tyrosyl-tRNA Synthetase Research Articles

In-silico prediction and in vitro validation of antioxidant, antibacterial and antifungal potential of Black Turmeric (Curcuma caesia Roxb.) essential oils and its constituents

The growing interest in the health and pharmaceutical industries has led to a significant increase in demand for essential oils. Curcuma caesia, as a member of the Zingiberaceae family, has been used for its high-quality essential oils (EOs) with remarkable therapeutic properties. The current study aimed at predicting the in-silico interactions of C. caesia volatile constituents against the protein responsible for oxidative and microbial stress in order to investigate their potential for industrial and pharmaceutical applications. The accuracy of the in-silico predictions was confirmed by carrying out the in vitro validation of the antioxidant, antibacterial, and antifungal activity of the EOs derived from the rhizome and leaves, as well as its volatile constituents. EOs from the rhizome and leaf samples of C. caesia were extracted through the hydro distillation method and yielded a percentage (%) of 1.80 ± 0.02 and 0.95 ± 0.02 (fresh weight basis, v/w), respectively. A total of 38 and 29 volatile constituents were identified in the rhizome and leaf EOs by gas-chromatography mass spectrometry analysis, representing 92.55% and 90.75% of the total peak area, respectively. The rhizome and leaf EOs showed oxygenated sesquiterpene (39.91% and 27.69%) as the predominate fractions followed by sesquiterpene hydrocarbons (13.36% and 18.44%). Curzerenone (18.09%), epicurzerenone (12.47%), eucalyptol (11.57%), camphor (5.94%), and germacrone (4.47%) were the major constituents in the rhizome EO, whereas, the leaf EO was dominated by eucalyptol (12.53%), camphor (7.23%), curzerenone (5.24%), germacrone (4.81%) and curzerene (4.9%). The in vitro biological activities such as antioxidant, antibacterial, and antifungal potential of C. caesia EOs were evaluated. The antioxidant evaluation using enzymatic and non-enzymatic assays, showed excellent potential of C. caesia EOs as compared to standard drugs. Specifically, in the enzymatic assay, leaf EO of C. caesia was resulted into the reduction of ROS and an increase in the activity of superoxide dismutase (SOD), catalase (CAT), and glutathione S-transferase (GST) in OZ-stimulated PMNs. The EOs also displayed a remarkable antibacterial activity against Staphylococcus aureus, elucidating it as the most susceptible strain. Further, the in-silico prediction of the constituents was conducted using Swiss-ADME, and molecular docking analysis. Swiss-ADME revealed the drug-likeness and safety properties of constituents present in C. caesia EOs. The molecular docking study was carried out to interpret the possible interactions of phytoconstituents qualified in the Swiss-ADME study with two bacterial proteins (Tyrosyl-tRNA synthetase from Staphylococcus aureus (PDB ID: 1JIJ) and Glucosamine 6-phosphate synthase from Escherichia coli (PDB ID: 1XFF)), one fungal protein (N-myristoyl transferase from Candida albicans (PDB ID: 1IYL)) and one oxidative protein (Human peroxiredoxin 5 (PDB ID: 1HD2)). Furthermore, to validate the result of molecular docking, the biological activity of higher affinity constituents was also evaluated. As a result, the in vitro findings supported the in-silico prediction. Therefore, C. caesia or its constituents like curzerenone, camphor, eucalyptol, epicurzerenone, germacrone, viridifloral, muurola-4,10(14)-dien-1-ol, and globulol might be a valuable source for developing antioxidant and antimicrobial drugs. To the best of present author’s knowledge, this is the first scientific report on the in-silico prediction of C. caesia constituents against bacterial, fungal and oxidative proteins through molecular docking, which may contribute to the development of various alternatives against multi-drug resistance.

Phytochemical and antibacterial analysis of Pistacia integerrima: An integrated in vitro and in silico approach

Antibiotic resistance is a global concern due to the ability of bacteria to continuously develop various mechanisms of resistance against diverse antimicrobial classes; therefore, there is a critical prerequisite to discover diverse antibiotics with novel chemical structures and unique mechanisms of action. The research work aimed to investigate the detailed antibacterial activity and phytochemical characterization of the methanolic extract of Pistacia integerrima galls. Antibacterial properties were analyzed through the well diffusion method and the minimum inhibitory concentration (MIC) was determined through the broth dilution method. MIC of Pistacia integerrima extract (PIE) was found to be 10 mg/mL against both E. coli and S. aureus. Biofilm inhibition was determined by the crystal violet method where PIE demonstrated significant inhibition of biofilms. In the presence of PIE, TEM demonstrated morphological changes in both strains. A total of 17 metabolites were identified through GC-MS analysis with most of the compounds exhibiting antibacterial properties, HPTLC shows the presence of the important metabolite quercetin. Furthermore, virtual ligand screening revealed quercetin and phthalic acid as the most medicinally active constituents and potential inhibitors of tyrosyl-tRNA synthetase (TyrRS) and Dihydrofolate reductase (DHFR). Further research into PIE's bioactive compounds could lead to the development of new antibacterial compounds.

Orthogonal translation with 5-cyanotryptophan as an infrared probe for local structural information, electrostatics, and hydrogen bonding.

Orthogonal translation is an efficient tool that provides many valuable spectral probes capable of covering different parts of the electromagnetic spectrum and thus enabling parameterization of various structural and dynamic phenomena in proteins. In this context, nitrile-containing tryptophan analogs are very useful probes to study local electrostatics and hydrogen bonding in both rigid and dynamic environments. Here, we report a semi-rational approach to engineer a tyrosyl-tRNA synthetase (TyrRS) variant of Methanocaldococcus jannaschii capable of incorporating 5-cyanotryptophan (5CNW) via orthogonal translation. We combined one round of the well-established positive selection system with saturation mutagenesis at preselected TyrRS positions, resulting in a novel 5CNW-specific enzyme that also exhibits high substrate tolerance to other aromatic noncanonical amino acids. We demonstrated the utility of our orthogonal pair by inserting 5CNW into the cyanobacteriochrome Slr1393g3, a bilin-binding photosensor of the phytochrome superfamily. The nitrile (CN) group of the inserted 5CNW provides non-invasive labeling in the local structural context while yielding information on local electrostatics and hydrogen bonding by IR spectroscopy. 5CNW is a versatile probe that can be used for both static and dynamic measurements.

Structural basis of antibacterial photodynamic action of curcumin against S. aureus

Antimicrobial photodynamic therapy (aPDT) is an alternative tool to commercial antibiotics for the inactivation of pathogenic bacteria (e.g., S. aureus). However, there is still a lack of understanding of the molecular modeling of the photosensitizers and their mechanism of action through oxidative pathways. Herein, a combined experimental and computational evaluation of curcumin as a photosensitizer against S. aureus was performed. The radical forms of keto-enol tautomers and the energies of curcumin's frontier molecular orbitals were evaluated by density functional theory (DFT) to point out the photodynamic action as well as the photobleaching process. Furthermore, the electronic transitions of curcumin keto-enol tautomers were undertaken to predict the transitions as a photosensitizer during the antibacterial photodynamic process. Moreover, molecular docking was used to evaluate the binding affinity with the S. aureus tyrosyl-tRNA synthetase as the proposed a target for curcumin. In this regard, the molecular orbital energies show that the curcumin enol form has a character of 4.5% more basic than the keto form – the enol form is a more promising electron donor than its tautomer. Curcumin is a strong electrophile, with the enol form being 4.6% more electrophilic than its keto form. In addition, the regions susceptible to nucleophilic attack and photobleaching were evaluated by the Fukui function. Regarding the docking analysis, the model suggested that four hydrogen bonds contribute to the binding energy of curcumin's interaction with the ligand binding site of S. aureus tyrosyl-tRNA synthetase. Finally, residues Tyr36, Asp40, and Asp177 contact curcumin and may contribute to orienting the curcumin in the active area. Moreover, curcumin presented a photoinactivation of 4.5 log unit corroborating the necessity of the combined action of curcumin, light, and O2 to promote the photooxidation damage of S. aureus. These computational and experimental data suggest insights regarding the mechanism of action of curcumin as a photosensitizer to inactivate S. aureus bacteria.

Nuclear translocation of an aminoacyl-tRNA synthetase may mediate a chronic “integrated stress response”

Various stress conditions are signaled through phosphorylation of translation initiation factor eukaryotic initiation factor 2α (eIF2α) to inhibit global translation while selectively activating transcription factor ATF4 to aid cell survival and recovery. However, this integrated stress response is acute and cannot resolve lasting stress. Here, we report that tyrosyl-tRNA synthetase (TyrRS), a member of the aminoacyl-tRNA synthetase family that responds to diverse stress conditions through cytosol-nucleus translocation to activate stress-response genes, also inhibits global translation. However, it occurs at a later stage than eIF2α/ATF4 and mammalian target of rapamycin (mTOR) responses. Excluding TyrRS from the nucleus over-activates translation and increases apoptosis in cells under prolonged oxidative stress. Nuclear TyrRS transcriptionally represses translation genes by recruiting TRIM28 and/or NuRD complex. We propose that TyrRS, possibly along with other family members, can sense a variety of stress signals through intrinsic properties of this enzyme and strategically located nuclear localization signal and integrate them by nucleus translocation to effect protective responses against chronic stress.

Synthesis, Crystal Structure, DFT Calculations, Hirshfeld Surface Analysis and In Silico Drug-Target Profiling of (R)-2-(2-(1,3-Dioxoisoindolin-2-yl)propanamido)benzoic Acid Methyl Ester.

The work here reflects synthesis, DFT studies, Hirshfeld charge analysis and crystal data exploration of pharmacologically important (R)-2-(2-(1,3-dioxoisoindolin-2-yl)propanamido)benzoic acid methyl ester (5) to understand its properties for further chemical transformations. The methyl anthranilate (2) was produced by the esterification of anthranilic acid in an acidic medium. The phthaloyl-protected alanine (4) was rendered by the fusion of alanine with phthalic anhydride at 150 °C, followed by coupling with (2) furnished isoindole (5). The characterization of products was performed using IR, UV-Vis, NMR and MS. Single-crystal XRD also verified the structure of (5) in which N-H⋯O bonding stabilizes the molecular configuration of (5), resulting in the formation of S(6) hydrogen-bonded loop. The molecules of isoindole (5) are connected in the form of dimers, and the π⋯π stacking interaction between aromatic rings further stabilizes the crystal packing. DFT studies suggest that HOMO is over the substituted aromatic ring, the LUMO is present mainly over the indole side, and nucleophilic and electrophilic corners point out the reactivity of the product (5). In vitro and in silico analysis of (5) shows its potential as an antibacterial agent targeting DNA gyrase and Dihydroorotase from E. coli and tyrosyl-tRNA synthetase and DNA gyrase from Staphylococcus aureus.

Therapeutic Potential of HMF and Its Derivatives: a Computational Study.

Over the past century, chemicals and energy have increasingly been derived from non-renewable resources. The growing demand for essential chemicals and shrinking inventory make reliable, sustainable sources essential. Carbohydrates offer by far the greatest carbon supply. Furan compounds, a particular family of dehydration products, are believed to offer high chemical potential. Here, we analyze 5-HMF (5, hydroxymethylfurfural) and some of its derivatives in particular, a furan-type platform chemical. To analyze the therapeutic potential of HMF and its derivatives, this study utilized cutting-edge technologies such as computer-aided drug design, virtual screening, molecular docking, and molecular dynamic simulation. We conducted 189 docking simulations and examined some of the most promising dock poses using the molecular dynamic simulator. As for the receptors for our compounds, the leading candidates are human acetylcholinesterase, beta-lactamases, P. aeruginosa LasR, and S. aureus tyrosyl-tRNA synthetases. Out of all derivatives considered in this study, 2,5-furandicarboxylic acid (FCA) performed best.

Synthesis, spectroscopic characterization, molecular studies, and biological evaluation of (E)-N'-((7-methyl-2-oxo-1,2-dihydroquinolin-3-yl)methylene)morpholine-4-carbothiohydrazide and some of its transition metal complexes

Novel Ni(II), Cu(II), Zn(II), Cd(II), and Pd(II) complexes (1–6) with (E)-N'-((7-methyl-2-oxo-1,2-dihydroquinolin-3-yl)methylene)morpholine-4-carbothiohydrazide ligand (HL) were prepared and characterized via different analytical and spectroscopic techniques. The spectral data showed that the ligand is bound with copper(II) chloride, zinc(II) chloride, cadmium(II) chloride, and potassium tetrachloropalladate(II) in its neutral thione form in complexes 2, 4, 5, and 6, respectively. Furthermore, the ligand was coordinated with nickel (II) chloride and copper(II) acetate in complexes 1 and 3 as a monobasic tridentate in its thiol form. Thermogravimetric studies were performed for the prepared compounds and the pyrolytic mechanism was proposed for some complexes. DFT, TD-DFT, and NBO calculations were achieved at the B3LYP/LanL2DZ level of theory. Computational studies showed that the investigated compounds have high hyperpolarizability values (β) suggesting their potential use in the creation of non-linear optical materials. Many bacterial and fungal strains were used to assess the ligand and its metal complexes' antibacterial activities. In general, metal complexes have been shown to possess a stronger antibacterial and antifungal effect thanthe free ligand. Complex 5 exhibited respectable antibacterial activity versus Gram-positive bacteria. Furthermore, Zn(II) and Cd(II), complexes 4 and 5 have shown excellent activity against Gram-negative bacteria. Complex 4 exhibited a superior antifungal activity against two types of tested fungi compared with other compounds and standard Ketoconazole. Molecular docking of the ligand and its complexes 1, 2, and 5 were performed against tyrosyl-tRNA synthetase. The more negative values of the binding energy indicate that complexes 1 and 5 have higher inhibition efficiency than the free ligand.

Antibacterial Activity of Legundi Leaf (Vitex trifolia) Essential Oil Using In-Vitro and In-Silico Methods

Staphylococcus aureus causes many severe diseases, such as meningitis, lung infection, and hematogenous osteomyelitis. The prolonged use of antibiotic drugs leads to antimicrobial resistance (AMR), decreasing their effectiveness against S. aureus. Therefore, novel drugs isolated from natural products have been the focus of many researchers to solve that problem. The essential oils isolated from Vitex trifolia leaf have many pharmacological activities, including antibacterial and antifungal activities. In this research, essential oil was isolated by distillation, followed by GC-MS analysis. The antibacterial activity of the essential oil was conducted using a disc diffusion test (KirbyBauer) and by molecular docking study. The essential oil yield from distillation was 0.13%, containing major compounds such as sabinene, eucalyptol, terpinen-4-ol, αterpineol, limonene, and caryophyllene. The essential oil gave intermediate inhibition against S. aureus with a 6.91 ± 0.03 mm inhibition zone in 20 mg/mL of the sample. Using molecular docking study, caryophyllene and α-terpineol were the key compounds for inhibiting the active site of tyrosyl-tRNA synthetase, sortase A, and dihydrofolate reductase that are responsible for the S. aureus growth and development

Phytochemical profiling, antimicrobial, antibiofilm, insecticidal, and anti-leishmanial properties of aqueous extract from Juglans regia L. root bark: In vitro and in silico approaches

ABSTRACT The Juglans regia root aqueous extract (JRRAE) phytochemical variability and the investigation of their antimicrobial, antibiofilm, insecticidal, and anti-leishmanial properties were studied. As a result, the JRRAE chemical profile revealed the presence of biomolecules using UV, HPLC, and FT-IR analysis. The investigations showed marked antibacterial activities, highlighted inhibited biofilm formation, induced lethality Leishmania amazonensis promastigotes (50%), and possess an insecticidal activity at 100 µg/ml. A molecular docking study was performed against S. aureus gyrase, S. aureus tyrosyl-tRNA synthetase, human peroxiredoxin 5, cyclooxygenase-2, and trypanothione reductase and confirmed that the activities are mainly due to coumarin, epicatechin, juglone, epicatechin, and epicatechin presence, respectively. The stability of these complexes is essentially related to the strong hydrogen bonds formed between the most active compounds and the binding site amino acids. The identified compounds were found to pass the absorption, distribution, metabolism, and excretion property as well as five Lipinski’s rules with good drug-likeness and pharmacokinetic behavior.

In silico study of antibacterial tyrosyl-tRNA synthetase and toxicity of main phytoconstituents from three active essential oils

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

Nuclear ATR lysine-tyrosylation protects against heart failure by activating DNA damage response

Dysregulated amino acid increases the risk for heart failure (HF) via unclear mechanisms. Here, we find that increased plasma tyrosine and phenylalanine levels are associated with HF. Increasing tyrosine or phenylalanine by high-tyrosine or high-phenylalanine chow feeding exacerbates HF phenotypes in transverse aortic constriction and isoproterenol infusion mice models. Knocking down phenylalanine dehydrogenase abolishes the effect of phenylalanine, indicating that phenylalanine functions by converting to tyrosine. Mechanistically, tyrosyl-tRNA synthetase (YARS) binds to ataxia telangiectasia and Rad3-related gene (ATR), catalyzes lysine tyrosylation (K-Tyr) of ATR, and activates the DNA damage response (DDR) in the nucleus. Increased tyrosine inhibits the nuclear localization of YARS, inhibits the ATR-mediated DDR, accumulates DNA damage, and elevates cardiomyocyte apoptosis. Enhancing ATR K-Tyr by overexpressing YARS, restricting tyrosine, or supplementing tyrosinol, a structural analog of tyrosine, promotes YARS nuclear localization and alleviates HF in mice. Our findings implicate facilitating YARS nuclear translocation as a potential preventive and/or interfering measure against HF.

Synthesis, Molecular Docking and Characterization of Pyrazole N-Mannich Base Derivatives as Antimicrobial Agents

In this work we aimed to design synthesis and evaluate the N-Mannich bases of pyrazole. A novel series of N-Mannich bases of pyrazole analogues were designed and synthesized with an effort to overcome the increasing antibiotic resistance. Tyrosyl-tRNA synthetase (TyrRS) comprises an N-terminal domain, which has the fold of the class I aminoacyl-tRNA synthetases. Computational Autodock 4.2 tools will be employed in this study for docking of pyrazole ligand molecules against Tyrosyl-tRNA synthetase (TyrRS) of Escherichia coli (PDB code: 1x8x) and Staphylococcus aureus (PDB code: 1jil.pdb). Molinspiration server was used for lead optimization. The ligand molecules were subjected to molecular docking studies with enzyme Tyrosyl-tRNA synthetase. The molecular docking studies are supported to compare in-vitro antibacterial activity by the use of binding energy of the docked ligand molecules. The newly synthesized compounds were characterized by UV, IR and various physico-chemical methods. Further, the antibacterial activity of N-Mannich bases of pyrazole compounds were assessed with zone of inhibition by agar well diffusion method using gram negative bacterial strain Escherichia coli and gram-positive strain staphylococcus aureus. These same compounds were subjected to find the antifungal activity against Aspergillus fumigates and Aspergillus Niger.

Minimizing the Anticodon-Recognized Loop of Methanococcus jannaschii Tyrosyl-tRNA Synthetase to Improve the Efficiency of Incorporating Noncanonical Amino Acids.

In the field of genetic code expansion (GCE), improvements in the efficiency of noncanonical amino acid (ncAA) incorporation have received continuous attention. By analyzing the reported gene sequences of giant virus species, we noticed some sequence differences at the tRNA binding interface. On the basis of the structural and activity differences between Methanococcus jannaschii Tyrosyl-tRNA Synthetase (MjTyrRS) and mimivirus Tyrosyl-tRNA Synthetase (MVTyrRS), we found that the size of the anticodon-recognized loop of MjTyrRS influences its suppression activity regarding triplet and specific quadruplet codons. Therefore, three MjTyrRS mutants with loop minimization were designed. The suppression of wild-type MjTyrRS loop-minimized mutants increased by 1.8-4.3-fold, and the MjTyrRS variants enhanced the activity of the incorporation of ncAAs by 15-150% through loop minimization. In addition, for specific quadruplet codons, the loop minimization of MjTyrRS also improves the suppression efficiency. These results suggest that loop minimization of MjTyrRS may provide a general strategy for the efficient synthesis of ncAAs-containing proteins.

Direct and Efficient Incorporation of DOPA into Resilin-Like Proteins Enables Cross-Linking into Tunable Hydrogels.

3,4-Dihydroxyphenylalanine (DOPA), a naturally occurring yet noncanonical amino acid, endows protein polymers with diverse chemical reactivities and novel functionalities. Although many efforts have been made to incorporate DOPA into proteins, the incorporation efficiency and production titer remain low and severely hinder the exploration of these peculiar proteins for biomaterial fabrication. Here, we report an efficient biosynthetic strategy to produce large amounts of DOPA-incorporated structural proteins for the fabrication of hydrogels with tunable mechanical properties. First, synthetic genes were constructed that encode repetitive resilin-like proteins (RLPs) with varying proportions of tyrosine residues and molecular weights (Mw). Decoding of these genes into RLPs incorporated with DOPA was achieved via mis-aminoacylation of DOPA by endogenous tyrosyl-tRNA synthetase (TyrRS) in recombinant Escherichia coli cells. By developing a stoichiometry-guided two-phase culture strategy, we achieved independent control of the bacterial growth and protein synthesis phases. This enabled hyperproduction of the DOPA-incorporated RLPs at gram-per-liter levels and with a high DOPA incorporation yield of 76-85%. The purified DOPA-containing RLPs were then successfully cross-linked into bulk hydrogels via facile DOPA-Fe3+ complexations. Interestingly, these hydrogels exhibited viscoelastic and self-healing properties that are highly dependent on the catechol content and Mw of the RLPs. Finally, exploration of the molecular cross-linking mechanisms revealed that higher DOPA contents of the proteins would result in the concomitant occurrence of metal coordination and oxidative covalent cross-linking. In summary, our results suggest a useful platform to generate DOPA-functionalized protein materials and provide deeper insights into the gelation systems based on DOPA chemistry.

Tyrosyl-tRNA synthetase has a noncanonical function in actin bundling

Dominant mutations in tyrosyl-tRNA synthetase (YARS1) and six other tRNA ligases cause Charcot-Marie-Tooth peripheral neuropathy (CMT). Loss of aminoacylation is not required for their pathogenicity, suggesting a gain-of-function disease mechanism. By an unbiased genetic screen in Drosophila, we link YARS1 dysfunction to actin cytoskeleton organization. Biochemical studies uncover yet unknown actin-bundling property of YARS1 to be enhanced by a CMT mutation, leading to actin disorganization in the Drosophila nervous system, human SH-SY5Y neuroblastoma cells, and patient-derived fibroblasts. Genetic modulation of F-actin organization improves hallmark electrophysiological and morphological features in neurons of flies expressing CMT-causing YARS1 mutations. Similar beneficial effects are observed in flies expressing a neuropathy-causing glycyl-tRNA synthetase. Hence, in this work, we show that YARS1 is an evolutionary-conserved F-actin organizer which links the actin cytoskeleton to tRNA-synthetase-induced neurodegeneration.

Antimicrobial, Antibiofilm, and Antioxidant Potentials of Four Halophytic Plants, Euphorbia chamaesyce, Bassia arabica, Fagonia mollis, and Haloxylon salicornicum, Growing in Qassim Region of Saudi Arabia: Phytochemical Profile and In Vitro and In Silico Bioactivity Investigations.

The current study aimed to investigate the phytochemical contents and antioxidant, antimicrobial, and antibiofilm activities of four halophytic plants, namely, Euphorbia chamaesyce, Bassia arabica, Fagonia mollis, and Haloxylon salicornicum, native to central Saudi Arabia. The alcoholic extract of E. chamaesyce was found to be the most potent in various bioactivities-based evaluations and rich in polyphenols and flavonoid secondary metabolites, with 68.0 mg/g and 39.23 mg/g gallic acid and quercetin equivalents, respectively. Among all plants' extracts, the alcoholic extract of E. chamaesyce had the highest DPPH scavenging and metal chelating antioxidant activities at 74.15 Trolox equivalents and 16.28 EDTA equivalents, respectively. The highest antimicrobial activity of E. chamaesyce extract was found to be against Shigella flexneri, with a mean zone of inhibition diameter of 18.1 ± 0.2 mm, whereas the minimum inhibitory concentration, minimum biocidal concentration, minimum biofilm inhibitory concentration, and minimum biofilm eradication concentration values were 12.5, 25, 25, and 50 mg/mL, respectively. The LC-ESI-MS/MS analysis of the E. chamaesyce extract showed the presence of six flavonoids and ten phenolic constituents. The in silico binding of the E. chamaesyce extract's constituents to Staphylococcus aureus tyrosyl-tRNA synthetase enzyme displayed -6.2 to -10.1 kcal/mol binding energy values, suggesting that these constituents can contribute to the antimicrobial properties of the plant extract, making it an essential medicinal ingredient. In conclusion, these results warrant further investigation to standardize the antimicrobial profiles of these plant extracts.

Phytochemical Composition and Insight into Antibacterial Potential of Origanum vulgare Essential Oil from Saudi Arabia Using In Vitro and In Silico Approaches

In Saudi Arabia, Origanum vulgare is widely disseminated. In the present work, we used GC-MS analysis to identify the components of Origanum vulgare essential oil. The disc diffusion assay was used to assess the essential oil’s in vitro antibacterial efficacy against Gram-positive and Gram-negative Staphylococcus aureus and Escherichia coli. The antimicrobial efficacy against many microbial proteins, including tyrosyl-tRNA synthetase (TyrRS), DNA gyrase, and dihydrofolate reductase (DHFR), was further evaluated using molecular docking. Eighteen compounds were identified using GC-MS analysis, which constituted 99.81% of the total essential oil content. Terpinen-4-ol (34.3%), Beta-Terpineol (16.96%), 3-Epimoretenol (11.84%), and Alpha-Terpineol (3.86%) were the main substances identified. According to the antibacterial investigation, the inhibition zone against Staphylococcus aureus was 8 mm and 6 mm against Escherichia coli. High affinities were found between 3-Epimoretenol and tyrosyl-tRNA synthetase (TyrRS) and dihydrofolate reductase (DHFR) compared to positive controls (Clorobiocin, SCHEMBL2181345); the affinity values were −8.3 Kcal/mol and −9.2, respectively. The results of the present study indicate that Origanum vulgare essential oil can be used as a nutraceutical to treat infectious diseases.

Synthesis, structure elucidation, Hirshfeld surface analysis, DFT, and molecular docking of new 6-bromo-imidazo[4,5-b]pyridine derivatives as potential tyrosyl-tRNA synthetase inhibitors

Novel 6-bromo-imidazo[4,5-b]pyridine derivatives (2-4, 5a-13a, and 6b, 8b-13b) have been synthesized based on a developed systematic approach involving the condensation of 5-Bromo-2,3-diaminopyridine with a suitable aromatic aldehyde in the presence of molecular iodine in water, followed by alkylation reactions using different alkyl dibromide agents. The synthesized compounds were characterized by the NMR spectroscopy technique. The structures of 8a, 9a, 12a, and 11b were confirmed using monocrystalline X-ray crystallography. Theoretical calculations have been carried out using DFT and TD-DFT methods at the B3LYP/6-31G++(d,p) level of theory. Intermolecular contacts between units of 8a, 9a, 12a, and 11b were determined through the Hirshfeld surface analysis. The molecular docking study has been performed to determine the binding affinity of 8a, 9a, 12a, and 11b into the binding site of S. aureus tyrosyl-tRNA synthetase as a target enzyme, and the results revealed that 9a is the most potent compound among the selected compounds with a binding affinity of −8.74 Kcal/mol. Communicated by Ramaswamy H. Sarma

TRANSFER RNA MODIFICATION CONTRIBUTE TO PATHOGENESIS OF INTESTINAL INFLAMMATION BY ALTERING EPITHELIAL BARRIERS

Abstract BACKGROUNDS Transfer RNA (tRNA) is the most extensively modified RNA in cells. Queuosine (Q)-modification is a fundamental process for fidelity and efficiency of translation from RNA to proteins. In eukaryotes, tRNA-Q-modification relies on the intestinal microbial product queuine. Growing evidence indicates that tRNA modifications play important roles in human diseases, e.g., type 2 diabetes. Q depletion led to endoplasmic reticulum stress in mouse liver. Q-tRNA modifications are dynamic and highly variable depending on the developmental stages and species type and tumorigenesis. However, the health consequences of disturbed availability of queuine and altered Q-tRNA modification remain to be investigated. The effects and mechanisms of Q-tRNA in intestinal bowel diseases (IBD) are unknown. METHODS We explored the Q-tRNA-related tRNA synthetases and expression of Q tRNA ribosyltransferase catalytic subunit 1 (QTRT1) in patients with IBD by investigating human biopsies and reanalyzing datasets. We used several colitis mouse models, organoids, and cultured cells for loss- and gain-of-function studies to investigate the mechanisms of Q-tRNA modifications in intestinal barrier functions, proliferation, and inflammation. RESULTS In ulcerative colitis and Crohn’s disease patients, QTRT1 expression was significantly downregulated. Altered QTRT1-related metabolites were found in human IBD. The four Q-tRNA-related tRNA synthetases, asparaginyl-aspartyl-, histidyl-, and tyrosyl-tRNA synthetase, were decreased in IBD patients. This reduction was further confirmed in DSS-induced colitis and IL10-deficient mice. Reduced QTRT1 was significantly correlated with intestinal junctions, including downregulated β-catenin and upregulated Claudin-2. These alterations were confirmed in vitro by deleting QTRT1 from cells. Queuine treatment significantly enhanced cell junctional functions and reduced inflammation in epithelial cells. CONCLUSION tRNA modifications play an unexplored novel role in the pathogenesis of intestinal inflammation by altering epithelial barriers. Insights into Q-tRNA modification in regulating barrier functions would facilitate the development of targeted interventions for IBD through queuine and tRNA modifications.