Computational methods have transformed target and drug discovery, significantly accelerating the identification of biological targets and lead compounds. Despite its limitations, in silico molecular docking represents a foundational tool. Molecular Dynamics (MD) simulations, employing accurate force fields, provide near-realistic insights into a compound’s behavior within a biological target. However, docking and MD predictions may be unreliable without precise knowledge of the target binding site. Through MD simulations, we investigated 100 co-crystal structures of biological targets complexed with active compounds, identifying key structural and energy dynamic features that govern target–ligand interactions. Our analysis provides a detailed quantitative description of these parameters, offering critical validation for improving the predictive reliability of docking and MD simulations. This work provides a robust framework for refining early-stage drug discovery and target identification.

This study presents an innovative approach to the sustainable valorization of industrial sweet cherry (Prunus avium L.) waste from the Vignola Region, Italy, transforming what is typically discarded into a high-value bioactive resource. Unlike conventional extractions, our hydroethanolic extract (VCE) was obtained from the entire cherry waste, including the pericarp, pulp, and stone, as generated by industrial processing. This full-fruit extraction strategy represents a novel and efficient use of agricultural by-products, aligning with circular bioeconomy principles. Sweet cherries are known for their phenolic richness, and spectrophotometric assays (TPC, TFC, reducing power, DPPH, and ABTS) confirmed the extract’s antioxidant capacity. In vitro studies using RAW 264.7 macrophages revealed no cytotoxic effects (MTT assay), along with significant anti-inflammatory activity, evidenced by reduced ROS and NO production and downregulation of iNOS and COX-2. Western blotting showed inhibition of NF-κB nuclear translocation and MAPK pathway signaling. Additionally, agarose gel electrophoresis showed protection against oxidative DNA damage. UPLC-MS/MS analysis identified sakuranetin, aequinetin, and dihydrowogonin as the most representative compounds in VCE. Molecular docking simulations revealed strong and specific binding affinities of these compounds to NF-κB p65 and key MAPK targets. These findings highlight whole sweet cherry waste—including the pit—as a potent and sustainable source of bioactive compounds with promising nutraceutical and pharmaceutical applications.

Currently, one-third of global food production, accounting for 1.3 billions tons, goes wasted due to major humanitarian and environmental challenges. In such a scenario, the circular bioeconomy model stands as an innovative solution by promoting sustainable production, utilizing agri-food waste, and converting non-renewable products into valuable resources. Here, the circular bioeconomy concept was applied on a previously obtained chestnut burr extract (agri-food waste) composed of gallic acid, quinic acid, protocatechuic acid, brevifolin carboxylic acid, and ellagic acid to evaluate its antimicrobial activity against four bacterial opportunistic pathogens (Enterococcus faecalis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli). Our results evidenced a modest but measurable antibacterial activity against Enterococcus faecalis, with a minimum inhibitory concentration (MIC) of 64 μg/mL. In silico studies allowed for identifying the potential molecular target, supporting the underlying antibacterial activity of the active principle and providing useful molecular findings regarding their interaction. In this study, we show a robust and comprehensive in vitro and in silico pipeline aimed at the identification of novel antibacterial scaffolds taking advantage of agri-food waste.

Agricultural and agro-industrial residues are increasingly recognized as sustainable, low-cost feedstocks for high-performance biomedical materials. This review critically examines the translational potential of polysaccharides, proteins, inorganic compounds, and phytochemical-rich extracts derived from agro-waste, highlighting their chemical features, structure–function relationships, and application-specific readiness. Polysaccharides such as nanocellulose, pectin, and chitosan emerge as the most advanced biopolymer platforms, particularly in wound healing, drug delivery, and 3D-printed scaffolds. Protein-derived materials—including collagen, gelatin, keratin, and soy protein—show strong promise in regenerative medicine, though challenges in mechanical stability and batch reproducibility remain. Inorganic phases such as hydroxyapatite and silica obtained from eggshells, rice husk ash, and marine shells demonstrate high bioactivity, with dental and bone applications approaching clinical translation. Finally, fruit-residue phytochemicals provide multifunctional antioxidant and antimicrobial enhancements to composite systems. By integrating material chemistry, processing strategies, and translational considerations, this review outlines the current state, challenges, and future perspectives for advancing agro-waste-derived biomaterials within a circular bioeconomy.

The circular bioeconomy is currently a promising model for repurposing natural sources; these sources include plants due to their abundance of bioactive compounds. This study evaluated the antimicrobial properties of a Chaetomorpha linum extract. Chaetomorpha linum is an invasive macroalga from the Orbetello Lagoon (Tuscany, Italy), which grows in nutrient-rich environments and has been forming extended mats since 2005. The biomass is mechanically harvested and treated as waste, consuming considerable manpower and financial resources. As a potential way to increase the value of such waste, this study found that C. linum extract (CLE) is a source of antimicrobial compounds. The phytochemical characterization of the extract revealed the predominant presence of palmitic acid, a fatty acid with known antimicrobial activity. Based on such findings, four bacterial species of high clinical relevance (Enterococcus faecalis, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli) were tested, revealing a notable antibacterial activity of the extract on Enterococcus faecalis (MIC, 32 μg/mL). Computational analyses identified a potential Enterococcus faecalis molecular target for palmitic acid, offering molecular insights on the interaction. This study presents a comprehensive in vitro and in silico approach for drug and target discovery studies by repurposing C. linum as a source of antimicrobial bioactive compounds.

In an era of escalating environmental challenges, converting organic residues into high-value bioactive compounds provides a sustainable way to reduce waste and enhance resource efficiency. This study explores the potential of the circular bioeconomy through the valorization of agricultural byproducts, with a focus on the antioxidant properties of specific chestnut burr cultivars. Currently, over one-third of food production is wasted, contributing to both humanitarian and environmental crises. Through circular bioeconomy, we can transform biological waste into valuable products for use in fields like food innovation and sustainability. The antioxidant effects of three chestnut cultivars, Bastarda Rossa, Cecio, and Marroni, were assessed through in vitro assays, highlighting their potential to combat oxidative stress—an important factor for health-related applications. The characterization of the three cultivars showed the major presence of ellagic acid and gallic acid in the extract, renowned for their antioxidant activity. In vitro assays evaluated the phenolic and flavonoid content, as well as the antioxidant activity of the three extracts, confirming the cultivar Cecio as the richest in these bioactive compounds and the most performative in antioxidant assays. In vitro antioxidant and oxidative stress recovery assays on SaOS-2, fibroblast, and chondrocyte cell lines displayed a strong antioxidant activity. Furthermore, the cytotoxicity assay demonstrated the safety of all three extracts in the tested human cell lines. In silico docking simulations further validated the biological relevance of these compounds by predicting strong hydrophobic and polar interactions with oxidative stress-related protein targets. Overall, this study demonstrates the antioxidant properties of chestnut byproducts. The findings contribute to the development of functional foods, nutraceuticals, and other applications, underscoring the role of chestnut cultivars in advancing circular bioeconomy practices.