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Daily Signal February 03, 2026 · 10 min read

Issue #39: Comparison of In Vitro Multiple Physiological Activities of Cys-Tyr-Gly-Ser-Arg (CYGSR) Linear and Cyclic Peptides and Analysis Based on Molecular Docking.

Protein Design Digest - 2026-02-03 - Comparison of In Vitro Multiple Physiological Activities of Cys-Tyr-Gly-Ser-Arg (CYGSR) Linear and Cyclic Peptides and Analysis Based on Molecular Docking.

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Comparison of In Vitro Multiple Physiological Activities of Cys-Tyr-Gly-Ser-Arg (CYGSR) Linear and Cyclic Peptides and Analysis Based on Molecular Docking.

Peptide cyclization is a strategy to improve biological stability and functional activity, but direct comparison between linear and cyclic peptides with the same sequence is still limited. In this study, linear (L-CR5) and cyclic (C-CR5) forms were synthesized, and biological functions such as antioxidant, whitening, and anti-wrinkle activity were compared and evaluated. C-CR5 showed about 22.3 times of DPPH radical scavenging activity, which was significantly stronger than L-CR5, and tyrosinase inhibition increased rapidly in C-CR5 to reach inhibition of 95% or more, whereas L-CR5 showed only moderate activity in the same range (about 6.5 times). MMP-1 expression in the evaluation of anti-wrinkle activity did not show a decreasing trend in L-CR5 at all, while C-CR5 showed an anti-wrinkle effect, which was reduced by about 92.8% at 400 μg/mL. As a result of molecular docking analysis, C-CR5 exhibited lower MolDock scores than L-CR5 toward both tyrosinase and MMP-1, indicating a potentially higher binding affinity and improved binding stability. This is expected to be due to reduced structural flexibility and optimized residue directions (especially Tyr and Arg). These results indicate that peptide cyclization is an example of enhanced functional bioactivity of CYGSR and provides a positive case for the structure-activity relationship.

Why this matters: Enhances small-molecule or peptide docking accuracy for targeted drug discovery.

Also Worth Reading

Decrypting potential mechanisms linking ochratoxin A to hepatocellular carcinoma: an integrated approach combining toxicology, machine learning, molecular docking, and molecular dynamics simulation.

Background Ochratoxin A (OTA), a common food-borne mycotoxin, is a potential human carcinogen, yet the specific molecular mechanisms linking it to hepatocellular carcinoma (HCC) remain unclear. Methods We integrated network toxicology to predict OTA targets and intersected them with HCC transcriptomic data to identify key candidate genes. Functional enrichment analysis was then conducted. Multiple machine learning algorithms were applied to screen and validate core genes. Furthermore, molecular docking and molecular dynamics (MD) simulations were employed to evaluate the binding stability between OTA and key target proteins. Results A total of 50 key genes were identified as potential targets for potential OTA-associated hepatocarcinogenesis. Enrichment analysis revealed their significant involvement in critical processes such as xenobiotic metabolism and oxidative stress response. Machine learning analysis prioritized eight core genes (AURKA, GABARAPL1, CA2, PARP1, LMNA, SLC27A5, EPHX2, and GSTP1), and a combined diagnostic model demonstrated outstanding performance (AUC = 0.986). Structural analyses via molecular docking and MD simulations confirmed stable binding interactions between OTA and these core targets. Conclusions This integrated computational study identifies a set of candidate genes through which OTA may potentially interact with HCC-associated molecular networks. The robust binding predicted between OTA and the core targets provides a structural basis for these interactions. These findings offer a prioritized list of targets and a theoretical framework for subsequent experimental validation and investigation into OTA’s toxicological role in HCC.

Study on the Mechanism of Ku Diding in the Treatment of Diabetes based on Network Pharmacology, Molecular Docking Technology, and Molecular Dynamics.

Introduction To explore how Ku Diding (KDD) works in managing Diabetes Mellitus (DM), researchers utilized network pharmacology, molecular docking, and molecular dynamics methodologies. Methods Key active components of KDD were identified using the Traditional Chinese Medicine Systematic Pharmacology Database and Analysis Platform (TCMSP). Data for diabetesrelated targets were retrieved from the Human Genetic Comprehensive Databases (Genecards) and the Online Mendelian Inheritance in Man (OMIM) database. The intersection of these targets was analyzed to determine potential therapeutic targets for diabetes treatment. Proteinprotein interaction networks (PPI) were constructed using the STRING database and Cytoscape software, followed by Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Molecular docking between the components and key targets was performed using the AutoDock Vina platform. Results This study identified that Dihydrosanguinarine, (S)-Scoulerine, among others, are the main active ingredients of KDD for treating DM, showing high affinity for critical targets like PTGS2 and PRKACA, through multiple pathways including vascular regulation, neuromodulation, metabolic regulation, and endocrine regulation. The molecular docking results showed that there are interactions between the active ingredients and the key targets, with the majority of the effective components exhibiting a stronger binding affinity than Metformin. Among them, (S)-Scoulerine and Dihydrosanguinarine demonstrated high docking affinity with the key target proteins PTGS2 and PRKACA. Discussion DM is closely linked to oxidative stress, chronic inflammation, and insulin signaling dysregulation. This study reveals that KDD exerts anti-diabetic effects via a multi-target network involving proteins such as PRKACA, PTGS2, ESR1, FOS, and DRD2. These targets are associated with glucose metabolism, inflammation, oxidative stress, and neural regulation. Modulation of these pathways likely enhances insulin sensitivity, lowers blood glucose, suppresses inflammation, and protects against oxidative damage. GO and KEGG analyses further indicate involvement in MAPK signaling, synaptic transmission, and vascular regulation, forming a multidimensional “metabolism-inflammation-neural” regulatory network. Compared to Metformin, most KDD-derived compounds showed stronger binding, highlighting their therapeutic potential. Molecular dynamics simulations support the stability of the observed binding conformations, suggesting their potential as therapeutic targets. These findings underscore KDD’s ability to simultaneously target multiple pathological mechanisms, offering a holistic treatment strategy for DM. Conclusion This study provides preliminary evidence that KDD is characterized by a multicomponent, multi-target, and multi-pathway approach in the treatment of diabetes mellitus (DM), thereby establishing a scientific foundation for further in-depth exploration of KDD’s molecular mechanisms.

Design, Docking, ADMET, Pass, Synthesis and Bio-Evaluation of Novel 7-O-Substituted Chrysin-Based VEGFR-2 Inhibitors.

VEGFR-2 is a critical target in cancer therapy, facilitating tumor angiogenesis, yet existing inhibitors face toxicity and resistance issues. Chrysin, a flavonoid with anticancer properties, has VEGFR-2 characteristics but suffers from poor pharmacokinetics. A series of 7-O-substituted chrysin derivatives was designed to improve binding and drug-like properties by integrating key hydrogen-bonding groups and hydrophobic elements, informed by VEGFR-2 structural analysis. To design and assess novel chrysin derivatives through computational predictions and molecular docking; synthesize and characterize selected derivatives; and evaluate their antioxidant and anticancer activities in vitro, to identify effective candidates that exhibit favourable pharmacokinetics and safety. Chrysin derivatives featuring alkylamino and ester substituents were designed using molecular docking against VEGFR-2. ADMET profiling was conducted to anticipate pharmacokinetics and toxicity. In silico cytotoxicity of chrysin and its hybrids was assessed using CLC-Pred 2.0 on the basis of PASS analysis and further analyzed on nine breast cancer cell lines via BC CLC-Pred. Selected derivatives were synthesized via alkylation and esterification and characterized using UV, IR, NMR, and mass spectrometry. Antioxidant activity was evaluated with the DPPH assay, whereas anticancer efficacy against MCF-7 and normal cell lines was measured through cell viability assays, comparing IC50 values to ascorbic acid and sorafenib. Docking studies indicated strong binding affinities, particularly for ester derivatives. ADMET predictions suggested favorable drug-like characteristics. Compound C7 demonstrated remarkable antioxidant activity (IC50 = 0.6 μM), exceeding both chrysin and ascorbic acid. In anticancer tests, C7 and C8 displayed significant cytotoxicity (IC50 = 1.0 and 1.5 μM, respectively), outperforming chrysin and nearing sorafenib efficacy. All other hybrids were found to have moderate inhibitory properties as compared to sorafenib, but better than chrysin. The improved bioactivity and predicted safety of C7 and C8 highlight the efficacy of rational structural modifications in optimizing natural products. Their dual antioxidant and anticancer properties underscore their potential as lead compounds for VEGFR-2-targeted breast cancer treatments. Ester-substituted chrysin derivatives, specifically C7 and C8, demonstrate promising VEGFR-2 inhibition and therapeutic potential, warranting further exploration as multifunctional anticancer agents.

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