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      Active ingredient and mechanistic analysis of traditional Chinese medicine formulas for the prevention and treatment of COVID-19: Insights from bioinformatics and in vitro experiments

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          Abstract

          Coronavirus disease 2019 (COVID-19) is an acute infectious disease caused by a novel coronavirus. Traditional Chinese medicine (TCM) has been proven to have a potential curative effect on COVID-19. This study preliminarily analyzed the existing TCM prescription’s key components and action mechanisms for preventing and treating COVID-19 using bioinformatic and experimental methods. Association and clustering analysis reveals that the “HQ + FF + BZ” drug combination had a strong correlation and confidence in 93 TCM prescriptions and may affect the progression of COVID-19 through inflammatory pathways such as the TNF signaling pathway. Further molecular docking revealed that quercetin has a higher affinity for IL6 and IL10 in the TNF signaling pathway associated with COVID-19. In vitro experiments demonstrated that quercetin could effectively reduce the levels of the inflammatory factor IL-6 and increase the anti-inflammatory factor IL-10, alleviating inflammation impact on cells. Our results provide a new understanding of the molecular mechanism of TCM prevention and treatment of COVID-19, which is helpful to the development of new diagnosis and treatment schemes for COVID-19.

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          Cytoscape: a software environment for integrated models of biomolecular interaction networks.

          Paul Shannon, Andrew Markiel, Owen Ozier … (2003)
          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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            A pneumonia outbreak associated with a new coronavirus of probable bat origin

            Peng Zhou, Xing-Lou Yang, Xian-Guang Wang … (2020)
            Since the outbreak of severe acute respiratory syndrome (SARS) 18 years ago, a large number of SARS-related coronaviruses (SARSr-CoVs) have been discovered in their natural reservoir host, bats 1–4 . Previous studies have shown that some bat SARSr-CoVs have the potential to infect humans 5–7 . Here we report the identification and characterization of a new coronavirus (2019-nCoV), which caused an epidemic of acute respiratory syndrome in humans in Wuhan, China. The epidemic, which started on 12 December 2019, had caused 2,794 laboratory-confirmed infections including 80 deaths by 26 January 2020. Full-length genome sequences were obtained from five patients at an early stage of the outbreak. The sequences are almost identical and share 79.6% sequence identity to SARS-CoV. Furthermore, we show that 2019-nCoV is 96% identical at the whole-genome level to a bat coronavirus. Pairwise protein sequence analysis of seven conserved non-structural proteins domains show that this virus belongs to the species of SARSr-CoV. In addition, 2019-nCoV virus isolated from the bronchoalveolar lavage fluid of a critically ill patient could be neutralized by sera from several patients. Notably, we confirmed that 2019-nCoV uses the same cell entry receptor—angiotensin converting enzyme II (ACE2)—as SARS-CoV.
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              SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor

              Markus Hoffmann, Hannah Kleine-Weber, Simon Schroeder … (2020)
              Summary The recent emergence of the novel, pathogenic SARS-coronavirus 2 (SARS-CoV-2) in China and its rapid national and international spread pose a global health emergency. Cell entry of coronaviruses depends on binding of the viral spike (S) proteins to cellular receptors and on S protein priming by host cell proteases. Unravelling which cellular factors are used by SARS-CoV-2 for entry might provide insights into viral transmission and reveal therapeutic targets. Here, we demonstrate that SARS-CoV-2 uses the SARS-CoV receptor ACE2 for entry and the serine protease TMPRSS2 for S protein priming. A TMPRSS2 inhibitor approved for clinical use blocked entry and might constitute a treatment option. Finally, we show that the sera from convalescent SARS patients cross-neutralized SARS-2-S-driven entry. Our results reveal important commonalities between SARS-CoV-2 and SARS-CoV infection and identify a potential target for antiviral intervention.
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                Author and article information

                Contributors
                Jiakai Yang:
                ORCID: https://orcid.org/0009-0002-0477-4698
                Qianqian Zhuang
                Chi Zhang
                Journal
                Journal ID (nlm-ta): Medicine (Baltimore)
                Journal ID (iso-abbrev): Medicine (Baltimore)
                Journal ID (publisher-id): MD
                Title: Medicine
                Publisher: Lippincott Williams & Wilkins (Hagerstown, MD )
                ISSN (Print): 0025-7974
                ISSN (Electronic): 1536-5964
                Publication date Collection: 01 December 2023
                Publication date (Electronic): 01 December 2023
                Volume: 102
                Issue: 48
                Electronic Location Identifier: e36238
                Affiliations
                [a ] Department of Biological Engineering, Qilu University of Technology, Jinan, China.
                Author notes
                [* ]Correspondence: Xinli Liu, Department of Biological Engineering, Qilu University of Technology, Jinan, Shandong Province 250303, China (e-mail: liuxl@ 123456qlu.edu.cn ).
                Author information
                https://orcid.org/0009-0002-0477-4698
                Article
                Accession ID: 00120
                DOI: 10.1097/MD.0000000000036238
                PMC ID: 10695544
                PubMed ID: 38050310
                SO-VID: 3d3c4667-f74c-465c-9f4c-50bcd2b31719
                Copyright © Copyright © 2023 the Author(s). Published by Wolters Kluwer Health, Inc.
                License:

                This is an open access article distributed under the Creative Commons Attribution License 4.0 (CCBY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 01 September 2023
                Date received : 30 October 2023
                Date accepted : 31 October 2023
                Categories
                Subject: 3800
                Subject: Research Article
                Subject: Observational Study
                Custom metadata
                OPEN-ACCESS TRUE
                SDC T

                Keywords: covid-19,in vitro ex,molecular docking,network pharmacology,prevention and treatment
                Data availability:
                Keywords: covid-19, in vitro ex, molecular docking, network pharmacology, prevention and treatment

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