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Objective@#To explore the molecular mechanism of resveratrol (RES) in the treatment of oral squamous cell carcinoma (OSCC) through the use of biological information methods such as network pharmacology and molecular docking and to provide a theoretical reference for the clinical application of RES in the treatment of OSCC.@*Methods@#The Swiss Target Prediction(http://www.swisstargetprediction.ch), SEA (http://sea.bkslab.org)database, and Pharm mapper database(http://lilab-ecust.cn) were used to retrieve RES-related targets, and the DISGENET (www.disgenet.org), OMIM (https://omim.org) and GeneCards (https://www.genecards.org) databases were used to screen OSCC disease targets. The intersection of drugs and disease targets was determined, and Cytoscape 3.7.2 software was used to construct a "drug-diseasetarget pathway" network. The Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database was used to construct a target protein interaction network, and the DAVID database was used for enrichment analysis of key proteins. Finally, molecular docking validation of key proteins was performed using AutoDock and PyMOL. The enrichment analysis and molecular docking results were integrated to predict the possible molecular mechanisms of RES treatment in OSCC; western blot was used to determine the effect of resveratrol at different concentrations (50, 100) μmol/L on the expression of Src tyrosine kinase (SRC), epidermal growth factor receptor (EGFR), estrogen receptor gene 1 (ESR1), and phosphatidylinositol 3 kinase/protein kinase B (PI3K/AKT) signaling pathway proteins in OSCC HSC-3 cells.@*Results@#A total of 243 targets of RES drugs and 6 094 targets of OSCC were identified. A total of 116 potential common targets were obtained by intersecting drugs with disease targets. These potential targets mainly participate in biological processes such as in vivo protein self-phosphorylation, peptide tyrosine phosphorylation, transmembrane receptor protein tyrosine kinase signaling pathway, and positive regulation of RNA polymerase Ⅱ promoter transcription, and they interfere with the PI3K/AKT signaling pathway to exert anti-OSCC effects. The docking results of resveratrol with OSCC molecules indicated that key targets, such as EGFR, ESR1, and SRC, have good binding activity. The results of cell-based experiments showed that resveratrol inhibited the protein expression of SRC, EGFR, ESR1, p-PI3K, and p-AKT in HSC-3 cells in a dose-dependent manner.@*Conclusion@#RES can inhibit the expression of its targets EGFR, ESR1, SRC, p-PI3K, and p-AKT in OSCC cells.
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Objective@#To investigate the potential caries prevention mechanism of the Xinjiang Mori cortex and to analyze its effect on the main cariogenic bacteria.@*Methods@#The active components of the Xinjiang Mori cortex and the main targets were predicted and screened using the TCMSP database. The GeneCards, DisGENET and TTD databases were used to obtain caries-related targets. The common targets were derived, and core genes were screened. The enrichment analysis was performed using the DAVID data platform. Molecular docking was performed using AutoDock software. In in vitro antibacterial experiments, first, the 50% minimum inhibitory concentration (MIC50) and the minimum bactericidal concentration (MBC) of the Xinjiang Mori Cortex extract against Streptococcus mutans, Streptococcus sanguis and Actinomyces viscosus were determined and the growth curves were measured. The effects of the Xinjiang Mori Cortex extract on acid production, polysaccharide production and adhesion ability of Streptococcus mutans, Streptococcus sanguis and Actinomyces viscosus in the planktonic state were determined. The 50% minimum biofilm inhibition concentration (MBIC50) and 50% minimum biofilm reduction concentration (MBRC50) were determined by crystal violet staining, and biofilm morphology was visualized using scanning electron microscopy (SEM).@*Results@#The main active components of the Xinjiang Mori cortex included quercetin, kaempferol, and β-sitosterol. Tumor necrosis factor (TNF), interleukin-6 (IL-6), and interleukin-1beta (IL-1β) could be the most important targets of the Xinjiang Mori cortex for the prevention of dental caries. The enrichment analysis results showed that Mori cortex extract may have effects on the AGE-RAGE signaling pathway, IL-17 signaling pathway, and TNF signaling pathway. The antibacterial experiment results showed that the MIC50 values of Xinjiang Mori Cortex extract against Streptococcus mutans, Streptococcus sanguis and Actinomyces viscosus were 0.5, 0.5 and 0.25 mg/mL, respectively, and the MBCs were 4.0, 2.0 and 1.0 mg/mL, respectively. The inhibitory effect of Xinjiang Mori Cortex extract on the acid production, polysaccharide production and adhesion ability of three major cariogenic bacteria in the planktonic state was stronger than that of the control group, and the differences were statistically significant (P<0.05). The MBIC50 was 1.0, 1.0, and 0.5 mg/mL, and the MBRC50 was 4.0, 4.0, and 2.0 mg/mL. SEM observation showed that the amount of biofilm formation decreased with the drug concentration compared with the control group.@*Conclusion@#Xinjiang Mori cortex extract can prevent caries through quercetin, kaempferol, and β-sitosterol active ingredients, TNF、IL-6、IL-1β key targets and multiple pathways and inhibit the growth, acid production, polysaccharide production, and adhesion ability of three major cariogenic bacteria in the planktonic state and has some inhibitory effect on corticogenic biofilm formation.
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Objective To investigate the mechanism of Qizhenziyin mixture in the treatment of hypogonadism by using the network pharmacology approach. Methods The active components of Qizhenziyin mixture were obtained by searching TCMSP ，TCMID and HIT databases.The related targets of candidate compounds were obtained by searching STITCH databases. The potential targets of Qizhenziyin mixture in the treatment of hypogonadism were obtained by mapping the disease genes of hypogonadism with Genecards and DisGeNet databases. The protein interaction platform database (STRING) was used to construct the interaction relationship between action targets. The target protein interaction （PPI） network was constructed by introducing Cytoscape software. The mechanism of Qizhenziyin mixture in the treatment of hypogonadism was explained through the enrichment analysis of GO, KEGG and molecular docking technology. Results A total of 148 drug-disease chemical compounds, 96 drug-disease intersection targets, 1085 disease targets were obtained；the components for treating diseases are: quercetin，kaempferol, luteolin, etc; enrichment analysis of GO revealed 1792 biological processes （BP）, 31 cellular components (CC) and 79 molecular functions (MF)；the results of KEGG pathway enrichment analysis indicated such as FOXO signaling pathway, prostate cancer, AGE-RAGE signaling pathway in diabetic complications, HIF-1 signaling pathway, etc.The results of molecular docking showed that kaempferol and LEP had the best and stable binding energy. Conclusion The active components of Qizhenziyin mixture may play a role of the treatment of hypogonadism by improving insulin resistance and the expression of testosterone synthetase of Leydig cells.
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Typhoid fever is a serious bacterial infection caused by Salmonella enterica serovar Typhi, and is a major public health issue in developing countries. The emergence of multidrug-resistant strains of S. Typhi has raised concerns about the effectiveness of existing treatments and has prompted the exploration of alternative therapies. Phytochemicals, which are bioactive compounds found in plants, have been investigated as potential sources of new antibacterial agents against typhoid. In this review, we conducted an in silico investigation of phytochemicals and their potential activity against S. Typhi. Our review examined current literature on phytochemicals and their antibacterial activity against S. Typhi. Using molecular docking studies, we investigated the potential binding of these phytochemicals to the target protein, DNA gyrase, which is an important drug target in S. Typhi. Our results indicate that several phytochemicals exhibit promising binding affinities to DNA gyrase, suggesting their potential as effective antibacterial agents against typhoid. Overall, our findings highlight the potential of phytochemicals as a source of new therapeutics for typhoid fever, particularly in regions where multidrug-resistant strains of S. Typhi are prevalent. The in silico approach used in this review provides a valuable tool for screening and identifying potential candidates for further investigation. Further studies are needed to validate the results of in silico studies and to explore the potential of phytochemicals as antibacterial agents against typhoid.
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Dyes are becoming more widely used around the world wide, but there is no effective bioremediation approach for removing them completely from the environment. Several dyes are mentioned to be degraded through bacteria; however, it's still unknown how the particular enzymes act throughout the dye degradation. The behavior and function of these enzymes in the biodegradation of azo dyes (Textile dyes) had been investigated experimentally by the numbers of the researchers, however, the molecular mechanisms remain unclear. Therefore, the interaction mechanisms of textile dye (methyl orange) with laccase from B. subtilis were explored through molecular docking and molecular dynamics simulations, the three selected dyes (methyl orange, malachite green, and acid blue 62) that interact positively with laccase on the basis of their maximum binding energy, molecular docking results indicate that one of the three dyes is more stable as a target for degradation through Bacillus subtilis laccase. Therefore, subsequent research focused solely on one substrate: methyl orange. Molecular Dynamics simulation study was applied after the molecular docking to determine the interaction between laccases and methyl orange dyes. The trajectory was proved with root mean square deviation and root mean square fluctuation analysis. According to the molecular dynamics simulation results, laccase-methyl orange complexes remain stable during the catalytic reaction. So, this study demonstrates how laccase is involved in methyl orange bioremediation.
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Background: Computer-aided repositioning of approved drugs is an increasingly popular strategy for the discovery of effective therapies. The potency of the newly repositioned drugs can be optimized using them as a component of an effective drug combination, thereby achieving the desired therapeutic effect at a lower and more tolerable drug concentration. Aim and Objectives: The aim of the study was to perform structure-based virtual screening and repurposing of FDA-approved drugs for the treatment of methicillin resistance by Staphylococcus aureus (SA) and perform an in vitro validation of the prediction. Materials and Methods: Following ethical clearance at the Department of Pharmacology and Therapeutics, College of Health Sciences, Usmanu Danfodiyo University Sokoto, molecular docking was performed against 5 validated protein targets involved in the development of methicillin resistance by SA and an in vitro validation of the prediction was done using 3 of the top-ranking drug candidates against methicillin-resistant vancomycin-susceptible strain of the pathogen (ATCC 43300). Results: Desmopressin and docetaxel, two of the 20 top-ranking repurposed drugs discovered through virtual screening, enhanced the inhibitory effect of oxacillin against the ATCC 43300 SA strain in a ratio-dependent manner, although each of the two drugs singly was only weakly effective against the bacterial strain. The standard drug, vancomycin (also among the top-scoring candidates), alone, was effective against ATCC 43300 strain and in combination with oxacillin, the two drugs produced a ratio-dependent synergistic effect against the bacterial strain. Conclusion: These findings suggest that oxacillin-based combinations with desmopressin, docetaxel, and the standard drug vancomycin, three of the 20 top-ranking drugs, at optimum ratios, may be beneficial in reversing the resistance of the ATCC 43300 SA strain to oxacillin, thus supporting the prediction of the molecular docking results.
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La proteína proteasa 3CLpro del SARS-CoV-2 es una enzima crucial para la replicación viral, razón por la cual se convierte en un blanco terapéutico de gran importancia. El timol (2-isopropil-5-me-tilfenol), un compuesto natural que se encuentra en el tomillo (Thymus vulgaris), exhibe potencial actividad antiviral contra la proteasa 3CLpro. En este estudio, usando acoplamiento molecular con AutoDockTools-1.5.6, se evaluaron las energías de interacción molecular entre el timol y los residuos de aminoácidos en el sitio activo de la proteína proteasa 3CLpro. Luego, con la teoría cuántica de Átomos en Moléculas (QTAIM) y la de Interacciones no covalentes (NCI) se analizaron los tipos de interacciones moleculares entre los residuos de aminoácidos identificados y el timol. Los cálculos cuánticos se llevaron con el software Orca-5.0.3, utilizando el método DFT con el funcional M06-2X y el conjunto base aug-cc-pVDZ en fase gaseosa. Los resultados de acoplamiento molecular indican que el timol se une a la proteína 3CL con una energía de interacción igual a -3,784 kcal/mol. El análisis QTAIM indica la presencia de puntos críticos de enlace entre el timol y los residuos HIS41 y CYS145. Además, se observa la formación de un enlace de hidrógeno entre el grupo OH del timol y el residuo CYS145, lo cual es corroborado por los análisis ELF (Electron Localization Function) y NCI (Non Covalent Interactions). Finalmente, el método NCI confirma la presencia de interacciones de Van der Waals con el residuo HIS41. Los resultados sugieren que el mecanismo de inhibición de la actividad de la proteína 3CLpro es controlado por interacciones moleculares tipo puente de hidrógeno e interacciones débiles.
The protease 3CLpro of the SARS-CoV-2 is a crucial enzyme for viral replication, becoming a highly important therapeutic target. Thymol (2-isopropyl-5-methyl-phenol), a naturally occurring compound found in thyme, exhibits potential antiviral activity against the 3CLpro protease. In this study, using molecular docking with AutoDockTools-1.5.6, the molecular interaction energies between thymol and amino acid residues in the active site of the protein protease 3CLpro were evaluated. Then, with the Atoms in Molecules (QTAIM) and Non-covalent Interactions (NCI) theories, the types of molecular interactions between identified amino acid residues and thymol were analyzed. Quantum calculations were carried out with the Orca-5.0.3 software using the DFT method with the M06-2X functional and the aug-cc-pVDZ basis set in the gas phase. The molecular docking results indicate that thymol is linked to the 3CL protein with an interaction energy equal to -3.784 kcal/mol. QTAIM analysis indicates the presence of critical binding sites between thymol and residues HIS41 and CYS145. In addition, the formation of a hydrogen bond between the OH group of thymol and the CYS145 residue is observed, which is corroborated by the ELF and NCI analyses. Finally, the NCI method confirms the presence of Van der Waals interactions with the HIS41 residue. The results suggest that the mechanism of inhibition of the activity of the 3CLpro protein is controlled by molecular interactions such as hydrogen bonding and weak interactions.
A protease 3CLpro do SARS-CoV-2 é uma enzima crucial para a replicação viral, tornando-se um alvo terapêutico de grande importÅncia. O timol (2-isopropil-5-me-tilfenol), um composto natural encontrado no tomilho, exibe potencial atividade antiviral contra a protease 3CLpro. Neste estudo, utilizando o docking molecular com o AutoDockTools-1.5.6, foram avaliadas as energias de interação molecular entre o timol e os residuos de aminoácidos no sítio ativo da proteína protease 3CLpro. Em seguida, com a teoria quantica de atomos em moleculas (QTAIM) e da interacões no-covalentes (NCI), foram analisados os tipos de interações moleculares entre os resíduos de aminoácidos identificados e o timol. Os cálculos quÅnticos foram realizados com o software Orca-5.0.3 usando o método DFT com o funcional M06-2X e a base aug-cc-pVDZ definida na fase gasosa. Os resultados do docking molecular indicam que o ti-mol está ligado à proteína 3CL com uma energia de interação igual a -3.784 kcal/ mol. A análise QTAIM indica a presença de sítios de ligação críticos entre o timol e os resíduos HIS41 e CYS145. Além disso, observa-se a formação de uma ponte de hidrogênio entre o grupo OH do timol e o resíduo CYS145, o que é corroborado pelas análises ELF e NCI. Finalmente, o método NCI confirma a presença das interações de Van der Waals com o resíduo HIS41. Os resultados sugerem que o mecanismo de inibição da atividade da proteína 3CLpro é controlado por interações moleculares como ligações de hidrogênio e interações fracas.
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The development of novel medications with previously unidentified action mechanisms is required due to the increasing in antibiotic resistance amongst dangerous microbes. The major goal of the research was to develop in silico and in vitro antibacterial methods for designing an active thiol substituted oxadiazole inhibitor targeting gram-negative and gram-positive bacteria's GlmS receptor. 1,3,4-Oxadiazole was proposed as a scaffold, and the possibility of its synthesis was examined. The least amount of free energy in the ligand configurations was chosen. Analyses of the novel molecules' characteristics were done using ADMET studies. There were four distinct reactions used in the synthesis processes. As the first reagent, substituted carboxylic acids were utilized. Synthesized compounds were characterized by spectral studies and minimum inhibitory concentration was evaluated by in vitro antibacterial examinations of synthesized compounds. Ciprofloxacin served as the study's reference drug. Based on in vitro studies and in silico molecular docking, ROS1-4 established strong binding energy, while ROS3 revealed significant antibacterial activity. These findings support the hypothesis that the proposed scaffold significantly inhibits the GlmS receptor protein.
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Polycystic Ovary Syndrome (PCOS) is one of the most prevalent endocrine disorder in women of reproductive age characterized by hyperandrogenism (HA). Current treatment options for PCOS are either with adverse effects or ineffective. Saptasaram kashayam (SK), an ayurvedic formulation is often been a safe traditional alternative medicine to improve the PCOS symptoms as well as its pathological development. However, its principle phytoconstituents or underlying mechanisms have not been investigated. In order to achieve this, the current study systematically utilized computational tools, network pharmacology approaches and molecular docking studies. All identified phytoconstituents of SK were screened by QikProp ADME prediction and 47 were selected based on oral bioavailability and drug likeliness scores. Their 3D structures were submitted to three online target fishing webservers PharmMapper, ChemMapper and Swiss Target Prediction which produced 1084 biological targets for SK comprehensively. 350 known PCOS therapeutic targets were retreived as common targets from three different interrogative disease centric bioinformatic platforms DisGeNET, OMIM and GeneCards. Intersection of 1084 biological targets of SK and 350 PCOS therapeutic targets produced, 88 potential therapeutic targets of SK against PCOS. STRING PPI and Compound-Target-Pathway networks were constructed and analysed using Cytoscape software. GO & KEGG pathway enrichment analysis was performed using DAVID database. 15 PCOS therapeutic target proteins were short listed from network analysis report- PIK3CA, PDPK1, AKT1, PIK3R1, STAT3, MAPK1, MAPK3, EGFR, AR, ESR1, ESR2, SHGB, NOS3, F2 & CREBBP. Targets that were likely to be inhibited/modulated by SK for treatment of PCOS were docked against the screened phytoconstituents and their respective standard inhibitors using GLIDE-SP of Schrodinger suite, Maestro version- 13.0. Results showed that Quercetin, Catechin, Boeravinone J, Genistein, Protocatechuic Acid, Gentisic Acid, Xanthoarnol, Luteolin, Boeravinone F, Tyrosine, Kaempferol, Dalbergioidin, etc exhibited good binding affinities when compared to standard drugs and might be responsible for synergistic/additive protective effect of SK against PCOS. Meanwhile PI3K-Akt signaling pathway, Prolactin signaling pathway, AGE-RAG diabetic complications, HIF-1 signaling pathway and Estrogen signaling pathway were found to be involving the hub genes of interest and in this way, they might be intervened during treatment of PCOS by SK. Present study succeeded in identifying the drug like principle phytoconstituents, probable PCOS therapeutic targets and the underlying molecular mechanism of SK apart from providing reliable evidence for therapeutic potential of SK against PCOS. However further validation by in vitro and in vivo investigations is necessary.
ABSTRACT
Polycystic Ovary Syndrome (PCOS) is one of the most prevalent endocrine disorder in women of reproductive age characterized by hyperandrogenism (HA). Current treatment options for PCOS are either with adverse effects or ineffective. Saptasaram kashayam (SK), an ayurvedic formulation is often been a safe traditional alternative medicine to improve the PCOS symptoms as well as its pathological development. However, its principle phytoconstituents or underlying mechanisms have not been investigated. In order to achieve this, the current study systematically utilized computational tools, network pharmacology approaches and molecular docking studies. All identified phytoconstituents of SK were screened by QikProp ADME prediction and 47 were selected based on oral bioavailability and drug likeliness scores. Their 3D structures were submitted to three online target fishing webservers PharmMapper, ChemMapper and Swiss Target Prediction which produced 1084 biological targets for SK comprehensively. 350 known PCOS therapeutic targets were retreived as common targets from three different interrogative disease centric bioinformatic platforms DisGeNET, OMIM and GeneCards. Intersection of 1084 biological targets of SK and 350 PCOS therapeutic targets produced, 88 potential therapeutic targets of SK against PCOS. STRING PPI and Compound-Target-Pathway networks were constructed and analysed using Cytoscape software. GO & KEGG pathway enrichment analysis was performed using DAVID database. 15 PCOS therapeutic target proteins were short listed from network analysis report- PIK3CA, PDPK1, AKT1, PIK3R1, STAT3, MAPK1, MAPK3, EGFR, AR, ESR1, ESR2, SHGB, NOS3, F2 & CREBBP. Targets that were likely to be inhibited/modulated by SK for treatment of PCOS were docked against the screened phytoconstituents and their respective standard inhibitors using GLIDE-SP of Schrodinger suite, Maestro version- 13.0. Results showed that Quercetin, Catechin, Boeravinone J, Genistein, Protocatechuic Acid, Gentisic Acid, Xanthoarnol, Luteolin, Boeravinone F, Tyrosine, Kaempferol, Dalbergioidin, etc exhibited good binding affinities when compared to standard drugs and might be responsible for synergistic/additive protective effect of SK against PCOS. Meanwhile PI3K-Akt signaling pathway, Prolactin signaling pathway, AGE-RAG diabetic complications, HIF-1 signaling pathway and Estrogen signaling pathway were found to be involving the hub genes of interest and in this way, they might be intervened during treatment of PCOS by SK. Present study succeeded in identifying the drug like principle phytoconstituents, probable PCOS therapeutic targets and the underlying molecular mechanism of SK apart from providing reliable evidence for therapeutic potential of SK against PCOS. However further validation by in vitro and in vivo investigations is necessary.
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Intercellular communication between the cell plays an essential role in cell growth and cell formation, including migration, metabolism, and cell differentiation. Cell function and tissue homeostasis are maintained through gap junction intercellular communication (GJIC), thus regulating connexin hemichannels. Mis regulation of such connexin, especially connexin (Cx) 43, affects a comprehensive process, including cell differentiation, inflammation, and cell death. Mis regulation may be due to the missense variant in Cx43. Thus, we screened the complete set of mutations from public mutational databases and obtained 219 missense variants, which were then classified based on their pathogenicity, functional impact, stability, conservation, and physiochemical properties. Variant L214P was scrutinized to have the most deleterious, which was then modelled using the I-TASSER server and performed molecular docking analysis to screen potent inhibitors. The compound Kanamycin, Ginsenoside, and Astragaloside IV have better interactions with Cx43 mutant with a maximum of 5 hydrogen bonds. Ginsenoside is a compound that follows a Lipinski rule of five. Thus, the result obtained from this study suggests that Ginsenoside would be a better potent inhibitor for native and mutant Cx43.
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Abstract In the current report, we studied the possible inhibitors of COVID-19 from bioactive constituents of Centaurea jacea using a threefold approach consisting of quantum chemical, molecular docking and molecular dynamic techniques. Centaurea jacea is a perennial herb often used in folk medicines of dermatological complaints and fever. Moreover, anticancer, antioxidant, antibacterial and antiviral properties of its bioactive compounds are also reported. The Mpro (Main proteases) was docked with different compounds of Centaurea jacea through molecular docking. All the studied compounds including apigenin, axillarin, Centaureidin, Cirsiliol, Eupatorin and Isokaempferide, show suitable binding affinities to the binding site of SARS-CoV-2 main protease with their binding energies -6.7 kcal/mol, -7.4 kcal/mol, -7.0 kcal/mol, -5.8 kcal/mol, -6.2 kcal/mol and -6.8 kcal/mol, respectively. Among all studied compounds, axillarin was found to have maximum inhibitor efficiency followed by Centaureidin, Isokaempferide, Apigenin, Eupatorin and Cirsiliol. Our results suggested that axillarin binds with the most crucial catalytic residues CYS145 and HIS41 of the Mpro, moreover axillarin shows 5 hydrogen bond interactions and 5 hydrophobic interactions with various residues of Mpro. Furthermore, the molecular dynamic calculations over 60 ns (6×106 femtosecond) time scale also shown significant insights into the binding effects of axillarin with Mpro of SARS-CoV-2 by imitating protein like aqueous environment. From molecular dynamic calculations, the RMSD and RMSF computations indicate the stability and dynamics of the best docked complex in aqueous environment. The ADME properties and toxicity prediction analysis of axillarin also recommended it as safe drug candidate. Further, in vivo and in vitro investigations are essential to ensure the anti SARS-CoV-2 activity of all bioactive compounds particularly axillarin to encourage preventive use of Centaurea jacea against COVID-19 infections.
Resumo No presente relatório, estudamos os possíveis inibidores de Covid-19 de constituintes bioativos de Centaurea jacea usando uma abordagem tripla que consiste em técnicas de química quântica, docking molecular e dinâmica molecular. Centaurea jacea é uma erva perene frequentemente usada em remédios populares de doenças dermatológicas e febre. Além disso, as propriedades anticâncer, antioxidante, antibacteriana e antiviral de seus compostos bioativos também são relatadas. A Mpro (proteases principais) foi acoplada a diferentes compostos de Centaurea jacea por meio de docking molecular. Todos os compostos estudados, incluindo apigenina, axilarina, Centaureidina, Cirsiliol, Eupatorina e Isokaempferide, mostram afinidades de ligação adequadas ao sítio de ligação da protease principal SARS-CoV-2 com suas energias de ligação -6,7 kcal / mol, -7,4 kcal / mol, - 7,0 kcal / mol, -5,8 kcal / mol, -6,2 kcal / mol e -6,8 kcal / mol, respectivamente. Dentre todos os compostos estudados, a axilarina apresentou eficiência máxima de inibidor, seguida pela Centaureidina, Isokaempferida, Apigenina, Eupatorina e Cirsiliol. Nossos resultados sugeriram que a axilarina se liga aos resíduos catalíticos mais cruciais CYS145 e HIS41 do Mpro, além disso a axilarina mostra 5 interações de ligações de hidrogênio e 5 interações hidrofóbicas com vários resíduos de Mpro. Além disso, os cálculos de dinâmica molecular em uma escala de tempo de 60 ns (6 × 106 femtossegundos) também mostraram percepções significativas sobre os efeitos de ligação da axilarina com Mpro de SARS-CoV-2 por imitação de proteínas como o ambiente aquoso. A partir de cálculos de dinâmica molecular, os cálculos RMSD e RMSF indicam a estabilidade e dinâmica do melhor complexo ancorado em ambiente aquoso. As propriedades ADME e a análise de previsão de toxicidade da axilarina também a recomendaram como um candidato a medicamento seguro. Além disso, as investigações in vivo e in vitro são essenciais para garantir a atividade anti-SARS-CoV-2 de todos os compostos bioativos, particularmente a axilarina, para encorajar o uso preventivo de Centaurea jacea contra infecções por Covid-19.
Subject(s)
Humans , Pharmaceutical Preparations , Centaurea , COVID-19 , Protease Inhibitors , Molecular Dynamics Simulation , Molecular Docking Simulation , SARS-CoV-2ABSTRACT
Objective:To explore the possible mechanism of Yangxue Qingnao Granule for the treatment of vascular dementia (VaD) based on network pharmacology and bioinformatics.Methods:The active components and potential targets of Yangxue Qingnao Granule in the treatment of VaD were obtained from TCMSP database, BATMAN-TCM database, GEO database and OMIM database, etc. The heatmap was visualized by using the pheatmap packages in R. Cytoscape 3.8.2 software and the CytoNCA plugin were utilized to build a network of "Chinese materia medica-active component-potential target". CytoNCA plug-in was used to analyze PPI network topology. Metascape was used for GO and KEGG pathway enrichment analyses. Finally, AutoDock Vina 1.5.6 software was applied to construct molecular docking between the active components and potential core targets. Resuls A total of 135 active components of Yangxue Qingnao Granule were screened and 186 potential targets of Yangxue Qingnao Granule against VaD were obtained. GO function enrichment analysis found protein kinase binding, transcription factor binding and other biological functions. KEGG pathway enrichment analysis identified PI3K-Akt signaling pathway, AGE-RAGE signaling pathway, TNF signaling pathway, etc. Molecular docking showed that the main active components of Yangxue Qingnao Granule had good binding activity with the potential targets. Conclusion:Yangxue Qingnao Granule has the characteristics of multi-targets and multi- pathways in the treatment of VaD. It may play a therapeutic role in VaD by inhibiting neuronal apoptosis and reducing inflammatory response.
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Objective:To study the active components and their potential mechanism of Yanghe Decoction for the treatment of chronic osteomyelitis (CO) via the methods of network pharmacology and molecular docking.Methods:Active components and action targets of Yanghe Decoction were screened from TCMSP, BATMAN-TCM and relevant literature. GeneCards, OMIM, DisGeNET, and PharmGKB databases were used to predict the targets for the CO. Cytoscape 3.8.0 software and STRING database were used to build the networks of "Chinese materia medica-active components-potential targets" and "protein-protein interaction", and according to topological parameters in the network, the core active components as well as Hub genes were screened. MCODE plug was used to accomplish clustering analysis of protein modules in PPI network. Then, intersection targets were enriched and analyzed by GO and KEGG in KOBAS database. Finally, molecular docking was carried out with the help of Autodock tool platform to predict the binding ability between the main active components and key targets.Results:A total of 120 active components of Yanghe Decoction and 402 targets were obtained; 1 464 CO-related targets were screened, and there were 103 intersection target genes of Yanghe Decoction-CO, 110 active components related to intersection targets, which mainly contained some flavonoids and Phytosterols, such as quercetin, Kaempferol, and Beta-Sitosterol. There were 9 Hub genes, including TNF, IL6, AKT1, etc., and 4 protein modules which involved the regulation of immune inflammatory response, vascular microcirculation, bone development, and formation, material synthesis and metabolism and other physiological processes. 193 signaling pathways and 1 552 GO results were acquired in KOBAS database. Molecular docking results showed that the active compounds had good binding activity with key targets based on the minimum binding energy of less than - 5 kcal/mol.Conclusion:The mechanism in the treatment of CO with Yanghe Decoction is a complex process of multiple components, multiple targets, and multiple pathways. It mainly regulates targets such as TNF, IL-6, CXCL8, VEGFA, and AKT1 through pathways such as TNF signaling pathway, IL-17 signaling pathway, and Toll-like receptors, participating in local inflammatory reactions, microcirculation, and bone cell metabolism in chronic osteomyelitis, and interfering with the immune escape mechanism of pathogenic bacteria.
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Objective:To explore the active components, targets and mechanism of Guizhi Fuling Pills in the treatment of atherosclerosis (AS) based on network pharmacology and molecular docking technology.Methods:The active components and potential target information of Guizhi Fuling Pills in the treatment of AS was obtained using Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), SwissTargetPrediction database and Genecards database. The target protein interaction network was constructed by using STRING database. The DAVID database was used to perform the Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment on potential targets. AutoDockVina and PyMOL software were used to verify the molecular docking of the main active components and key targets of Guizhi Fuling Pills.Results:A total of 74 active components, 239 potential targets and 4 710 AS-related disease targets were screened, and 182 intersection targets were obtained. A total of 484 biological process items, 132 molecular function items and 74 cellular component items were obtained by GO functional enrichment analysis, and 116 signal pathways were screened by KEGG enrichment analysis. The results of molecular docking suggested that the active components of Guizhi Fuling Pills have good binding activity to the key intersection targets.Conclusion:The active components of Guizhi Fuling Pills, such as sitosterol and paeoniflorin, mainly treat AS by regulating estrogen signal pathway and inflammatory signal pathway through TNF, VEGFA and other targets.
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Objective:To explore the mechanism of Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma medicinal pair in delaying heart aging based on animal experiments, network pharmacology and molecular docking. Methods:Mice were divided into control group, aging group, metformin group and TCM group according to random number table method. All the groups were injected subcutaneously by D-galactose except the control group to build the subacute aging model. Two weeks later, the metformin group was given metformin suspension (150 mg/kg), the TCM group was given Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma lyophilized powder solution (650 mg/kg), and the control group and aging group were given an equivalent volume of ultrapure water by gastric gavage, once a day, six times a week, for 10 weeks. The level of heart TERT mRNA was detected by PCR; the expression of heart p53 was observed by immunohistochemical staining; the morphology of heart tissue was observed by HE staining. TCMSP and SwissTargetPrediciton databases were used to retrieve the active components and targets of Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma medicinal pair; TTD, OMIM, Gene, HAGR, DisGeNET and other data platforms were used to screen the targets of heart aging; after the drug and disease targets were intersected, the active components of them were collected; STRING database, Cytoscape 3.8.0 software, etc. were used to make PPI of the intersection targets, and screen out the key targets; FunRich was used to perform enrichment analysis of cellular components, molecular functions, biological processes, and biological signal pathways for key targets; Schr?dinger Maestro software was used to do the molecular docking of the screened active components and key targets, and docking results were visualized via PyMOL 2.1 software. Results:Experiment results showed that Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma could significantly ameliorate the damage of aging heart tissues, elevate TERT mRNA level, while significantly reducing the positive expression of p53. A total of 32 active components from the medicinal pair were screened, corresponding to 637 target genes. There were 263 targets for heart aging, and 67 intersection targets of drug active component targets and heart aging targets. 31 key targets were obtained after screening. Enrichment analysis showed that molecular functions were related to transcription factor activity and protein-tyrosine kinase activity. Biological processes involved signal transduction and cell communication. Signaling pathways mainly involved PDGFR-beta, PI3K-Akt, S1P1, Glypican, TRAIL, and Glypican 1. The molecular docking results showed that kaempferol, suchilactone, and ginsenoside Rg5_qt in the medicinal pair had a strong binding ability to p53. Conclusion:Ginseng Radix et Rhizoma- Notoginseng Radix et Rhizoma- Chuanxiong Rhizoma may achieve the effect of delaying heart aging by inhibiting p53 expression, providing a foundation for further research on mechanism of invigorating qi and activating blood circulation drugs to delay heart aging.
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Objective:To analyze the molecular mechanism of Zhenqi Fuzheng Capsules in the adjuvant treatment of AIDS by network pharmacology method and molecular docking technology.Methods:The active components and targets of Zhenqi Fuzheng Capsules were obtained through TCMSP, and the AIDS-related targets were obtained through GeneCards, OMIM and DrugBank databases. The intersection target PPI network was constructed through STRING 11.5 database, and Cytoscape 3.9.1 software was used for network topology analysis; Metascape database was used for GO function and KEGG pathway enrichment analysis of core targets; Cytoscape 3.9.1 was used to construct Zhenqi Fuzheng Capsules component-target-pathway network; Autodock Tools software was used to carry out molecular docking of core targets and active components.Results:Totally 31 active components and 180 targets of Zhenqi Fuzheng Capsules were screened out. TNF, IL6, AKT1, IL1B, TP53, VEGFA, RELA, EGFR and CASP3 were identified as the core targets. GO functional enrichment analysis obtained 1 436 biological processes, 53 cellular components, and 117 molecular functions. KEGG pathway enrichment analysis obtained 167 pathways, which were related to pathways in cancer, AGE-RAGE signaling pathway in diabetic complications, and IL-17 signaling pathway was closely related. Molecular docking results showed that core targets such as AKT1 and TNF had good binding activity to quercetin, kaempferol, and luteolin.Conclusion:The main active components of Zhenqi Fuzheng Capsules in the adjuvant treatment of AIDS are quercetin, kaempferol and luteolin, which may treat AIDS through the IL-17 signaling pathway.
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Objective:The mechanism of Indigo Naturalis in the treatment of ulcerative colitis (UC) was predicted by GEO chip combined with network pharmacology, and preliminarily verified by molecular docking. Methods:The main active components and targets of Indigo Naturalis were obtained by searching TCMSP, SymMap database, SwissTargetPrediction and Pharmmapper. The UC disease targets were obtained from DrugBank database, OMIM database, TTD database, Disgenet database and GEO gene chips. Venn diagram was used to show drug-disease common targets. The protein-protein interaction (PPI) network of intersection targets was analyzed by String platform, and Cytoscape 3.8.2 software was used to construct the PPI network of components and disease targets. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed on the core targets. AutoDock Vina 1.2.1 was used for molecular docking, and the results were visualized by Discovery studio Visualizer. Results:A total of 10 active components and 184 compound targets of IN-UC, of which 42 were core targets, were enriched and analyzed by GO and KEGG. The therapeutic effect of Indigo Naturalis on UC may involve activation of various process, such as reactive oxygen species metabolism, heme binding, protein phosphatase binding, secretory granule exocytosis, cytoplasmic vesicles, cell focal adhesion and cell substrate connection, and regulates PI3K/Akt signal pathway, human cytomegalovirus infection signal pathway, EB virus infection signal pathway HF1 signaling pathway and insulin resistance signaling pathway to treat UC. Conlusion:Indigo Naturalis has the characteristics of multi-component, multi target and multi pathway in the treatment of ulcerative colitis. Through PTGS2, CAT and other core targets, it can regulate PI3K/Akt signal pathway, human giant cell signal pathway, HIF-1 signal pathway to play a therapeutic role.
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Objective:To predict the mechanism of Danggui Buxue Decoction for anti-myocardial ischemia-reperfusion injury and "treating different diseases with the same method" in ischemic stroke based on network pharmacology and molecular docking.Methods:The active components and targets of Danggui Buxue Decoction were screened by retrieving the database of TCMSP and literature; the corresponding targets of myocardial ischemia-reperfusion injury and ischemic stroke were found by OMIM and GeneCards database; the intersection targets of Danggui Buxue Decoction and disease were obtained by using Venny diagram, and the common target network and protein-protein interaction network were constructed by Cytoscape 3.7.1 software and STRING database. The GO and KEGG pathways were enriched by David Database, and the Bio GPS database was used to obtain the tissue distribution information of the key targets. The molecular docking technology was used to verify the results.Results:There were 21 active components in Danggui Buxue Decoction, 181 effective targets and 93 cross targets with diseases. The key components were quercetin, Kaempferol, β-sitosterol, formononetin and isorhamnetin. The key targets were AKT1, TNF, IL6, IL-1β and VEGFA. The enrichment results showed that the main action pathways were fluid shear force and arteriosclerosis, lipid and arteriosclerosis, AGE-RAGE signal pathway in diabetic complications, and the core targets were mainly located in the medullary cells, dendritic cell, smooth muscle, prostate, thyroid and other tissues. The results of molecular docking showed that quercetin had the best binding effect to IL-1β, while isorhamnetin had the best binding effect to IL-1β.Conclusion:Danggui Buxue Decoction is against myocardial ischemia-reperfusion injury and ischemic stroke through hemodynamics, lipid metabolism, inflammatory reaction, oxidative stress, immune reaction and cell apoptosis, plays the role of "treating different diseases with the same method".
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Objective:To explore the material basis and mechanism of Linggui Zhugan Decoction in treating hypertension and obesity by means of network pharmacology and molecular docking technique.Methods:The TCMSP was retrieved and the main active components and action targets of Linggui Zhugan Decoction were screened. The GeneCards, OMIM, TTD, DisGeNET and DrugBank databases were used to screen disease-related targets of hypertension and obesity. The Cytoscape 3.9.0 was used to draw Chinese materia medica-composition-intersection target-disease network diagram. The STRING 11.5 database was used to draw PPI network. The cytoNCA plug-in was used to screen core active components and targets. The bioenrichment analysis of GO and KEGG was carried out in the R4.1.2, and the Chinese materia medica-intersection target-path diagram was drawn, and the core active components and core targets were docked in PyMOL and AutoDockTools 1.5.7.Results:A total of 102 potentially active components and 62 intersection targets were obtained, and 8 active components and 7 core targets were screened. Enrichment analysis showed that the key targets were mainly enriched through the signaling pathways of fluid shear stress and atherosclerosis, lipid and atherosclerosis, and AGE-RAGE, which were involved in biological processes such as the response to nutritional levels and the regulation of small molecule metabolism. Molecular docking showed that there were 37 groups with addinity < -7 kcal/mol.Conclusion:The main active components of Linggui Zhugan Decoction are quercetin, kaempferol and naringenin, which may play a role in fluid shear stress and atherosclerosis pathway, lipid and atherosclerosis pathway and AGE-RAGE signal pathway through AKT1, EGFR, IL1B and other targets.