In silico tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides. However, restricted sampling of both ligand and receptor conformations and use of approximated scoring functions can produce results that do not correlate with actual experimental binding affinities. Molecular dynamics simulations (MDS) can provide valuable information in deciphering functional mechanisms of proteins/peptides and other biomolecules, overcoming the rigid sampling limitations in docking analysis. This review will discuss the information related to the traditional use of in silico models, such as molecular docking, and its application for studying food proteins and bioactive peptides, followed by an in-depth introduction to the theory of MDS and description of why these molecular simulation techniques are important in the theoretical prediction of structural and functional dynamics of food proteins and bioactive peptides. Applications, limitations, and future prospects of MDS will also be discussed.

Pleurotus ostreatus strains were cultured in liquid medium and on wheat straw. The yields of lovastatin were compared

High-risk strains of human papillomavirus (HPV) have been identified as the etiologic agent of some anogenital tract, head, and neck cancers. Although prophylactic HPV vaccines have been approved; it is still necessary a drug-based treatment against the infection and its oncogenic effects. The E6 oncoprotein is one of the most studied therapeutic targets of HPV, it has been identified as a key factor in cell immortalization and tumor progression in HPV-positive cells. E6 can promote the degradation of p53, a tumor suppressor protein, through the interaction with the cellular ubiquitin ligase E6AP. Therefore, preventing the formation of the E6-E6AP complex is one of the main strategies to inhibit the viability and proliferation of infected cells. Herein, we propose an in silico pipeline to identify small-molecule inhibitors of the E6-E6AP interaction. Virtual screening was carried out by predicting the ADME properties of the molecules and performing ensemble-based docking simulations to E6 protein followed by binding free energy estimation through MM/PB(GB)SA methods. Finally, the top-three compounds were selected, and their stability in the E6 docked complex and their effect in the inhibition of the E6-E6AP interaction was corroborated by molecular dynamics simulation. Therefore, this pipeline and the identified molecules represent a new starting point in the development of anti-HPV drugs.

Water contamination is a worldwide concerning problem. Emerging contaminants have made conventional water treatment processes ineffective. This makes the search for new materials with improved physical-chemical properties for water treatment an urgent necessity. Doping metal oxides nanostructures can improve the photocatalytic degradation of contaminants and the antimicrobial activity of the material. During this process, water treatment not only involves the degradation of toxic pollutants, but also the elimination of virus and bacteria. Then, it is important to study not only the effect of a dopant in a material as photocatalyst but also the effect in its antimicrobial properties. In this work ZnO nanorods, Ga doped ZnO nanorods and Ag doped ZnO nanorods are synthesized and supported in polyethylene by a fast-hydrothermal microwave heating synthesis. Their photocatalytic performance and antimicrobial properties for water treatment were evaluated. Experiments show that Ag and Ga can improve the photocatalytic and antimicrobial properties of ZnO nanorods; the relationship between doping concentrations, with both the toxicity effect of the nanorods toward bacteria and the nanorods photocatalytic performance, is shown.