Molecular Docking Methods Research Articles

Exploring the mechanism of Scleromitrion diffusum (Willd.) in treating lung cancer based on network pharmacology and experimental validation

This study aims to elucidate the mechanisms by which the effective components of Scleromitrion diffusum (Willd.) (SDW) treat lung cancer, using network pharmacology, in vitro cell experiments, and molecular docking methods. Network pharmacology techniques were employed to construct a network of SDW components, lung cancer targets, and signaling pathways. A proteinprotein interaction (P P I) network was built for target genes, identifying core gene targets. Signaling pathway and biological process analyses were conducted. MT T assays measured cell viability, and Western blot analysis assessed the impact of core protein targets and key pathway proteins on the stemness of three lung cancer cell lines. Molecular docking was performed to link SDW components with core proteins and key pathway targets related to lung cancer. SDW was found to target 88 genes and 5 active components (2-methoxy-3-methyl-9-10-anthraquinone, stigmasterol, beta-sitosterol, quercetin, and poriferasterol) relevant to lung cancer treatment. The P I3K/Akt and MEK/ERK pathways were identified as major signaling pathways. Extracts from SDW roots significantly inhibited the proliferation of three lung cancer cell lines (A549, HCC827, and NCIH-1395), primarily via P I3K/Akt and MEK/ERK pathways, significantly reducing the expression of p-Akt and p-Erk1/2 and slightly inhibiting caspase-9, p-P I3K, and EGFR expression. Molecular docking confirmed the strong binding activities of SDW components with lung cancer-related core proteins and key pathway targets. SDW may regulate apoptosis and proliferation in lung cancer treatment through P I3K-Akt and MAP K/ERK signaling pathways. The combination of network pharmacology, molecular docking, and experimental validation provides valuable insights into the molecular mechanisms of SDW in lung cancer therapy.

Inhibition of soluble epoxide hydrolase by natural isothiocyanates

GoalThe long-term goal of our research is to develop safe and effective soluble epoxide hydrolase (sEH) inhibitors. The objective of this study is to evaluate the potency and selectivity of six natural isothiocyanates (ITCs) as sEH inhibitors. MethodsMolecular docking was used to model likely interactions between the ligands and receptors. The sEH inhibitory activity was tested using a validated fluorescence-based assay and PHOME as a substrate. To evaluate their selectivity as sEH inhibitors, the inhibitory potential of the ITCs was determined on microsomal epoxide hydrolase (mEH) and cytochrome P450 (CYP) enzymes in human liver microsomes. Probe substrates such as styrene oxide (mEH substrate) and established substrates for CYP2A6, CYP2C9, CYP2C19, CYP2D6, CYP2E1, and CYP3A4 were used in this study. The metabolites of these substrates were analyzed using validated LC-MS/MS and HPLC-UV assays. ResultsMolecular Docking revealed significant differences in binding site preference among the ITCs in silico and pointed to important interactions between the ligands and the catalytic residues of the sEH enzyme. In vitro, the ITCs showed varying degrees of sEH inhibition, but sulforaphane (SFN) and phenyl isothiocyanate (PITC) were the most potent inhibitors with IC50 values of 3.65 and 7.5 μM, respectively. mEH was not significantly inhibited by any of the ITCs. Erucin and iberin were the only ITCs that did not inhibit the activity of any of the tested CYP enzymes. ConclusionOur results demonstrate that natural ITCs have the potential to offer safe, selective, and potent sEH inhibition.

Molecular docking and MD simulation studies of 4-thiazol-N-(pyridin-2-yl)pyrimidin-2-amine derivatives as novel inhibitors targeted to CDK2/4/6

PurposeNowadays, cyclin-dependent kinase 4/6 (CDK4/6) inhibitors have been approved for treating metastatic breast cancer and have achieved inspiring curative effects. But some discoveries have indicated that CDK 4/6 are not the requisite factors in some cell types because CDK2 partly compensates for the inhibition of CDK4/6. Thus, it is urgent to design CDK2/4/6 inhibitors for significantly enhancing their potency. This study aims to explore the mechanism of the binding of CDK2/4/6 kinases and their inhibitors to design novel CDK2/4/6 inhibitors for significantly enhancing their potency in different kinds of cancers.Materials and methodsA series of 72 disparately functionalized 4-substituted N-phenylpyrimidin-2-amine derivatives exhibiting potent inhibitor activities against CDK2, CDK4 and CDK6 were collected to apply to this research. The total set of these derivatives was divided into a training set (54 compounds) and a test set (18 compounds). The derivatives were constructed through the sketch molecule module in SYBYL 6.9 software. A Powell gradient algorithm and Tripos force field were used to calculate the minimal structural energy and the minimized structure was used as the initial conformation for molecular docking. By the means of 3D-QSAR models, partial least squares (PLS) analysis, molecular dynamics (MD) simulations and binding free energy calculations, we can find the relationship between structure and biological activity.ResultsIn this study, we used molecular docking, 3D-QSAR and molecular dynamics simulation methods to comprehensively analyze the interaction and structure–activity relationships of 72 new CDK2/4/6 inhibitors. We used detailed statistical data to reasonably verify the constructed 3D-QSAR models for three receptors (q2 of CDK2 = 0.714, R2pred = 0.764, q2 = 0.815; R2pred of CDK4 = 0.681, q2 = 0.757; R2pred of CDK6 = 0.674). MD simulations and decomposition energy analysis validated the reasonability of the docking results and identified polar interactions as crucial factors that influence the different bioactivities of the studied inhibitors of CDK2/4/6 receptors, especially the electrostatic interactions of Lys33/35/43 and Asp145/158/163. The nonpolar interaction with Ile10/12/19 was also critical for the differing potencies of the CDK2/4/6 inhibitors. We concluded that the following probably enhanced the bioactivity against CDK2/4/6 kinases: (1) electronegative groups at the N1-position and electropositive and moderate-sized groups at ring E; (2) electrogroups featured at R2; (3) carbon atoms at the X-position or ring C replaced by a benzene ring; and (4) an electrogroup as R4.ConclusionPrevious studies, to our knowledge, only utilized a single approach of 3D-QSAR and did not integrate this method with other sophisticated techniques such as molecular dynamics simulations to discover new potential inhibitors of CDK2, CDK4, or CDK6. So we applied the intergenerational technology, such as 3D-QSAR technology, molecular docking simulation techniques, molecular dynamics simulations and MMPBSA19/MMGBSA20-binding free energy calculations to statistically explore the correlations between the structure with biological activities. The constructed 3D-QSAR models of the three receptors were reasonable and confirmed by the excellent statistical data. We hope the results obtained from this work will provide some useful references for the development of novel CDK2/4/6 inhibitors.

Molecular Docking and Dynamic Simulation of Erythrina fusca Lour Chemical Compounds Targeting VEGFR-2 Receptor for Anti-Liver Cancer Activity

Liver cancer is a serious health concern characterized by abnormal cell growth, but currently, available treatment options are limited, suggesting the need for a new therapeutic method. Therefore, this research aimed to investigate the potential of chemical compounds obtained from the cangkring plant (Erythrina fusca) as anti-liver cancer agents targeting Vascular Endothelial Growth Factor Receptor 2 (VEGFR-2). The investigation was conducted in silico through molecular docking and dynamic method. Molecular docking was performed using AutoDock Tools, followed by visualization with Biovia Discovery Studio. Additionally, molecular dynamics simulation was conducted using GROMACS software and visualized with Grace. A total of 36 chemical compounds from E. fusca were used as ligands for molecular docking. The results showed that Isobavachalcone (ISB) was the most effective test compound with a binding energy of -11.45 kcal/mol, compared to the positive control Sorafenib with a value of - 11.51 kcal/mol. In this context, hydrogen bonding, as well as hydrophobic, electrostatic, and unfavorable molecular interactions were identified. Moreover, molecular dynamics simulation provided RMSD, RMSF, Radius of Gyration (Rg), and hydrogen bond parameters. Analysis of these parameters further confirmed the superior stability of ISB in binding to VEGFR-2, suggesting the potential to suppress angiogenesis by blocking the receptor.

ANTIBACTERIAL ACTIVITY OF AMPHIPHILES BASED ON INDOLYL-3-CARBOXYLIC ACIDS AND L-LYSINE WITH ETHYLENEDIAMINE LINKER

Recently, due to the growth of bacterial infections resistant to antibiotics, there is an urgent need to develop alternative antibacterial drugs. Alkyl-indolyl-L-lysine is a promising class of compounds; their amphiphilic structure is key in antimicrobial ef cacy. A scheme was developed and the synthesis of ve new derivatives of indolylbutyric and indolylacetic acids containing a polar amino acid residue with an ethylenediamine linker binding alkyl fragments of different lengths was carried out. The antibacterial activity of new amphiphiles against gram-positive and gram-negative bacterial strains was evaluated. The minimum binding energy of synthesized compounds with human serum albumin (HSA) was determined by the method of molecular docking. A lower af nity of the studied objects was shown compared to the control indolmycin.

Mechanism of network pharmacology of Erzhi Pill and Erxian Decoction in treating climacteric syndrome with "treating the same disease with different methods": A review.

Network pharmacology and molecular docking methods were used in the present study to clarify the molecular mechanism of two traditional Chinese medicine prescriptions of climacteric syndrome. Based on oral availability and drug similarity, the main active components of Erzhi Pill and Erxian Decoction were screened through the platform of traditional Chinese medicine system pharmacology. The target database of climacteric syndrome was established by using GENECARD, OMIM, PharmGKB, Targets and Drugbank. The "component - target" network diagram was constructed using Cytoscape software (version 3.8.2). Topology analysis, module analysis, and GO and KEGG enrichment analyses were used to explore the core target and action pathway of Erzhi Pill-Erxian Decoction for treating climacteric syndrome of same disease with different treatments. There were 16 active components and 103 corresponding targets found in Erzhi Pill; 69 active components and 121 corresponding targets were found in Erxian Decoction; and 100 potential targets were found in Erzhi Pill and Erxian Decoction. Through network analysis, topology and module analysis, TP53, AKT1, Jun, ESR1, IL1B, CASP3, MMP9, PTGS2, HIF1A, MYC and EGFR could be considered as potential targets of the 2 prescriptions for alleviating climacteric syndrome. The effects of Erzhi pill and Erxian Decoction on climacteric syndrome are mainly in the pathway of lipid and atherosclerosis, AGE-RAGE signaling pathway and PI3K-Akt signaling pathway in diabetic complications. The active components in Erzhi Pill - Erxian Decoction, such as quercetin, show considerable potential as a candidate drug for the treatment of climacteric syndrome.

Functional constituents of Colchicum lingulatum Boiss. & Spruner subsp. Rigescens K. Perss. Extracts and their biological activities with different perspectives

The genus Colchicum comprises medicinal plants with important bioactive alkaloids, mainly colchicine, and phenolics. The present study was aimed to determine for the first time the phytoconstituents, antioxidant, enzyme inhibition and cytotoxic properties of corms of C. lingulatum. Different solvents extracts (hexane, ethyl acetate, methanol and water) were obtained. The extracts were examined for chemical characterization, antioxidant, enzyme inhibition and cytotoxic properties. To gain more insights, in silico and network pharmacological analysis were performed. Results of GC/MS analysis of the hexane extract revealed that the extract was dominated by oxygenated diterpenes (37%). UHPLC/MS analysis of ethyl acetate, methanol and aqueous extracts indicated the presence of flavonoids as the most abundant class in addition to phenolic acids and alkaloids. The alkaloid colchicine together with its derivatives colchiceine, colchiciline and isomers were detected in the methanol and aqueous extracts. Results of antioxidant activity showed that the methanol extract exhibited the highest DPPH radical scavenging. At 100 μg/mL, the ethyl acetate, methanol and aqueous extracts displayed potent cytotoxicity against the human embryonic (HEK 293), murine macrophages (RAW 264.7). In silico analyzes have investigated the potential of C. lingulatum in cancer therapy using network pharmacology and molecular docking methods. These results demonstrate C. lingulatum can be a valuable source of bioactive compounds in the development of functional applications including nutraceuticals.

A potential role of arcadia in conditioned media - umbilical cord derived mesenchymal stem cell on cartilage repair

Background Certain conditions can stimulate stem cells to produce secretory factors that differ from each condition, such as hypoxia. Umbilical Cord-derived Mesenchymal Stem Cells have been known to have higher proliferation rates, plasticity, and better self-improvement ability than MSCs from other sources. The objective was to analyze the secreting proteins in the Conditioned Medium - Umbilical cord-derived Mesenchymal Stem Cells (CM-UCMSCs) which potentially has a role in the chondrogenesis of cartilage defect. Methods We used SDS PAGE combined with electrospray ionization mass spectrometry using mass spectrometer to perform a proteomic analysis of CM-UCMSCs which conditioned in a state of fasting (without serum albumin). Then, we continue to analyze to identify proteins of interest using Mascot sequence matching software. Then Analyzed using in silico / molecular docking to know the interaction of each protein with the cartilage repair factor. Results SDS PAGE performed on all secreted products in CM-UCMSCs. We found one dominant band, then we used Mass Spectrometry continued Mascot sequencing protein that band, conclude that the protein was a D4A9T1/ RNF-111/ Arkadia Protein. And then using in silico/ molecular docking method analyzed that Arkadia Protein worked synergistically with TGF-β1 Protein through activation of TGF-β1 receptors to induce the chondrogenesis. Conclusions Our results show that the fasting state on CM-UCMSCs promoted secreted Arkadia protein. From in silico model prediction, this protein suspects to have an important role in the process of repairing cartilage defects. However, further research is needed before feasible and safe for the clinical application of CM-UCMSCs in cartilage repair.

Molecular docking and molecular dynamics simulation of wheat gluten-derived antioxidant peptides acting through the Keap1-Nrf2 pathway.

In our previous study, we successfully identified five peptides from wheat gluten: Ala-Pro-Ser-Tyr (APSY), Leu-Tyr (LY), Pro-Tyr (PY), Arg-Gly-Gly-Tyr (RGGY) and Tyr-Gln (YQ). Molecular docking and molecular dynamics simulation methods were employed to investigate the interaction between these antioxidant peptides and the Kelch-like ECH-associated protein 1 (Keap1 protein), revealing the molecular mechanism of their non-competitive binding. In addition, the total antioxidant capacity of the five peptides was determined using the 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS) method. The affinities of APSY, LY, PY, RGGY and YQ were -8.9, -8.3, -8.5, -9.1 and - 7.9 kcal mol-1, respectively. The five peptides effectively bound to Keap1 protein through hydrogen, π-σ, π-alkyl and alkyl interactions. Significant roles were observed for the P1 pocket residue ARG-415 and the P3 pocket residue ALA-556 in the interactions of the Keap1-peptide complexes. Molecular dynamics simulations further elucidated the dynamic process of peptide binding to the Keap1 protein. All five peptides formed stable complexes with Keap1 protein, with van der Waals forces playing crucial roles in these complex systems, indicative of the peptides' strong binding ability to Keap1 protein. The van der Waals forces were -178.74, -123.11, -134.36, -132.59, and -121.44 kJ mol-1 for the Keap1-APSY, Keap1-LY, Keap1-PY, Keap1-RGGY and Keap1-YQ complexes, respectively. These peptides exhibited excellent antioxidant effects. Among them, the YQ peptide exhibited the highest total antioxidant capacity, with an activity value of 1.18 ± 0.06 mmol Trolox equivalent (TE) L-1 at a concentration of 0.10 mg mL-1. The RGGY, PY, LY and APSY peptides followed in descending order, with activity values of 0.91 ± 0.05, 0.72 ± 0.06, 0.62 ± 0.04 and 0.60 ± 0.05 mmol TE L-1, respectively. These results unveiled the molecular mechanism by which the five antioxidant peptides act on active pockets through the Keap1-Nrf2 signaling pathway, providing a theoretical basis for the development of antioxidants. © 2024 Society of Chemical Industry.

Anti-inflammatory effect and its mechanism of Saracae Cortex based on zebrafish model and network pharmacology

This paper aims to explore the anti-inflammatory mechanism of Saracae Cortex by using network pharmacology and molecular docking methods and verify it through the inflammation model of zebrafish. The effective components, potential core targets, and signaling pathways of Saracae Cortex were obtained by using network pharmacology. A lipopolysaccharide(LPS)-induced inflammation model of zebrafish was established to evaluate the anti-inflammatory activity of aqueous extract and 70% ethanol extract of Saracae Cortex with cell apoptosis rate and reactive oxygen species(ROS) production rate as indicators. q PCR was performed to verify the main targets predicted by network pharmacology. The prediction found that there were 121 potential anti-inflammatory targets in Saracae Cortex. Protein-protein interaction(PPI) analysis showed that Saracae Cortex mainly acted on signal transducer and activator of transcription 3(STAT3), vascular endothelial growth factor A( VEGFA), epidermal growth factor( EGF), tumor necrosis factor( TNF),tumor protein p53(TP53), matrix metalloprotein 9(MMP9), c-fos proto-oncogene protein(FOS), estrogen receptor 1(ESR1), cx-c motif chemokine ligand 8(CXCL8), cluster of differentiation 8(CD8), and other targets. Gene Ontology(GO) analysis showed the biological process mainly acted on the inhibition of apoptosis, the positive regulation of gene expression, and the positive regulation of cell proliferation. Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis showed that the mitogen-activated protein kinase(MAPK) signaling pathway, PI3K-Akt signaling pathway, and hypoxia-inducible factor 1(HIF-1) signaling pathway may play a key role in anti-inflammation of Saracae Cortex. Molecular docking verified that five key compounds had a strong binding force with their corresponding core target. Zebrafish animal experiments showed that Saracae Cortex could significantly inhibit ROS formation and reduce cell apoptosis in juvenile fish caused by inflammation and inhibit the further enhancement of inflammatory response in tissue. In addition, compared with the blank group, the transcription levels of nuclear factor kappa-B(NF-κB), TP53, FOS, adaptor protein complex-1(AP-1), and mitogen-activated protein kinases P38(P38) were significantly up-regulated in the model group. Compared with the model group, the m RNA expression of NF-κB, TP53, FOS, AP-1, and P38 was significantly down-regulated in zebrafish tissue treated with aqueous extract and 70% ethanol extract of Saracae Cortex. Saracae Cortex plays an anti-inflammatory role through multiple components and targets, and its anti-inflammatory effect may be related to the inhibition of the MAPK signaling pathway.

Network Pharmacology and Molecular Docking Reveal the Antioxidant Potential of Mangiferin from Mango Peel

Background: As one of the main by-products of mango production, the mango peel is rich in multiple polyphenols, such as mangiferin. Therefore, there is an urgent need to explore the potential mechanism of mangiferin for nutrition intervention of oxidative stress-related diseases. Methods: Mangiferin was extracted and purified from the mango peel and was identified by the reverse phase high-performance liquid chromatography. The antioxidant potential of mangiferin was determined in vitro (potassium ferricyanide reducing capacity, DPPH, hydroxyl radicals scavenging ability, and superoxide anion radicals reducing capacity). In order to explore the potential mechanism for the antioxidant activity of mangiferin, a combination of network pharmacology and molecular docking approaches was performed. Results: The purity of mangiferin from the mango peel was ≥ 95.0%, and its antioxidant activity was confirmed by different in vitro assays. ALB, ESR1, CASP8, CASP3, BCL2L1, CXCL8, AKT1, CTNNB, and EGFR were identified as the potential oxidative stress-related targets of mangiferin. These results suggested that mangiferin might play a key role in the antioxidant process through multi-targets. Conclusion: Integrated with network pharmacology and molecular docking methods, this work demonstrated the potential mechanism of mangiferin for nutrition intervention of oxidative stress-related diseases.

Discovery of New Dual-Target Agents Against PPAR-γ and α-Glucosidase Enzymes with Molecular Modeling Methods: Molecular Docking, Molecular Dynamic Simulations, and MM/PBSA Analysis.

Type 2 diabetes mellitus (T2DM) has become a serious public health problem both in our country and worldwide, being the most prevalent type of diabetes. The combined use of drugs in the treatment of T2DM leads to serious side effects, including gastrointestinal problems, liver toxicity, hypoglycemia, and treatment costs. Hence, there has been a growing emphasis on drugs that demonstrate dual interactions. Several studies have suggested that dual-target agents for peroxisome proliferator-activated receptor-γ (PPAR-γ) and alpha-glucosidase (α-glucosidase) could be a potent approach for treating patients with diabetes. We aim to develop new antidiabetic agents that target PPAR-γ and α-glucosidase enzymes using molecular modeling techniques. These compounds show dual interactions, are more effective, and have fewer side effects. The molecular docking method was employed to investigate the enzyme-ligand interaction mechanisms of 159 newly designed compounds with target enzymes. Additionally, we evaluated the ADME properties and pharmacokinetic suitability of these compounds based on Lipinski and Veber's rules. Compound 70, which exhibited favorable ADME properties, demonstrated more effective binding energy with both PPAR-γ and α-glucosidase enzymes (-12,16kcal/mol, -10.07kcal/mol) compared to the reference compounds of Acetohexamide (-9.31kcal/mol, -7.48kcal/mol) and Glibenclamide (-11.12kcal/mol, -8.66kcal/mol). Further, analyses of MM/PBSA binding free energy and molecular dynamics (MD) simulations were conducted for target enzymes with compound 70, which exhibited the most favorable binding affinities with both enzymes. Based on this information, our study aims to contribute to the development of new dual-target antidiabetic agents with improved efficacy, reduced side effects, and enhanced reliability for diabetes treatment.

Coronavirus Inhibitory Activity of Tamarind Indica

Background: SARS-COVID-19 is an infectious disease, the causative agent Caroni virus. WHO announced the pandemic on 3rd November 2020 to the whole world. Objective: Severe Acute Respiratory Syndrome COVID-19 is an infectious disease globally declared a pandemic by WHO. There is a need to find the proper medication for recovery. The study uses the molecular docking method to predict the anti-covid activity of plant phytoconstituents of Tamarind indica. Methods: Molecular docking techniques were accomplished to search the binding pattern of plant phytoconstituents of T. indica against the crystal structure SARS-CoV-2 enzyme (PDB ID: 6LU7) with the help of PyRx virtual screening software to study the amino acid interaction and inhibitory potential of phytoconstituents of T. indica. In addition, we performed a pharmacokinetic and toxicological study of plant phytoconstituents of T. indica using SwissADME and the pkCSM online server. Results: The phytoconstituents of Plant T. indica docking results proposed that apigenin (-7.8 kcal/mol), epicatechin (-7.1 kcal/mol) and taxifolin (-7.5 kcal/mol) show the best binding energy as compared to favipiravir (-5.2 kcal/mol). The phytoconstituents exposed promising interaction with amino acid residue, leading to an inhibitory effect against the SARS-CoV-2 enzyme (PDB ID: 6LU7). Further, ADMET studies showed that pharmacokinetics and toxicological parameters are within acceptable limits. Conclusion: In silico study revealed that the phytochemicals of T.indica show promising inhibitory results against the SARS-CoV-2 enzyme (PDB ID: 6LU7). Moreover, the traditional benefits of T.indica were clinical treatment and drug discovery.

Prediction of Treatment Mechanisms of Scutellariae Radix on Viral Pneumonia Through Network Pharmacology: Focus on Hypoxic State Regulation Through HIF-1α and HSP90

Objectives: In this study, we used network-based systems pharmacology analysis and molecular docking methods to predict the therapeutic mechanism of Scutellariae Radix on viral pneumonia.Methods: We screened active components of Scutellariae Radix and its’ genes by TCMSP. Also, we extracted viral pneumonia related target genes through Gene Cards, CTD and DisGeNet. To construct Protein-protein Interaction, STRING database was used. For functional enrichment, using SRplot platform, genes were classified by 3 categories: cellular component (CC), molecular function (MF) and biological process (BP). Molecular docking was conducted by AutoDockTools (version 4.2.6).Results: 32 Network-based systematic pharmacology analysis identified 37 target genes associated with baicalein. Based on the network and gene ontology analysis of the active ingredient's target genes and disease target genes, we identified nine core genes (AKT1, BAX, BCL2, CASP3, HIF1A, PTGS2, RELA, TP53, VEGFA) and HSP90 as involved. Notably, HIF1A showed the highest relevance, overlapping with two or more utilized programs. Hypoxia-inducible factor 1-alpha (HIF-1α) has been implicated in the expression of inflammatory cytokines, the induction of hypoxia, and the triggering of cytokine storms. Baicalein, a major component of SR, binds to both HIF-1 α and HSP90, suggesting that it may be a possible targeted treatment for viral pneumonia.Conclusions: Baicalein may bind to HIF-1α to control inflammation caused by viral infectious diseases and may also regulate hypoxic conditions to prevent impairment of lung function caused by an overactive immune system. These findings suggest further research into the molecular mechanisms involved in hypoxia and provide a scientific basis for improving the treatment of viral infectious diseases.

Investigating mechanistic insights of curcumin in blocking the Interleukin-8 signaling pathway associated with Breast Cancer: An in-silico approach

Interleukin-8 (IL-8) is a chemokine, a type of signaling molecule that has a role in immunological responses and inflammation. In recent years, IL-8 is additionally related to cancer growth and recurrence. Breast cancer growth, progression, and metastatic developmentare all linked to IL-8. Breast cancer cells are known to develop faster when IL-8 stimulates their proliferation and survival. It can also cause angiogenesis, or the creation of new blood vessels, which is necessary for tumor nutrition and growth. IL-8 and curcumin have been subjects of interest in drug design, particularly in the context of inflammation-related disorders and cancer. This study aims to give an overview of the role of IL-8. Inhibitor-based treatment approaches were being used to target IL-8 with curcumin. Molecular docking method was employed to find a potential interaction to supress competitive inhibition of IL-8 with curcumin. PASS analysis and ADMET characteristics were also being carried out. In the end, IL-8 complexed with curcumin is chosen for MD simulations. Overall, our results showed that during the simulation, the complex stayed comparatively stable. It is also possible to investigate curcumin further as a possible treatment option. The combined results imply that IL-8 and their genetic alterations can be studied in precision cancer therapeutic treatments, utilizing target-driven therapy and early diagnosis.

From petals to healing: consolidated network pharmacology and molecular docking investigations of the mechanisms underpinning Rhododendron arboreum flower's anti-NAFLD effects.

Rhododendron arboreum: Sm., also known as Burans is traditionally used as an anti-inflammatory, anti-diabetic, hepatoprotective, adaptogenic, and anti-oxidative agent. It has been used since ancient times in Indian traditional medicine for various liver disorders. However, the exact mechanism behind its activity against NAFLD is not known. The aim of the present study is to investigate the molecular mechanism of Rhododendron arboreum flower (RAF) in the treatment of NAFLD using network pharmacology and molecular docking methods. Bioactives were also predicted for their drug-likeness score, probable side effects and ADMET profile. Protein-protein interaction (PPI) data was obtained using the STRING platform. For the visualisation of GO analysis, a bioinformatics server was employed. Through molecular docking, the binding affinity between potential targets and active compounds were assessed. A total of five active compounds of RAF and 30 target proteins were selected. The targets with higher degrees were identified through the PPI network. GO analysis indicated that the NAFLD treatment with RAF primarily entails a response to the fatty acid biosynthetic process, lipid metabolic process, regulation of cell death, regulation of stress response, and cellular response to a chemical stimulus. Molecular docking and molecular dynamic simulation exhibited that rutin has best binding affinity among active compounds and selected targets as indicated by the binding energy, RMSD, and RMSF data. The findings comprehensively elucidated toxicity data, potential targets of bioactives and molecular mechanisms of RAF against NAFLD, providing a promising novel strategy for future research on NAFLD treatment.

An in silico study on human carcinogenicity mechanism of polybrominated biphenyls exposure

Polybrominated biphenyls (PBBs) are associated with an increased risk of thyroid cancer; however, relevant mechanistic studies are lacking. In this study, we investigated the mechanisms underlying PBB-induced human thyroid cancer. Molecular docking and molecular dynamics methods were employed to investigate the metabolism of PBBs by the cytochrome P450 enzyme under aryl hydrocarbon receptor mediation into mono- and di-hydroxylated metabolites. This was taken as the molecular initiation event. Subsequently, considering the interactions of PBBs and their metabolites with the thyroxine-binding globulin protein as key events, an adverse outcome pathway for thyroid cancer caused by PBBs exposure was constructed. Based on 2D quantitative structure activity relationship (2D-QSAR) models, the contribution of amino acid residues and binding energy were analyzed to understand the mechanism underlying human carcinogenicity (adverse effect) of PBBs. Hydrogen bond and van der Waals interactions were identified as key factors influencing the carcinogenic adverse outcome pathway of PBBs. Analysis of non-bonding forces revealed that PBBs and their hydroxylation products were predominantly bound to the thyroxine-binding globulin protein through hydrophobic and hydrogen bond interactions. The key amino acids involved in hydrophobic interactions were alanine 330, arginine 381 and lysine 270, and the key amino acids involved in hydrogen bond interactions were arginine 381 and lysine 270. This study provides valuable insights into the mechanisms underlying human health risk associated with PBBs exposure.

Cross-species molecular docking method to support predictions of species susceptibility to chemical effects

The advancement of protein structural prediction tools, exemplified by AlphaFold and Iterative Threading ASSEmbly Refinement, has enabled the prediction of protein structures across species based on available protein sequence and structural data. In this study, we introduce an innovative molecular docking method that capitalizes on this wealth of structural data to enhance predictions of chemical susceptibility across species. We demonstrated this method using the androgen receptor as a pertinent modulator of endocrine function. By using protein structures, this method contextualizes species susceptibility within a functional framework and helps to integrate molecular docking into the repertoire of New Approach Methodologies (NAMs) that support the Next-Generation Risk Assessment (NGRA) paradigm through the novel integration of various open-source tools.

Molecular docking of orphan receptors with fatty acid amide

One of the promising directions for development of new pharmacological drugs for analgesia and other consequences of peripheral nerve damage is the study of the physiological effects of fatty acid amides. The potential selectivity of G-protein receptor antagonists has been evaluated using molecular docking and quantum chemistry methods, and its complexes with fatty acid amides have been constructed. As a result of docking, it was found that PSB-CB5 is a selective antagonist for GPR18 receptors, and O-1918 is a selective antagonist for GPR55. It was found that stable complexes are formed between fatty acid amides (REA, SEO) and orphan receptors (GPR 18, GPR55). Numerous van der Waals contacts and hydrogen bonds play a major role in the interaction of these compounds with receptors.

Exploration of Potential Targets and Molecular Mechanisms of the Yiqi Jianpi Tongqiao Formula in Treating Allergic Rhinitis Mouse Model based on Network Pharmacology and Molecular Docking.

To investigate the therapeutic effect of Yiqi Jianpi Tongqiao (YJT) formula (Hedysarum Multijugum Maxim, Magnoliae Flos, Xanthii Fructus, Notopterygii Rhizoma Et Radix, Kaempferiae Rhizoma, Acoritataninowii Rhizoma, Saposhnikoviae Radix) on an allergic rhinitis mouse model, and to explore the active ingredients, key targets, and molecular mechanisms of this formula using network pharmacology and molecular docking methods. An allergic rhinitis mouse model was established to observe changes in rhinitis symptoms, nasal mucosal morphology, and serum indicators after administering the YJT formula. The TCMSP, GeneCards, OMIM, and DisGeNET databases were used to screen for the active ingredients, action targets, and disease targets of the YJT formula. The Cytoscape software was used to construct a network of the active ingredients and action targets. The protein-protein interaction (PPI) network was used to predict hub genes. The corresponding active compounds with the hub genes' highest oral bioavailability (OB) values were identified, followed by molecular docking analysis. Animal experiments demonstrated that the YJT formula reduced rhinitis symptoms (nasal itching, runny nose, and face scratching) in allergic rhinitis mice, as well as decreased nasal mucosal inflammatory reactions and serum inflammatory indicators (histamine, OVAspecific IgE, IL-1β levels). Furthermore, 63 active components and 101 potential indicator targets of the YJT formula were identified, along with 5 hub genes (IL6, AKT1, IL1B, VEGFA, and PTGS2), and the corresponding active compounds with the highest OB values were quercetin, aloe-emodin, and denudanolide b. Molecular docking results revealed the binding energy between quercetin, aloe-emodin, denudanolide b and 5 hub genes (IL6, AKT1, IL1B, VEGFA, and PTGS2) were -5.78 to -10.22 kcal/mol, the binding energy between dexamethasone and 5 hub genes were -6.3 to -9.7 kcal/mol. In addition, GO and KEGG analysis suggested significant enrichment of these genes in biological processes such as response to lipopolysaccharide, response to molecule of bacterial origin, and response to reactive oxygen species, as well as signaling pathways like AGE-RAGE signaling pathway in diabetic complications, Lipid and atherosclerosis, and IL-17 signaling pathway. The YJT formula has therapeutic effects in an allergic rhinitis mouse model, with the main active components being quercetin, aloe-emodin, and denudanolide b, and the key targets being IL6, AKT1, IL1B, VEGFA, and PTGS2, involving multiple signaling pathways.