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      Potential mechanism prediction of Cold-Damp Plague Formula against COVID-19 via network pharmacology analysis and molecular docking

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          Abstract

          Background

          Coronavirus disease 2019 (COVID-19) is a new global public health emergency. The therapeutic benefits of Cold‒Damp Plague Formula (CDPF) against COVID-19, which was used to treat “cold‒dampness stagnation in the lung” in Trial Versions 6 and 7 of the “Diagnosis and Treatment Protocol for COVID-19”, have been demonstrated, but the effective components and their mechanism of action remain unclear.

          Methods

          In this study, a network pharmacology approach was employed, including drug-likeness evaluation, oral bioavailability prediction, protein‒protein interaction (PPI) network construction and analysis, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, and virtual docking, to predict the bioactive components, potential targets, and molecular mechanism of CDPF for COVID-19 treatment.

          Results

          The active compound of herbs in CDPF and their candidate targets were obtained through database mining, and an herbs—ingredients—targets network was constructed. Subsequently, the candidate targets of the active compounds were compared to those relevant to COVID-19, to identify the potential targets of CDPF for COVID-19 treatment. Subsequently, the PPI network was constructed, which provided a basis for cluster analysis and hub gene screening. The seed targets in the most significant module were selected for further functional annotation. GO enrichment analysis identified four main areas: (1) cellular responses to external stimuli, (2) regulation of blood production and circulation, (3) free radical regulation, (4) immune regulation and anti-inflammatory effects. KEGG pathway analysis also revealed that CDPF could play pharmacological roles against COVID-19 through “multi components‒multi targets‒multi pathways” at the molecular level, mainly involving anti-viral, immune-regulatory, and anti-inflammatory pathways; consequently, a “CDPF—herbs—ingredients—targets—pathways—COVID-19” network was constructed. In hub target analysis, the top hub target IL6, and ACE2, the receptor via which SARS-CoV-2 typically enters host cells, were selected for molecular docking analyses, and revealed good binding activities.

          Conclusions

          This study revealed the active ingredients and potential molecular mechanism by which CDPF treatment is effective against COVID-19, and provides a reference basis for the wider application and further mechanistic investigations of CDPF in the fight against COVID-19.

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          Most cited references52

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          A pneumonia outbreak associated with a new coronavirus of probable bat origin

          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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            Incidence of thrombotic complications in critically ill ICU patients with COVID-19

            Introduction COVID-19 may predispose to both venous and arterial thromboembolism due to excessive inflammation, hypoxia, immobilisation and diffuse intravascular coagulation. Reports on the incidence of thrombotic complications are however not available. Methods We evaluated the incidence of the composite outcome of symptomatic acute pulmonary embolism (PE), deep-vein thrombosis, ischemic stroke, myocardial infarction or systemic arterial embolism in all COVID-19 patients admitted to the ICU of 2 Dutch university hospitals and 1 Dutch teaching hospital. Results We studied 184 ICU patients with proven COVID-19 pneumonia of whom 23 died (13%), 22 were discharged alive (12%) and 139 (76%) were still on the ICU on April 5th 2020. All patients received at least standard doses thromboprophylaxis. The cumulative incidence of the composite outcome was 31% (95%CI 20-41), of which CTPA and/or ultrasonography confirmed VTE in 27% (95%CI 17-37%) and arterial thrombotic events in 3.7% (95%CI 0-8.2%). PE was the most frequent thrombotic complication (n = 25, 81%). Age (adjusted hazard ratio (aHR) 1.05/per year, 95%CI 1.004-1.01) and coagulopathy, defined as spontaneous prolongation of the prothrombin time > 3 s or activated partial thromboplastin time > 5 s (aHR 4.1, 95%CI 1.9-9.1), were independent predictors of thrombotic complications. Conclusion The 31% incidence of thrombotic complications in ICU patients with COVID-19 infections is remarkably high. Our findings reinforce the recommendation to strictly apply pharmacological thrombosis prophylaxis in all COVID-19 patients admitted to the ICU, and are strongly suggestive of increasing the prophylaxis towards high-prophylactic doses, even in the absence of randomized evidence.
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              Angiotensin-converting enzyme 2 (ACE2) as a SARS-CoV-2 receptor: molecular mechanisms and potential therapeutic target

              A novel infectious disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was detected in Wuhan, China, in December 2019. The disease (COVID-19) spread rapidly, reaching epidemic proportions in China, and has been found in 27 other countries. As of February 27, 2020, over 82,000 cases of COVID-19 were reported, with > 2800 deaths. No specific therapeutics are available, and current management includes travel restrictions, patient isolation, and supportive medical care. There are a number of pharmaceuticals already being tested [1, 2], but a better understanding of the underlying pathobiology is required. In this context, this article will briefly review the rationale for angiotensin-converting enzyme 2 (ACE2) receptor as a specific target. SARS-CoV-2 and severe acute respiratory syndrome coronavirus (SARS-CoV) use ACE2 receptor to facilitate viral entry into target cells SARS-CoV-2 has been sequenced [3]. A phylogenetic analysis [3, 4] found a bat origin for the SARS-CoV-2. There is a diversity of possible intermediate hosts for SARS-CoV-2, including pangolins, but not mice and rats [5]. There are many similarities of SARS-CoV-2 with the original SARS-CoV. Using computer modeling, Xu et al. [6] found that the spike proteins of SARS-CoV-2 and SARS-CoV have almost identical 3-D structures in the receptor-binding domain that maintains van der Waals forces. SARS-CoV spike protein has a strong binding affinity to human ACE2, based on biochemical interaction studies and crystal structure analysis [7]. SARS-CoV-2 and SARS-CoV spike proteins share 76.5% identity in amino acid sequences [6] and, importantly, the SARS-CoV-2 and SARS-CoV spike proteins have a high degree of homology [6, 7]. Wan et al. [4] reported that residue 394 (glutamine) in the SARS-CoV-2 receptor-binding domain (RBD), corresponding to residue 479 in SARS-CoV, can be recognized by the critical lysine 31 on the human ACE2 receptor [8]. Further analysis even suggested that SARS-CoV-2 recognizes human ACE2 more efficiently than SARS-CoV increasing the ability of SARS-CoV-2 to transmit from person to person [4]. Thus, the SARS-CoV-2 spike protein was predicted to also have a strong binding affinity to human ACE2. This similarity with SARS-CoV is critical because ACE2 is a functional SARS-CoV receptor in vitro [9] and in vivo [10]. It is required for host cell entry and subsequent viral replication. Overexpression of human ACE2 enhanced disease severity in a mouse model of SARS-CoV infection, demonstrating that viral entry into cells is a critical step [11]; injecting SARS-CoV spike into mice worsened lung injury. Critically, this injury was attenuated by blocking the renin-angiotensin pathway and depended on ACE2 expression [12]. Thus, for SARS-CoV pathogenesis, ACE2 is not only the entry receptor of the virus but also protects from lung injury. We therefore previously suggested that in contrast to most other coronaviruses, SARS-CoV became highly lethal because the virus deregulates a lung protective pathway [10, 12]. Zhou et al. [13] demonstrated that overexpressing ACE2 from different species in HeLa cells with human ACE2, pig ACE2, civet ACE2 (but not mouse ACE2) allowed SARS-CoV-2 infection and replication, thereby directly showing that SARS-CoV-2 uses ACE2 as a cellular entry receptor. They further demonstrated that SARS-CoV-2 does not use other coronavirus receptors such as aminopeptidase N and dipeptidyl peptidase 4 [13]. In summary, the SARS-CoV-2 spike protein directly binds with the host cell surface ACE2 receptor facilitating virus entry and replication. Enrichment distribution of ACE2 receptor in human alveolar epithelial cells (AEC) A key question is why the lung appears to be the most vulnerable target organ. One reason is that the vast surface area of the lung makes the lung highly susceptible to inhaled viruses, but there is also a biological factor. Using normal lung tissue from eight adult donors, Zhao et al. [14] demonstrated that 83% of ACE2-expressing cells were alveolar epithelial type II cells (AECII), suggesting that these cells can serve as a reservoir for viral invasion. In addition, gene ontology enrichment analysis showed that the ACE2-expressing AECII have high levels of multiple viral process-related genes, including regulatory genes for viral processes, viral life cycle, viral assembly, and viral genome replication [14], suggesting that the ACE2-expressing AECII facilitate coronaviral replication in the lung. Expression of the ACE2 receptor is also found in many extrapulmonary tissues including heart, kidney, endothelium, and intestine [15–19]. Importantly, ACE2 is highly expressed on the luminal surface of intestinal epithelial cells, functioning as a co-receptor for nutrient uptake, in particular for amino acid resorption from food [20]. We therefore predict that the intestine might also be a major entry site for SARS-CoV-2 and that the infection might have been initiated by eating food from the Wuhan market, the putative site of the outbreak. Whether SARS-CoV-2 can indeed infect the human gut epithelium has important implications for fecal–oral transmission and containment of viral spread. ACE2 tissue distribution in other organs could explain the multi-organ dysfunction observed in patients [21–23]. Of note, however, according to the Centers for Disease Control and Prevention [24], whether a person can get COVID-19 by touching surfaces or objects that have virus on them and then touching mucus membranes is yet to be confirmed. Potential approaches to address ACE2-mediated COVID-19 There are several potential therapeutic approaches (Fig. 1). Spike protein-based vaccine. Development of a spike1 subunit protein-based vaccine may rely on the fact that ACE2 is the SARS-CoV-2 receptor. Cell lines that facilitate viral replication in the presence of ACE2 may be most efficient in large-scale vaccine production. Inhibition of transmembrane protease serine 2 (TMPRSS2) activity. Hoffman et al. [25] recently demonstrated that initial spike protein priming by transmembrane protease serine 2 (TMPRSS2) is essential for entry and viral spread of SARS-CoV-2 through interaction with the ACE2 receptor [26, 27]. The serine protease inhibitor camostat mesylate, approved in Japan to treat unrelated diseases, has been shown to block TMPRSS2 activity [28, 29] and is thus an interesting candidate. Blocking ACE2 receptor. The interaction sites between ACE2 and SARS-CoV have been identified at the atomic level and from studies to date should also hold true for interactions between ACE2 and SARS-CoV-2. Thus, one could target this interaction site with antibodies or small molecules. Delivering excessive soluble form of ACE2. Kuba et al. [10] demonstrated in mice that SARS-CoV downregulates ACE2 protein (but not ACE) by binding its spike protein, contributing to severe lung injury. This suggests that excessive ACE2 may competitively bind with SARS-CoV-2 not only to neutralize the virus but also rescue cellular ACE2 activity which negatively regulates the renin-angiotensin system (RAS) to protect the lung from injury [12, 30]. Indeed, enhanced ACE activity and decreased ACE2 availability contribute to lung injury during acid- and ventilator-induced lung injury [12, 31, 32]. Thus, treatment with a soluble form of ACE2 itself may exert dual functions: (1) slow viral entry into cells and hence viral spread [7, 9] and (2) protect the lung from injury [10, 12, 31, 32]. Notably, a recombinant human ACE2 (rhACE2; APN01, GSK2586881) has been found to be safe, with no negative hemodynamic effects in healthy volunteers and in a small cohort of patients with ARDS [33–35]. The administration of APN01 rapidly decreased levels of its proteolytic target peptide angiotensin II, with a trend to lower plasma IL-6 concentrations. Our previous work on SARS-CoV pathogenesis makes ACE2 a rational and scientifically validated therapeutic target for the current COVID-19 pandemic. The availability of recombinant ACE2 was the impetus to assemble a multinational team of intensivists, scientists, and biotech to rapidly initiate a pilot trial of rhACE2 in patients with severe COVID-19 (Clinicaltrials.gov #NCT04287686). Fig. 1 Potential approaches to address ACE2-mediated COVID-19 following SARS-CoV-2 infection. The finding that SARS-CoV-2 and SARS-CoV use the ACE2 receptor for cell entry has important implications for understanding SARS-CoV-2 transmissibility and pathogenesis. SARS-CoV and likely SARS-CoV-2 lead to downregulation of the ACE2 receptor, but not ACE, through binding of the spike protein with ACE2. This leads to viral entry and replication, as well as severe lung injury. Potential therapeutic approaches include a SARS-CoV-2 spike protein-based vaccine; a transmembrane protease serine 2 (TMPRSS2) inhibitor to block the priming of the spike protein; blocking the surface ACE2 receptor by using anti-ACE2 antibody or peptides; and a soluble form of ACE2 which should slow viral entry into cells through competitively binding with SARS-CoV-2 and hence decrease viral spread as well as protecting the lung from injury through its unique enzymatic function. MasR—mitochondrial assembly receptor, AT1R—Ang II type 1 receptor
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                Author and article information

                Contributors
                melonzhao@163.com
                tongxiaolin@vip.163.com
                Journal
                Chin Med
                Chin Med
                Chinese Medicine
                BioMed Central (London )
                1749-8546
                30 July 2020
                30 July 2020
                2020
                : 15
                : 78
                Affiliations
                [1 ]GRID grid.464297.a, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, ; Beijing, 100053 China
                [2 ]GRID grid.24695.3c, ISNI 0000 0001 1431 9176, Beijing University of Chinese Medicine, ; Beijing, 100029 China
                [3 ]GRID grid.418117.a, ISNI 0000 0004 1797 6990, Gansu University of Chinese Medicine, ; Lanzhou, 730000 China
                Article
                360
                10.1186/s13020-020-00360-8
                7391051
                32754224
                bdd418ff-ecc2-4064-94ef-5139ad0c7ce6
                © The Author(s) 2020

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 14 May 2020
                : 24 July 2020
                Funding
                Funded by: the Special Project for Emergency of the Ministry of Science and Technology
                Award ID: 2020YFC0845000
                Award Recipient :
                Categories
                Research
                Custom metadata
                © The Author(s) 2020

                Complementary & Alternative medicine
                covid-19,cold‒damp plague formula (cdpf),network pharmacology,molecular mechanism,molecular docking

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