Recep Adiyaman
bioinformatics

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.

February 03, 2026 Daily Intelligence
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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.

🧬 Abstract

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

⭐ Additional Signals

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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The Role of the Electronic Structure during Protein Folding through Electron Density-Based Quantum Chemical Descriptors.

One of the major challenges in protein folding is understanding the role that the electronic structure of proteins plays during their folding. We emphasize that the structural and dynamic properties of proteins are extremely important for understanding how their conformational changes occur during folding. However, since the electronic structure is intrinsically related to the atomic structure, further analysis of the electronic structure during folding may assist in the development of methods for predicting protein biological activity. In this study, we applied statistical sampling in molecular dynamics folding trajectories, and subsequent calculations of global and local quantum chemical molecular descriptors calculated by DFT-D3 and semiempirical quantum chemical methods for three fast-folding proteins (NTL9, BBA, and α3D). We observe an intriguing trend in the local hardness per residue (η j ). Specifically, soft residues do not become softer as the trajectory progresses until they reach the expected softness, and hard residues do not become progressively harder. Rather, a subtle process occurs in which the local hardness fluctuates above and below the final native values for each residue. The point is not that the folded structures have more favorable hard or soft interactions in their residues, but that η j becomes stable as the conformation approaches the folded state. In addition, we observed that η j can distinguish non-native from native-like structures, revealing that intrinsic aspects of the electronic structure play a highly relevant role in the protein folding process. These observations could show an electronic structure signature during protein folding.

In-silico characterization of deleterious non-synonymous SNPs in the human S1PR1 gene reveals structural instability and altered ligand affinity.

S1PR1 is a G protein-coupled receptor that plays a key role in regulating lymphocyte trafficking, immune response, cardiovascular system function, cell proliferation and survival, tumor angiogenesis, and metastasis. It is also recognized as a pharmacotherapeutic target for the treatment of autoimmune diseases like relapsing multiple sclerosis and ulcerative colitis. This study aimed to identify deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) in the S1PR1 gene that may impact its functional properties and pharmacotherapeutic responses though in-silico approaches. A total of 3,259 SNPs were identified in the human S1PR1 gene, with 6.51% being non-synonymous (nsSNPs). Functional predictions from eight computational tools prioritized 25 deleterious variants. Further structural and evolutionary evaluation highlighted R120P, F125S, C184Y, Y198C, and L275P as the most damaging nsSNPs. These mutations were found to cluster within the seven-transmembrane (7-TM) domain (residues 46-322), directly affecting receptor stability and signaling. Structural modeling revealed disrupted hydrogen bonds, void formations, and loss of critical disulfide bonding (C184Y), severely compromising folding. Conservation analysis confirmed R120P, F125S, and C184Y as highly conserved (score 9), underscoring their functional importance. Molecular docking and dynamics simulations showed that R120P and F125S weaken binding affinity for natural agonist sphingosine-1-phosphate (S1P) and FTY720P, while antagonist W146 retained strong binding. Our analysis further revealed significant changes in binding interactions and protein-ligand complex stability under simulated physiological conditions. Collectively, these findings identified high-risk nsSNPs in S1PR1 gene with potential structural and functional implications, particularly in diseases involving impaired receptor signaling. These findings enhanced our understanding of how specific nsSNPs can influence disease susceptibility, drug response, and receptor function, paving the way for precision medicine approaches in treating autoimmune and inflammatory disorders.

Discovery of a novel Keap1 inhibitor for neurodegeneration through virtual screening and molecular dynamics simulations.

Oxidative stress is a key feature of Alzheimer’s disease (AD) and other neurodegenerative disorders. The Kelch-like ECH-associated protein 1 (Keap1)-nuclear factor erythroid 2-related factor 2 (Nrf2) pathway controls redox balance, and disrupting the Keap1-Nrf2 protein-protein interaction (PPI) has become a promising therapeutic approach. Marine natural products (MNPs), because of their structural diversity and bioactivity, are an underexplored source of potential neuroprotective compounds. This study aimed to identify novel marine-derived inhibitors of the Keap1-Nrf2 interaction using a comprehensive in silico pipeline. A total of 14,492 compounds from an open-access MNP database were virtually screened against the Keap1 Kelch domain through molecular docking. The top 1,329 candidates exhibited strong binding affinities, with several reaching scores comparable to the co-crystallized reference ligand L5F. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) profiling was employed to assess pharmacokinetic properties, brain penetration, and safety, leading to the identification of compound 145398-61-4 as the most promising hit. Molecular dynamics (MD) simulations verified the structural stability of the Keap1-145398-61-4 complex, while binding free energy calculations indicated energetically favorable interactions. Additional validation using principal component analysis (PCA) and highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy analysis further confirmed the stability of this interaction. Overall, our in silico study identified compound 145398-61-4 as a novel Keap1-Nrf2 inhibitor, highlighting its potential as a lead candidate for developing treatments for Alzheimer’s disease and other neurodegenerative disorders, such as amyotrophic lateral sclerosis and multiple sclerosis.

Integrating metabolomics, network pharmacology and molecular dynamics simulations reveals that Xiehuang San targets CLCF1-STAT3 to restore insulin signaling in T2DM.

Xiehuang San (XHS) is a classical Chinese herbal formula with analgesic, anti-inflammatory, gastrointestinal-regulating and hypoglycemic effects, but its specific regulatory mechanisms remain incompletely understood. To evaluate the effects of XHS on T2DM, with a particular focus on its metabolic and molecular mechanisms. C57BL/6J mice were induced with T2DM using a high-fat diet combined with streptozotocin. T2DM mice were treated with XHS for 4 weeks to assess blood glucose control and metabolism. Serum metabolomics were analyzed by UPLC-Q-TOF/MS. Network pharmacology integrated drug-metabolite-disease associations. Molecular docking and dynamics simulations assessed the binding of active compounds to targets. RT-qPCR and Western blot were used to determine gene and protein expression levels. An in vitro model was established to validate the effects of XHS on T2DM. XHS significantly improved T2DM pathology. Compared to the diabetic Mod group, XHS reduced fasting blood glucose levels, enhances glucose tolerance and improves insulin resistance and sensitivity. 24 dysregulated metabolites were corrected after treatment. Network pharmacology predicted that the key target of XHS in T2DM treatment is the CLCF1-STAT3 pathway. Licochalcone B, Wogonin and Apigenin are predicted to exhibit strong binding affinity for this pathway. Both in vitro and in vivo models, XHS effectively inhibits the activation of the CLCF1-STAT3 signalling pathway and protects insulin signalling. This study combines metabolomics and network pharmacology to reveal that XHS exerts anti-diabetic effects by remodeling glycerophospholipid metabolism and inhibiting CLCF1-STAT3 signaling. These findings support the application of XHS in the treatment of T2DM.

Mechanistic insights into PCBP1-driven unfolding of selected i-motif DNA at G1/S checkpoint.

I-motifs are non-canonical, four-stranded DNA structures in cytosine-rich genomic regions, yet their protein-mediated regulation remains underexplored. Here, we identify PCBP1 (Poly(rC)-binding protein 1) as a selective i-motif-binding protein that unfolds specific i-motifs depending on their protonation and hairpin-forming propensities. Systematic truncation reveals that individual K-homology (KH) domains of PCBP1 cannot selectively bind or unfold i-motifs, but their coordinated actions restore wild-type PCBP1 functions. Using biochemical, biophysical, and molecular dynamics studies, we demonstrate that KH1+2 domains remodel i-motifs, recruiting KH3 to facilitate unfolding and efficient DNA replication. Chromatin and cell-based investigations reveal that PCBP1-knockdown increases i-motif formation at specific genomic loci, coinciding with G1/S arrest and elevated γH2AX, indicative of genomic instability. During G1/S transition, PCBP1 occupancy peaks at these i-motif loci, ensuring i-motif resolution in early S phase. These findings establish PCBP1 as a critical regulator of i-motif dynamics, directly linking its unfolding activity to G1/S transition and genome stability.

From Hit to Lead: Discovery of Novel Selective RIPK1 Inhibitor with Pyridoimidazole Scaffold for the Treatment of Autoimmune Diseases through Phenotypic Screening and Structural Optimization.

Autoimmune diseases remain challenging to treat due to the limitations of TNFα-targeted biologics and the inefficacy of small molecules directly targeting TNFα. RIPK1, a central mediator of TNFα-driven inflammation and necroptosis, offers a promising alternative therapeutic target. Using drug repurposing and phenotype-based high-content screening of 378 clinical-stage kinase inhibitors, TAK-117 (a PI3Kα inhibitor) was identified as a RIPK1 hit compound with a novel pyridoimidazole scaffold. Guided by structure-based optimization and four iterative SAR cycles, WJH-C19 was developed, exhibiting >1000-fold increased RIPK1 potency (IC50 = 5.7 nM) and negligible PI3Kα activity (IC50 > 10 μM). Mechanistically, WJH-C19 suppressed the RIPK1/RIPK3/MLKL signaling axis, attenuating inflammatory responses. Oral administration of WJH-C19 achieved robust efficacy in DSS-induced colitis and CFA-induced arthritis models, with favorable pharmacokinetics and no observable toxicity. These results establish WJH-C19 as a potent lead and highlight the pyridoimidazole scaffold as a privileged chemotype for RIPK1-targeted drug discovery in autoimmune diseases.

Glycine at Position 93 in SOD1: Mutation-Sensitivity Landscape and Context-Dependent Folding Requirements.

Glycine, the simplest amino acid with a single hydrogen atom as its side chain, plays a crucial role in protein folding and structural flexibility. In this study, we used copper/zinc superoxide dismutase (SOD1) as a model system to investigate how the substitution of glycine at position 93 with various amino acids affects the protein structure and stability. We engineered 19 G93 SOD1 mutants and evaluated their folding patterns and aggregation propensities using immunoblotting, fluorescence microscopy, and fluorescence loss in photobleaching (FLIP) assays. All mutants, regardless of the amino acid substitution, form protein aggregates with varying degrees of stability, demonstrating that position 93 exhibits extreme mutation sensitivity, with different substitutions producing distinct destabilization pathways. Our findings demonstrate that alteration of glycine’s minimal side chain─consisting of a single hydrogen atom─ disrupts native protein structure. The physicochemical properties of the substituting amino acid, such as polarity, charge, and steric bulk, critically modulate the nature and extent of the resulting misfolding. Nonpolar residues promote aggregation primarily through hydrophobic interactions, while polar and charged residues drive aggregation via hydrogen bonding and electrostatic interactions. This study provides fundamental insights into glycine’s unique structural contributions to protein architecture and presents a conceptual framework for understanding how side chain properties influence protein folding and stability. These findings also provide mechanistic implications for protein aggregation processes in neurodegenerative diseases.

Molecular Dynamics and Experimental Validation of Natural Products from Chuanxiong Rhizoma as VEGFR2 Inhibitors for nAMD Therapy.

Age-related macular degeneration (AMD) is a leading cause of blindness among the elderly worldwide. Neovascular AMD (nAMD) is a significant subtype of AMD, responsible for the blindness of over 90% of patients with AMD. The hallmark of nAMD is choroidal angiogenesis dysregulation, a condition that can result in severe inflammation, leakage, and bleeding, ultimately leading to a precipitous decline in visual acuity. Inhibition of the vascular endothelial growth factor (VEGF) pathway has been proven to be an effective therapeutic strategy for this disease. Intraocular injection of anti-VEGF macromolecule drugs is a clinical therapy for this disease, but it has shortcomings, such as severe side effects, high cost, long treatment cycle, and complex administration methods. Consequently, the identification of novel small-molecule drugs and the development of innovative delivery mechanisms are of paramount importance for the treatment of this condition. Chuanxiong Rhizoma (CX), a type of traditional Chinese medicine (TCM), has been employed in the treatment of vascular-related diseases. Contemporary pharmacological research has demonstrated that CX contains a substantial quantity of natural compounds that exhibit anti-VEGF activity. In this study, we employed molecular simulation docking and molecular dynamics (MD) to examine the anti-VEGFR2 effects of 10 natural compounds derived from CX. Sorafenib was selected as the reference ligand, which is a marketed VEGFR2 inhibitor for cancer treatment. As a DFG-out inhibitor, sorafenib stabilizes the inactive conformation of the kinase by binding to an allosteric site near the ATP-binding pocket. In our research, natural products exhibiting a strong binding affinity were identified using computer-simulated docking technology and detailed binding sites were predicted. The findings of the research indicate that apigenin exhibits the strongest affinity for the VEGFR2 receptor with the formation of three hydrogen bonds. The molecular docking results indicate that the CYS919 and ASP1046 amino acid residues of VEGFR2 are the primary groups that form hydrogen bonds with the ligands. Furthermore, the AutoQSAR module of Schrödinger Suite predicted apigenin to have the highest predicted pIC50 value among the ten candidate compounds, suggesting its potential for significant VEGFR2 inhibitory activity. A subsequent MD simulation revealed that the binding of apigenin to the protein was more stable, and the conformation was stronger. According to the ADMET prediction results, apigenin is characterized by low toxicity. To ascertain the capacity of apigenin to impede the proliferation of choroidal angiogenesis, the choroid sprouting assay was utilized as a methodological framework. An in vitro experiment demonstrated that apigenin can significantly inhibit the growth of choroidal vessels in a dose-dependent manner. The present study was conducted with the objective of assessing the potential of natural products in the treatment of nAMD. In addition, the study offered valuable insights for the development of new natural agents.

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The protein structure is the language of life; design is its poetry. — Recep Adiyaman

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