Sweetness in food delivers a delightful sensory experience, underscoring the crucial role of sweeteners in the food industry. However, the widespread use of sweeteners has sparked health concerns. This underscores the importance of developing and screening natural, health-conscious sweeteners. Our study represents a groundbreaking venture into the discovery of such sweeteners derived from egg and soy proteins. Employing virtual hydrolysis as a novel technique, our research entailed a comprehensive screening process that evaluated biological activity, solubility, and toxicity of the derived compounds. We harnessed cutting-edge machine learning methodologies, specifically the latest graph neural network models, for predicting the sweetness of molecules. Subsequent refinements were made through molecular docking screenings and molecular dynamics simulations. This meticulous research approach culminated in the identification of three promising sweet peptides: DCY(Asp-Cys-Tyr), GGR(Gly-Gly-Arg), and IGR(Ile-Gly-Arg). Their binding affinity with T1R2/T1R3 was lower than −15 kcal/mol. Using an electronic tongue, we verified the taste profiles of these peptides, with IGR emerging as the most favorable in terms of taste with a sweetness value of 19.29 and bitterness value of 1.71. This study not only reveals the potential of these natural peptides as healthier alternatives to traditional sweeteners in food applications but also demonstrates the successful synergy of computational predictions and experimental validations in the realm of flavor science.

The disease of SARS-CoV-2 has caused considerable morbidity and mortality globally. Spike proteins on the surface of SARS-CoV-2 allow it to bind with human cells, leading to infection. Fullerenes and their derivatives are promising SARS-CoV-2 inhibitors and drug-delivery vehicles. In this study, Gaussian accelerated molecular dynamics simulations and the Markov state model were employed to delve into the inhibitory mechanism of Fullerene–linear-polyglycerol-b-amine sulfate (F–LGPS) on spike proteins. During the study, it was discovered that fullerene derivatives can operate at the interface of the receptor-binding domain (RBD) and the N-terminal domain (NTD), keeping structural domains in a downward conformation. It was also observed that F-LGPS demonstrated superior inhibitory effects on the XBB variant in comparison to the wild-type variant. This study yielded invaluable insights for the potential development of efficient therapeutics targeting the spike protein of SARS-CoV-2.

Chitosanase CsnMY002 is a new type of enzyme isolated from Bacillus subtilis that is used to prepare chitosan oligosaccharide. Although mutants G21R and G21K could increase Chitosan yield and thus increase the commercial value of the final product, the mechanism by which this happens is not known. Herein, we used molecular dynamics simulations to explore the conformational changes in CsnMY002 wild type and mutants when they bind substrates. The binding of substrate changed the conformation of protein, stretching and deforming the active and catalytic region. Additionally, the mutants caused different binding modes and catalysis, resulting in different degrees of polymerization of the final Chitooligosaccharide degradation product. Finally, Arg37, Ile145 ~ Gly148 and Trp204 are important catalytic residues of CsnMY002. Our study provides a basis for the engineering of chitosanases.

Chrysanthemum (Chrysanthemum morifolium Ramat.) has been recognized as both a food and medicinal substance in China since 2002 and possesses antioxidant, anti-inflammatory, antibacterial, and immunomodulatory activities. Previous studies suggest that Chrysanthemum may alleviate skin lesions resembling atopic dermatitis (AD); however, its underlying mechanisms remain unclear. In this study, we integrated network pharmacology and machine learning to systematically explore the potential mechanisms of Chrysanthemum in AD treatment. Four algorithms—Random Forest (RF), Lasso regression with cross-validation (LassoCV), Elastic Net (EN), and Extreme Gradient Boosting (XGB)—were compared, among which the XGB model achieved the best performance (accuracy = 0.9393). Further analysis identified 15 optimal features, two core targets (PTGS2 and MMP9), and one critical pathway (NF-κB signaling). To experimentally validate these findings, HaCaT keratinocytes were co-stimulated with TNF-α and IFN-γ to establish an in vitro inflammatory model, and co-treatment with three major flavonoids from Chrysanthemum—Acacetin, Diosmetin, and Chryseriol—significantly suppressed cytokine-induced COX-2 overexpression and reduced NF-κB p65 phosphorylation, confirming their inhibitory effects on NF-κB activation. These results were consistent with molecular docking and dynamics simulations, which demonstrated that these flavonoids, along with celecoxib, could stably bind to COX-2, thereby enhancing system stability and reducing residue fluctuations at the binding interface, revealing the molecular basis by which Chrysanthemum alleviates AD and supporting its modernization and therapeutic potential.

Background: Root resorption, an unwanted side effect often seen in orthodontics, depends largely on osteoclasts. Osteoclastic protein tyrosine phosphatase (PTP-oc) plays a major role in controlling osteoclast activity. This study aimed to investigate the effects of Ursolic acid (UA), a novel PTP-oc inhibitor, on osteoclastogenesis and root resorption. Methods: UA was pinpointed using a PTP inhibition assay. Its inhibitory characteristics, inhibitor constant (Ki) against ∆PTP-oc, and selectivity were through an Inhibition Kinetics assay. The effects of UA on osteoclastogenesis were examined by treating human U937 histiocytic lymphoma cells with or without UA and then assessing osteoclastogenesis mediated by phorbol 12-myristate 13-acetate /1α, 25 di-hydroxy vitamin D₃ (1,25(OH)₂D₃). The cell counting kit-8 (CCK-8) evaluated how a UA affects U937 cell proliferation in vitro. Osteoclast-like cell development was examined using tartrate-resistant acid phosphatase (TRAP) Staining, while Real-time-polymerase chain reaction (qPCR) was used to assess the expression of tartrate-resistant acid phosphatase (TRAP), receptor activator of nuclear factor-κB (RANK), matrix metalloproteinase-9 (MMP-9), cathepsin K (CK), and calcitonin receptor (CTR). Tyrosine kinase c-Src (c-Src) protein was measured using Western Blot. A rat model was used to study the levels of root resorption and tyrosine phosphorylation of c-Src (PY-527) by histology and immunohistochemistry. Results: UA displayed a strong and reversible inhibitory effect on PTP-oc in a competitive manner, showing selective in vitro (p < 0.001). The compound did not impact the viability of U937 cells at concentrations between 1–5 μM UA. UA's inhibition of osteoclastogenesis depends on its concentration, and the compound effectively suppresses the expression of osteoclast marker genes, TRAP, RANK, MMP-9, CK, and CTR. Additionally, the area of TRAP-positive cells was reduced. This effect is facilitated by inhibiting enzymatically active PTP-oc, which elevates the levels of c-Src tyrosine phosphorylation, thereby decreasing the activity of c-Src Protein Tyrosine Kinases (PTK). In animal studies, as UA concentration increased, there was a noticeable delay and weakening in root resorption. Finally, IHC staining results revealed that compared to the 0 μM UA (control) group, c-Src PY-527 in the model groups increased alongside the rise in UA concentration (p < 0.05). Conclusions: This study demonstrates that UA application effectively suppresses osteoclastogenesis and root resorption by inhibiting the enzymatic activity of PTP-oc. This effect is dose-dependent and may be mediated by the regulation of c-Src signaling pathway.