Inhibition of Aspergillus VosA protein by lactic acid bacteria metabolites (in silico study)

In this work, we performed an in silico study using 3D structure protein of VosA, and analyzed the protein interaction via molecular docking using PyRx to test the inhibition efficacy of 15 metabolites compounds produced by lactic acid bacteria in conidia germination protein of Aspergillus. The antifungal docking findings revealed that these compounds showed good interactions and binding affinity against the target involved in conidia germination. The highest binding energy (-6.3 kcal/mol) was given by stearic acid. This interaction is due to the residue amines Ser and Phe. Palmitic acid also showed a good binding affinity with -6 kcal/mol. Lactic acid has not the same efficiency as palmitic, and stearic acid, which represented a value of -3.6 kcal/mol, the values recorded by cytidine was from -5 kcal/mol, which was also important compared to oxalic and acetic acid. DOI: http://dx.doi.org/10.5281/zenodo.560999

The inhibitory effect of vitamins on O micron virus via targeting the ACE2 receptor. In silico analysis

Objectives: The wide and rapid spread of epidemics like COVID 19, highlighted the need for the rapid development of effective solutions. In the present work, a therapeutic approach based on the use of vitamins against the Omicron variant spike was investigated through bioinformatics tools. Methods: The inhibitory effect of vitamins A, B2, B3, C, E, D, K1 and K7 were tested in silico through a molecular docking and molecular dynamic simulation against four ACE2 grid boxes binding specifically the Omicron proteins 7T9K, 7T9L, 7WBL and 7WBP. Results: The docking study showed that vitamins K1, A, D and E bind strongly and efficiently to ACE2 receptor. High docking scores with low binding energies and strong interactions with crucial amino acids residues were generally noted for these four vitamins. The dynamic simulation analysis for 100 ns of the best docked complexes using Gromacs tools at a temperature of 300 K allowed screening vitamin A-grid2, vitamin E- grid4, vitamin K1-grid2 and vitamin D-grid 2 as the most stable complexes compared to rest of systems. Conclusion: These findings indicate that vitamins could interact directly with ACE2 receptor blocking in this way the Omicron binding to its host

Application of 16S rRNA virtual RFLP for the discrimination of some closely taxonomic-related lactobacilli species

Abstract Background Several species in Lactobacillaceae family were recognized as potential probiotic bacteria. In this group of lactic acid bacteria, species are taxonomically closed and usually share similar 16S rRNA gene, thus, instead of so their identification and discrimination are too difficult. Method In the present study, virtual restriction fragment length polymorphism (RFLP) is instead of was used as a tool to discriminate between the closely related species Lactiplantibacillus plantarum (L plantarum), Lactiplantibacillus paraplantarum (L paraplantarum), and Lactiplantibacillus pentosus (L pentosus); Latilactobacillus sakei (L sakei), Latilactobacillus curvatus(L curvatus), and Latilactobacillus graminis (L graminis); Lacticaseibacillus casei (L casei), Lacticaseibacillus paracasei (L paracasei), Lacticaseibacillus zeae, and Lacticaseibacillus rhamnosus; Lactobacillus gasseri (L gasseri) and Lactobacillus johnsonii (L johnsonii). In silico comparative analysis of 16S rRNA sequences digested by 280 restriction enzymes was performed in order to search the key enzymes which gives different profiles. Results Results revealed that L casei, L paracasei, L zeae, and Lb rhamnosus could be separated from each other on the basis of AlwI, BpuEI, BsgI, BsrDI, BstYI, EarI, MluCI, and NsPI RFLP. Results showed also that different RFLP patterns were obtained from L sakei, L graminis and L curvatus by using both AflI and NspI endonucleases (in separated restriction) and L plantarum, L paraplantarum, and L pentosus were distinguished each one from the other by MucI, NspI, and TspDTI PCR-RFLP. Lb gasseri and L johnsonii were also separated on the basis of Mse I, Taq I, and Dra I RFLP. Conclusion In this study, we proved that too closely related species could be separated in virtual analysis on basis of their 16S rRNA RFLP patterns using key restriction enzymes method