As the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) pandemic continues to spread, several variants of the virus, with mutations distributed all over the viral genome, are emerging. While most of the variants present mutations having little to no effects at the phenotypic level, some of these variants are spreading at a rate that suggests they may present a selective advantage. In particular, these rapidly spreading variants present specific mutations on the spike protein. These observations call for an urgent need to characterize the effects of these variants’ mutations on phenotype features like contagiousness and antigenicity. With this aim, we performed molecular dynamics simulations on a selected set of possible spike variants in order to assess the stabilizing effect of particular amino acid substitutions on the molecular complex. We specifically focused on the mutations that are both characteristic of the top three most worrying variants at the moment, i.e the English, South African, and Amazonian ones, and that occur at the molecular interface between SARS-CoV-2 spike protein and its human ACE2 receptor. We characterize these variants’ effect in terms of (i) residue mobility, (ii) compactness, studying the network of interactions at the interface, and (iii) variation of shape complementarity via expanding the molecular surfaces in the Zernike basis. Overall, our analyses highlighted greater stability of the three variant complexes with respect to both the wild type and two negative control systems, especially for the English and Amazonian variants. In addition, in the three variants, we investigate the effects a not-yet observed mutation in position 501 could provoke on complex stability. We found that a phenylalanine mutation behaves similarly to the English variant and may cooperate in further increasing the stability of the South African one, hinting at the need for careful surveillance for the emergence of these mutations in the population. Ultimately, we show that the proposed observables describe key features for the stability of the ACE2-spike complex and can help to monitor further possible spike variants.

The present investigation focuses on the analysis of the interactions among human lactoferrin (LF), SARS-CoV-2 receptor-binding domain (RBD) and human angiotensin-converting enzyme 2 (ACE2) receptor in order to assess possible mutual interactions that could provide a molecular basis of the reported preventative effect of lactoferrin against CoV-2 infection. In particular, kinetic and thermodynamic parameters for the pairwise interactions among the three proteins were measured via two independent techniques, biolayer interferometry and latex nanoparticle-enhanced turbidimetry. The results obtained clearly indicate that LF is able to bind the ACE2 receptor ectodomain with significantly high affinity, whereas no binding to the RBD was observed up to the maximum “physiological” lactoferrin concentration range. Lactoferrin, above 1 µM concentration, thus appears to directly interfere with RBD–ACE2 binding, bringing about a measurable, up to 300-fold increase of the K_D value relative to RBD–ACE2 complex formation.

Lactoferrins and lactoferrin-derived peptides display numerous functions linked to innate immunity in mammalians, spanning from antimicrobial to anti-inflammatory and immunomodulatory actions, and even demonstrate antitumor properties. To date, the proposed mechanisms for their biological actions are varied, although the molecular basis that governs lactoferrin interactions with molecular targets has been clarified only in a limited number of specific cases. However, key in silico methods have recently moved the topic to the fore, thus greatly expanding the possibilities of large-scale investigations on macromolecular interactions involving lactoferrins and their molecular targets. This review aims to summarize the current knowledge on the structural determinants that drive lactoferrin recognition of molecular targets, with primary focus on the mechanisms of activity against bacteria and viruses. The understanding of the structural details of lactoferrins’ interaction with their molecular partners is in fact a crucial goal for the development of novel pharmaceutical products.

Gallic acid, a major phenolic compound in wine, significantly influences its sensory profile and health-related properties, making its accurate measurement essential for both enological and nutritional studies. In this context, a derivatization protocol for gallic acid using ethyl chloroformate (ECF) was developed and optimized for GC-MS analysis, with experimental conditions refined through a Box–Behnken Design (BBD). The BBD systematically investigated the effects of three critical reagent volumes: ethyl chloroformate, pyridine, and ethanol. This approach elucidated complex interactions and quadratic effects, leading to a predictive second-order polynomial model and identifying the optimal derivatization conditions for maximum yield (137 µL of ethyl chloroformate, 51 µL of pyridine, and 161 µL of ethanol per 150 µL of wine). The BBD-optimized GC-MS method was validated and successfully applied to quantify gallic acid in diverse commercial wine samples (white, red, conventional, natural). A key finding was the method’s wide dynamic range, enabling accurate quantification from 5 up to over 600 µg/mL without sample dilution. This work represents, to our knowledge, the first application of a BBD for optimizing the ethyl chloroformate derivatization of gallic acid, providing a robust, efficient, and widely applicable analytical tool for routine quality control and enological research.

Dihydrolevoglucosenone (DHL) shows great promise as an alternative to conventional toxic organic solvents widely used for industrial purposes. In this framework, evaluating the potential of DHL (commercially known as Cyrene) as a solvent for dissolving proteins is of great importance. Here, the effect of DHL/water mixtures on protein stability and solubility has been assessed. Several proteins, namely, hemoglobin, ferritin, ribonuclease, and albumin, were readily dissolved in buffer solutions containing up to 50-60% DHL and were stable at room temperature, as indicated by gel electrophoresis and matrix-assisted laser desorption/ionization analysis. Turbidimetry assays were performed in order to assess the solubility limitations derived from DHL/water mixtures. Finally, protein secondary structures in such mixtures, investigated by attenuated total reflectance Fourier-transform infrared spectroscopy, were found to be comparable to those obtained in phosphate buffer up to 50% DHL/water, with small spectral changes in the case of ribonuclease. DHL/water mixtures may thus represent highly convenient solvents for studies of protein chemistry.

In this study, we focused on the computational analysis of a selected single-point mutation identified by a NGS screening panel in the TET2 enzyme classified as “variant of uncertain clinical significance.” The mutation, namely Q1084P, occurs at the interface between TET2, an important epigenetic regulator, and NANOG, a transcription factor fundamental for hematopoietic cells differentiation. Notably, the mutation occurs in a protein region distant from the active site; moreover, the experimental structures of the interacting region of both proteins are unknown, making it difficult to validate the impact of TET2 mutation on its binding with NANOG. To address these challenges, we employed an integrated computational approach combining molecular docking, molecular dynamics simulations and protein-protein interaction prediction. Our findings indicate that the single-point mutation might effectively reduce the TET2-NANOG interaction, which would consequently impair cells differentiation and hematopoiesis process, consistent with the clinical presentation of pure red cell aplastic anemia. These results, along with the proposed computational method, provide insights for establishing clinical correlations between variants of uncertain significance and anemias in general, comprising common hematological problems widespread in the world population and for which dedicated NGS panels are still not available.