Antibacterial, antibiofilm, and chemical profiles of Ammi visnaga L. and Foeniculum vulgare mill. Essential oils, and ADMET, molecular docking investigation of essential oils major components.

This study determined chemical profiles, antibacterial and antibiofilm activities of the essential oils (EOs) obtained by A. visnaga aerial parts and F. vulgare fruits. Butanoic acid, 2-methyl-, 3-methylbutyl ester (38.8%), linalyl propionate (34.7%) and limonene (8.5%) resulted as main constituents of A. visnaga EO. In F. vulgare EO trans-anethole (76.9%) and fenchone (14.1%) resulted as main components. The two EOs were active against five bacterial strains (Acinetobacter baumannii, Escherichia coli, Listeria monocytogenes, Pseudomonas aeruginosa, and Staphylococcus aureus) at different degrees. The MIC values ranged from 5 ± 2 to 10 ± 2 µL/mL except for S. aureus (MIC >20 µL/mL). EOs exhibited inhibitory effect on the formation of biofilm up to 53.56 and 48.04% against E. coli and A. baumannii, respectively and activity against bacterial metabolism against A. baumannii and E. coli, with biofilm-inhibition ranging from 61.73 to 73.55%. The binding affinity of the identified components was estimated by docking them into the binding site of S. aureus gyrase (PDB code 2XCT) and S. aureus tyrosyl-tRNA synthetase (PDB code 1JIJ). trans-Anethole and butanoic acid, 2-methyl-, 3-methylbutyl ester showed relatively moderate binding interactions with the amino acid residues of S. aureus tyrosyl-tRNA synthetase. In addition, almost all predicted compounds possess good pharmacokinetic properties with no toxicity, being inactive for cytotoxicity, carcinogenicity, hepatotoxicity, mutagenicity and immunotoxicity parameters. The results encourage the use of these EOs as natural antibacterial agents in food and pharmaceutical industries.

Structural impact, ligand-protein interactions, and molecular phenotypic effects of TGF-ß1 gene variants: In silico analysis with implications for idiopathic pulmonary fibrosis.

BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) is a chronic interstitial lung disease resulting in progressively deteriorating lung function. Transforming growth factor-ß1 (TGF-ß1) belongs to the TGF superfamily and exerts a profibrotic role in promoting lung fibrosis by facilitating fibroblast infiltration and activity, extracellular matrix deposition, and inhibition of collagen breakdown, thus promoting tissue remodelling and IPF. MATERIALS AND METHODS: We evaluated the link between pathogenic TGF-ß1 SNPs and IPF pathogenesis and the structure-activity functional consequences of those SNPs on the TGF-ß1 protein. Several computational algorithms were merged to address the functional consequences of TGF-ß1 gene mutations to protein stability, putative post-translational modification sites, ligand-protein interactions, and molecular phenotypic effects. These included FATHMM, POLYPHEN2, PROVEAN, and SIFT tools (identifying deleterious nsSNPs in the TGF-ß1 gene), along with Pmut, PhD-SNP, SNAP, MutPred and the related TMHMM, MARCOIL, and DisProt algorithms (predicting structural disorders). INPS-MD was also used to evaluate the mutation-induced TGF-ß1 protein's stability and MODPRED for recognition of post-translational TGF-ß1 modification. RESULTS: In total, 14 major pathogenic variants markedly impact the destabilization of the TGF-ß1 protein, with most of these high-risk mutations associated with decreased stability of the TGF-ß1 protein as per the I-Mutant, MUpro, and INPS-MD tools. R205W, R185W, R180Q, D86Y, and I300T variants were proposed to participate in the post-translational modifications, thus affecting affect protein-ligand interactions. Furthermore, at-risk genetic variants appear to target conserved regions in the alpha helices, random coils, and extracellular loops, resulting in a varied composition of amino acids, charge, hydrophobicity, and spatial architecture. CONCLUSIONS: This study manuscript comprehensively analyzes gene variants within the TGF-ß1 gene, offering novel insights into their structural and functional implications in interacting with target sites. This study is significant for the development of targeted therapeutic strategies and personalized treatment approaches for patients with inflammatory lung diseases such as IPF.