Molecular Docking Results Research Articles

Design, Synthesis, and Antifungal Activities of Phenylpyrrole Analogues Based on Alkaloid Lycogalic Acid.

Plant diseases caused by pathogenic fungi seriously affect the yield and quality of crops, cause huge economic losses, and pose a considerable threat to global food security. Phenylpyrrole analogues were designed and synthesized based on alkaloid lycogalic acid. All target compounds were characterized by 1H NMR, 13C NMR, and HRMS. Their antifungal activities against seven kinds of phytopathogenic fungi were evaluated. The results revealed that most compounds had broad-spectrum fungicidal activities at 50 μg/mL; 14 compounds displayed more than 60% fungicidal activities against Rhizoctonia cerealis and Sclerotinia sclerotiorum, and in particular, the fungicidal activities of compounds 8g and 8h against Rhizoctonia cerealis were more than 90%, which could be further developed as lead agents for water-soluble fungicides. The molecular docking results indicate that compounds 8g and 8h can interact with 14α-demethylase (RcCYP51) through hydrogen bonding with strong affinity.

The mechanism of Taohong Siwu decoction in treating chemotherapy-induced peripheral neuropathy: a network pharmacology and molecular docking study.

Taohong Siwu decoction (THSWD) is a classic traditional Chinese medicine (TCM) formula known for its effects in promoting blood circulation, removing blood stasis, and rejuvenating energy. There have been clinical reports of THSWD treating chemotherapy-induced peripheral neuropathy (CIPN) caused by paclitaxel. We conducted a network pharmacology and molecular docking analysis to further clarify the molecular mechanisms by which THSWD exerts its protective effects against CIPN. Chemical components of THSWD and their corresponding targets were obtained through the traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP), and related targets of CIPN were searched in disease databases including Online Mendelian Inheritance in Man (OMIM), Therapeutic Target Database (TTD), GeneCards, and DrugBank. Common targets between THSWD and CIPN were identified using Venn diagrams. A protein-protein interaction (PPI) network was constructed using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), which was followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. AutoDock and PyMOL were used for the molecular docking validation of the key components of THSWD with core targets. At total of 69 chemical components of THSWD were identified, corresponding to 856 targets; 2,297 targets were associated with CIPN, with an intersection of 105 common targets. PPI analysis identified eight core targets: MYC, TNF, MAPK14, AKT1, ESR1, RELA, TP53, and HSP90AA1; KEGG enrichment analysis implicated signaling pathways such as PI3K-Akt, NF-κB, and HIF-1, etc. Molecular docking results indicated that the selected active components and their corresponding target proteins have good binding activity. Through network pharmacology, this study found that THSWD has significant advantages in treating CIPN. By analyzing potential core targets, biological functions, and involved signaling pathways, we clarified the potential molecular biological mechanisms involved in THSWD's treatment effect. This study provides a theoretical basis for the clinical application of THSWD in treating CIPN.

Research on bitter taste and efficacy of Ginkgo biloba extract based on UPLC-Q-TOF-MS~E integrated with molecular docking

Based on high performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry(UPLC-Q-TOF-MS~E) and molecular docking technique, bitter compounds of Ginkgo biloba extract(GBE) were characterized, and their relationship with bitter efficacy was investigated. Firstly, UPLC-Q-TOF-MS~E was used for qualitative analysis of GBE components, and 60 chemical components were identified. These chemical components were molecular-docked with bitter receptors, and 26 bitter substances were selected, mainly flavonoids. Secondly, sensory and electronic tongue bitterness evaluation techniques were used to verify that total flavones of GBE were the main bitter substances, which was consistent with the molecular docking results. Finally, network pharmacology was used to predict and analyze bitter substances. The relationship between the target of bitter substance and bitter effect was explored. The key targets of bitter substances are CYP2B6, ALOX15, and PTGS2, etc., and bitter substances may exert a bitter efficacy by ac-ting on related disease targets, indicating that bitter substances of GBE are the material basis of the bitter effect. In summary, the study indicated that the molecular docking technique had a guiding effect on the screening of bitter substances in traditianal Chinese medicine(TCM), and bitter substances of GBE had a bitter efficacy. It provides ideas and references for the study of the "taste-efficacy relationship" of TCM in the future.

Icariside II in NSCLC and COVID-19: Network pharmacology and molecular docking study.

Patients with non-small cell lung cancer (NSCLC) are susceptible to coronavirus disease-2019 (COVID-19), but current treatments are limited. Icariside II (IS), a flavonoid compound derived from the plant epimedin, showed anti-cancer,anti-inflammation and immunoregulation effects. The present study aimed to evaluate the possible effect and underlying mechanisms of IS on NSCLC patients with COVID-19 (NSCLC/COVID-19). NSCLC/COVID-19 targets were defined as the common targets of NSCLC (collected from The Cancer Genome Atlas database) and COVID-19 targets (collected from disease database of Genecards, OMIM, and NCBI). The correlations of NSCLC/COVID-19 targets and survival rates in patients with NSCLC were analyzed using the survival R package. Prognostic analyses were performed using univariate and multivariate Cox proportional hazards regression models. Furthermore, the targets in IS treatment of NSCLC/COVID-19 were defined as the overlapping targets of IS (predicted from drug database of TMSCP, HERBs, SwissTarget Prediction) and NSCLC/COVID-19 targets. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis of these treatment targets were performed aiming to understand the biological process, cellular component, molecular function and signaling pathway. The hub targets were analyzed by a protein-protein interaction network and the binding capacity with IS was characterized by molecular docking. The hub targets for IS in the treatment of NSCLC/COVID-19 includes F2, SELE, MMP1, MMP2, AGTR1 and AGTR2, and the molecular docking results showed that the above target proteins had a good binding degree to IS. Network pharmacology showed that IS might affect the leucocytes migration, inflammation response and active oxygen species metabolic process, as well as regulate the interleukin-17, tumor necrosus factor and hypoxia-inducible factor-1 signaling pathway in NSCLC/COVID-19. IS may enhance the therapeutic efficacy of current clinical anti-inflammatory and anti-cancer therapy to benefit patients with NSCLC combined with COVID-19.

Qingxiong Ointment and its Active Ingredient, Shikonin Treat Psoriasis through HIF-1 Signaling Pathway.

Psoriasis is a common chronic inflammatory skin disorder. Qingxiong ointment (QX) is a natural medicinal combination frequently employed in clinical treatment of psoriasis. However, the active ingredients of QX and its precise mechanisms of improving psoriasis remain unclear. This study elucidated the effects of QX on an Imiquimod (IMQ)-induced mouse model of psoriasis while also exploring the regulation of the active ingredient of QX, shikonin, on the HIF-1 signaling pathway in HaCaT cells. A mouse model of psoriasis was established through topical application of IMQ, and the local therapeutic effect of QX was evaluated using dorsal skin tissue with mouse psoriatic lesion and Psoriasis Area Severity Index (PASI) scores, hematoxylin-eosin (HE) staining, and immunohistochemical staining. Elisa and qPCR were employed to identify changes in the expression of inflammation-related factors in the mouse dorsal skin. Immunofluorescence was used to assess changes in the expression of T cell subsets before and after treatment with various doses of QX. HPLC was used to analyze the content of shikonin, and network pharmacology was employed to analyze the main targets of shikonin. Immunofluorescence was used to identify the effects of shikonin on the HIF-1 signaling pathway in IL6-induced psoriasis HaCaT cells. Finally, qPCR was used to identify the differential expression of the HIF-1 signaling pathway in skin tissues. QX significantly reduces PASI scores on the backs of IMQ-induced psoriasis mice. HE staining reveals alleviated epidermal thickness in the QX group. Immunohistochemical analysis shows a significant reduction in ICAM, KI67, and IL17 expression levels in the QX group. Immunofluorescence results indicate that QX can notably decrease the proportions of CD4+ T cells, γδ T cells, and CD8+ T cells while increasing the proportion of Treg cells. Network pharmacology analysis demonstrates that the main targets of shikonin are concentrated in the HIF-1 signaling pathway. Molecular docking results show favorable binding affinity between shikonin and key genes of the HIF-1 signaling pathway. Immunofluorescence results reveal that shikonin significantly reduces p-STAT3, SLC2A1, HIF1α, and NOS2 expression levels. qPCR results show significant downregulation of the HIF-1 signaling pathway at cellular and tissue levels. Our study revealed that QX can significantly reduce the dorsal inflammatory response in the IMQ-induced psoriasis mouse model. Furthermore, we discovered that its main component, shikonin, exerts its therapeutic effect by diminishing the HIF-1 signaling pathway in HaCaT cells.

The Potential Mechanism of Eriodictyol in Treating Alzheimer's Disease: A Study on Computer-assisted Investigational Strategies.

At present, drug development for treating Alzheimer's disease (AD) is still highly challenging. Eriodictyol (ERD) has shown great potential in treating AD, but its molecular mechanism is unknown. We aimed to explore the potential targets and mechanisms of ERD in the treatment of AD through network pharmacology, molecular docking, and molecular dynamics simulations. ERD-related targets were predicted based on the CTD, SEA, PharmMapper, Swiss TargetPrediction, and ETCM databases, and AD-related targets were predicted through the TTD, OMIM, DrugBank, GeneCards, Disgenet, and PharmGKB databases. Protein-protein interaction, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomics analyses (KEGG) were used to analyse the potential targets and key pathways of the anti-AD effect of ERD. Subsequently, potential DEGs affected by AD were analysed using the AlzData database, and their relationships with ERD were evaluated through molecular docking and molecular dynamics simulations. A total of 198 ERD-related targets, 3716 AD-related targets, and 122 intersecting targets were identified. GO annotation analysis revealed 1497 biological processes, 78 cellular components, and 132 molecular functions of 15 core targets. KEGG enrichment analysis identified 168 signalling pathways. We ultimately identified 9 DEGs associated with AD through analysis of the AlzData data. Molecular docking results showed good affinity between the selected targets and ERD, with PTGS2, HSP90AA1, and BCL2. The interactions were confirmed by molecular dynamics simulations. ERD exerts anti-AD effects through multiple targets, pathways, and levels, providing a theoretical foundation and valuable reference for the development of ERD as a natural anti-AD drug.

Network Pharmacological Study of the Active Ingredient of Panax Notoginseng Saponins for the Treatment of Lung Cancer by Inhibiting AKR1C3

Background: Lung cancer is the malignancy with the second highest diagnostic rate and the leading cause of cancer-related death. Objective: This study aims to investigate the potential mechanism and molecular targets of Panax notoginseng saponins (PNS) in inhibiting lung cancer through network pharmacology. Methods: Pharmacodynamic targets of each compound of PNS were searched from TargetNet, SwissTargetPrediction, and BatMan-TCM databases. Next, the differential expression genes (DEGs) in lung cancer were obtained from the Gene Expression Omnibus (GEO) database and screened by R package. Later, the STRING 11.0 database was utilized to analyze the protein-protein interaction (PPI) network of common targets of PNS-lung cancer, clusterProfiler to perform gene ontology (GO) annotation, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for the common targets, and Cytoscape 3.8.0 to construct and analyze the "ingredient-target" network for the common targets of PNS-lung cancer. Results: A total of 154 potential pharmacodynamic targets of PNS, 2399 DEGs of lung cancer-related diseases, and 21 common targets of PNS-lung cancer were obtained by database search and screening. The 21 common targets were mainly involved in biological processes (such as small molecule metabolism and cytokine production) and were major components of cellular structures (such as neuronal cell bodies and membrane rafts). Besides, these targets could function as carboxylic ester hydrolases, G protein-coupled amine receptors, and oxidoreductase. They were mainly enriched in 14 signaling pathways, like neuroactive ligand-receptor interaction, regulation of lipolysis in adipocytes, and calcium signaling pathway. Furthermore, the molecular docking results revealed that aldo-keto reductase family 1 member C3 (AKR1C3) and melanin metabolic enzyme (MME) may be direct targets of ginsenoside Rg1 and notoginsenoside R2. Conclusion: Our study showed that ginsenosides inhibit the progression of lung cancer through multiple targets and pathways. More importantly, PNS may treat lung cancer by directly inhibiting AKR1C3.

Effects of genetic diversity on the allergenicity of peanut (Arachis hypogaea) proteins: identification of the hypoallergenic accessions using BALB/c mice model and in silico analysis of Ara h 3 allergen cross-reactivity

This study investigated the effects of genetic diversity in the allergenicity of peanut and assessed the allergenic capacity of six Arachis hypogaea accessions using a Balb/c mouse model. It also explored potential cross-reactivities between Ara h 3 (peanut allergen) and Gly m (soybean allergen) using computational tools. Female Balb/c mice were injected with peanut protein extracts and alum. Serum-specific antibodies (IgE, IgGt, IgG1, IgG2a) were measured using ELISA, and allergic protein profiles were examined via western blot. Structural homology, B cell epitopes, and molecular interactions between Ara h 3 and Gly m with human IgE were also investigated. The mice developed high sIgE and sIgG1 responses, with antibodies recognizing 19 bands on western blot. Notably, Saharan accessions showed unique features such as no bands on western blot profiles, reduced anaphylactic symptoms, lower IgE titers, and less intestinal tissue damage. Molecular docking results suggest significant cross-allergenicity, supported by allergenicity predictions and structural homology analysis. This comprehensive analysis provides insights into shared epitopes, potential competition for binding sites, and molecular dynamics of cross-reactive responses, enhancing understanding of food allergen interactions. The study recommends using Algerian Sahara peanut accessions in breeding, genomics studies, and industry for safer peanut options for individuals with allergies. SignificanceThe significance of this study lies in its contribution to addressing a major public health issue: peanut allergy, which represents a significant cause of anaphylaxis affecting numerous individuals and families worldwide. By exploring the genetic diversity of peanut proteins and identifying hypoallergenic accessions through experimental and computational approaches, this research offers valuable insights for mitigating allergic reactions. The findings highlight that certain accessions from the Saharan region exhibit reduced allergenicity, resulting in attenuated anaphylactic symptoms, lower IgE levels, and reduced intestinal damage in murine models. Furthermore, the study's in silico analysis sheds light on the issue of cross-reactivity between peanut and soybean allergens, providing crucial information for understanding allergen interactions at the molecular level. Overall, this research contributes to advancing knowledge in the field of food allergen research and has practical implications for improving the quality of life for individuals allergic to peanuts, particularly through the selection of safer peanut varieties and their cultivation.

Material basis and mechanism of Bletillae Rhizoma for melasma, gastrointestinal hemorrhage, lung cancer and bronchoplumonary inflammation as "homotherapy for heteropathy" based on UHPLC-Q-Exactive Orbitrap HRMS coupled with network pharmacology and molecular docking

Based on UHPLC-Q-Exactive Orbitrap HRMS coupled with the network pharmacology and molecular docking, the common material basis and molecular mechanisms of Bletillae Rhizoma for melasma, gastrointestinal hemorrhage, lung cancer and bronchoplumonary inflammation as "homotherapy for heteropathy" were explored. The fingerprint of 17 batches of Bletillae Rhizoma from different areas was established using HPLC, and the similarity analysis was carried out. The common chemical components of the 17 batches of Bletillae Rhizoma were identified using UHPLC-Q-Exactive Orbitrap HRMS. Depending on the bioavailability and drug-like properties of the common components, the active chemical components were screened, and then their protein targets were collected using the Traditional Chinese Medicine Database and Analysis Platform(TCMSP) and SwissTargetPrediction database. The protein targets related to diseases were retrieved from the databases DrugBank, TTD and GeneCards to produce a Venn diagram. The shared targets were obtained between drugs and diseases as "homotherapy for heteropathy" targets. The protein-protein interaction(PPI) was analyzed with the STRING database, and KEGG and GO analyses of the "homotherapy for heteropathy" targets were performed using the Bioconductor database. Cytoscape 3.7.2 software was employed to construct the "chemical components of Bletillae Rhizoma-homotherapy for heteropathy targets" network and PPI network, and topological analysis was conducted to screen out the key active chemical components and core targets. Finally, the affinity between the active components and core targets was evaluated using the molecular docking by AutoDock Vina 4.2.6, which verified the interaction between them. Thirteen common peaks were identified by fingerprint chromatography, and the similarity between different batches was 0.941-0.998. Fifty-three chemical components were identified by mass spectrometry in Bletillae Rhizoma, and 18 common chemical constituents were obtained in the 17 batches of Bletillae Rhizoma. Network pharmacologic screening showed that the pharmacodynamic substances of Bletillae Rhizoma for melasma, gastrointestinal hemo-rrhage, lung cancer and bronchoplumonary inflammation with "homotherapy for heteropathy" were 11 compounds, such as polysaccharides, biphenanthrenes, dihydrophenanthrenes and bibenzyls. There were 42 common targets identified for the treatment of different diseases. These targets were involved in biological processes such as cell response to chemical stress, reactive oxygen species and positive regulation of protein kinase B signal transduction. They were also involved in 121 signaling pathways, encompassing vital pathways such as PI3K-Akt, ErbB, Rap1, FoxO, MAPK and estrogen. Molecular docking results showed a strong affinity between the key active components and the core targets. This study provides a preliminary explanation of how Bletillae Rhizoma exerts its therapeutic effect on chloasma, gastrointestinal hemorrhage, lung cancer, and bronchopneumonic lesions as "homotherapy for heteropathy" through a combined action involving multiple components, targets, and pathways. These findings offer a certain theoretical basis for the further deve-lopment and application of Bletillae Rhizoma.

Computer-aided rational design and synthesis of new potential antihypertensive agents among 1,2,3-triazole-containing nifedipine analogs

1,2,3-Triazole-containing Nifedipine analogues offer the opportunity to increase biostability, bioavailability, efficacy and binding selectivity to target receptors. Here, we applied a computer-aided rational design for identifying new Nifedipine analogues containing a 1,2,3-triazole moiety. First, a new chemical library of 796 derivatives combining the DHP fragment and 1,2,3-triazole moiety was generated. Second, to reduce the library size, the library was pre-filtered using two 3D-pharmacophore models with different complexity, which allowed us to gradually reduce the chemical space, ending up with 26 hit candidates. Molecular docking calculations against the rCav1.1 receptor allowed the identification of eight derivatives 5a-h, characterized by the binding affinity towards the rCav1.1 receptor of the same level as approved Nifedipine-like drugs. Next, our molecular docking results were used to guide and optimize the retrosynthetic approaches for new analogues of Nifedipine as promising antihypertensive agents. So, a retrosynthetic approach for Nifedipine analogues with a 1,2,3-triazole ring in position 4 was proposed. Finally, eight analogues 5a-h determined by molecular docking calculations were synthesized using the suggested retrosynthetic approach. The aim of this study is to identify new Nifedipine analogues using a computer-aided drug design and a retrosynthetic approach. Materials and Methods. The organic synthesis of new Nifedipine analogues containing a 1,2,3-triazole moiety. Computer-aided drug design of new DHP derivatives using pharmacophore screening and molecular docking calculations. Results. Molecular docking of new Nifedipine analogues made it possible to estimate the binding affinity of new Nifedipine derivatives to the rCav1.1 receptor. Pharmacophore screening of a chemical library of analogues, consisting of 796 derivatives, allowed gradually reducing the chemical space and obtaining 26 candidates with high affinity to the rCav1.1 receptor. Using the method of molecular docking, eight hits 5a-h were identified, and the synthesis of the recommended compounds was proposed and performed. Conclusions. The results of molecular docking showed that Nifedipine analogues are characterized by binding affinity to the rCav1.1 receptor at the same level as approved Nifedipine-like drugs. Pharmacophore screening and molecular docking calculations indicate key features of the ligand-receptor interaction that can guide and optimize the synthesis of new Nifedipine analogues as promising new antihypertensive agents. A retrosynthetic approach was proposed, and the recommended compounds were synthesized

Synthesis, crystal structure, Hirshfeld surface analysis, energy frameworks, molecular docking and DFT calculation of new pyrazole-4-carboxamide compound as antifungal agent

A new compound 3-(difluoromethyl)-N-((3,4-difluorophenyl)carbamoyl)-1-methyl-1H- pyrazole-4-carboxamide (7) was synthesized. The structure of 3-(difluoromethyl)-N-((3,4-difluorophenyl)carbamoyl)-1-methyl-1H-pyrazole-4-carboxamide was confirmed by 1H NMR, HRMS and X-ray single crystal diffraction. The in vivo greenhouse fungicidal activity showed that 3-(difluoromethyl)-N-((3,4-difluorophenyl)carbamoyl)-1-methyl-1H-pyrazole-4-carboxamide (7) possessed good control efficacy against Botrytis cinerea. The title compound exhibited intermolecular hydrogen bonds of the type N–H…O and C–H…F. Hirshfeld surface analysis shows that the major intermolecular interaction is mainly due to H…H contacts. Furthermore, energy frameworks, molecular docking results and DFT calculation were done and the results indicated that pyrazole carboxamide group is important for the fungicidal activity.

In Silico Analysis for Exploring the Potential Inhibitors Against Breast Cancer (MCF7) Using Curcumin Analogue Compounds

Breast cancer is one of the most problematic diseases in the world. Currently, there are no potential vaccines for the treatment of this disease. Therefore, finding effective compounds, such as curcumin analogs, is crucial to inhibit breast cancer. Forty-five synthesized curcumin analogs were tested on the MCF7 cell line using the MTT assay. It was shown that nine curcumin compounds, Cpd 5, Cpd 9, Cpd 17, Cpd 18, Cpd 21, Cpd 25, Cpd 28, Cpd 32, and Cpd 45, had better inhibitory activities against breast cancer. Furthermore, in silico analysis was developed using 2D and 3D QSAR models with high predictive ability, with an r2 value of 0.834. In addition, based on molecular docking, molecular dynamics, and pharmacophore results, it was shown that these nine compounds had the lowest binding free energy and were also stable during the simulation. The presence of methoxy groups, hydrogen bond donors, and aromatic ring features are the main factors that enhance the biological activity of curcumin analogs. Therefore, these compounds could serve as references for the next stage of drug design.

MOLECULAR DOCKING STUDY OF EPIGALLOCATECHIN GALLATE (EGCG) AS A THERAPY FOR TYPE 2 DIABETES MELLITUS

Epigallocatechin gallate (EGCG) has an effect in reducing sugar levels in the blood by inhibiting α-glucosidase enzyme, which is connected explicitly by hydrogen bonds and modifies the secondary structure and micro-environment of the enzyme reversibly and non-competitive. This study looks at the activity and interaction of EGCG as α-glucosidase inhibitors in the form of binding affinity and compound bonding profiles with receptors, including toxicity predictions and drug-likeness results. The research was performed in silico with molecular docking on Autodock Vina that integrated through PyRx, then viewed the compound's binding profile with receptor using Discovery Studio 2021 Client, toxicity prediction using ProTox-II and determination of drug-likeness using SwissADME based on Lipinski's rule of five guidelines. The control drugs used were acarbose and miglitol. The molecular docking results obtained that the binding affinity of EGCG is -8.4 kcal/mol while acarbose and miglitol are -13.8 kcal/mol and -5.3 kcal/mol respectively. There are amino acid residues similar to the drug control with various interactions like electrostatic, hydrophobic, and hydrogen bonds; then it has an inactive target for each toxicity parameter and has a molecular weight of 458.37 g/mol; Log P value of 1.01; H-bond donor of 8; and H-bond acceptor of 11 in the determination of drug-likeness. Based on these results, EGCG has effectiveness as α-glucosidase inhibitors predicted to be non-toxic; however, there are violations in determining drug-likeness.

Dihydromyricetin ameliorates diabetic renal fibrosis via regulating SphK1 to suppress the activation of NF-κB pathway

Dihydromyricetin (DHM) is a flavonoid from vine tea with broad pharmacological benefits, which improve inflammation by blocking the NF-κB pathway. A growing body of research indicates that chronic kidney inflammation is vital to the pathogenesis of diabetic renal fibrosis. Sphingosine kinase-1 (SphK1) is a key regulator of diabetic renal inflammation, which triggers the NF-κB pathway. Hence, we evaluated whether DHM regulates diabetic renal inflammatory fibrosis by acting on SphK1. Here, we demonstrated that DHM effectively suppressed the synthesis of fibrotic and inflammatory adhesion factors like ICAM-1, and VCAM-1 in streptozotocin-treated high-fat diet-induced diabetic mice and HG-induced glomerular mesangial cells (GMCs). Moreover, DHM significantly suppressed NF-κB pathway activation and reduced SphK1 activity and protein expression under diabetic conditions. Mechanistically, the results of molecular docking, molecular dynamics simulation, and cellular thermal shift assay revealed that DHM stably bound to the binding pocket of SphK1, thereby reducing sphingosine-1-phosphate content and SphK1 enzymatic activity, which ultimately inhibited NF-κB DNA binding, transcriptional activity, and nuclear translocation. In conclusion, our data suggested that DHM inhibited SphK1 phosphorylation to prevent NF-κB activation thus ameliorating diabetic renal fibrosis. This supported the clinical use and further drug development of DHM as a potential candidate for treating diabetic renal fibrosis.

Manganese(III) complexes with a tetradentate thiosemicarbazone. Structural characterization, electrochemistry, antioxidant capability, molecular docking and dynamics simulation on the potential inhibitory activity of cyclin-dependent kinase 2

Two manganese(III) complexes with the general formula [MnIII(L)X] (where L is a tetradentate thiosemicarbazone; X = Cl (Mn1) or N3 (Mn2 is new) were synthesized and verified the expected structures by experimental and theoretical methods. Electrochemical behavior of the manganese complexes were studied using cyclic voltammetry (CV) and square wave voltammetry (SWV). TEAC and DPPH values were determined and compared with those of ascorbic acid (AA). Further, the correlation between the antioxidant data and redox potentials was discussed. Molecular dynamics (MD) simulations were performed after calculating the binding affinities to cyclin-dependent kinase 2 for Mn1, Mn2, and AA to clarify some information about their thermodynamic and dynamic properties and to validate the molecular docking results. The calculations gave the binding affinities that are −6.0, −8.6 and −9.4 kcal/mol for AA, Mn1 and Mn2, respectively. The experimental and theoretical results revealed that complex Mn2 having azide ion has a better antioxidant performance and also the highest docking score with the protein. The study demonstrated that such manganese complexes are suitable candidates to drug development against diseases caused by oxidative stress.

Novel Antioxidant Self-Assembled Peptides Extracted from Azumapecten farreri Meat: In Vitro- and In Silico-Assisted Identification.

Previous studies have found that the self-assembled supramolecules of Azumapecten farreri meat peptides have antioxidant effects. Therefore, this study aims to isolate and identify novel antioxidant peptides with self-assembly characteristics and analyze their structure-activity relationship through molecular docking and molecular dynamics simulation. The in vitro results show that as the purification steps increased, the antioxidant activity of peptides became stronger. Additionally, the purification step did not affect its pH-responsive self-assembly. Using LC-MS/MS, 298 peptide sequences were identified from the purified fraction PF1, and 12 safe and antioxidant-active peptides were acquired through in silico screening. The molecular docking results show that they had good binding interactions with key antioxidant-related protein ligands (KEAP1 (Kelch-like ECH-associated protein 1) and MPO (myeloperoxidase)). The peptide QPPALNDSYLYGPQ, with the lowest docking energy, was selected for a 100 ns molecular dynamics simulation. The results show that the peptide QPPALNDSYLYGPQ exhibited excellent stability when docked with KEAP1 and MPO, thus exerting antioxidant effects by regulating the KEAP1-NRF2 pathway and inhibiting MPO activity. This study further validates the antioxidant and self-assembling properties of the self-assembled supramolecules of Azumapecten farreri meat peptide and shows its potential for developing new, effective, and stable antioxidants.

Phytochemical analysis, in-vitro and in-silico study of antiproliferative activity of ethyl acetate fraction of Launaea cornuta (Hochst. ex Oliv. & Hiern) C. Jeffrey against human cervical cancer cell line.

Introduction: Cervical cancer is one of the leading causes of death among women globally due to the limitation of current treatment methods and their associated adverse side effects. Launaea cornuta is used as traditional medicine for the treatment of a variety of diseases including cancer. However, there is no scientific validation on the antiproliferative activity of L. cornuta against cervical cancer. Objective: This study aimed to evaluate the selective antiproliferative, cytotoxic and antimigratory effects of L. cornuta and to explore its therapeutical mechanisms in human cervical cancer cell lines (HeLa-229) through a network analysis approach. Materials and methods: The cytotoxic effect of L. cornuta ethyl acetate fraction on the proliferation of cervical cancer cells was evaluated by 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) bioassay and the antimigratory effect was assessed by wound healing assays. Compounds were analysed using the qualitative colour method and gas chromatography-mass spectroscopy (GC-MS). Subsequently, bioinformatic analyses, including the protein-protein interaction (PPI) network analysis, Gene Ontology (GO), and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analysis, were performed to screen for potential anticervical cancer therapeutic target genes of L. cornuta. Molecular docking (MD) was performed to predict and understand the molecular interactions of the ligands against cervical cancer. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was performed to validate the network analysis results. Results: L. cornuta ethyl acetate fraction exhibited a remarkable cytotoxic effect on HeLa-229 proliferation (IC50 of 20.56 ± 2.83μg/mL) with a selectivity index (SI) of 2.36 with minimal cytotoxicity on non-cancerous cells (Vero-CCL 81 (IC50 of 48.83 ± 23.02). The preliminary screening revealed the presence of glycosides, phenols, saponins, terpenoids, quinones, and tannins. Thirteen compounds were also identified by GC-MS analysis. 124 potential target genes associated with the effect of L. cornuta ethyl acetate fraction on human cervical cancer were obtained, including AKT1, MDM2, CDK2, MCL1 and MTOR were identified among the top hub genes and PI3K/Akt1, Ras/MAPK, FoxO and EGFR signalling pathways were identified as the significantly enriched pathways. Molecular docking results showed that stigmasteryl methyl ether had a good binding affinity against CDK2, ATK1, BCL2, MDM2, and Casp9, with binding energy ranging from -7.0 to -12.6kcal/mol. Tremulone showed a good binding affinity against TP53 and P21 with -7.0 and -8.0kcal/mol, respectively. This suggests a stable molecular interaction of the ethyl acetate fraction of L. cornuta compounds with the selected target genes for cervical cancer. Furthermore, RT-qPCR analysis revealed that CDK2, MDM2 and BCL2 were downregulated, and Casp9 and P21 were upregulated in HeLa-229 cells treated with L. cornuta compared to the negative control (DMSO 0.2%). Conclusion: The findings indicate that L. cornuta ethyl acetate fraction phytochemicals modulates various molecular targets and pathways to exhibit selective antiproliferative and cytotoxic effects against HeLa-229 cells. This study lays a foundation for further research to develop innovative clinical anticervical cancer agents.

Screening of Poria cocos polysaccharide with immunomodulatory activity and its activation effects on TLR4/MD2/NF-κB pathway

PCP-W1, the Poria cocos polysaccharide with the strong immunomodulatory activity, was isolated through column chromatography and screened for in vitro immune activity in RAW 264.7 cells in this study. The structure analysis results revealed that the PCP-W1 were composed of galactose, glucose, fucose and mannose in a molar percentage of 35.87: 28.56: 21.77: 13.64. And it exhibited a random coil and branched conformational features with a molecular weight of 18.38 kDa. The main chain consisted of residues→3)-β-D-Glcp-(1 → 3,6)-β-D-Glcp-(1 → 3)-β-D-Glcp-(1 → 6)-β-D-Glcp-(1 → 6)-α-D-Galp-(1 → 6)-α-D-Galp-(1 → 2,6)-α-D-Galp-(1→6)-α-D-Galp-(1 → 6)-α-D-Galp-(1 → , while branching occurred at β-D-Glcp-(1→, α-D-Manp-(1→, and α-L-Fucp-(1 → 3)- α-L-Fucp-(1→. The pharmacodynamic studies demonstrated that PCP-W1 activated the release of NO, IL-6, IL-β, TNF-α, CD86, and ROS to induce polarization of RAW 264.7 murine macrophages towards M1-type through modulation of the TLR4/MD2/NF-κB pathway. The molecular docking results showed that PCP-W1 could primarily dock onto the hydrophobic binding site of TLR4/MD2 complex via its galactose chain. Furthermore, molecular dynamics simulation displayed stable modeling for TLR4-MD2-PCP-W1 complex. Overall, we screened the most immunoactive components of the polysaccharide, analyzed its structure, demonstrated its impact on TLR4/MD2/NF-kB pathway, and studied the interaction between TLR4/MD2 and the polysaccharide fragments. These results provide further support for the structure-activity relationship study of the immunomodulatory effects of Poria cocos polysaccharide.

Study of the immune disorder and metabolic dysregulation underlying mental abnormalities caused by exposure to narrow confined spaces

Prolonged confinement in cramped spaces can lead to derangements in brain function/structure, yet the underlying mechanisms remain unclear. To investigate, we subjected mice to restraint stress to simulate long-term narrow and enclosed space confinement, assessing their mental state through behavioral tests. Stressed mice showed reduced center travel and dwell time in the Open Field Test and increased immobility in the Tail Suspension Test. We measured lower hippocampal brain-derived neurotrophic factor levels and cortical monoamine neurotransmitters (5-HT and NE) in the stressed group. Further examination of the body’s immune levels and serum metabolism revealed immune dysregulation and metabolic imbalance in the stressed group. The results of the metabolic network regulation analysis indicate that the targets affected by these differential metabolites are involved in several metabolic pathways that the metabolites themselves participate in, such as the “long-term depression” and “purine metabolism” pathways. Additionally, these targets are also associated with numerous immune-related pathways, such as the TNF, NF-κB, and IL-17 signaling pathways, and these findings were validated using GEO dataset analysis. Molecular docking results suggest that differential metabolites may regulate specific immune factors such as TNF-α, IL-1β, and IL-6, and these results were confirmed in experiments. Our research findings suggest that long-term exposure to confined and narrow spaces can lead to the development of psychopathologies, possibly mediated by immune system dysregulation and metabolic disruption.

Developing of pharmacophore and three-dimensional structure-activity relationship models of VCP/p97 ligands and their synthesis and biological evaluation

VCP/p97 is a valosine-containing protein mediating the ubiquitin-proteasome degradation pathway and many cancer pathways, which was considered as a potential drug target. The identification of ligands targeting p97 protein is challenging. Here we report the development of the optimal pharmacophore DHRRR_3 based on the N-benzylpyrimidin-4-amine derivatives, cyclopentanes and pyrimidine derivatives of previous works. A robust 3D-QSAR model with desirable prediction rate in internal and external verification was constructed, where R2, Q2, and Pearson-R were 0.72, 0.76, and 0.95, respectively. Consistent to molecular docking result, THR688 and ASP478 interacted with lead compound CB5339, which was essential for VCP/p97 inhibition activity. Additionally, three novel VCP/p97 inhibitors D1-D3 were designed based on the theoretical models and then chemically synthesized. Biological results showed that molecule D1 (IC50 34 nM) was more active than CB5339 (IC50 44 nM) in inhibition of VCP/p97. Molecule D2 was as active as CB5339 against the viability of both HCT-116 and RPMI-8226 cell lines. The pharmacokinetic properties and binding free energies of synthesized compounds were theoretically estimated. And the results were consistent with the experimental ones, which indicated the high prediction accuracy of the developed models and could provide theoretical guidance for the design of VCP/p97 inhibitors.