosis aspartyl-tRNA synthetase (Mt-AspRS), an essential component of the protein synthesis machinery of tuberculosis, using a whole-cell target-based screening strategy against a genetically modified Mycobacterium bovis BCG strain. We also provide further evidence of protein inhibition and inhibitor profiling through a classical aminoacylation reaction and a tRNA-independent assay, respectively. Altogether, our results have identified a number of hit new molecules with novel mechanism of action for further development through medicinal chemistry as hits and leads.
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Barh D, Tiwari S, Kumavath RN, Ghosh P, Azevedo V. Linking common non-coding RNAs of human lung cancer and M. tuberculosis. Bioinformation 2018; 14:337-345. [PMID: 30237679 PMCID: PMC6137563 DOI: 10.6026/97320630014337] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 06/29/2018] [Accepted: 06/30/2018] [Indexed: 02/07/2023] Open
Abstract
Lung cancer and pulmonary tuberculosis caused by Mycobacterium are two major causes of deaths worldwide. Tuberculosis linked lung cancer is known. However, the precise molecular mechanism of Mycobacterium associated increased risk of lung cancer is not understood. We report 45 common human miRNAs deregulated in both pulmonary tuberculosis and lung cancer. We show that sRNA_1096 and sRNA_1414 from M. tuberculosis have sequence homology with human mir-21. Hence, the potential role of these three small non-coding RNAs in rifampicin resistance in pulmonary tuberculosis is implied. Further, the linking of sRNA_1096 and sRNA_1414 from M. tuberculosis with the host lung tumorigenesis is inferred. Nonetheless, further analysis and validation is required to associate these three non-coding RNAs with Mycobacterium associated increased risk of lung cancer.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
- Laboratorio de Genetica Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciencias Biologicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
- Division of Bioinformatics and Computational Genomics, NITTE University Center for Science Education and Research (NUCSER), NITTE (Deemed to be University), Deralakatte, Mangaluru, Karnataka, India
| | - Sandeep Tiwari
- Laboratorio de Genetica Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciencias Biologicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
| | - Ranjith N. Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Tejaswini Hills, Periya (P.O) Kasaragod, Kerala-671316, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Virginia 23284, USA
| | - Vasco Azevedo
- Laboratorio de Genetica Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciencias Biologicas (ICB), Universidade Federal de Minas Gerais, Pampulha, Belo Horizonte, Minas Gerais, Brazil
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A Metabolomics Pilot Study on Desmoid Tumors and Novel Drug Candidates. Sci Rep 2018; 8:584. [PMID: 29330550 PMCID: PMC5766559 DOI: 10.1038/s41598-017-18921-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/19/2017] [Indexed: 12/21/2022] Open
Abstract
Desmoid tumors (aggressive fibromatosis) are locally invasive soft tissue tumors that lack the ability to metastasize. There are no directed therapies or standard treatment plan, and chemotherapeutics, radiation, and surgery often have temporary effects. The majority of desmoid tumors are related to T41A and S45F mutations of the beta-catenin encoding gene (CTNNB1). Using broad spectrum metabolomics, differences were investigated between paired normal fibroblast and desmoid tumor cells from affected patients. There were differences identified, also, in the metabolomics profiles associated with the two beta-catenin mutations, T41A and S45F. Ongoing drug screening has identified currently available compounds which inhibited desmoid tumor cellular growth by more than 50% but did not affect normal fibroblast proliferation. Two drugs were investigated in this study, and Dasatinib and FAK Inhibitor 14 treatments resulted in unique metabolomics profiles for the normal fibroblast and desmoid tumor cells, in addition to the T41A and S45F. The biochemical pathways that differentiated the cell lines were aminoacyl-tRNA biosynthesis in mitochondria and cytoplasm and signal transduction amino acid-dependent mTORC1 activation. This study provides preliminary understanding of the metabolic differences of paired normal and desmoid tumors cells, their response to desmoid tumor therapeutics, and new pathways to target for therapy.
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Abrahams KA, Cox JAG, Fütterer K, Rullas J, Ortega-Muro F, Loman NJ, Moynihan PJ, Pérez-Herrán E, Jiménez E, Esquivias J, Barros D, Ballell L, Alemparte C, Besra GS. Inhibiting mycobacterial tryptophan synthase by targeting the inter-subunit interface. Sci Rep 2017; 7:9430. [PMID: 28842600 PMCID: PMC5573416 DOI: 10.1038/s41598-017-09642-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 07/25/2017] [Indexed: 01/22/2023] Open
Abstract
Drug discovery efforts against the pathogen Mycobacterium tuberculosis (Mtb) have been advanced through phenotypic screens of extensive compound libraries. Such a screen revealed sulfolane 1 and indoline-5-sulfonamides 2 and 3 as potent inhibitors of mycobacterial growth. Optimization in the sulfolane series led to compound 4, which has proven activity in an in vivo murine model of Mtb infection. Here we identify the target and mode of inhibition of these compounds based on whole genome sequencing of spontaneous resistant mutants, which identified mutations locating to the essential α- and β-subunits of tryptophan synthase. Over-expression studies confirmed tryptophan synthase as the biological target. Biochemical techniques probed the mechanism of inhibition, revealing the mutant enzyme complex incurs a fitness cost but does not prevent inhibitor binding. Mapping of the resistance conferring mutations onto a low-resolution crystal structure of Mtb tryptophan synthase showed they locate to the interface between the α- and β-subunits. The discovery of anti-tubercular agents inhibiting tryptophan synthase highlights the therapeutic potential of this enzyme and draws attention to the prospect of other amino acid biosynthetic pathways as future Mtb drug targets.
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Affiliation(s)
- Katherine A Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jonathan A G Cox
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Klaus Fütterer
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Joaquín Rullas
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Fátima Ortega-Muro
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Patrick J Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Esther Pérez-Herrán
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Elena Jiménez
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Jorge Esquivias
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - David Barros
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Lluís Ballell
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain
| | - Carlos Alemparte
- Tres Cantos Medicines Development Campus, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Madrid, Spain.
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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Anti-tubercular drug discovery: in silico implications and challenges. Eur J Pharm Sci 2017; 104:1-15. [PMID: 28341614 DOI: 10.1016/j.ejps.2017.03.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/08/2017] [Accepted: 03/19/2017] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) has been reported as a major public health concern, especially in the developing countries. WHO report on tuberculosis 2016 shows a high mortality rate caused by TB leading to 1.8 million deaths worldwide (including deaths due to TB in HIV positive individuals), which is one of the top 10 causes of mortality in 2015. However, the main therapy used for the treatment of TB is still the Direct Observed Therapy Short-course (DOTS) that consists of four main first-line drugs. Due to the prolonged and unorganized use of these drugs, Mycobacterium tuberculosis (Mtb) has developed drug-resistance against them. To overcome this drug-resistance, efforts are continuously being made to develop new therapeutics. New drug-targets of Mtb are pursued by the researchers to develop their inhibitors. For this, new methodologies that comprise of the computational drug designing techniques are vigorously applied. A major limitation that is found with these techniques is the inability of the newly identified target-based inhibitors to inhibit the whole cell bacteria. A foremost factor for this limitation is the inability of these inhibitors to penetrate the bacterial cell wall. In this regard, various strategies to overcome this limitation have been discussed in detail in this review, along with new targets and new methodologies. A bunch of in silico tools available for the prediction of physicochemical properties that need to be explored to deal with the permeability issue of the Mtb inhibitors has also been discussed.
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Abstract
Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis (TB), is recognized as a global health emergency as promoted by the World Health Organization. Over 1 million deaths per year, along with the emergence of multi- and extensively-drug resistant strains of Mtb, have triggered intensive research into the pathogenicity and biochemistry of this microorganism, guiding the development of anti-TB chemotherapeutic agents. The essential mycobacterial cell wall, sharing some common features with all bacteria, represents an apparent ‘Achilles heel’ that has been targeted by TB chemotherapy since the advent of TB treatment. This complex structure composed of three distinct layers, peptidoglycan, arabinogalactan and mycolic acids, is vital in supporting cell growth, virulence and providing a barrier to antibiotics. The fundamental nature of cell wall synthesis and assembly has rendered the mycobacterial cell wall as the most widely exploited target of anti-TB drugs. This review provides an overview of the biosynthesis of the prominent cell wall components, highlighting the inhibitory mechanisms of existing clinical drugs and illustrating the potential of other unexploited enzymes as future drug targets.
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Spectrophotometric assays for monitoring tRNA aminoacylation and aminoacyl-tRNA hydrolysis reactions. Methods 2016; 113:3-12. [PMID: 27780756 DOI: 10.1016/j.ymeth.2016.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/17/2016] [Accepted: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Aminoacyl-tRNA synthetases play a central role in protein synthesis, catalyzing the attachment of amino acids to their cognate tRNAs. Here, we describe a spectrophotometric assay for tyrosyl-tRNA synthetase in which the Tyr-tRNA product is cleaved, regenerating the tRNA substrate. As tRNA is the limiting substrate in the assay, recycling it substantially increases the sensitivity of the assay while simultaneously reducing its cost. The tRNA aminoacylation reaction is monitored spectrophotometrically by coupling the production of AMP to the conversion of NAD+ to NADH. We have adapted the tyrosyl-tRNA synthetase assay to monitor: (1) aminoacylation of tRNA by l- or d-tyrosine, (2) cyclodipeptide formation by cyclodipeptide synthases, (3) hydrolysis of d-aminoacyl-tRNAs by d-tyrosyl-tRNA deacylase, and (4) post-transfer editing by aminoacyl-tRNA synthetases. All of these assays are continuous and homogenous, making them amenable for use in high-throughput screens of chemical libraries. In the case of the cyclodipeptide synthase, d-tyrosyl-tRNA deacylase, and post-transfer editing assays, the aminoacyl-tRNAs are generated in situ, avoiding the need to synthesize and purify aminoacyl-tRNA substrates prior to performing the assays. Lastly, we describe how the tyrosyl-tRNA synthetase assay can be adapted to monitor the activity of other aminoacyl-tRNA synthetases and how the approach to regenerating the tRNA substrate can be used to increase the sensitivity and decrease the cost of commercially available aminoacyl-tRNA synthetase assays.
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21
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Abrahams KA, Chung CW, Ghidelli-Disse S, Rullas J, Rebollo-López MJ, Gurcha SS, Cox JAG, Mendoza A, Jiménez-Navarro E, Martínez-Martínez MS, Neu M, Shillings A, Homes P, Argyrou A, Casanueva R, Loman NJ, Moynihan PJ, Lelièvre J, Selenski C, Axtman M, Kremer L, Bantscheff M, Angulo-Barturen I, Izquierdo MC, Cammack NC, Drewes G, Ballell L, Barros D, Besra GS, Bates RH. Identification of KasA as the cellular target of an anti-tubercular scaffold. Nat Commun 2016; 7:12581. [PMID: 27581223 PMCID: PMC5025758 DOI: 10.1038/ncomms12581] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 07/14/2016] [Indexed: 12/12/2022] Open
Abstract
Phenotypic screens for bactericidal compounds are starting to yield promising hits against tuberculosis. In this regard, whole-genome sequencing of spontaneous resistant mutants generated against an indazole sulfonamide (GSK3011724A) identifies several specific single-nucleotide polymorphisms in the essential Mycobacterium tuberculosis β-ketoacyl synthase (kas) A gene. Here, this genomic-based target assignment is confirmed by biochemical assays, chemical proteomics and structural resolution of a KasA-GSK3011724A complex by X-ray crystallography. Finally, M. tuberculosis GSK3011724A-resistant mutants increase the in vitro minimum inhibitory concentration and the in vivo 99% effective dose in mice, establishing in vitro and in vivo target engagement. Surprisingly, the lack of target engagement of the related β-ketoacyl synthases (FabH and KasB) suggests a different mode of inhibition when compared with other Kas inhibitors of fatty acid biosynthesis in bacteria. These results clearly identify KasA as the biological target of GSK3011724A and validate this enzyme for further drug discovery efforts against tuberculosis.
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Affiliation(s)
- Katherine A. Abrahams
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Chun-wa Chung
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Joaquín Rullas
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - María José Rebollo-López
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Sudagar S. Gurcha
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jonathan A. G. Cox
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Alfonso Mendoza
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Elena Jiménez-Navarro
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | | | - Margarete Neu
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Paul Homes
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Ruth Casanueva
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Nicholas J. Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Patrick J. Moynihan
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Joël Lelièvre
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Carolyn Selenski
- GlaxoSmithKline, 709 Swedeland Road, PO Box 1539, King of Prussia, Pennsylvania 19406-0939, USA
| | - Matthew Axtman
- GlaxoSmithKline, 709 Swedeland Road, PO Box 1539, King of Prussia, Pennsylvania 19406-0939, USA
| | - Laurent Kremer
- Centre National de la Recherche Scientifique FRE 3689, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé, Université de Montpellier, 1919 route de Mende, 34293 Montpellier, France
- INSERM, CPBS, 34293 Montpellier, France
| | - Marcus Bantscheff
- Cellzome—a GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Iñigo Angulo-Barturen
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Mónica Cacho Izquierdo
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Nicholas C. Cammack
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Gerard Drewes
- Cellzome—a GSK Company, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Lluis Ballell
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - David Barros
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
| | - Gurdyal S. Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert H. Bates
- Diseases of the Developing World, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, 28760 Madrid, Spain
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Abstract
Aminoacyl-tRNA synthetases (aaRSs) are modular enzymes globally conserved in the three kingdoms of life. All catalyze the same two-step reaction, i.e., the attachment of a proteinogenic amino acid on their cognate tRNAs, thereby mediating the correct expression of the genetic code. In addition, some aaRSs acquired other functions beyond this key role in translation. Genomics and X-ray crystallography have revealed great structural diversity in aaRSs (e.g., in oligomery and modularity, in ranking into two distinct groups each subdivided in 3 subgroups, by additional domains appended on the catalytic modules). AaRSs show huge structural plasticity related to function and limited idiosyncrasies that are kingdom or even species specific (e.g., the presence in many Bacteria of non discriminating aaRSs compensating for the absence of one or two specific aaRSs, notably AsnRS and/or GlnRS). Diversity, as well, occurs in the mechanisms of aaRS gene regulation that are not conserved in evolution, notably between distant groups such as Gram-positive and Gram-negative Bacteria. The review focuses on bacterial aaRSs (and their paralogs) and covers their structure, function, regulation, and evolution. Structure/function relationships are emphasized, notably the enzymology of tRNA aminoacylation and the editing mechanisms for correction of activation and charging errors. The huge amount of genomic and structural data that accumulated in last two decades is reviewed, showing how the field moved from essentially reductionist biology towards more global and integrated approaches. Likewise, the alternative functions of aaRSs and those of aaRS paralogs (e.g., during cell wall biogenesis and other metabolic processes in or outside protein synthesis) are reviewed. Since aaRS phylogenies present promiscuous bacterial, archaeal, and eukaryal features, similarities and differences in the properties of aaRSs from the three kingdoms of life are pinpointed throughout the review and distinctive characteristics of bacterium-like synthetases from organelles are outlined.
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Affiliation(s)
- Richard Giegé
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 67084 Strasbourg, France
| | - Mathias Springer
- Université Paris Diderot, Sorbonne Cité, UPR9073 CNRS, IBPC, 75005 Paris, France
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Ravishankar S, Ambady A, Swetha RG, Anbarasu A, Ramaiah S, Sambandamurthy VK. Essentiality Assessment of Cysteinyl and Lysyl-tRNA Synthetases of Mycobacterium smegmatis. PLoS One 2016; 11:e0147188. [PMID: 26794499 PMCID: PMC4721953 DOI: 10.1371/journal.pone.0147188] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 12/30/2015] [Indexed: 12/02/2022] Open
Abstract
Discovery of mupirocin, an antibiotic that targets isoleucyl-tRNA synthetase, established aminoacyl-tRNA synthetase as an attractive target for the discovery of novel antibacterial agents. Despite a high degree of similarity between the bacterial and human aminoacyl-tRNA synthetases, the selectivity observed with mupirocin triggered the possibility of targeting other aminoacyl-tRNA synthetases as potential drug targets. These enzymes catalyse the condensation of a specific amino acid to its cognate tRNA in an energy-dependent reaction. Therefore, each organism is expected to encode at least twenty aminoacyl-tRNA synthetases, one for each amino acid. However, a bioinformatics search for genes encoding aminoacyl-tRNA synthetases from Mycobacterium smegmatis returned multiple genes for glutamyl (GluRS), cysteinyl (CysRS), prolyl (ProRS) and lysyl (LysRS) tRNA synthetases. The pathogenic mycobacteria, namely, Mycobacterium tuberculosis and Mycobacterium leprae, were also found to possess two genes each for CysRS and LysRS. A similar search indicated the presence of additional genes for LysRS in gram negative bacteria as well. Herein, we describe sequence and structural analysis of the additional aminoacyl-tRNA synthetase genes found in M. smegmatis. Characterization of conditional expression strains of Cysteinyl and Lysyl-tRNA synthetases generated in M. smegmatis revealed that the canonical aminoacyl-tRNA synthetase are essential, while the additional ones are not essential for the growth of M. smegmatis.
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Affiliation(s)
- Sudha Ravishankar
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, 560024, India
| | - Anisha Ambady
- AstraZeneca India Pvt Ltd, Bellary Road, Hebbal, Bengaluru, 560024, India
| | - Rayapadi G. Swetha
- School of Biosciences & Technology, VIT University, Vellore, 632014, India
| | - Anand Anbarasu
- School of Biosciences & Technology, VIT University, Vellore, 632014, India
| | - Sudha Ramaiah
- School of Biosciences & Technology, VIT University, Vellore, 632014, India
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Cox JAG, Abrahams KA, Alemparte C, Ghidelli-Disse S, Rullas J, Angulo-Barturen I, Singh A, Gurcha SS, Nataraj V, Bethell S, Remuiñán MJ, Encinas L, Jervis PJ, Cammack NC, Bhatt A, Kruse U, Bantscheff M, Fütterer K, Barros D, Ballell L, Drewes G, Besra GS. THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria. Nat Microbiol 2016; 1:15006. [DOI: 10.1038/nmicrobiol.2015.6] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/02/2015] [Indexed: 01/18/2023]
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Punina NV, Makridakis NM, Remnev MA, Topunov AF. Whole-genome sequencing targets drug-resistant bacterial infections. Hum Genomics 2015; 9:19. [PMID: 26243131 PMCID: PMC4525730 DOI: 10.1186/s40246-015-0037-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 07/03/2015] [Indexed: 01/07/2023] Open
Abstract
During the past two decades, the technological progress of whole-genome sequencing (WGS) had changed the fields of Environmental Microbiology and Biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of Public Health, Epidemiology, Health Economics, and national productivity. Today’s WGS technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in clinical laboratories and in long-term epidemiological investigations. WGS gives rise to an exciting future direction for personalized Genomic Epidemiology. One of the most vital and growing public health problems is the emerging and re-emerging of multidrug-resistant (MDR) bacterial infections in the communities and healthcare settings, reinforced by a decline in antimicrobial drug discovery. In recent years, retrospective analysis provided by WGS has had a great impact on the identification and tracking of MDR microorganisms in hospitals and communities. The obtained genomic data are also important for developing novel easy-to-use diagnostic assays for clinics, as well as for antibiotic and therapeutic development at both the personal and population levels. At present, this technology has been successfully applied as an addendum to the real-time diagnostic methods currently used in clinical laboratories. However, the significance of WGS for public health may increase if: (a) unified and user-friendly bioinformatics toolsets for easy data interpretation and management are established, and (b) standards for data validation and verification are developed. Herein, we review the current and future impact of this technology on diagnosis, prevention, treatment, and control of MDR infectious bacteria in clinics and on the global scale.
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Affiliation(s)
- N V Punina
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia.
| | - N M Makridakis
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - M A Remnev
- The Federal State Unitary Enterprise All-Russia Research Institute of Automatics, Moscow, 127055, Russia
| | - A F Topunov
- Bach Institute of Biochemistry, Russian Academy of Science, Moscow, 119071, Russia
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