In silico prediction and in vitro analysis of bacteriocin and probiotic properties of Weissella cibaria NM1 isolated from Asian sea bass

Aims@#This study aims to predict the presence of bacteriocin- and probiotic-associated genes in the genome of Weissella cibaria NM1 isolated from Asian sea bass using a machine learning-based NeuBI prediction approach, followed by the investigation of the crude bacteriocin antimicrobial and probiotic properties via in vitro analysis.@*Methodology and results@#This study utilized the machine learning-based NeuBI prediction approach with a homology search of highly conserved bacteriocin-associated genes present in the genome of W. cibaria NM1. This approach discovered a putative bacteriocin gene (WC_2064) and bacteriocin operon with complete immunity, transporter, regulator and modifier genes. Furthermore, the genome of W. cibaria NM1 was found to harboured specific probiotic*associated genes that would contribute to acid and bile tolerance, adhesion on thehost cell and exhibited cholesterolreducing ability. On top of that, the genome also shows the absence of virulence and antibiotic resistance genes, which signifies the safety of W. cibaria NM1 as a potential probiotic candidate. In vitro study has confirmed the antipseudomonal activity of crude bacteriocin NM1 with MIC of 62.5 mg/mL. Weissella cibaria NM1 can tolerate 0.3% (v/v) of bile salt condition and the transit through the simulated gastric (pH 3 and 4) and small intestinal (pH 8) tract.@*Conclusion, significance and impact of study@#Current findings suggested in silico approach can speed up the search for putative bacteriocin and probiotic-associated genes from the genome of W. cibaria NM1. Nevertheless, further verification through experimental works will be deemed essential.

Synthesis, in-vitro antioxidant activity and in-silico prediction of drug-likeness properties of a novel compound: 4-(3,5-Di-tert-butyl- 4-hydroxybenzylidene)-3-methylisoxazol-5(4H)-one

A simple and eco-friendly method has been used for the synthesis of novel compound 4-(3,5-di-tert-butyl-4-hydroxybenzylidene)-3-methylisoxazol-5(4H)-one. The synthesized compound was characterized by its physical andspectral data. This compound was screened for in-vitro antioxidant activity by 1,1-diphenyl-2-picrylhydrazyl (DPPH)and nitric oxide free radical scavenging assays at 100 µM concentration. The DPPH scavenging ability of evaluatedcompound was superior to the synthetic antioxidant butylated hydroxytoluene (BHT) and comparable to the standardascorbic acid. The nitric oxide scavenging ability of the compound was also found greater than the BHT. The insilico prediction of molecular properties and bioactivity scores of synthesized compound and BHT were carried outusing Molinspiration Cheminformatics online software. The study revealed that the predicted compounds obeyedLipinski’s rule of five and showed good intestinal absorption and membrane permeability indicating the drug-likenessproperties of predicted compounds. Finally, the in silico study identified the title compound as a nuclear receptorligand compared to BHT.

In silico prediction of exposure amino acid sequences of outer inflammatory protein A of Helicobacter pylori for surface display on Eschierchia coli.

BACKGROUND: Outer inflammatory protein A (OipA) is an outer membrane protein of Helicobacter pylori that is involved in inducing IL-8 and intracellular signaling. In this study, we have predicted exposure amino acid sequences of OipA for insertion in permissive sites of CstH subunit of Eschierchia coli CS3 pilli for bacterial surface display. MATERIALS AND METHODS: Databases: National Center for Biotechnology Institute and Protein Data Bank. Servers: PHD, SABLE, GOR 4, SignalP3.0, TBBpred, PRODIV-TMHMM, TMRPres2D, CPH Models, PHYRE, GETAREA, VADAR, Pep state and pep window. Software: Swiss PDB viewer and Discovery studio. RESULTS: In silico prediction of exposure amino acid sequences of OipA led to detection of six sequences of amino acid, 76-87, 106-112, 170-182, 222-230, 242-258, and 278-290. These sequences inserted between amino acid sequences 66-67, 100-101, and 109-110 of CstH that were predicted by Eskandari et al. as permissive sites of CstH. CONCLUSION: OipA has the ability to induce IL-8 from gastric epithelial cells and some papers are mentioned that this outer membrane protein involve to attachment and intracellular signaling. Receptor of OipA and adhesion motifs on this protein is unknown. Detection of exposure motifs aids to recognition of adhesion motifs and receptor of OipA on gastric epithelial cells. In this study, we have predicted exposure amino acid sequences for insert to subunit CstH of CS3 pilli E. coli for surface display.