AutoDock Tools Research Articles

In silico Rationalization for Leads from Oldenlandia umbellata L. to Inhibit Multiple Molecular Targets Regulating Osteoporosis

Background Osteoporosis is a chronic metabolic bone disease caused due to the dysregulation in the functioning of osteoblast and osteoclast cells leading to increased bone resorption predominantly in postmenopausal women and the elderly, thereby affecting a significant global population. Purpose The present study aims to computationally screen the phytochemical constituents of Oldenlandia umbellata Linn against the unique molecular therapeutic targets of osteoporosis and validate the results using Molecular Dynamics (MD) Simulation. Materials and Methods The molecular docking analysis of the selected phytoconstituents against the molecular targets were performed using AutoDock 4.2.6 – AutoDock Tools 1.5.6. In addition, the drug likeliness, ADME, bioactivity, and toxicity were predicted using Molinspiration ADMELAB2.0, ProTox-II and Orisis DataWarrior online tools. Molecular Dynamic Simulation studies were performed using WebGRO macromolecular simulation server. Results Molecular docking results and data analysis revealed that deacetylasperuloside possesses good drug-likeness, ADME properties, and bioactive scores and did not indicate any toxicity compared to other phytochemicals exhibiting binding energies below –8.00 Kcal/mol against the targets. Together, the study emphasized that deacetylasperuloside could bind with the molecular targets of osteoporosis, and the lead is a potential therapeutic candidate for osteoporosis treatment. Further, molecular dynamic simulation analysis for 100 ns revealed that the ligand–protein complexes, including glycogen synthase kinase 3β (GSK3β)-deacetylasperuloside and cathepsin K (CTSK)-deacetylasperuloside complexes, were stable and highly compact assessed from their trajectories. Hence, it can be emphasized that deacetylasperuloside could be a potential therapeutic molecule that could inhibit the targets, including GSK3β and CTSK. Conclusion Oldenlandia umbellata L. is a potential candidate for identifying therapeutic leads for osteoporosis treatment. Further, in vitro and in vivo studies are needed as an output of this research to evaluate its therapeutic efficacy.

In silico and in vitro investigation of the role of Asparagus racemosus lead compound Shatavarin IV and associated silver nanoparticles

Antibiotic-resistant microbes are a global threat, necessitating the need for new antibacterials. Bioactive compounds obtained from Asparagus racemosus and silver nanoparticles synthesized from it were tested for antibacterial activity. The nanoparticles exhibited a UV absorbance peak at 415nm. SEM image revealed elliptical nanoparticles from 32.6 nm to 78.6 nm while the FTIR study of aromatic amine N-H and C-O stretching indicates the stability of the silver nanoparticle. Zeta potential and XRD tests confirmed the presence of silver nanoparticles in the root extract under stable conditions. Methanolic root extract and silver nanoparticles were found to be very effective against Bacillus subtilis (20mm), Salmonella typhimurium (20mm), Escherichia coli (20mm), Klebsiella pneumoniae (18mm), Staphylococcus aureus (17mm) and Pseudomonas aeruginosa (15mm) in comparison to ampicillin. AutoDock Tools 1.5.7 was used to perform molecular docking of Shatavarin IV against target proteins involved in breast cancer (PDB ID: 3O96), bacterial infections (PDB ID: 2ZCO), viral infections angiotensin (PDB ID: 4APH) and inflammation (PDB ID: 7PHS). The respective best docking scores are -18.66, -18.07 -14.57 and -15.84 Kcal/Mol respectively. Sarsasapogenin and Kaempferol also showed favorable docking scores with specific target proteins. Shatavarin IV is found to target amino acid(s) and the standard drugs of each category such as Remdesivir for viral, Diclofenac for inflammation, Tamoxifen for cancer and Plazomicin for bacterial infections. This study reveals that Asparagus racemosus bioactive compound Shatavarin IV is a suitable lead compound for the treatment of cancer, viral, bacterial infections and inflammatory conditions.

Exploration of the main active metabolites from Tinospora crispa (L.) Hook. f. & Thomson stem as insulin sensitizer in L6.C11 skeletal muscle cell by integrating in vitro, metabolomics, and molecular docking

Ethnopharmacological relevanceTinospora crispa (L.) Hook. f. & Thomson stem (TCS) has long been used as folk medicine for the treatment of diabetes mellitus. Previous study revealed that TCS possesses multi-ingredients and multi-targets characteristic potential as insulin sensitizer activity. However, its mechanisms of action and molecular targets are still obscure. Aim of the studyIn the present study, we investigated the effects of TCS against insulin resistance in muscle cells through integrating in vitro experiment and identifying its active biomarker using metabolomics and in molecular docking validation. Materials and methodsWe used centrifugal partition chromatography (CPC) to isolate 33 fractions from methanolic extract of TCS, and then used UHPLC-Orbitrap-HRMS to identify the detectable metabolites in each fraction. We assessed the insulin sensitization activity of each fraction using enzyme-linked immunosorbent assay (ELISA), and then used confocal immunocytochemistry microscopy to measure the translocation of glucose transporter 4 (GLUT4) to the cell membrane. The identified active metabolites were further simulated for its molecular docking interaction using Autodock Tools. ResultsThe polar fractions of TCS significantly increased insulin sensitivity, as measured by the inhibition of phosphorylated insulin receptor substrate-1 (pIRS1) at serine-312 residue (ser312) also the increasing number of translocated GLUT4 and glycogen content. We identified 58 metabolites of TCS, including glycosides, flavonoids, alkaloids, coumarins, and nucleotides groups. The metabolomics and molecular docking simulations showed the presence of minor metabolites consisting of tinoscorside D, higenamine, and tinoscorside A as the active compounds. ConclusionsOur findings suggest that TCS is a promising new treatment for insulin resistance and the identification of the active metabolites in TCS could lead to the development of new drugs therapies for diabetes that target these pathways.

Sijunzi Decoction Targets IL1B and TNF to Reduce Neutrophil Extracellular Traps (NETs) in Ulcerative Colitis: Evidence from Silicon Prediction and Experiment Validation.

This study was conducted to explore the mechanism of Sijunzi Decoction (SJZ) in the treatment of ulcerative colitis (UC). The study aimed to investigate the active components and targets of SJZ in the treatment of UC by screening databases such as TCMSP, GeneCards, OMIM, Distinct, TTD, and Drugbank. An online Venn tool, Cytoscape 3.7.2, and Autodock Tools were used to analyze the components and targets. The study also used a mouse model of UC to further investigate the effects of SJZ. HE staining, immunofluorescence, ELISA, qPCR, and Western blot were used to detect various indices. Eighty-three active components and 112 action targets were identified from SJZ, including 67 targets for treating UC-related NETs. The five core targets identified were AKT1, JUN, IL1B, PTGS2, and TNF, and molecular docking studies indicated that the five targets were well-docked with ginsenoside Rh2, isoflavones, and formononetin. Animal experiments demonstrated that SJZ could alleviate various parameters such as weight, colon length, spleen index, disease activity index, and intestinal pathology of the UC mice. Immunofluorescence and Western blot showed that SJZ could reduce the expression of IL1B and TNF in intestinal neutrophils while increasing the expression of Occludin. Cellular immunofluorescence suggests that SJZ can reduce the expression of TNF and IL1B in NETs. The qPCR results also suggested that SJZ could inhibit TNF signal. Furthermore, ELISA results suggested that SJZ could inhibit the expression of pro-inflammatory cytokines (TNF-α, IL-1β, IL-6) while promoting the expression of anti-inflammatory cytokines (IL-10, IL-37, TGF-β). SJZ treats UC by reducing the content of intestinal NETs, with primary targets on the NETs being IL1B and TNFand suppress TNF signal. The practical components of SJZ may be ginsenoside Rh2, isoflavones, and formononetin.

Molecular Docking Insights of Newly Synthesized Schiff Base Monomers and Evaluating the Anticancer Activity of Their Polymers

Introduction The molecular docking technique has shown efficacy with small molecules but faces challenges when applied to macromolecules. To overcome this limitation, a focused approach targeting the active repeat units (monomers) of macromolecules was adopted. This study synthesized ten new dihydroxy Schiff base monomers (SBM1-SBM10) featuring azo moieties and alkoxy side groups. These were attached to human 3-alpha-hydroxysteroid dehydrogenase type 3 (4XO6), a protein linked to breast cancer, using molecular docking via the AutoDock tool. Materials and Methods The synthesis of dihydroxy Schiff base monomers SBM1-SBM10 with azo moieties and alkoxy side groups was carried out. These synthesized monomers were then docked with human 3-alpha-hydroxysteroid dehydrogenase type 3 (4XO6) utilizing AutoDock. Among these, the most promisingly docked monomer, SBM8, was selected for further experimentation. SBM8 was polymerized with terephthaloyl chloride to produce a novel polyester termed PolySyringaldehydeDiaminodiphenylSulfone (PSDS). The anticancer activity of PSDS was assessed using the MCF7 human breast cancer cell line. Concurrently, its cytotoxicity was evaluated via the MTT assay employing a normal VERO cell line. Results The molecular docking analysis revealed the best-docked monomer, SBM8, which was subsequently used for the synthesis of PSDS. The newly formed polyester, PSDS, demonstrated significant anticancer properties against the MCF7 human breast cancer cell line. Simultaneously, the cytotoxicity evaluation on the normal VERO cell line indicated a favorable safety profile for PSDS. Conclusion The study's findings highlight the successful synthesis and docking of dihydroxy Schiff base monomers with 4XO6, resulting in the creation of PSDS. This newly synthesized polyester, PSDS, exhibited promising anticancer activity against the MCF7 cell line while demonstrating minimal cytotoxicity towards normal VERO cells. These results suggest the potential of PSDS as a targeted therapeutic agent against breast cancer, warranting further investigation and development.

Exploring the Mechanism of Buyang Huanwu Decoction Alleviating Restenosis by Regulating VSMC Phenotype Switching and Proliferation by Network Pharmacology and Molecular Docking.

Buyang Huanwu Decoction (BHD) is used to regulate blood circulation and clear collaterals and is widely used in coronary heart disease. However, the active compounds and the mechanism of BHD used to treat restenosis are less understood. The study aimed to explore the potential mechanism of Buyang Huanwu decoction BHD for the treatment of restenosis using network pharmacology and molecular docking experiments. The bioactive components of BHD and their corresponding targets were retrieved from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) and Encyclopaedia of Traditional Chinese Medicine (ETCM) databases as well as literature. Restenosisassociated therapeutic genes were identified from the OMIM, Drugbank, GEO, and Dis- GeNET databases. Genes related to the vascular smooth muscle cell (VSMC) phenotype were obtained from the gene ontology (GO) database and literature. The core target genes for the drug-disease-VSMC phenotype were identified using the Venn tool and Cytoscape software. Moreover, the "drug-component-target-pathway" network was constructed and analyzed, and pathway enrichment analysis was performed. The connection between the main active components and core targets was analyzed using the AutoDock tool, and PyMOL was used to visualize the results. The "compound-target-disease" network included 80 active ingredients and 599 overlapping targets. Among the bioactive components, quercetin, ligustrazine, ligustilide, hydroxysafflor yellow A, and dihydrocapsaicin had high degree values, and the core targets included TP53, MYC, APP, UBC, JUN, EP300, TGFB1, UBB, SP1, MAPK1, SMAD2, CTNNB1, FOXO3, PIN1, EGR1, TCF4, FOS, SMAD3, and CREBBP. A total of 365 items were obtained from the GO functional enrichment analysis (p < 0.05), whereas the enrichment analysis of the KEGG pathway identified 30 signaling pathways (p < 0.05), which involved the TGF-β signaling pathway, Wnt signaling pathway, TRAF6-mediated induction of NF-κB and MAPK pathway, TLR7/8 cascade, and others. The molecular docking results revealed quercetin, luteolin, and ligustilide to have good affinity with the core targets MYC and TP53. The active ingredients in BHD might act on TP53, MYC, APP, UBC, JUN, and other targets through its active components (such as quercetin, ligustrazine, ligustilide, hydroxysafflor yellow A, and dihydrocapsaicin). This action of BHD may be transmitted via the involvement of multiple signaling pathways, including the TGF-β signaling pathway, Wnt signaling pathway, TRAF6-mediated induction of NF-κB and MAPK pathway, and TLR7/8 cascade, to treat restenosis by inhibiting the phenotype switching and proliferation of VSMC.

Analyzing Active Compounds in Elateriospermum tapos Yogurt for Maternal Obesity: A Network Pharmacology and Molecular Docking Study.

Maternal obesity, characterized by an elevated body mass index (BMI) during pregnancy, is known to have adverse effects on the offspring. However, a recent study suggests that Elateriospermum tapos (E. tapos) yogurt may hold potential in mitigating excessive weight retention post-pregnancy. Thus, this study aims to employ network pharmacology to explore the pharmacological effects of the bioactive compounds present in E. tapos yogurt against maternal obesity. Initially, a screening process is conducted to identify the bioactive compounds in E. tapos yogurt, followed by the prediction of potential gene targets for these compounds using Swiss Target Prediction and the SuperPred databases. Maternal obesity-associated genes are sourced from the OMIM, DisGeNet, and GeneCards databases. The interaction between the identified compounds and maternal obesity genes is established via protein-protein interaction analysis, gene ontology examination, and KEGG pathway analysis. To validate the results, molecular docking studies are conducted using AutoDock Tools software. The findings reveal that out of the 64 compounds analyzed, three meet the screening criteria, resulting in a total of 380 potential gene targets. Among these targets, 240 are shared with maternal obesity-related genes. Further analysis demonstrates the favorable affinity of these active compounds with key targets, linking them to biological processes involving protein phosphorylation, inflammation, as well as the pathways related to lipid metabolism, atherosclerosis, and the other signaling pathways. In conclusion, this study provides valuable insights into the potential pharmacological effects of the bioactive compounds found in E. tapos yogurt against maternal obesity. These findings open avenues for further exploration and potential therapeutic interventions targeting maternal obesity.

Herbal Metabolites as Potential Carbonic Anhydrase Inhibitors: Promising Compounds for Cancer and Metabolic Disorders.

Human carbonic anhydrases (CAs) play a role in various pathological mechanisms by controlling intracellular and extracellular pH balance. Irregular expression and function of CAs have been associated with multiple human diseases, such as obesity, cancer, glaucoma, and epilepsy. In this work, we identify herbal compounds that are potential inhibitors of CA VI. We used the AutoDock tool to evaluate binding affinity between the CA VI active site and 79 metabolites derived from flavonoids, anthraquinones, or cinnamic acids. Compounds ranked at the top were chosen for molecular dynamics (MD) simulations. Interactions between the best CA VI inhibitors and residues within the CA VI active site were examined before and after MD analysis. Additionally, the effects of the most potent CA VI inhibitor on cell viability were ascertained in vitro through the 2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. Kaempferol 3-rutinoside-4-glucoside, orientin, kaempferol 3-rutinoside-7-sophoroside, cynarin, and chlorogenic acid were estimated to establish binding with the CA VI catalytic domain at the picomolar scale. The range of root mean square deviations for CA VI complexes with kaempferol 3-rutinoside-4-glucoside, aloe-emodin 8-glucoside, and cynarin was 1.37 to 2.05, 1.25 to 1.85, and 1.07 to 1.54 Å, respectively. The MTT assay results demonstrated that cynarin had a substantial effect on HCT-116 cell viability. This study identified several herbal compounds that could be potential drug candidates for inhibiting CA VI.

The inhibitory mechanism of echinacoside against Staphylococcus aureus Ser/Thr phosphatase Stp1 by virtual screening and molecular modeling.

Stp1 is a new potential target closely related to the pathogenicity of Staphylococcus aureus (S. aureus). In this study, effective Stp1 inhibitors were screened via virtual screening and enzyme activity experiments, and the inhibition mechanism was analyzed using molecular dynamics simulation. AutoDock Vina 4.0 software was used for virtual screening. The molecular structures of Stp1 and ligands were obtained from the RCSB Protein Data Bank and Zinc database, respectively. The molecular dynamics simulation used the Gromacs 4.5.5 software package with the Amberff99sb force field and TIP3P water model. AutoDock Tools was used to add polar hydrogen atoms to Stp1 and distribute part of the charge generated by Kollman's combined atoms. The binding free energies were calculated using the Amber 10 package. The theoretical calculation results are consistent with the experimental results. We found that echinacoside (ECH) substantially inhibits the hydrolytic activity of Stp1. ECH competes with the substrate by binding to the active center of Stp1, resulting in a decrease in Stp1 activity. In addition, Met39, Gly41, Asp120, Asn162, and Ile163 were identified to play key roles in the binding of Stp1 to ECH. The benzene ring of ECH also plays an important role in complex binding. These findings provide a robust foundation for the development of innovative anti-infection drugs.

Network pharmacology and molecular docking predictions of the active compounds and mechanism of action of Huangkui capsule for the treatment of idiopathic membranous nephropathy.

Huangkui Capsule is a single herbal concoction prepared from the flower of Abelmoschus manihot, which is used to treat idiopathic membranous nephropathy (IMN), a frequent pathologically damaging kidney condition. It has been widely utilized to treat a variety of renal disorders, including IMN, in clinical practice. However, the active compounds and mechanism of action underlying the anti-IMN effects of Huangkui Capsule remain unclear. In this study, we aimed to predict the potential active compounds and molecular targets of Huangkui Capsule for the treatment of IMN. The possible active components of Huangkui were located using the SymMap v2 database. The targets of these drugs were predicted using Swiss Target Prediction, while IMN-related genes with association scores under 5 were gathered from the GeneCards and DisGeNET databases. The common targets of the disease and the components were determined using VENNY 2.1. Using Cytoscape 3.8.0, a drug-disease network diagram was created. Molecular docking was carried out with Pymol, AutoDock Tools, and AutoDock Vina. With 1260 IMN-related illness genes gathered from GeneCards and DisGeNET databases, we were able to identify 5 potentially active chemicals and their 169 target proteins in Huangkui. Based on degree value, the top 6 targets for Huangkui treatment of IMN were chosen, including AKT, MAPK3, PPARG, MMP9, ESR1, and KDR. This work theoretically explains the mechanism of action of Huangkui Capsule in treating IMN and offers a foundation for using Huangkui Capsule in treating IMN in clinical settings. The findings require additional experimental validation.

Alpha-mangostin, piperine and beta-sitosterol as hepatitis C antivirus (HCV): In silico and in vitro studies

Hepatitis C is still a serious liver case of health. Up to now the development of anti-Hepatitis C Virus (HCV) drugs is challenging, especially the development of natural material compounds as anti-HCV. In the present study, we evaluated the probability of α-mangostin, piperine, and β-sitosterol as anti-HCV with the in silico and in vitro approaches. Molecular docking was performed between nonstructural protein 5B (NS5B, PDB ID 3FQL) with α-mangostin, piperine, and β-sitosterol by Autodock Tools® and BIOVIA Discovery Studio®. Subsequently, molecular dynamics simulations were conducted for 200 ns, evaluating the dynamic interaction between the ligands and the viral protein NS5B. Furthermore, compound characterization at the hepatocarcinoma cell line was employed. α-Mangostin with NS5B complex demonstrated the most negative binding free energy value based on MM-PBSA calculation with a value of −9.13 kcal/mol. In vitro test showed that IC50 of α -mangostin was 2.70 ± 0.92 μM, IC50 of piperine was 52.18 ± 3.21 μM, IC50 of β-sitosterol was >100 μM. α-Mangostin can serve as a valuable lead compound for further development of the anti-HCV.

A novel small molecule inhibitor of p38⍺ MAP kinase augments cardiomyocyte cell cycle entry in response to direct cell cycle stimulation.

Myocardial infarction (MI) is the leading cause of mortality globally due in part to the limited ability of cardiomyocytes (CMs) to regenerate. Recently, we demonstrated that overexpression of four-cell cycle factors, CDK1, CDK4, cyclin B1 and cyclin D1 (4F), induced cell division in ~20% of the post-mitotic CMs overexpressed 4F. The current study aims to identify a small molecule that augments 4F-induced CM cycle induction. Screening of small molecules with a potential to augment 4F-induced cell-cycle induction in 60-day-old mature human induced pluripotent cardiomyocytes (hiPS-CMs) revealed N-(4,6-Dimethylpyridin-2-yl)-4-(pyridine-4-yl)piperazine-1-carbothioamide (NDPPC), which activates cell cycle progression in 4F-transduced hiPS-CMs. Autodock tool and Autodock vina computational methods showed that NDPPC has a potential interaction with the binding site at the human p38⍺ mitogen-activated protein kinase (p38⍺ MAP kinase), a critical negative regulator of the mammalian cell cycle. A p38 MAP kinase activity assay showed that NDPPC inhibits p38⍺ with 5-10 times lower IC50 compared to the other P38 isoforms in a dose-dependent manner. Overexpression of p38⍺ MAP kinase in CMs inhibited 4F cell cycle induction, and treatment with NDPPC reversed the cell cycle inhibitory effect. NDPPC is a novel inhibitor for p38 MAP kinase and is a promising drug to augment CM cell cycle response to the 4F. NDPPC could become an adjunct treatment with other cell cycle activators for heart failure treatment.

Duhuo Jisheng decoction alleviates neuroinflammation and neuropathic pain by suppressing microglial M1 polarization: a network pharmacology research

BackgroundNeuropathic pain (NP) is the most prevalent form of chronic pain resulting from nerve damage or injury. Despite the widespread use of Duhuo Jisheng decoction (DHJSD) in traditional Chinese medicine (TCM) to treat chronic pain, the mechanism underlying its analgesic action remains unclear.MethodsUsing network pharmacology, we obtained DHJSD and NP-related target information from public databases to construct protein–protein interactions (PPI) and compound-target networks based on common target genes. These networks were further analyzed using gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG). The interaction between molecules was verified through molecular docking using AutoDock Tools software. Additionally, we treated a chronic constriction injury (CCI) rat model with DHJSD and determined the mechanical withdrawal threshold (MWT). We used an enzyme-linked immunosorbent assay kit to determine the levels of inflammatory cytokines. Furthermore, qRT-PCR was employed to analyze ACHE, NOS2, MAPK3, PTGS2, AKT1, and PPARG mRNA expression, and immunofluorescence was used to evaluate changes in microglia.ResultsOur screening of compounds and targets identified 252 potential targets of DHJSD associated with NP. PPI analysis, along with GO and KEGG analyses, revealed that the potential mechanism of DHJSD in NP treatment may be related to inflammatory reactions, the IL-17 signaling pathway, MAP kinase activity, and endocrine activity. Based on molecular docking, the core target showed significant affinity for DHJSD's active components. Moreover, DHJSD treatment repaired the CCI-induced inflammatory reaction in the spinal cord while regulating the expression of ACHE, NOS2, MAPK3, PTGS2, AKT1, and PPARG mRNA. Immunofluorescence results indicated that the active components of DHJSD may regulate microglial M1 polarization to improve neuroinflammation, PPARG may have been involved in the process.ConclusionThe multi-component, multi-target, and multi-pathway actions of DHJSD provide new insights into its therapeutic mechanism in NP.

Integrated network pharmacology analysis and in vitro validation revealed the underlying mechanism of Xiyanping injection in treating coronavirus disease 2019.

Coronavirus disease 2019 (COVID-19) has spread rapidly worldwide, leading to a pandemic. In China, Xiyanping injection (XYP) has been recommended as a drug for COVID-19 treatment in the Guideline on Diagnosis and Treatment of COVID-19 by the National Health Commission of the People Republic of China and National Administration of Traditional Chinese Medicine (Trial eighth Edition). However, the relevant mechanisms at the molecular-level need to be further elucidated. In this study, XYP related active ingredients, potential targets and COVID-19 related genes were searched in public databases. Protein-protein interaction network and module analyzes were used to screen for key targets. gene ontology and Kyoto encyclopedia of genes and genomes were performed to investigate the potentially relevant signaling pathways. Molecular docking was performed using Autodock Tools and Vina. For the validation of potential mechanism, PolyI:C was used to induce human lung epithelial cells for an inflammation model. Subsequently, CCK-8 assays, enzyme-linked immunosorbent assay, reverse transcription quantitative polymerase chain reaction and western blot were employed to determine the effect of XYP on the expression of key genes. Seven effective active ingredients in XYP were searched for 123 targets in the relevant databases. Furthermore, 6446 COVID-19 disease targets were identified. Sodium 9-dehydro-17-hydro-andrographolide-19-yl sulfate was identified as the vital active compounds, and IL-6, TNF, IL-1β, CXCL8, STAT3, MAPK1, MAPK14, and MAPK8 were considered as the key targets. In addition, molecular docking revealed that the active compound and the targets showed good binding affinities. The enrichment analysis predicted that the XYP could regulate the IL-17, Toll-like receptor, PI3K-Akt and JAK-STAT signaling pathways. Consistently, further in vitro experiments demonstrated that XYP could slow down the cytokine storm in the lung tissue of COVID-19 patients by down-regulating IL-6, TNF-α, IL-1β, CXCL8, and p-STAT3. Through effective network pharmacology analysis and molecular docking, this study suggests that XYP contains many effective compounds that may target COVID-19 related signaling pathways. Moreover, the in vitro experiment confirmed that XYP could inhibit the cytokine storm by regulating genes or proteins related to immune and inflammatory responses.

Huoxin Pill Reduces Myocardial Ischemia Reperfusion Injury in Rats via TLR4/NFκB/NLRP3 Signaling Pathway.

To explore the protective effect of Huoxin Pill (HXP) on acute myocardial ischemia-reperfusion (MIRI) injury in rats. Seventy-five adult SD rats were divided into the sham-operated group, model group, positive drug group (diltiazem hydrochloride, DH), high dose group (24 mg/kg, HXP-H) and low dose group (12 mg/kg, HXP-L) of Huoxin Pill (n=15 for every group) according to the complete randomization method. After 1 week of intragastric administration, the left anterior descending coronary artery of the rat's heart was ligated for 45 min and reperfused for 3 h. Serum was separated and the levels of creatine kinase (CK), creatine kinase isoenzyme (CK-MB) and lactate dehydrogenase (LDH), superoxide dismutase (SOD), and malondialdehyde (MDA), hypersensitive C-reactive protein (hs-CRP) and interleukin-1β (IL-1β) were measured. Myocardial ischemia rate, myocardial infarction rate and myocardial no-reflow rate were determined by staining with Evans blue and 2,3,5-triphenyltetrazolium chloride (TTC). Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine (BATMAN) databases were used to screen for possible active compounds of HXP and their potential therapeutic targets; the results of anti-inflammatory genes associated with MIRI were obtained from GeneCards, Drugbank, Online Mendelian Inheritance in Man (OMIM), and Therapeutic Target Datebase (TTD) databases was performed; Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were used to analyze the intersected targets; molecular docking was performed using AutoDock Tools. Western blot was used to detect the protein expression of Toll-like receptor 4 (TLR4)/nuclear factor kappa-B (NFκB)/NOD-like receptor protein 3 (NLRP3). Compared with the model group, all doses of HXP significantly reduced the levels of LDH, CK and CK-MB (P<0.05, P<0.01); HXP significantly increased serum activity of SOD (P<0.05, P<0.01); all doses of HXP significantly reduced the levels of hs-CRP and IL-1β (P<0.05, P<0.01) and the myocardial infarction rate and myocardial no-reflow rate (P<0.01). GO enrichment analysis mainly involved positive regulation of gene expression, extracellular space and identical protein binding, KEGG pathway enrichment mainly involved PI3K-Akt signaling pathway and lipid and atherosclerosis. Molecular docking results showed that kaempferol and luteolin had a better affinity with TLR4, NFκB and NLRP3 molecules. The protein expressions of TLR4, NFκB and NLRP3 were reduced in the HXP group (P<0.01). HXP has a significant protective effect on myocardial ischemia-reperfusion injury in rats, and its effect may be related to the inhibition of redox response and reduction of the inflammatory response by inhibiting the TLR4NFκB/NLRP3 signaling pathway.

Experimental, computational investigations and biological evaluation on 1-(3-acetamidophenyl)-5-mercaptotetrazole-cytotoxicity MTT assay

The current research is Experimental, Computational investigations and biological evaluation on 1-(3-Acetamidophenyl)-5-mercaptotetrazole which is a tetrazole derivative. Tetrazole moiety has wide spectrum of pharmaceutical applications. Density Functional Theory is employed for theoretical analysis and optimized structure, molecular geometry was obtained. Vibrational assignments and PED values were calculated. Experimentally and theoretically FT-IR, FT-Raman studies were carried out. Topology studies ELF, LOL and RDG were done on the title compound. UV analysis was done and peaks were obtained by both experimentally and theoretically with different solvents. HOMO LUMO energies and energy gap were also identified. MEP, NLO and Natural Bonding Orbital calculations were performed on title compound. Drug likeness properties and Ramachandran plot were identified. Finally, Molecular docking against anti-convulsant targets were performed using autodock tools and visualized with Discovery studio software. Theoretical results are compared with experimental results, which is in good agreement. Cytotoxicity assay studies were done on title compound. Results reveals that this compound is nontoxic and can be used as a anti – convulsant.

Molecular docking and molecular dynamics simulation analysis of bioactive compounds of Cichorium intybus L. seed against hepatocellular carcinoma

In this article, bioactive compounds present in Cichorium intybus L. seeds were collected from literature review and analyzed for probable remedy for hepatocellular carcinoma. Cichorium intybus L. is a traditional plant used all over the world mainly in hepatic disorders and renal diseases. This therapeutic plant has many bioactive compounds like chicoric acid, chlorogenic acid, sesquiterpne lactones, stigmasterols etc are found in seeds. Here, the target protein p53 (PDB ID: 2OCJ) which is involved in many cancerous pathways, is chosen. The preADMET study filtered out some compounds which were then subjected to molecular docking studies by Autodock tool 4.2. Afterwards, two best compounds (Esculetin and Isochlorogenic acid) were screened out on the basis of binding energy as compared to the standard compound (Doxorubicin). All these complexes were then analyzed for stability by molecular dynamics using online GROMACS tool. In the comparative simulation study, the compound Esculetin shows a stable interaction with the p53 over the 100 ns trajectory. Hepatocellular carcinoma accounts for high mortality of cancer related death worldwide. These findings suggest that these compound can be used to treat the hepatocellular carcinoma. Communicated by Ramaswamy H. Sarma

Bacterial network construction and molecular docking approach to study interaction of Myristica fragrans on Acne infections

Acne vulgaris is a very common bacterial infection caused. Herbal remedies have always give a positive response in treatment of various disease in disorders. The present study works on predicting the probable interactions between the Myristica fragrans bioactives with the bacterial targets via network pharmacology and docking techniques. The bio-actives and disease targets were obtained from open databases and literature review. Protein and pathway enrichment analysis was done by utilizing metascape and STRING tool. Cytoscape tool were utilized for construction of network. The compounds were further assessed using molsoft tools and docking was done using auto-dock tools. The potential bio-actives were selected further the network construction gave insights on the highest degree values. The targets with highest interactions were docked and the complex which showed good binding was selected. It was found that Stigmasterol and Campesterol have the highest potential and can be considered as hit compounds for further studies too. &#x0D;

Investigation of target genes and potential mechanisms related to compound Xiao-ai-fei honey ointment based on network pharmacology and bioinformatics analysis.

Compound Xiao-ai-fei honey ointment (CXHO) is an anticancer preparation with a long history in Uyghur folk medicine in China and has been used for the treatment of gastric cancer (GC) in Xinjiang, China. Nevertheless, the mechanism of its anticancer effect remains to be investigated. Bioactive ingredients of CXHO were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database. Target genes of ingredients were acquired via the PubChem and Swiss target prediction database. Gene expression profiling of GC was obtained from GSE54129 in the GEO database and analyzed using the limma package in R. The hub genes associated with CXHO in GC were validated using the TIMER2.0 database, GEPIA2 database and Auto Dock tools. The effect of CXHO on migration of GC cells was detected by Transwell chamber assay and Wound healing assay. The effect of CXHO on expression levels of MMP2/MMP9 and NF-κb, PI3K/AKT signaling pathway was detected by Western blot assay. Forty-five bioactive ingredients and their 819 related genes were found. A total of 462 differentially expressed genes were identified between GC patients and healthy controls. Seventeen common target genes were identified as hub genes CXHO against GC. Among them, MMP2 and MMP9 were significantly associated with tumor immune infiltrates and had good binding affinity with effective ingredients. Moreover, we validated the mRNA and protein expression levels and prognostic value of MMP2 and MMP9 by different databases. In addition, Kyoto encyclopedia of genes and genomes and gene ontology analyses showed that the 17 common target genes were mainly involved in steroid hormone biosynthesis and cancer-related pathways. Experimental results showed that CXHO inhibited migration of GC cells and down regulated the expression levels of MMP2/MMP9, NF-κb. In addition, CXHO can inhibited PI3K/AKT signaling pathway. We identified and experimental validated 2 pivotal target genes of CXHO against GC and preliminarily analyzed the potential mechanisms by which CXHO inhibits the development of GC. All these findings support CXHO as a promising drug for the treatment of GC.

Integrating network analysis and pharmacokinetics to investigate the mechanisms of Danzhi Tiaozhi Decoction in metabolic-associated fatty liver disease (MAFLD)

Ethnopharmacological relevanceBased on ancient classics, Danzhi Tiaozhi Decoction has been successfully used to treat nonalcoholic fatty liver disease for decades. However, its therapeutic mechanisms remain unclear. Aim of the studyThis study aimed to investigate the effects of Danzhi Tiaozhi Decoction (DZTZD) on metabolic-associated fatty liver disease (MAFLD). Materials and methodsFirst, we identified the active ingredients of DZTZD and their potential targets in the Traditional Chinese Medicine System Pharmacology database. Using the overlapped genes, we selected the key MAFLD-associated genes, then conducted GO and KEGG pathway enrichment analyses. Furthermore, DZTZD was administered orally to rats, and their serum and liver tissues were examined for absorbed compounds using pharmacochemistry. UPLC-Q-Exactive Orbitrap/MS was used to determine the main compounds. Then, we validated the binding association of the key targets with their active compounds with AutoDock Tools and other software. Finally, the predicted hub targets were experimentally validated. ResultsWe found 254 active compounds in DZTZD corresponding to 208 targets. Sixteen key genes were identified, and the enrichment analysis revealed multiple signaling pathways, including the AGE-RAGE pathway in diabetic complications and the lipid and atherosclerosis signaling pathway. Next, 160 absorbed components and metabolites were characterized in vivo, and 53 absorbed components and metabolites were characterized in liver tissue. Thirteen parent compounds were identified, including coptisine, quercetin, luteolin, and aloe-emodin. The molecular docking data demonstrated the strongest binding between the active compounds and the core proteins. Moreover, the animal experiments showed that DZTZD decreased body weight, liver weight, lipid accumulation, and ALT, AST, CRP, FFA, IL-6, PEPCK, G6P, TG, TC, and LDL-c serum levels, and increased serum HDL-c levels compared to high-fat induced rats. Besides, the RT-PCR and Western blot showed that DZTZD inhibited the SREBP1c and FAS and increased hyperlipidemia-induced CPT-1A levels. In the high-fat group, JNK phosphorylation increased, and AKT protein phosphorylation decreased, while DZTZD reversed these effects. ConclusionBased on the pharmacological network analysis, pharmacochemistry, and experimental validation, DZTZD can potentially improve MAFLD via the JNK/AKT pathway.