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Mechanism of Polygala-Acorus in Treating Autism Spectrum Disorder Based on Network Pharmacology and Molecular Docking 基于网络药理学和分子对接的茯苓治疗自闭症谱系障碍的机制研究
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-12-01 DOI: 10.2174/0115734099266308231108112058
Haozhi Chen, Changlin Zhou, Wen Li, Yaoyao Bian
Background:: Recent epidemic survey data have revealed a globally increasing prevalence of autism spectrum disorders (ASDs). Currently, while Western medicine mostly uses a combination of comprehensive intervention and rehabilitative treatment, patient outcomes remain unsatisfactory. Polygala–Acorus, used as a pair drug, positively affects the brain and kidneys, and can improve intelligence, wisdom, and awareness; however, the underlying mechanism of action is unclear. background: Recent epidemic survey data revealed a globally increasing prevalence of autism spectrum disorders (ASDs). Currently, Western medicine mostly uses a combination of comprehensive intervention and rehabilitative treatment, but patient outcomes remain unsatisfactory. Polygala–Acorus, used as a pair drug, positively affects the brain and kidneys and can improve intelligence, wisdom, and awareness. However, the underlying mechanism is unclear. Objective:: We performed network pharmacology analysis of the mechanism of Polygala– Acorus in treating ASD and its potential therapeutic effects to provide a scientific basis for the pharmaceutical’s clinical application. Methods:: The chemical compositions and targets corresponding to Polygala–Acorus were obtained using the Traditional Chinese Medicine Systematic Pharmacology Database and Analysis Platform, ChemSource.com, and PharmMapper database. Disease targets in ASD were screened using the DisGeNET, DrugBank, and GeneCards databases. Gene Ontology functional analysis and metabolic pathway analysis (Kyoto Encyclopedia of Genes and Genomes) were performed using the Metascape database and validated via molecular docking using AutoDock Vina and PyMOL software. Results:: Molecular docking analysis showed that the key active components of Polygala- Acorus interacted with the following key targets: EGFR, SRC, MAPK1, and ALB. Thus, the key active components of Polygala-Acorus (sibiricaxanthone A, sibiricaxanthone B tenuifolin, polygalic acid, cycloartenol, and 8-isopentenyl-kaempferol) have been found to bind to EGFR, SRC, MAPK1, and ALB. Conclusion:: This study has preliminarily revealed the active ingredients and underlying mechanism of Polygala-Acorus in the treatment of ASD, and our predictions need to be proven by further experimentation.
背景:最近的流行病调查数据显示,全球范围内自闭症谱系障碍(ASDs)的患病率正在上升。目前西医多采用综合干预与康复治疗相结合的方法,但患者的治疗效果并不理想。金银花,作为配对药物使用,对大脑和肾脏有积极影响,可以提高智力,智慧和意识;然而,其潜在的作用机制尚不清楚。背景:最近的流行病调查数据显示,全球范围内自闭症谱系障碍(ASDs)的患病率正在上升。目前西医多采用综合干预与康复治疗相结合的方法,但患者的治疗效果并不理想。宝丽花,作为配对药物使用,对大脑和肾脏有积极影响,可以提高智力,智慧和意识。然而,潜在的机制尚不清楚。目的:通过网络药理学方法分析茯苓治疗ASD的作用机制及潜在的治疗效果,为该药的临床应用提供科学依据。方法:利用中药系统药理学数据库及分析平台、ChemSource.com、PharmMapper数据库获取茯茯灵对应的化学成分及靶点。使用DisGeNET、DrugBank和GeneCards数据库筛选ASD的疾病靶点。使用metscape数据库进行基因本体功能分析和代谢途径分析(京都基因与基因组百科全书),并使用AutoDock Vina和PyMOL软件进行分子对接验证。结果:分子对接分析表明,Polygala- Acorus的关键活性成分与EGFR、SRC、MAPK1、ALB等关键靶点相互作用。因此,已发现聚没食子酸、环蒿烯醇和8-异戊烯基山奈酚与EGFR、SRC、MAPK1和ALB结合的关键活性成分(西伯利亚杉烷酮A、西伯利亚杉烷酮B、tenuifolin)。结论:本研究初步揭示了金银花治疗ASD的有效成分及其作用机制,有待进一步实验验证。
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引用次数: 0
DeepTransformer: Node Classification Research of a Deep Graph Network on an Osteoporosis Graph based on GraphTransformer DeepTransformer:基于GraphTransformer的骨质疏松图深度图网络节点分类研究
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-12-01 DOI: 10.2174/0115734099266731231115065030
Yixin Liu, Guowei Jiang, Miaomiao Sun, Ziyan Zhou, Pengchen Liang, Qing Chang
Background:: Osteoporosis (OP) is one of the most common diseases in the elderly population. It is mostly treated with medication, but drug research and development have the disadvantage of taking a long time and having a high cost. Objective:: Therefore, we developed a graph neural network with the help of artificial intelligence to provide new ideas for drug research and development for OP. Methods:: In this study, we built a new osteoporosis graph (called OPGraph) and proposed a deep graph neural network (called DeepTransformer) to predict new drugs for OP. OPGraph is a graph data model established by gathering features and their interrelationships from a vast amount of OP data. DeepTransformer uses GraphTransformer as its foundational network and applies residual connections for deep layering. Results:: The analysis and results showed that DeepTransformer outperformed numerous models on OPGraph, with area under the curve (AUC) and area under the precision-recall curve (AUPR) reaching 0.9916 and 0.9911, respectively. In addition, we conducted an in vitro validation experiment on two of the seven predicted compounds (Puerarin and Aucubin), and the results corroborated the predictions of our model. Conclusion:: The model we developed with the help of artificial intelligence can effectively reduce the time and cost of OP drug development and reduce the heavy economic burden brought to patient's family by complications caused by osteoporosis.
背景:骨质疏松症(Osteoporosis, OP)是老年人最常见的疾病之一。它主要是通过药物治疗,但药物研究和开发的缺点是耗时长,成本高。为此,我们借助人工智能技术开发了一种图神经网络,为OP的药物研发提供新的思路。方法:在本研究中,我们构建了一种新的骨质疏松症图(OPGraph),并提出了一种深度图神经网络(DeepTransformer)来预测OP的新药。OPGraph是通过收集大量OP数据中的特征及其相互关系而建立的图数据模型。DeepTransformer使用GraphTransformer作为其基础网络,并应用剩余连接进行深层分层。结果:分析和结果表明,DeepTransformer在OPGraph上优于众多模型,曲线下面积(AUC)和精确召回曲线下面积(AUPR)分别达到0.9916和0.9911。此外,我们对预测的7种化合物中的2种(葛根素和Aucubin)进行了体外验证实验,结果证实了我们的模型的预测。结论:我们借助人工智能开发的模型可以有效减少OP药物开发的时间和成本,减轻骨质疏松症并发症给患者家庭带来的沉重经济负担。
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引用次数: 0
Insights into the Molecular Mechanisms of Bushen Huoxue Decoction in Breast Cancer via Network Pharmacology and in vitro experiments 网络药理学及体外实验探讨补肾活血汤治疗乳腺癌的分子机制
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-12-01 DOI: 10.2174/0115734099269728231115060827
Hongyi Liang, Guoliang Yin, Guangxi Shi, Xiaofei Liu, Zhiyong Liu, Jingwei Li
Aim:: Breast cancer (BC) is by far seen as the most common malignancy globally, with 2.261 million patients newly diagnosed, accounting for 11.7% of all cancer patients, according to the Global Cancer Statistics Report (2020). The luminal A subtype accounts for at least half of all BC diagnoses. According to TCM theory, Bushen Huoxue Decoction (BSHXD) is a prescription used for cancer treatment that may influence luminal A subtype breast cancer (LASBC). Objectives:: To analyze the clinical efficacy and underlying mechanisms of BSHXD in LASBC. Materials and Methods:: Network pharmacology and in vitro experiments were utilized to foresee the underlying mechanism of BSHXD for LASBC. Results:: According to the bioinformatics analysis, BSHXD induced several proliferation and apoptosis processes against LASBC, and the presumed targets of active components in BSHXD were mainly enriched in the HIF-1 and PI3K/AKT pathways. Flow cytometry assay and western blotting results revealed that the rate of apoptosis enhanced in a dose-dependent manner with BSHXD concentration increasing, respectively. BSHXD notably downregulated the expressions of HIF-1α, P-PI3K, PI3K, P-AKT and AKT proteins. However, adding an HIF-1α agonist restored those protein levels. Conclusion:: The study proved that the mechanism of BSHXD in LASBC may be connected to suppressing proliferation by inhibiting the activity of the HIF-1α/PI3K/AKT signaling pathway and promoting apoptosis via the Caspase cascade in LASBC cells.
目的:根据《全球癌症统计报告(2020)》,乳腺癌(BC)是迄今为止全球最常见的恶性肿瘤,新确诊患者226.1万例,占所有癌症患者的11.7%。腔内A亚型至少占所有BC诊断的一半。根据中医理论,补肾活血汤(BSHXD)是一种用于癌症治疗的方剂,可能影响腔内a亚型乳腺癌(LASBC)。目的:分析BSHXD治疗LASBC的临床疗效及机制。材料与方法:采用网络药理学和体外实验方法,探讨白芍散治疗LASBC的作用机制。结果:生物信息学分析表明,BSHXD可诱导LASBC的多种增殖和凋亡过程,推测BSHXD的活性成分主要富集于HIF-1和PI3K/AKT通路。流式细胞术和western blotting结果显示,BSHXD浓度升高,细胞凋亡率呈剂量依赖性增强。BSHXD显著下调HIF-1α、P-PI3K、PI3K、P-AKT和AKT蛋白的表达。然而,添加HIF-1α激动剂可以恢复这些蛋白水平。结论:本研究证实BSHXD在LASBC中的作用机制可能通过抑制HIF-1α/PI3K/AKT信号通路活性,通过Caspase级联促进LASBC细胞凋亡,从而抑制LASBC细胞增殖。
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引用次数: 0
Acknowledgements to Reviewers 审稿人致谢
4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-10-01 DOI: 10.2174/157340991906230407123048
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引用次数: 0
Investigation of Iminosugars as Antiviral Agents against SARS-CoV-2 Main Protease: Inhibitor Design and Optimization, Molecular Docking, and Molecular Dynamics Studies to Explore Potential Inhibitory Effect of 1-Deoxynojirmycin Series. 亚糖抗SARS-CoV-2主要蛋白酶的研究:抑制剂设计与优化、分子对接及1-脱氧诺吉霉素系列潜在抑制作用的分子动力学研究。
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-08-23 DOI: 10.2174/1573409920666230823094343
Vashima Miglani, Parul Sharma, Anudeep Kumar Narula
<p><strong>Background: </strong>The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) poses an enormous challenge to human health and economy at a global level. According to WHO's latest data, till now, there have been a total of 641,435,884 confirmed cases of COVID-19, and the associated deaths are 6,621,060. Though few vaccinations have been approved for emergency usage, antiviral medications for long-term therapeutics are still being sought. The current research seeks to identify the inhibitory effect of iminosugars, particularly 1-deoxynojirmycin (IDNJ) series, against SARS-CoV-2 main protease (SARS-CoV2-Mpro) using an inhibitor optimization approach for 1DNJ series.</p><p><strong>Aim: </strong>The aim of this study was to investigate the inhibitory effect of iminosugars, specifically 1-deoxynojirmycin (1-DNJ) derivatives, on SARS-CoV-2 main protease (Mpro) as it plays a vital role in viral propagation and transcription and is shaped like a heart.</p><p><strong>Objective: </strong>The main objective of this study was to find the possibility of 1-DNJ derivatives being potent inhibitors against SARS CoV2 Mpro. This study was focused on finding the most probable conformation in which DNJ derivatives could bind to Mpro. Another objective was to obtain molecular-level details by getting insights into stable interactions formed between the ligand and receptor.</p><p><strong>Method: </strong>In silico molecular mechanics (MM) based techniques were employed to identify the best-docked inhibitors using molecular docking, and complexes that showed stable interactions were further subjected to 200 ns of molecular dynamics (MD) simulations to check the stability of ligand into the binding pocket of SARS-CoV2-Mpro. The inhibitors that formed stable complexes were further tested for their ADME properties in order to check the pharmacokinetic parameters as well as their therapeutic importance.</p><p><strong>Result: </strong>Docking was performed on 29 compounds from two different series against SARS-CoV-2 main protease, Mpro (PDB ID: 6LZE). Twelve compounds were found to have high docking scores and better interactions with the active site of Mpro, as compared to the co-crystallized ligand. Furthermore, the three highest-scoring docked compounds (17a, 7, and 8) depicted strong and stable complex formation, throughout the 200 ns molecular dynamics simulation, by analyzing the binding energy (MM/GBSA). The molecules were discovered to form stable interactions with conserved active-site residues, which play an important role in demonstrating activity in structure-based drug design. The ADMET analysis was performed using Qikprop, and the proposed stable derivatives passed all of the needed drug discovery standards, potentially inhibiting the Mpro of SARS-CoV-2.</p><p><strong>Conclusion: </strong>The present findings confer opportunities for compounds 17a, 7, and 8 that could be developed as new therapeutic agents against COVID-19. These compounds are
背景:严重急性呼吸综合征冠状病毒2型(SARS-CoV-2)在全球范围内对人类健康和经济构成巨大挑战。根据世界卫生组织的最新数据,截至目前,全球共有641435884例新冠肺炎确诊病例,死亡人数为6621060人。虽然很少有疫苗被批准用于紧急用途,但用于长期治疗的抗病毒药物仍在寻求中。本研究旨在通过对1-脱氧诺吉霉素(IDNJ)系列的抑制剂优化方法,确定亚糖特别是1-脱氧诺吉霉素(IDNJ)系列对SARS-CoV-2主要蛋白酶(SARS-CoV2-Mpro)的抑制作用。目的:本研究的目的是研究亚糖,特别是1-脱氧诺吉霉素(1-DNJ)衍生物对SARS-CoV-2主蛋白酶(Mpro)的抑制作用,因为它在病毒传播和转录中起着至关重要的作用,形状像心脏。目的:本研究的主要目的是寻找1-DNJ衍生物作为SARS CoV2 Mpro的有效抑制剂的可能性。本研究的重点是寻找DNJ衍生物与Mpro结合的最可能的构象。另一个目标是通过深入了解配体和受体之间形成的稳定相互作用来获得分子水平的细节。方法:采用基于硅分子力学(MM)的技术,通过分子对接鉴定最佳对接抑制剂,并对表现出稳定相互作用的配合物进行200 ns的分子动力学(MD)模拟,以检验进入SARS-CoV2-Mpro结合袋的配体的稳定性。进一步测试形成稳定复合物的抑制剂的ADME特性,以检查药代动力学参数及其治疗重要性。结果:两个不同系列的29个化合物对SARS-CoV-2主要蛋白酶Mpro (PDB ID: 6LZE)进行了对接。与共结晶配体相比,有12个化合物具有较高的对接分数,并且与Mpro活性位点的相互作用更好。此外,通过分析结合能(MM/GBSA),在整个200 ns分子动力学模拟中,三个得分最高的对接化合物(17a、7和8)描绘了强大而稳定的络合物形成。这些分子被发现与保守的活性位点残基形成稳定的相互作用,这在基于结构的药物设计中发挥了重要作用。使用Qikprop进行ADMET分析,所提出的稳定衍生物通过了所有所需的药物发现标准,可能抑制SARS-CoV-2的Mpro。结论:目前的研究结果为化合物17a、7和8提供了开发新的COVID-19治疗剂的机会。这些化合物是根据药代动力学参数和治疗重要性提出的,因此可以在体外进行测试。
{"title":"Investigation of Iminosugars as Antiviral Agents against SARS-CoV-2 Main Protease: Inhibitor Design and Optimization, Molecular Docking, and Molecular Dynamics Studies to Explore Potential Inhibitory Effect of 1-Deoxynojirmycin Series.","authors":"Vashima Miglani,&nbsp;Parul Sharma,&nbsp;Anudeep Kumar Narula","doi":"10.2174/1573409920666230823094343","DOIUrl":"https://doi.org/10.2174/1573409920666230823094343","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) poses an enormous challenge to human health and economy at a global level. According to WHO's latest data, till now, there have been a total of 641,435,884 confirmed cases of COVID-19, and the associated deaths are 6,621,060. Though few vaccinations have been approved for emergency usage, antiviral medications for long-term therapeutics are still being sought. The current research seeks to identify the inhibitory effect of iminosugars, particularly 1-deoxynojirmycin (IDNJ) series, against SARS-CoV-2 main protease (SARS-CoV2-Mpro) using an inhibitor optimization approach for 1DNJ series.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Aim: &lt;/strong&gt;The aim of this study was to investigate the inhibitory effect of iminosugars, specifically 1-deoxynojirmycin (1-DNJ) derivatives, on SARS-CoV-2 main protease (Mpro) as it plays a vital role in viral propagation and transcription and is shaped like a heart.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Objective: &lt;/strong&gt;The main objective of this study was to find the possibility of 1-DNJ derivatives being potent inhibitors against SARS CoV2 Mpro. This study was focused on finding the most probable conformation in which DNJ derivatives could bind to Mpro. Another objective was to obtain molecular-level details by getting insights into stable interactions formed between the ligand and receptor.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Method: &lt;/strong&gt;In silico molecular mechanics (MM) based techniques were employed to identify the best-docked inhibitors using molecular docking, and complexes that showed stable interactions were further subjected to 200 ns of molecular dynamics (MD) simulations to check the stability of ligand into the binding pocket of SARS-CoV2-Mpro. The inhibitors that formed stable complexes were further tested for their ADME properties in order to check the pharmacokinetic parameters as well as their therapeutic importance.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Result: &lt;/strong&gt;Docking was performed on 29 compounds from two different series against SARS-CoV-2 main protease, Mpro (PDB ID: 6LZE). Twelve compounds were found to have high docking scores and better interactions with the active site of Mpro, as compared to the co-crystallized ligand. Furthermore, the three highest-scoring docked compounds (17a, 7, and 8) depicted strong and stable complex formation, throughout the 200 ns molecular dynamics simulation, by analyzing the binding energy (MM/GBSA). The molecules were discovered to form stable interactions with conserved active-site residues, which play an important role in demonstrating activity in structure-based drug design. The ADMET analysis was performed using Qikprop, and the proposed stable derivatives passed all of the needed drug discovery standards, potentially inhibiting the Mpro of SARS-CoV-2.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;The present findings confer opportunities for compounds 17a, 7, and 8 that could be developed as new therapeutic agents against COVID-19. These compounds are","PeriodicalId":10886,"journal":{"name":"Current computer-aided drug design","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10049798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Anti-inflammatory and Anti-arthritic Properties of Mucuna gigantea Plant Extracts: Establishing by Molecular Docking Study. 巨茶树提取物抗炎抗关节炎作用的分子对接研究
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-08-17 DOI: 10.2174/1573409920666230817142114
Satish Kumar, Pratima Srivastava, Somdutt Mujwar, Vinod Gauttam, Sumeet Gupta

Background Mucuna giganteais a traditional plant reported in the management of nervous disorders, male infertility, etc., and also exhibits aphrodisiac, anti-oxidant, and anti-diabetic properties. Very few studies are conducted on Mucuna gigantea. It has not been pharmacologically evaluated for rheumatoid arthritis (RA). In RA, the body's natural defence mechanism gets confused and begins to target the healthy tissues in the body, which leads to joint pain, swelling, bone erosion, and joint stiffness. It is a condition that is classified as an auto-immune disorder. Methods In-silico docking depicted that beta-sitosterol is present in Mucuna gigantea out of ligand library prepared based on a literature survey using computational analysis. Inflammation was induced by carrageen and chronic inflammation was induced by Freund's complete adjuvant in the plantar surface of the rats. The petroleum ether, ethanolic and aqueous extracts in three divided doses (75, 150, and 300 mg/kg) were administered orally. Diclofenac sodium (10 mg/kg), prednisolone (5 mg/kg), and methotrexate (0.5 mg/kg) were used as standard. The statistical significance between means was analyzed using one-way ANOVA, followed by Dunnett's multiple range test. The values are expressed as mean ± SD for each group (n=6), and aP<0.0001, bP<0.001, and cP<0.05 were compared with a negative control group. Results Ethanolic and petroleum ether extracts showed a statistically significant aP<0.0001 effect at 3hr with 300mg/kg effect in analgesic activity, whereas aqueous extracts showed statistically significant aP<0.0001 effect at 1.5hr with 150 and 300mg/kg. In the carrageen-induced model, all three extracts at 300 mg/kg showed a statistically significant aP<0.0001 effect from 2- 4hr. In Freund's adjuvant model, all three extracts at all doses showed a statistically significant aP<0.0001 effect. Also, Mucuna gigantea remarkably ameliorated altered WBCs, rheumatoid factor, and positively modified radiographic and histopathological changes. Conclusion Taken together, these results support the traditional use of Mucuna gigantea as a potent anti-inflammatory and anti-arthritic agent that may be proposed for rheumatoid arthritis treatment.

巨型粘虫是一种传统植物,据报道用于治疗神经障碍、男性不育等,也具有壮阳、抗氧化和抗糖尿病的特性。很少有研究对巨木茶进行。尚未对类风湿关节炎(RA)进行药理学评价。在类风湿性关节炎中,身体的自然防御机制被混淆,并开始针对身体的健康组织,从而导致关节疼痛、肿胀、骨质侵蚀和关节僵硬。这是一种被归类为自身免疫性疾病的疾病。方法通过计算机对接分析,从文献综述的配体文库中发现-谷甾醇存在于巨型麻豆中。角叉菜胶诱导大鼠足底炎症,弗氏完全佐剂诱导大鼠足底慢性炎症。分别以75、150、300 mg/kg三种剂量口服石油醚、乙醇和水提取物。以双氯芬酸钠(10mg /kg)、强的松龙(5mg /kg)、甲氨蝶呤(0.5 mg/kg)为标准品。采用单因素方差分析(one-way ANOVA)分析均数间的统计学显著性,然后进行Dunnett多元极差检验。每组的数值以mean±SD表示(n=6), aP
{"title":"Anti-inflammatory and Anti-arthritic Properties of Mucuna gigantea Plant Extracts: Establishing by Molecular Docking Study.","authors":"Satish Kumar,&nbsp;Pratima Srivastava,&nbsp;Somdutt Mujwar,&nbsp;Vinod Gauttam,&nbsp;Sumeet Gupta","doi":"10.2174/1573409920666230817142114","DOIUrl":"https://doi.org/10.2174/1573409920666230817142114","url":null,"abstract":"<p><p>Background Mucuna giganteais a traditional plant reported in the management of nervous disorders, male infertility, etc., and also exhibits aphrodisiac, anti-oxidant, and anti-diabetic properties. Very few studies are conducted on Mucuna gigantea. It has not been pharmacologically evaluated for rheumatoid arthritis (RA). In RA, the body's natural defence mechanism gets confused and begins to target the healthy tissues in the body, which leads to joint pain, swelling, bone erosion, and joint stiffness. It is a condition that is classified as an auto-immune disorder. Methods In-silico docking depicted that beta-sitosterol is present in Mucuna gigantea out of ligand library prepared based on a literature survey using computational analysis. Inflammation was induced by carrageen and chronic inflammation was induced by Freund's complete adjuvant in the plantar surface of the rats. The petroleum ether, ethanolic and aqueous extracts in three divided doses (75, 150, and 300 mg/kg) were administered orally. Diclofenac sodium (10 mg/kg), prednisolone (5 mg/kg), and methotrexate (0.5 mg/kg) were used as standard. The statistical significance between means was analyzed using one-way ANOVA, followed by Dunnett's multiple range test. The values are expressed as mean ± SD for each group (n=6), and aP<0.0001, bP<0.001, and cP<0.05 were compared with a negative control group. Results Ethanolic and petroleum ether extracts showed a statistically significant aP<0.0001 effect at 3hr with 300mg/kg effect in analgesic activity, whereas aqueous extracts showed statistically significant aP<0.0001 effect at 1.5hr with 150 and 300mg/kg. In the carrageen-induced model, all three extracts at 300 mg/kg showed a statistically significant aP<0.0001 effect from 2- 4hr. In Freund's adjuvant model, all three extracts at all doses showed a statistically significant aP<0.0001 effect. Also, Mucuna gigantea remarkably ameliorated altered WBCs, rheumatoid factor, and positively modified radiographic and histopathological changes. Conclusion Taken together, these results support the traditional use of Mucuna gigantea as a potent anti-inflammatory and anti-arthritic agent that may be proposed for rheumatoid arthritis treatment.</p>","PeriodicalId":10886,"journal":{"name":"Current computer-aided drug design","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2023-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10018708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Prediction of Rhizoma Drynariae Targets in the Treatment of Osteonecrosis of the Femoral Head based on Network Pharmacology and Experimental Verification. 基于网络药理学的干连治疗股骨头坏死靶点预测及实验验证。
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-01-01 DOI: 10.2174/1573409918666221006122426
Yong Zhang, Xiaohan Shen, Tongzhou Hu, Qiuyan Weng, Jinming Han

Background: Rhizoma drynariae, a classic prescription in traditional Chinese medicine, has long been used for the treatment of osteonecrosis of the femoral head (ONFH), but its potential targets and molecular mechanisms remain to be further explored.

Objective: This study aims to explore the mechanism of Rhizoma drynariae in ONFH treatment via network pharmacology and in vitro experiments.

Methods: Targets of Rhizoma drynariae and ONFH were predicted using relevant databases, and intersection analysis was conducted to screen for shared targets. A PPI network of the shared targets was built using STRING to identify the key targets. Functional enrichment analyses of Gene Ontology and KEGG pathway data were carried out using R software. The compound-target-pathway network was constructed for Rhizoma Drynariae in the treatment with ONFH using Cytoscape 3.9.0. Cell proliferation was assessed using CCK8 and apoptosis was detected using (Propidium Iodide) PI staining and western blotting.

Results: This study depicts the interrelationship of the bioactive compounds of Rhizoma drynariae with ONFH-associated signaling pathways and target receptors and is a potential reagent for ONFH treatment.

Conclusion: Based on a network pharmacology analysis and in vitro experiment, we predicted and validated the active compounds and potential targets of Rhizoma drynariae, provide valuable evidence of Rhizoma Drynariae in future ONFH treatment.

背景:干连是治疗股骨头坏死(ONFH)的经典中药方剂,但其潜在的靶点和分子机制仍有待进一步探索。目的:通过网络药理学和体外实验,探讨干连治疗ONFH的作用机制。方法:利用相关数据库对干参和ONFH的靶点进行预测,并进行交叉分析筛选共享靶点。利用STRING识别关键靶点,构建了共享靶点的PPI网络。利用R软件对Gene Ontology和KEGG通路数据进行功能富集分析。利用Cytoscape 3.9.0软件构建ONFH处理干参的化合物靶点通路网络。CCK8检测细胞增殖,PI染色和western blotting检测细胞凋亡。结果:本研究揭示了干连生物活性化合物与ONFH相关信号通路和靶受体的相互关系,是治疗ONFH的潜在试剂。结论:通过网络药理分析和体外实验,预测并验证了干连的活性成分和潜在靶点,为今后干连治疗ONFH提供了有价值的依据。
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引用次数: 1
Network Pharmacological Study of Compound Kushen Injection in Esophageal Cancer. 复方苦参注射液治疗食管癌的网络药理研究。
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-01-01 DOI: 10.2174/1573409919666230111155954
Dongli Guo, Jing Jin, Jianghui Liu, Meng Ren, Yutong He

Aim: To provide new methods and ideas for the clinical application of integrated traditional Chinese and Western medicine in the treatment of esophageal cancer.

Background: Traditional Chinese medicine compound Kushen injection (CKI) has been widely used in the clinic with adjuvant radiotherapy and chemotherapy. However, the mechanism of action of CKI as adjuvant therapy for esophageal cancer has not yet been described.

Methods: This study is based on network pharmacology, data mining, and molecular docking technology to explore the mechanism of action of CKI in the treatment of esophageal cancer. We obtained the effective ingredients and targets of CKI from the traditional Chinese medicine system pharmacology database and analysis platform (TCMSP) and esophageal cancer-related genes from the Online Mendelian Inheritance in Man (OMIM) and GeneCards databases.

Results: CKI mainly contains 58 active components. Among them, the top 5 active ingredients are quercetin, luteolin, naringenin, formononetin, and beta-sitostero. The target protein of the active ingredient was matched with the genes associated with esophageal cancer. The active ingredients targeted 187 esophageal cancer target proteins, including AKT1, MAPK1, MAPK3, TP53, HSP90AA1, and other proteins. Then, we enriched and analyzed the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) and used AutoDockVina to dock the core targets and compounds. Finally, PyMOL and Ligplot were used for data visualization.

Conclusion: This study provides a new method and ideas for the clinical application of integrated traditional Chinese and Western medicine in the treatment of esophageal cancer.

目的:为中西医结合治疗食管癌的临床应用提供新的方法和思路。背景:中药复方苦参注射液(CKI)已广泛应用于临床辅助放化疗。然而,CKI作为食管癌辅助治疗的作用机制尚不清楚。方法:本研究基于网络药理学、数据挖掘和分子对接技术,探讨CKI治疗食管癌的作用机制。我们从中药系统药理学数据库和分析平台(TCMSP)中获得CKI的有效成分和靶点,从人类在线孟德尔遗传(OMIM)和GeneCards数据库中获得食管癌相关基因。结果:CKI主要含有58种有效成分。其中,排名前5位的有效成分分别是槲皮素、木犀草素、柚皮素、刺芒柄花素和β -谷甾醇。活性成分的靶蛋白与食管癌相关基因匹配。活性成分靶向187种食管癌靶蛋白,包括AKT1、MAPK1、MAPK3、TP53、HSP90AA1等蛋白。然后,我们对基因本体(GO)和京都基因与基因组百科全书(KEGG)进行了丰富和分析,并使用AutoDockVina对接核心靶点和化合物。最后使用PyMOL和Ligplot进行数据可视化。结论:本研究为中西医结合治疗食管癌的临床应用提供了新的方法和思路。
{"title":"Network Pharmacological Study of Compound Kushen Injection in Esophageal Cancer.","authors":"Dongli Guo,&nbsp;Jing Jin,&nbsp;Jianghui Liu,&nbsp;Meng Ren,&nbsp;Yutong He","doi":"10.2174/1573409919666230111155954","DOIUrl":"https://doi.org/10.2174/1573409919666230111155954","url":null,"abstract":"<p><strong>Aim: </strong>To provide new methods and ideas for the clinical application of integrated traditional Chinese and Western medicine in the treatment of esophageal cancer.</p><p><strong>Background: </strong>Traditional Chinese medicine compound Kushen injection (CKI) has been widely used in the clinic with adjuvant radiotherapy and chemotherapy. However, the mechanism of action of CKI as adjuvant therapy for esophageal cancer has not yet been described.</p><p><strong>Methods: </strong>This study is based on network pharmacology, data mining, and molecular docking technology to explore the mechanism of action of CKI in the treatment of esophageal cancer. We obtained the effective ingredients and targets of CKI from the traditional Chinese medicine system pharmacology database and analysis platform (TCMSP) and esophageal cancer-related genes from the Online Mendelian Inheritance in Man (OMIM) and GeneCards databases.</p><p><strong>Results: </strong>CKI mainly contains 58 active components. Among them, the top 5 active ingredients are quercetin, luteolin, naringenin, formononetin, and beta-sitostero. The target protein of the active ingredient was matched with the genes associated with esophageal cancer. The active ingredients targeted 187 esophageal cancer target proteins, including AKT1, MAPK1, MAPK3, TP53, HSP90AA1, and other proteins. Then, we enriched and analyzed the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) and used AutoDockVina to dock the core targets and compounds. Finally, PyMOL and Ligplot were used for data visualization.</p><p><strong>Conclusion: </strong>This study provides a new method and ideas for the clinical application of integrated traditional Chinese and Western medicine in the treatment of esophageal cancer.</p>","PeriodicalId":10886,"journal":{"name":"Current computer-aided drug design","volume":"19 5","pages":"367-381"},"PeriodicalIF":1.7,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9842273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Benzothiazole Clubbed Imidazolone Derivatives: Synthesis, Molecular Docking, DFT Studies, and Antimicrobial Studies. 苯并噻唑棒状咪唑酮衍生物:合成、分子对接、DFT研究和抗菌研究。
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-01-01 DOI: 10.2174/1573409919666221121115556
Nisheeth Desai, Abhay Maheta, Aratiba Jethawa, Iqrar Ahmad, Harun Patel, Bharti Dave
<p><strong>Aim: </strong>This study aims to synthesize antimicrobial agents and their molecular docking, and DFT studies of benzothiazole-imidazolone scaffolds.</p><p><strong>Background: </strong>Benzothiazole and imidazolone analogues are of interest due to their potential activity against microbial infections. In search of suitable antimicrobial compounds, we report here the synthesis, characterization, and biological activities of benzothiazole and imidazolone analogues (4a-l).</p><p><strong>Objective: </strong>The benzothiazole clubbed imidazolone motifs were synthesized, characterized, and screened for their antimicrobial activity. Molecular docking was carried out for the development of antimicrobial agents based on the results of biological activity obtained.</p><p><strong>Methods: </strong>We have synthesized a new series of benzothiazole-clubbed imidazolone hybrids by using multi-step reactions in the search for antimicrobial agents (4a-l). The structures were determined by <sup>1</sup>H NMR, <sup>13</sup>C NMR, IR, and mass spectroscopy techniques. Moreover, synthesized compounds were evaluated for their antimicrobial activity by using a Serial Broth Dilution method. In addition, molecular electrostatic potential, geometric optimization, and molecular reactivity analyses (HOMO-LUMO) of 4c, which is one of the compounds with the highest antibacterial activity, were performed.</p><p><strong>Results: </strong>The in vitro antimicrobial activity was evaluated against pathogenic strains. Among them, compounds 4c showed the most potent biological activity against Gram-negative bacteria, E. coli with MIC values of 50 μg/mL, and compound 4c active against A. clavatus with MIC values of 100 μg/mL. Active compound 4c HUMO-LUMO energies, molecular electrostatic potential analysis, and geometric optimization parameters were calculated with a 6-31G ** base set using DFT/B3LYP theory, and the results were displayed. Molecular docking studies were performed on E. coli DNA Gyrase B to understand the binding interaction of compound 4c, and it was observed that compound 4c interacted with Arg76 amino acid of the active site through hydrophobic interaction.</p><p><strong>Conclusion: </strong>Benzothiazole-clubbed imidazolone hybrids (4a-l) indicated promising antimicrobial activity. Among them, compounds 4b (MIC=50 μg/mL C. albicans), 4c (MIC=50 μg/mL, E. coli), 4e (MIC= 100 μg/mL, A. niger), and 4g (MIC= 50 μg/mL, S. pyogenes) with electronwithdrawing bromo, chloro, and fluoro group at the para position of the phenyl ring on benzothiazole-imidazolone hybrids indicated remarkable potency compared to the standard drug. The geometric optimization, molecular reactivity, and MESP analyses of 4c were calculated with the B3LYP/6-31G ** base set and ΔE = ELUMO-EHOMO, which was found to be - 0.12096 eV. In addition, the binding affinity scores correlated well with the in vitro antimicrobial activity (4c), while their binding modes proposed the involvement of ster
目的:本研究旨在合成抗菌药物及其分子对接,并对苯并噻唑-咪唑酮类支架进行DFT研究。背景:苯并噻唑和咪唑酮类似物因其潜在的抗微生物感染活性而受到关注。为了寻找合适的抗菌化合物,我们报道了苯并噻唑和咪唑酮类似物的合成、表征和生物活性(4a- 1)。目的:合成并表征苯并噻唑棒状咪唑酮基序,并对其抗菌活性进行筛选。根据获得的生物活性结果,进行了抗菌药物开发的分子对接。方法:采用多步反应法合成了一系列新的苯并噻唑-棒状咪唑酮杂化合物,以寻找抗菌药物(4a- 1)。通过1H NMR, 13C NMR, IR和质谱技术对其结构进行了表征。此外,用连续肉汤稀释法评价合成的化合物的抗菌活性。此外,对抗菌活性最高的化合物之一4c进行了分子静电势、几何优化和分子反应性分析(HOMO-LUMO)。结果:对病原菌进行了体外抑菌活性评价。其中,化合物4c对革兰氏阴性菌、大肠杆菌的生物活性最强,MIC值为50 μg/mL;化合物4c对钉螺的生物活性最强,MIC值为100 μg/mL。采用DFT/B3LYP理论,在6-31G **的碱基集上计算了活性化合物4c的HUMO-LUMO能量、分子静电势分析和几何优化参数,并对结果进行了显示。对大肠杆菌DNA Gyrase B进行分子对接研究,了解化合物4c的结合相互作用,发现化合物4c通过疏水相互作用与活性位点的Arg76氨基酸相互作用。结论:苯并噻唑-棒状咪唑酮复合物(4a-l)具有良好的抗菌活性。其中,化合物4b (MIC=50 μg/mL,白色念珠菌)、4c (MIC=50 μg/mL,大肠杆菌)、4e (MIC= 100 μg/mL,黑曲霉)和4g (MIC=50 μg/mL,化脓性念珠菌)在苯并噻唑-咪唑类杂化合物苯基环对位上具有吸电子的溴、氯、氟基团,与标准药物相比药效显著。利用B3LYP/6-31G **碱基集和ΔE = ELUMO-EHOMO对4c进行几何优化、分子反应性和MESP分析,得到4c的几何优化、分子反应性和MESP分析结果为- 0.12096 eV。此外,结合亲和力评分与体外抗菌活性相关良好(4c),而它们的结合模式表明与活性位点存在空间、静电和氢键相互作用。
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引用次数: 0
Exploring the Mechanism of Buyang Huanwu Decoction Alleviating Restenosis by Regulating VSMC Phenotype Switching and Proliferation by Network Pharmacology and Molecular Docking. 补阳还五汤通过调节VSMC表型转换和增殖减轻再狭窄的网络药理学和分子对接机制研究
IF 1.7 4区 医学 Q4 CHEMISTRY, MEDICINAL Pub Date : 2023-01-01 DOI: 10.2174/1573409919666230203144207
Xueqin Chen, Jingyue Yu, Huan Lei, Lei Li, Xupin Liu, Bo Liu, Yanfei Xie, Haihong Fang

Background: 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.

Objective: 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.

Methods: 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.

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.

Conclusion: 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.

背景:补阳还五汤具有活血通络的作用,在冠心病治疗中应用广泛。然而,BHD用于治疗再狭窄的活性化合物和机制尚不清楚。目的:通过网络药理学和分子对接实验,探讨补阳还五汤治疗再狭窄的潜在作用机制。方法:从中国中医系统药理学(TCMSP)和中国中医百科全书(ETCM)数据库及文献中检索BHD的生物活性成分及其相应的靶点。从OMIM、Drugbank、GEO和Dis- GeNET数据库中鉴定出再狭窄相关的治疗基因。从基因本体(GO)数据库和文献中获得与血管平滑肌细胞(VSMC)表型相关的基因。使用Venn工具和Cytoscape软件鉴定药物- vsmc表型的核心靶基因。构建并分析了“药物-成分-靶点-途径”网络,并进行了途径富集分析。使用AutoDock工具分析主要活性成分与核心目标之间的联系,并使用PyMOL将结果可视化。结果:“化合物-靶点-疾病”网络包含80个有效成分和599个重叠靶点。其中槲皮素、川芎嗪、川芎内酯、羟基红花黄A、二氢辣椒素度值较高,核心靶点包括TP53、MYC、APP、UBC、JUN、EP300、TGFB1、UBB、SP1、MAPK1、SMAD2、CTNNB1、FOXO3、PIN1、EGR1、TCF4、FOS、SMAD3、CREBBP。GO功能富集分析共获得365个项目(p < 0.05),而KEGG途径富集分析共鉴定出30条信号通路(p < 0.05),涉及TGF-β信号通路、Wnt信号通路、traf6介导的NF-κB和MAPK信号通路、TLR7/8级联等。分子对接结果显示槲皮素、木犀草素和藁本内酯与核心靶点MYC和TP53具有良好的亲和力。结论:BHD有效成分可能通过槲皮素、川芎嗪、川芎内酯、羟基红花黄A、二氢辣椒素等有效成分作用于TP53、MYC、APP、UBC、JUN等靶点。BHD的这种作用可能通过多种信号通路参与传递,包括TGF-β信号通路、Wnt信号通路、traf6介导的NF-κB和MAPK信号通路以及TLR7/8级联,通过抑制VSMC的表型转换和增殖来治疗再狭窄。
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引用次数: 0
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Current computer-aided drug design
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