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Identification of the Anti-COVID-19 Mechanism of Action of Han-Shi Blocking Lung Using Network Pharmacology- Integrated Molecular Docking

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Identification of the Anti-COVID-19 Mechanism of Action of Han-Shi Blocking Lung Using Network Pharmacology- Integrated Molecular Docking Yuan et al Tropical Journal of Pharmaceutical Research June 2021; 20 (6): 1241-1249 ISSN: 1596-5996 (print); 1596-9827 (electronic) © Pharmacotherapy Group, Faculty of Pharmacy, University of Benin, Benin City, 300001 Nigeria. Available online at http://www.tjpr.org http://dx.doi.org/10.4314/tjpr.v20i6.21 Original Research Article Identification of the anti-COVID-19 mechanism of action of Han-Shi Blocking Lung using network pharmacology- integrated molecular docking Chong Yuan1, Fei Wang1, Peng-Yu Chen1, Zong-Chao Hong1, Yan-Fang Yang1,2, He-Zhen Wu1,2* 1Faculty of Pharmacy, Hubei University of Chinese Medicine, Wuhan 430065, 2Key Laboratory of Traditional Chinese Medicine Resources and Chemistry of Hubei Province, Wuhan 430061, China *For correspondence: Email: [email protected], [email protected]; Tel: +86-13667237629, +86-13545341663 Sent for review: 30 June 2020 Revised accepted: 16 May 2021 Abstract Purpose: To investigate the bio-active components and the potential mechanism of the prescription remedy, Han-Shi blocking lung, with network pharmacology with a view to expanding its application. Methods: Chemical components were first collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). Pharmmapper database and GeneCards were used to predict the targets related to active components and COVID-19. Using DAVIDE and KOBAS 3.0 databases, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were enriched. A “components-targets-pathways” (C-T-P) network was conducted by Cytoscape 3.7.1 software. With the aid of Discovery Studio 2016 software, bio-active components were selected to dock with SARS-COV-2 3CL and ACE2. Results: From the prescription, 47 bio-active components, 83 targets and 103 signaling pathways were obtained in total (p < 0.05). 126 GO entries (p < 0.05) were screened by GO enrichment analysis. Molecular docking results showed that procyanidin B1 eriodictyol, (4E, 6E)-1, 7-bis(4- hydroxyphenyl)hepta-4, 6-dien-3-one, and quercetin had higher docking scores with SARS-COV-2 3CL and ACE2. Conclusion: With network pharmacology and molecular docking, the bio-active components and targets of this prescription, Han-Shi blocking lung, against COVID-19 were identified. Taken together, this study provided a basis for the treatment of COVID-19 and further promotion of this prescription. Keywords: Prescription, Han-Shi blocking lung, COVID-19, Mechanism of action, Bioactive components, Network pharmacology, Molecular docking This is an Open Access article that uses a funding model which does not charge readers or their institutions for access and distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0) and the Budapest Open Access Initiative (http://www.budapestopenaccessinitiative.org/read), which permit unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. Tropical Journal of Pharmaceutical Research is indexed by Science Citation Index (SciSearch), Scopus, International Pharmaceutical Abstract, Chemical Abstracts, Embase, Index Copernicus, EBSCO, African Index Medicus, JournalSeek, Journal Citation Reports/Science Edition, Directory of Open Access Journals (DOAJ), African Journal Online, Bioline International, Open-J-Gate and Pharmacy Abstracts INTRODUCTION cumulative number of cases worldwide has exceeded 121,076,777, and the number of COVID-19 has swept the world from the end of deaths has exceeded 2,673,579, and this has 2019 to now, with hundreds of thousands of attracted special attention all over the world. people infected. As at March 17, 2021, the COVID-19 is often accompanied by clinical -------------------------------------------------------------------------------------------------------------------------------Trop J Pharm Res, June 2021;---------------------- 20(6): 1241 © 2021 The authors. This work is licensed under the Creative Commons Attribution 4.0 International License Yuan et al manifestations such as fever and dry cough at Screening of potential bio-active components the early stage. Ill patients may have dyspnea, hypoxemia, or even acute respiratory distress Drugs play an important role in human body syndrome [1-2]. The world is in urgent need of through absorption, distribution, metabolism and effective tests and drugs to help fight the excretion (ADME). Higher oral bioavailability epidemic. (OB) and drug likeness (DL) values usually indicate that the drug has better biological In Traditional Chinese Medicine (TCM) theory, activity. In this study, a comprehensive model of Han-Shi blocking lung is often manifested as low OB ≥ 30 %, and DL ≥ 0.18 were constructed for fever, nausea, dry cough with little phlegm or screening potential bio-active components of this fatigue. The people’s Republic of China prescription [12]. published the COVID-19 Clinical Protocols: Seventh Edition, which gives corresponding Targets prediction of bio-active components treatment prescription consisting of Cangzhu (ATRACTYLODIS RHIZOMA) [3], Chenpi (CITRI The potentially bio-active components were RETICULATAE PERICARPIUM) [4], Houpo imported into the Pharmmapper database (MAGNOLIAE OFFICINALIS CORTEX) [5], Huo (http://lilab.ecust.edu.cn/pharmmapper/index.php xiang (POGOSTEMONIS HERBA) [6], Caoguo ) to match the candidate targets, and the plug-in (TSAOKO FRUCTUS), Shengmahuang of Uniprot database (limit species to humans) (EPHEDRAE HERBA) [7] Qianghuo was used to obtain the Gene Official Symbol (NOTOPTERYGII RHIZOMA ET RADIX) [8], format. Shengjiang (ZINGIBERIS RHIZOMA RECENS) [9], and Binglang (ARECAESEMEN) [10]. At Screening of COVID-19-related targets present, the efficacy of this prescription has been verified in China. Therefore, it is necessary to By searching GeneCards database further investigate its bio-active components and (https://www.genecards.org/) for the keywords mechanism of action, so as to increase the “novel coronavirus”, the COVID-19-related genes popularity and use of this prescription. were obtained. The candidate targets of COVID- 19-related genes with the bio-active components Network pharmacology method integrates multi- were compared by Venn diagram. direction pharmacology, systems biology, and computer analysis technology. It establishes a Gene function and KEGG pathway “C-T-P” network to study the interaction between enrichment bio-active components and candidate targets, so as to systematically and comprehensively The KOBAS3.0 database correlate drugs and diseases [11], which is (http://kobas.cbi.pku.edu.cn/anno_iden.php) and consistent with the holistic and systematic the Database for Annotation, Visualization and characteristics of TCM treatment. The high Integrated Discovery (DAVID, molecular docking technique simulates the https://david.ncifcrf.gov/) for a large number of interaction between the receptors and bio-active genes provide comprehensive biofunctional components, and demonstrates the docking annotations. The potential targets were activity of the drug molecules. In this study, using introduced into the two databases. Then, the network pharmacology and molecular docking species and identifier were selected as “Homo technology, the “C-T-P” network was conducted sapiens” and “GENE OFFICIAL SYMBOL” to predict the potentially bio-active components respectively for GO enrichment and KEGG and mechanism of this prescription against pathway annotations. And p < 0.05 was set as COVID-19, which provided ideas and basis for the threshold to screen meaningful results. Using further research. Omicshare database (http: //www.omicshare.com), the top ten relevant GO METHODS enrichment and KEGG pathways were plotted as bubble plots respectively. Collection of prescription components Constructing a network TCMSP (http://lsp.nwu.edu.cn/tcmsp.php) which provided pharmacokinetic properties of bio-active Through Cytoscape 3.7.1 software components, was used to collect all the (https://cytoscape.org/download.html), the "C-T- components of the prescription. With PubChem P" network was conducted. The nodes of database (https://pubchem.ncbi.nlm.nih.gov/), a different colors represented bio-active component library was established. components, candidate targets and pathways respectively., and the edges represented the Trop J Pharm Res, June 2021; 20(6): 1242 Yuan et al correlation between different nodes. Topological of the component’s 2D structure which was analysis of the constructed pharmacological downloaded from the PubChem database network was performed to screen the important (https://pubchem.ncbi.nlm.nih.gov/), their energy bio-active components. It is generally believed was minimized. It is generally believed that the that the node's degree is significant when it is docking ability with protein is stronger when greater than twice the median. LiDockscore≥90. Construction of protein-protein interaction RESULTS (PPI) network Screening bio-active components The interaction between proteins was integrated through the STRING database (https://string- The TCMSP database was used to screen the db.org/) which collects, scores, and integrates all bio-active components of this prescriptions. By publicly available PPI information. OB ≥ 30% and DL ≥ 0.18, 68 chemical components were screened totally. After Molecular docking removing no corresponding target components and repeated chemical components, information SARS-CoV-2 is a newly discovered β- of 47 potentially bio-active components were coronavirus closely related
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