1
|
Elkolli M, Elkolli H, Alam M, Benguerba Y. In silico study of antibacterial tyrosyl-tRNA synthetase and toxicity of main phytoconstituents from three active essential oils. J Biomol Struct Dyn 2024; 42:1404-1416. [PMID: 37066614 DOI: 10.1080/07391102.2023.2199865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 04/01/2023] [Indexed: 04/18/2023]
Abstract
The misuse and overuse of antibiotics have resulted in antibiotic resistance. However, there are alternative approaches that could either substitute antibiotics or enhance their effectiveness without harmful side effects. One such approach is the use of terpene-rich essential oils. In this study, we aimed to demonstrate the antibacterial activity of the main components of three plant essential oils, namely Anthemis punctata, Anthemis pedunculata and Daucus crinitus. Specifically, we targeted bacterial tyrosyl-tRNA synthetase, an enzyme that plays a critical role in bacterial protein synthesis. To investigate how the phytocompounds interact with the enzyme's active sites, we employed a molecular docking study using Autodock Software Tools 1.5.7. Our findings revealed that all 28 phytocompounds bound to the enzyme's active sites with binding energies ranging from -6.96 to -4.03 kcal/mol. These results suggest that terpene-rich essential oils could be a potential source of novel antimicrobial agents.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Meriem Elkolli
- Laboratoire de Microbiologie Appliquée, Faculté des Sciences de la Nature et de la Vie, Setif, Algeria
| | - Hayet Elkolli
- Laboratoire des Matériaux Polymériques Multiphasiques, Département de Génie des Procédés, Faculté de Technologie, Sétif, Algeria
| | - Manawwer Alam
- Department of Chemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Yacine Benguerba
- Laboratoire de Biopharmacie et Pharmacotechnie (LPBT), Ferhat Abbas Setif 1 University, Setif, Algeria
| |
Collapse
|
2
|
Avila‐Cobian LF, Hoshino H, Horsman ME, Nguyen VT, Qian Y, Feltzer R, Kim C, Hu DD, Champion MM, Fisher JF, Mobashery S. Amber-codon suppression for spatial localization and in vivo photoaffinity capture of the interactome of the Pseudomonas aeruginosa rare lipoprotein A lytic transglycosylase. Protein Sci 2023; 32:e4781. [PMID: 37703013 PMCID: PMC10536563 DOI: 10.1002/pro.4781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
The 11 lytic transglycosylases of Pseudomonas aeruginosa have overlapping activities in the turnover of the cell-wall peptidoglycan. Rare lipoprotein A (RlpA) is distinct among the 11 by its use of only peptidoglycan lacking peptide stems. The spatial localization of RlpA and its interactome within P. aeruginosa are unknown. We employed suppression of introduced amber codons at sites in the rlpA gene for the introduction of the unnatural-amino-acids Νζ -[(2-azidoethoxy)carbonyl]-l-lysine (compound 1) and Nζ -[[[3-(3-methyl-3H-diazirin-3-yl)propyl]amino]carbonyl]-l-lysine (compound 2). In live P. aeruginosa, full-length RlpA incorporating compound 1 into its sequence was fluorescently tagged using strained-promoted alkyne-azide cycloaddition and examined by fluorescence microscopy. RlpA is present at low levels along the sidewall length of the bacterium, and at higher levels at the nascent septa of replicating bacteria. In intact P. aeruginosa, UV photolysis of full-length RlpA having compound 2 within its sequence generated a transient reactive carbene, which engaged in photoaffinity capture of neighboring proteins. Thirteen proteins were identified. Three of these proteins-PBP1a, PBP5, and MreB-are members of the bacterial divisome. The use of the complementary methodologies of non-canonical amino-acid incorporation, photoaffinity proximity analysis, and fluorescent microscopy confirm a dominant septal location for the RlpA enzyme of P. aeruginosa, as a divisome-associated activity. This accomplishment adds to the emerging recognition of the value of these methodologies for identification of the intracellular localization of bacterial proteins.
Collapse
Affiliation(s)
- Luis F. Avila‐Cobian
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Hidekazu Hoshino
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Mark E. Horsman
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Van T. Nguyen
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Yuanyuan Qian
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Rhona Feltzer
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Choon Kim
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Daniel D. Hu
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Matthew M. Champion
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| |
Collapse
|
3
|
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.
Collapse
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.
| |
Collapse
|
4
|
Obiștioiu D, Hulea A, Cocan I, Alexa E, Negrea M, Popescu I, Herman V, Imbrea IM, Heghedus-Mindru G, Suleiman MA, Radulov I, Imbrea F. Boswellia Essential Oil: Natural Antioxidant as an Effective Antimicrobial and Anti-Inflammatory Agent. Antioxidants (Basel) 2023; 12:1807. [PMID: 37891886 PMCID: PMC10603989 DOI: 10.3390/antiox12101807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The research aimed to determine the chemical composition, the antioxidant and anti-inflammatory activity as well as the antimicrobial activity against Gram-positive, Gram-negative and two fungal Candida ATCC strains of a commercial Boswellia essential oil (BEO) containing Boswellia carteri, Boswellia sacra, Boswellia papryfera, and Boswellia frereana. Additionally, molecular docking was carried out to show the molecular dynamics of the compounds identified from the essential oil against three bacterial protein targets and one fungal protein target. The major components identified by GC-MS (Gas Chromatography-Mass Spectrometry) were represented by α-pinene, followed by limonene. Evaluation of antioxidant activity using the DPPH (2,2-Diphenyl-1-Picrylhydrazyl) method showed high inhibition comparable to the synthetic antioxidant used as a control. Oxidative stability evaluation showed that BEO has the potential to inhibit primary and secondary oxidation products with almost the same efficacy as butylated hydroxyanisole (BHA). The use of BEO at a concentration of 500 ppm provided the best protection against secondary oxidation during 30 days of storage at room temperature, which was also evident in the peroxide value. Regarding the in vitro anti-inflammatory activity, the membrane lysis assay and the protein denaturation test revealed that even if the value of protection was lower than the value registered in the case of dexamethasone, the recommendation of using BEO as a protective agent stands, considering the lower side effects. Gram-positive bacteria proved more sensitive, while Pseudomonas aeruginosa presented different sensitivity, with higher MICs (minimal inhibitory concentration). Haemophilus influenzae demonstrated a MIC at 2% but with consecutive inhibitory values in a negative correlation with the increase in concentration, in contrast to E. coli, which demonstrated low inhibitory rates at high concentrations of BEO. The computational tools employed revealed interesting binding energies with compounds having low abundance. The interaction of these compounds and the proteins (tyrosyl-tRNA synthetase, DNA gyrase, peptide deformylase, 1,3-β-glucan synthase) predicts hydrogen bonds with amino acid residues, which are reported in the active sites of the proteins. Even so, compounds with low abundance in BEO could render the desired bioactive properties to the overall function of the oil sustained by physical factors such as storage and temperature. Interestingly, the findings from this study demonstrated the antioxidant and antimicrobial potential of Boswellia essential oil against food-related pathogens, thus making the oil a good candidate for usage in food, feed or food-safety-related products.
Collapse
Affiliation(s)
- Diana Obiștioiu
- Faculty of Agriculture, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (D.O.); (I.P.); (I.R.); (F.I.)
| | - Anca Hulea
- Faculty of Veterinary Medicine, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania;
| | - Ileana Cocan
- Faculty of Food Engineering, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (E.A.); (M.N.); (G.H.-M.)
| | - Ersilia Alexa
- Faculty of Food Engineering, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (E.A.); (M.N.); (G.H.-M.)
| | - Monica Negrea
- Faculty of Food Engineering, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (E.A.); (M.N.); (G.H.-M.)
| | - Iuliana Popescu
- Faculty of Agriculture, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (D.O.); (I.P.); (I.R.); (F.I.)
| | - Viorel Herman
- Faculty of Veterinary Medicine, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania;
| | - Ilinca Merima Imbrea
- Faculty of Engineering and Applied Technologies, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania;
| | - Gabriel Heghedus-Mindru
- Faculty of Food Engineering, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (E.A.); (M.N.); (G.H.-M.)
| | - Mukhtar Adeiza Suleiman
- Faculty of Life Science, Department of Biochemistry, Ahmadu Bello University, Zaria 810107, Kaduna State, Nigeria;
| | - Isidora Radulov
- Faculty of Agriculture, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (D.O.); (I.P.); (I.R.); (F.I.)
| | - Florin Imbrea
- Faculty of Agriculture, University of Life Sciences “King Michael I” from Timisoara, Calea Aradului 119, 300645 Timisoara, Romania; (D.O.); (I.P.); (I.R.); (F.I.)
| |
Collapse
|
5
|
Triazole-containing hybrids with anti- Mycobacterium tuberculosis potential - Part I: 1,2,3-Triazole. Future Med Chem 2021; 13:643-662. [PMID: 33619989 DOI: 10.4155/fmc-2020-0301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Tuberculosis regimens currently applied in clinical practice require months of multidrug therapy, which imposes a major challenge of patient compliance and drug resistance development. Moreover, because of the increasing emergence of hard-to-treat tuberculosis, this disease continues to be a significant threat to the human population. 1,2,3-triazole as a privileged structure has been widely used as an effective template for drug discovery, and 1,2,3-triazole-containing hybrids that can simultaneously act on dual or multiple targets in Mycobacterium tuberculosis have the potential to circumvent drug resistance, enhance efficacy, reduce side effects and improve pharmacokinetic as well as pharmacodynamic profiles. Thus, 1,2,3-triazole-containing hybrids are useful scaffolds for the development of antitubercular agents. This review aims to highlight recent advances of 1,2,3-triazole-containing hybrids with potential activity against various forms of M. tuberculosis, covering articles published between 2015 and 2020. The structure-activity relationship and the mechanism of action are also discussed to facilitate further rational design of more effective drug candidates.
Collapse
|
6
|
De Ruysscher D, Pang L, Lenders SMG, Cappoen D, Cos P, Rozenski J, Strelkov SV, Weeks SD, Van Aerschot A. Synthesis and structure-activity studies of novel anhydrohexitol-based Leucyl-tRNA synthetase inhibitors. Eur J Med Chem 2020; 211:113021. [PMID: 33248851 DOI: 10.1016/j.ejmech.2020.113021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/20/2020] [Accepted: 11/10/2020] [Indexed: 12/01/2022]
Abstract
Leucyl-tRNA synthetase (LeuRS) is a clinically validated target for the development of antimicrobials. This enzyme catalyzes the formation of charged tRNALeu molecules, an essential substrate for protein translation. In the first step of catalysis LeuRS activates leucine using ATP, forming a leucyl-adenylate intermediate. Bi-substrate inhibitors that mimic this chemically labile phosphoanhydride-linked nucleoside have proven to be potent inhibitors of different members of the aminoacyl-tRNA synthetase family but, to date, they have demonstrated poor antibacterial activity. We synthesized a small series of 1,5-anhydrohexitol-based analogues coupled to a variety of triazoles and performed detailed structure-activity relationship studies with bacterial LeuRS. In an in vitro assay, Kiapp values in the nanomolar range were demonstrated. Inhibitory activity differences between the compounds revealed that the polarity and size of the triazole substituents affect binding. X-ray crystallographic studies of N. gonorrhoeae LeuRS in complex with all the inhibitors highlighted the crucial interactions defining their relative enzyme inhibitory activities. We further examined their in vitro antimicrobial properties by screening against several bacterial and yeast strains. While only weak antibacterial activity against M. tuberculosis was detected, the extensive structural data which were obtained could make these LeuRS inhibitors a suitable starting point towards further antibiotic development.
Collapse
Affiliation(s)
- Dries De Ruysscher
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium
| | - Luping Pang
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium; Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium
| | - Stijn M G Lenders
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene, Department of Pharmaceutical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium
| | - Sergei V Strelkov
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium
| | - Stephen D Weeks
- Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 822, 3000, Leuven, Belgium.
| | - Arthur Van Aerschot
- Medicinal Chemistry, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Herestraat 49 - Box 1030, 3000, Leuven, Belgium.
| |
Collapse
|