Integrative transcriptomic and proteomic analyses revealed that SRP reversed the downregulation of core genes and key proteins, modulating multiple vascular homeostasis pathways including calcium signaling, vascular smooth muscle contraction, Toll-like receptor signaling, and neuroactive ligand-receptor interaction.
Abstract
A Peptidase A1 domain-containing protein (SRP, 43.1 kDa, >95% purity) was isolated from the edible mushroom Stropharia rugosoannulata and characterized for its structural properties, and ACE inhibitory and vascular modulatory activities. This represents the first report of an intact Peptidase A1 family protein exhibiting bioactivities beyond its canonical proteolytic role. SRP inhibited ACE (IC50 = 108.84 ± 3.42 μg mL-1) through strong intermolecular interactions, with Glu264 contributing 45% (-20.76 kcal mol-1) of the total binding energy and additional contributions from conserved active-site residues. Isothermal titration calorimetry confirmed high-affinity binding to ACE (KD = 1.12 × 10-8 M), driven by both enthalpic and entropic contributions with entropy as the dominant thermodynamic force, suggesting a complex binding mode involving both primary and secondary interaction sites. In a zebrafish hypertension model, SRP at 62.5 μg mL-1 decreased cardiac output by 20-24% and increased vessel diameter by 17-18%, with effects comparable to those of captopril at the tested concentration. Integrative transcriptomic and proteomic analyses revealed that SRP reversed the downregulation of core genes and key proteins, modulating multiple vascular homeostasis pathways including calcium signaling, vascular smooth muscle contraction, Toll-like receptor signaling, and neuroactive ligand-receptor interaction. These findings expand the known functional repertoire of Peptidase A1 family proteins and highlight the multi-pathway modulatory potential of food-derived intact proteins.
The development of isoform-selective inhibitors for homologous cysteine proteases remains challenging due to structural similarity and overlapping specificities. Metabolites isolated from Tabebuia aurea were investigated as modulators of Cathepsins B and L. Bioassay-guided fractionation yielded three compounds: 2,3-DH-5-HMB (1), veratric acid (2), and iridoid specioside (3). Enzymatic assays identified veratric acid as the most active compound (IC∼50∼ = 4.23 ± 0.17 μM for Cathepsin B and 1.28 ± 0.03 μM for Cathepsin L). Steady-state kinetic analyses revealed marked mechanistic divergence between isoforms. Against Cathepsin B, compounds 1 and 2 acted as competitive inhibitors with strong positive cooperativity, quantitatively captured by the cooperativity factor β (0.00041 and 0.0129, respectively), corresponding to 2,400-fold and 78-fold increases in affinity upon binding of a second inhibitor molecule. For compound 2, where extreme cooperativity precluded independent estimation of microscopic parameters, the quadratic cooperativity parameter γ (0.273 μM-2) enabled robust quantification of the cooperative effect. In contrast, all three compounds inhibited Cathepsin L via a simple linear non-competitive mechanism (α ≈ 1), reflecting its more accessible active-site architecture. Cellular assays confirmed selective antiproliferative activity of veratric acid in K562 leukemia cells (EC∼50∼ = 12.47 μM) while sparing non-tumor HaCaT cells. Molecular docking and molecular dynamics simulations of 1:1 complexes provided structural context for the observed isoform-specific binding modes. These results demonstrate that structurally simple phenolic compounds can induce fundamentally different inhibition mechanisms in closely related enzymes, establishing a structure-mechanism framework for isoform-selective modulation of cysteine proteases.
Marli de Fátima Corrêa Emiliano, Mariele Rondon Santos Gonçalves, L. M. R. de Novais et al.· Archives of Biochemistry and...· 0 citations
Phycocyanobilin, a bioactive compound derived from Arthrospira platensis C1, was investigated for its potential role in systemic lupus erythematosus (SLE) based on its structural similarity to bilirubin, with a Tanimoto score of 93%. Molecular docking revealed favorable binding affinities between phycocyanobilin and several protein targets, including EGFR, FYN, HLA-B, LCK, LYN, and TP53. Target prediction further identified LYN kinase as a key candidate. Molecular dynamics simulations demonstrated stable binding of the phycocyanobilin–LYN complex, with interaction profiles comparable to those of the native ligand, staurosporine. Binding free energy and residue-level analyses supported strong and stable interactions, highlighting key contributions to complex stability. Overall, these findings provide mechanistic insight into the interaction between phycocyanobilin and LYN, suggesting that this compound may modulate LYN-associated signaling pathways and warrants further investigation in the context of SLE.
A. Chaiprasert, Ping Han, Teeraphan Laomettachit et al.· PLoS ONE· 0 citations
Nine previously undescribed prenylated xanthones, aspxanthones A-I (1-9), were isolated and characterized from the endophytic fungus Aspergillus sp. TJ507. Their structures were established through comprehensive spectroscopic analyses, single-crystal X-ray diffraction, and DP4+ probability analysis. Compounds 1, 2, and 4 exhibited modest in vitro SIRT1 activating effects, with EC50 values ranging from 9.3 to 13.7 μM. The positive control resveratrol yielded an EC50 of 2.4 ± 0.4 μM under identical assay conditions. Molecular docking was conducted with resveratrol as a reference ligand, which revealed obvious differences in binding modes between resveratrol and the tested xanthones. To further clarify their dynamic binding behaviors, molecular dynamics simulations, free-energy landscape analysis, and MM/GBSA calculations were carried out on these active compounds. Among them, compound 4 displayed the most stable simulated binding profile and the most favorable estimated binding free energy among the three complexes, broadly consistent with the experimental activity ranking. In contrast, compound 2 exhibited higher conformational flexibility throughout the simulation, indicating a distinct binding mode. This study expands the chemical diversity of fungal-derived xanthones and provides valuable templates for the design and development of potential SIRT1 activators.
Xueqi Lan, Dong-Chun Liang, Li Tang et al.· Bioorganic chemistry (Print)· 0 citations
Biochemical oxidase and reductase assays on PDI showed that punicalagin inhibits both activities with micromolar potency, thereby extending earlier work that described disulfide reductase inhibition.
Osamede C. Owegie, Rong-guang Xu, Quinn P. Kennedy et al.· Biochemical and Biophysical...· 0 citations
Kawista (Limonia acidissima) is a plant known for its potential pharmacological properties, includingantihypertensive activity. This study aimed to evaluate the inhibitory potential of kawista secondary metabolitesagainst angiotensin-converting enzyme (ACE) using an in silico approach. A total of 31 compounds were identifiedand screened for oral bioavailability using the BOILED-Egg model, resulting in 20 compounds with favourablepharmacokinetic properties. Molecular docking analysis revealed that limodissimin A (mol 17) exhibitedthestrongest binding affinity toward ACE (−9.09 kcal/mol; Ki = 215.73 nM), with key interactions involving Lys511, His353, and His513. Molecular dynamics simulations further confirmed the stability of the ACE–ligand complex, asindicated by lower RMSD, reduced structural fluctuations, and decreased solvent exposure compared to the apoprotein. These findings suggest that limodissimin A is a promising candidate for ACE inhibition. Further experimental validation is required to confirm its potential as a natural antihypertensive agent.
E.J. Astuti, M.A. Muchlisin, D. Elvina et al.· RASAYAN Journal of Chemistry· 0 citations
Malaria, caused by the Plasmodium parasites, remains a major global health burden, and resistance to current antimalarials drives the need for drugs with new mechanisms of action. Plasmepsin V (PMV), an essential aspartic protease required for PEXEL processing and protein export, is structurally divergent from human aspartic proteases, offering a path to selective inhibition. Here, we applied a structure‐informed, deconstruction‐based approach to identify non‐peptidomimetic PMV inhibitors by mining catalytic dyad‐binding motifs from experimentally solved aspartic protease–inhibitor complexes and assembling a focused fragment‐like library. Fragment‐inspired model compounds based on pyrrolidine, piperidine, and piperazine cores showed measurable PMV inhibition in a Forster resonance energy transfer (FRET)‐based assay, and a trans‐3,4‐disubstituted pyrrolidine hit (7a; IC50 70 µM) was selected for optimization. Guided by PMV structural data and a renin cocrystal structure of a related pyrrolidine inhibitor, we explored SAR around substituents intended to engage the S1 and S2 regions. Optimization identified N‐sulfonamide analogs bearing two aromatic substituents as a preferred chemotype, with meta‐substitution on the N‐aryl group improving potency to the low micromolar range. The most potent compounds obtained displayed ~10 µM potency, establishing a promising non‐peptidomimetic scaffold for further development of selective PMV inhibitors.
M. Skvorcova, Laura Ruduša, D. Zelencova-Gopejenko et al.· ChemMedChem· 0 citations
