Molecular docking and network connections of active compounds from the classical herbal formula Ding Chuan Tang (original) (raw)

Systems Pharmacology and In Silico Docking Analysis Uncover Association of CA2, PPARG, RXRA, and VDR with the Mechanisms Underlying the Shi Zhen Tea Formula Effect on Eczema

Evidence-Based Complementary and Alternative Medicine, 2021

Eczema is a complex chronic inflammatory skin disease impacted by environmental factors, infections, immune disorders, and deficiencies in skin barrier function. Shi Zhen Tea (SZT), derived from traditional Chinese medicine Xiao-Feng-San, has shown to be an effective integrative therapy for treating skin lesions, itching, and sleeping loss, and it facilitates reduction of topical steroid and antihistamine use in pediatric and adult patients with severe eczema. Yet, its active compounds and therapeutic mechanisms have not been elucidated. In this study, we sought to investigate the active compounds and molecular mechanisms of SZT in treating eczema using systems pharmacology and in silico docking analysis. SZT is composed of 4 medicinal herbs, Baizhu (Atractylodis macrocephalae rhizome), Jingjie (Schizonepetae herba), Kushen (Sophorae flavescentis radix), and Niubangzi (Arctii fructus). We first identified 51 active compounds from SZT and their 81 potential molecular targets by high-...

Identification of Natural Compounds as Possible Anti-Allergic Drugs using Molecular Docking Analysis

2017

Allergic diseases have been increasing all over the world, especially allergic respiratory diseases whose incidence is rising at an alarming. Less side effects and low cost of natural resources open new avenues for the treatment of various diseases including allergy and also using computational approaches minimizes experimental time in drug design. Therefore, this study aimed to target C-Chemokine receptor 3 (CCR3) as potential therapeutic target for Allergic respiratory diseases because it mediates the chemotactic response to binding of several chemokines which are highly expressed in the airways of asthmatic patients. The homology model of the target protein was built using MODELLER 9v16 and validated by Ramachandran plot. The modeled structure was virtually screened against natural product database by means of molecular docking approaches. Ligands with low binding affinity were further studied for their pharmacokinetics and drug-likeness properties. Those that are non-substrate t...

Network pharmacology-based identification of key pharmacological pathways of Yin-Huang-Qing-Fei capsule acting on chronic bronchitis

International journal of chronic obstructive pulmonary disease, 2017

For decades in China, the Yin-Huang-Qing-Fei capsule (YHQFC) has been widely used in the treatment of chronic bronchitis, with good curative effects. Owing to the complexity of traditional Chinese herbal formulas, the pharmacological mechanism of YHQFC remains unclear. To address this problem, a network pharmacology-based strategy was proposed in this study. At first, the putative target profile of YHQFC was predicted using MedChem Studio, based on structural and functional similarities of all available YHQFC components to the known drugs obtained from the DrugBank database. Then, an interaction network was constructed using links between putative YHQFC targets and known therapeutic targets of chronic bronchitis. Following the calculation of four topological features (degree, betweenness, closeness, and coreness) of each node in the network, 475 major putative targets of YHQFC and their topological importance were identified. In addition, a pathway enrichment analysis based on the K...

Target Prediction and Molecular Mechanism of Compound Honggencao for Upper Respiratory Tract Infection Based on Network Pharmacology

Chinese Medicine, 2020

Objective: The target prediction and molecular mechanism of compound Honggencao in the treatment of upper respiratory tract infection were investigated based on network pharmacology. Methods: In the database of Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform , chemical composition and potential targets of compound Honggencao were mined, and the target gene of upper respiratory tract infection of compound Honggencao was extracted from GeneCards databases. The protein protein interaction of target genes was constructed. Then, the essential genes of enrichment of KEGG pathway analysis and functional analysis were analysed. Results: Compound Honggencao had 69 kinds of active ingredients. The upper respiratory tract infection of the target gene was 186 that built compound Honggencao on the relationship between upper respiratory tract infections of protein interaction networks, which had a total of 186 nodes, 3515 sides. Fifty-six essential genes were including IL-17, EGFR and CDND1, and so on. Gene ontology analysis had 2567 items, and pathway analysis was 166 items. The main signaling pathways involved with IL-17 signaling pathways, tumour necrosis factor signal pathway and human cyto-megalovirus infection, and so on. Conclusion: The pharmacological action of compound Honggencao on upper respiratory tract infection was characterized by the synergistic effect of multiple components and multiple targets, which provided an absolute theoretical basis for the research on the pharmacological direction of molecular signaling pathway and a specific theoretical basis for clinical use.

Virtual Screening and Molecular Docking studies for discovery of potent drug candidates among compounds of Adhatoda vasica against Bronchial Asthma

Indian Journal of Pharmacology | December 2014 | Vol 46 | Supplement S37, 2014

Indian Journal of Pharmacology | December 2014 | Vol 46 | Supplement S37 Virtual Screening and Molecular Docking studies for discovery of potent drug candidates among compounds of Adhatoda vasica against Bronchial Asthma Rigom Pegu 1, Bishnu Prasad Sarma1, Rupali Borua1, Subrata Sinha2*, Surabhi Johari2 , Arabinda Ghosh3 1Govt, Ayurvedic College and Hospital, Jalukbari, Guwahati, Assam, 2Center for Bioinformatics Studies, Dibrugarh University, Dibrugarh, Assam, 3Department of Bio Technology, Indian Institute of Technology Guwahati, Guwahati, Assam, India Objective: Bronchial Asthma is a syndrome characterized by airflow obstruction with reduced airflow, symptomatic wheezing and dyspnea. Asthma is a multi factorial disease for which many genes are responsible. Ayurveda has mentioned in various Samhitas, that Adhatoda vasica can be used in the treatment of Asthma. However, the role of its compounds at the molecular level is yet to be known. In this study, an attempt has been made on in silico molecular studies for discovery of naturally derived from Adhatoda vasica as potent drug candidates for Bronchial Asthma. Methodology: Target protein of Bronchial Asthma was identified using KEGG Pathway Database for Asthma and cross validated using PDTD. The 3D structure files of the identified target protein were retrieved from RCSB-PDB Server. Compounds of Adhatoda vasica retrieved from Knapsack Family DB and toxicity was assessed using OSIRIS Property Explorer and Biological Activity assessed using Schrodinger QuickProp utility. Finally molecular docking was carried out between identified target protein and the screened ligands using Autodock Vina. Results: Out of 12 phytochemicals of Adhotada vasica, 8 phytochemicals viz. Vasicolinone, Vasicoline, Vasicol, Vasicinolone, Vasicinone, Vasicinol, Peganine, Deoxyvasicinon passed the virtual screening phase. Molecular docking studies of 8 compounds with target protein of Asthma (IL3, IL4, IL5, IL13, TNF-α and EOTAXIN) showed vasicinolone binds with IL-5 with the minimum binding affinity of -7.7 kcal/mol. Conclusion: The in-silico methods adopted in the present study helped to identify that vasicinolone can be used as a potent drug candidate for Asthma

Effects of Qinghuang Powder on Acute Myeloid Leukemia Based on Network Pharmacology, Molecular Docking, and In Vitro Experiments

Evidence-Based Complementary and Alternative Medicine, 2021

Qinghuang powder (QHP) is a traditional Chinese herbal medicine. This is a unique formula that is frequently used to treat malignant hematological diseases such as acute myeloid leukemia (AML) in modern clinical practice. An approach of network pharmacology and experimental validation were applied to investigate the pharmacological mechanisms of QHP in AML treatment. First, public databases for target genes known to be associated with AML are searched and compared to the target genes of the active compounds in QHP. Second, AML-associated genes and QHP target genes are compared to identify overlapping enriched genes, and these were used to predict selected target genes that may be implicated in the effects of QHP on AML. Additionally, we conducted functional enrichment analyses, such as gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The significantly enriched pathway associated with potential target proteins was the PI3K-Akt signaling pathway, sug...

Prediction of Active Compounds of Muntingia Calabura as Potential Treat-Ment for Chronic Obstructive Pulmonary Diseases by Network Pharmacology Integrated with Molecular Docking

International Journal of Applied Pharmaceutics

Objective: Electronic cigarettes (E-Cigarettes) are often advertised as a safe alternative to smoke cessation. The number of E-Cigarettes users (vapers) has increased in many countries. The health impact of E-Cigarettes research topics still counting constitutes initiating Chronic Obstructive Pulmonary Disease (COPD). This research aimed to analyze the interaction between genes from E-Cigarettes causing COPD with Muntingia Calabura leaves, which has umpteen pharmacological effects through Bioinformatics. Methods: The related genes in E-Cigarettes compounds underlying COPD conditions were screened and intersected towards M. Calabura's genes target. The constructed networks were analyzed for their protein-protein interaction and pathway possibilities. The gene with the best betweenness centrality, closeness centrality, and degree value was validated using molecular docking methods for its interaction with M. Calabura leaves. Results: 12 target genes of M. Calabura and COPD were AL...

PREDICTION OF ACTIVE COMPOUNDS OF MUNTINGIA CALABURA AS POTENTIAL TREAT-MENT FOR CHRONIC OBSTRUCTIVE PULMONARY DISEASES BY NETWORK PHARMACOLOGY INTEGRATED WITH MOLECULAR DOCKING Original Article

International Journal of Applied Pharmaceutics, 2023

Objective: Electronic cigarettes (E-Cigarettes) are often advertised as a safe alternative to smoke cessation. The number of E-Cigarettes users (vapers) has increased in many countries. The health impact of E-Cigarettes research topics still counting constitutes initiating Chronic Obstructive Pulmonary Disease (COPD). This research aimed to analyze the interaction between genes from E-Cigarettes causing COPD with Muntingia Calabura leaves, which has umpteen pharmacological effects through Bioinformatics. Methods: The related genes in E-Cigarettes compounds underlying COPD conditions were screened and intersected towards M. Calabura's genes target. The constructed networks were analyzed for their protein-protein interaction and pathway possibilities. The gene with the best betweenness centrality, closeness centrality, and degree value was validated using molecular docking methods for its interaction with M. Calabura leaves.

Molecular Docking Analysis: Interaction Studies of Natural Compounds to Anti-inflammatory Targets

2017

A variety of compounds from medicinal plants have been reported to possess antiinflammatory properties. Selected natural compounds that exhibit anti-inflammatory properties were subjected to docking simulation using AutoDock Vina to investigate their interaction modes to the potential macromolecular targets. The docking was performed using different molecular targets, i.e., cyclooxygenase-2, phospholipase A2, NF-κB inhibitor, and interleukin-1 receptor. It revealed that flavonoids have the highest affinity to the macromolecular targets (the lowest binding energy values) and the highest consistency of interaction model. Some terpenoids were identified to have potential inhibitor of phospholipase A2.