Anti-listerial peptides from a marine Bacillus velezensis FTL7: production optimization, characterizations and molecular docking studies.

Antimicrobial peptides (AMPs) with potent anti-listerial activity were characterized from a novel marine Bacillus velezensis FTL7. A Box-Behnken statistical experimental design was used to study the combined impact of culture conditions on the production of AMPs by B. velezensis FTL7. The conditions optimized by statistical experimental design were 34.5 °C incubation temperature, 23 h incubation time, and 7.6 initial pH of the medium. AMP purification was performed by ammonium sulphate fractionation and butanol extraction followed by reversed-phase C18 solid-phase extraction. Tricine-SDS-PAGE analysis revealed a peptide with a molecular mass of ~ 6.5 kDa in an active AMPs fraction, whereas the mass spectrometry (MS) analysis showed the presence of AMPs in the mass range of 1-1.6 kDa, along with a 6.5 kDa peptide. Both MS and MS/MS analysis confirmed the AMPs as lipopeptides including surfactin, fengycins and iturin A and a circular bacteriocin amylocyclicin. The minimum inhibitory concentration of these AMPs against L. monocytogenes Scott A was 2.5 µg/mL. Further, the in-silico docking studies showed that the AMPs from B. velezensis FTL7 have high binding energy and stable binding patterns towards L. monocytogenes target proteins. Thus, this new combination of AMPs can serve as an effective food bio-preservative. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-024-03944-5.

Nrf2-regulated antioxidant response ameliorating ionizing radiation-induced damages explored through in vitro and molecular dynamics simulations.

This study aims to investigate the mechanism of natural antioxidant ferulic acid (FA) in reducing oxidative stress followed by its inhibitory effect on the Keap1-Nrf2 complex. FA was treated ex vivo with human blood for 30 min at 37 °C ± 1 °C and exposed to 1.5 Gy of γ- rays of 60Co (0.789 Gy/min) and allowed for repair for an hour at 37 °C ± 1 °C. FA's free radical scavenging capacity was measured using 2,7-dichlorofluorescein diacetate assay and cytogenetic assays. Further, a possible mechanism of protein-ligand interaction between FA and Keap1-Nrf2 pathway protein as a cellular drug target was studied using docking and molecular dynamics simulation. The 1.5 Gy of γ- rays exposed to pre-treated blood with FA showed a significant (p < 0.05) reduction in reactive oxygen species and DNA damage compared to the normal control blood group sample. The ligand-protein transient binding interaction in molecular dynamic simulation over a period of 100 ns was consistent and stable emphasizing complementary charge between the protein and ligand, speculating higher hydrophobic amino acid residues in the Keap1 active pocket. This might sway the Keap1 from interaction with Nrf2, and could lead to nuclear translocation of Nrf2 during radiation-induced oxidative stress. The present study emphasizes the radioprotective effect of FA against 1.5 Gy of γ- rays exposed to human blood and the application of in silico approaches helpful for the possible protective effect of FA.Communicated by Ramaswamy H. Sarma.

Structure-based screening of natural product libraries in search of potential antiviral drug-leads as first-line treatment to COVID-19 infection.

The study focuses on identifying and screening natural products (NPs) based on their structural similarities with chemical drugs followed by their possible use in first-line treatment to COVID-19 infection. In the present study, the in-house natural product libraries, consisting of 26,311 structures, were screened against potential targets of SARS-CoV-2 based on their structural similarities with the prescribed chemical drugs. The comparison was based on molecular properties, 2 and 3-dimensional structural similarities, activity cliffs, and core fragments of NPs with chemical drugs. The screened NPs were evaluated for their therapeutic effects based on their predicted in-silico pharmacokinetic and pharmacodynamics properties, binding interactions with the appropriate targets, and structural stability of the bound complex using molecular dynamics simulations. The study yielded NPs with significant structural similarities to synthetic drugs currently used to treat COVID-19 infections. The study proposes the probable biological action of the selected NPs as Anti-retroviral protease inhibitors, RNA-dependent RNA polymerase inhibitors, and viral entry inhibitors.

Evolutionary selectivity of amino acid is inspired from the enhanced structural stability and flexibility of the folded protein.

AIM: The present study attempts to decipher the site-specific amino acid alterations at certain positions experiencing preferential selectivity and their effect on proteins' stability and flexibility. The study examines the selection preferences by considering pair-wise non-bonded interaction energies of adjacent and interacting amino acids present at the interacting site, along with their evolutionary history. MATERIALS AND METHODS: For the study, variations in the interacting residues of spike protein (S-Protein) receptor-binding domain (RBD) of different coronaviruses were examined. The MD simulation trajectory analysis revealed that, though all the variants studied were structurally stable at their native and bound confirmations, the RBD of 2019-nCoV/SARS-CoV-2 was found to be more flexible and more dynamic. Furthermore, a noticeable change observed in the non-bonded interaction energies of the amino acids interacting with the receptor corroborated their selection at respective positions. KEY FINDINGS: The conformational changes exerted by the altered amino acids could be the reason for a broader range of interacting receptors among the selected proteins. SIGNIFICANCE: The results envisage a strong indication that the residue selection at certain positions is governed by a well-orchestrated feedback mechanism, which follows increased stability and flexibility in the folded structure compared to its evolutionary predecessor.

Augmentation of pyrethrins content in callus of Chrysanthemum cinerariaefolium and establishing its insecticidal activity by molecular docking of NavMS Sodium Channel Pore receptor.

Pyrethrins are effective food-grade bio-pesticides obtained from the flowers of Chrysanthemum cinerariaefolium and this crop cannot be cultivated widely in India due to its specific agro-climatic requirement. Hence pyrethrins are mostly imported from Kenya. Therefore, the present study aims to develop a process for augmentation of pyrethrin contents in C. cinerariaefolium callus and establish the correlation between early knockdown effects through docking on grain storage insect. In vitro seedlings were used as explants to induce callus on MS medium with different concentrations of auxins and cytokinins. Pyrethrin extracted from the callus was estimated by RP-HPLC. In callus, total pyrethrin was found to be 17.5 µg/g, which is higher than that found in natural flowers of certain Pyrethrum cultivars. The concentrations of cinerin II, pyrethrin II and jasmoline II were quite high in callus grown on solid medium. Bio-efficacy of pyrethrum extracts of flower and callus on insect Tribolium sp., showed higher repellency and early knock-down effect when compared with pure compound pestanal. Further, the rapid knockdown effect of all pyrethrins components was established by molecular docking studies targeting NavMS Sodium Channel Pore receptor docking followed by multiple ligands simultaneous docking, performed to investigate the concurrent binding of different combinations of pyrethrin. Among the six pyrethrin components, the pyrethrin I and II were found to be a more efficient, binding more firmly to the target, exhibiting higher possibilities of insecticidal effect by an early knockdown mechanism.