key: cord-0907972-6w9ncuch
authors: Su, Jinsong; Liu, Zixuan; Liu, Chuan; Li, Xuanhao; Wang, Yi; Zhao, Jing; Wu, Qingjiang; Zheng, Shichao; Zhang, Yi
title: Network Pharmacology Integrated Molecular Docking Reveals the Mechanism of Anisodamine Hydrobromide Injection against Novel Coronavirus Pneumonia
date: 2020-08-05
journal: Evid Based Complement Alternat Med
DOI: 10.1155/2020/5818107
sha: 212249720993818d88827ecfe307e984f873547d
doc_id: 907972
cord_uid: 6w9ncuch

BACKGROUND: The Coronavirus Disease 2019 (COVID-19) outbreak in Wuhan, China, was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Anisodamine hydrobromide injection (AHI), the main ingredient of which is anisodamine, is a listed drug for improving microcirculation in China. Anisodamine can improve the condition of patients with COVID-19. MATERIALS AND METHODS: Protein-protein interactions obtained from the String databases were used to construct the protein interaction network (PIN) of AHI using Cytoscape. The crucial targets of AHI PIN were screened by calculating three topological parameters. Gene ontology and pathway enrichment analyses were performed. The intersection between the AHI component proteins and angiotensin-converting enzyme 2 (ACE2) coexpression proteins was analyzed. We further investigated our predictions of crucial targets by performing molecular docking studies with anisodamine. RESULTS: The PIN of AHI, including 172 nodes and 1454 interactions, was constructed. A total of 54 crucial targets were obtained based on topological feature calculations. The results of Gene Ontology showed that AHI could regulate cell death, cytokine-mediated signaling pathways, and immune system processes. KEGG disease pathways were mainly enriched in viral infections, cancer, and immune system diseases. Between AHI targets and ACE2 coexpression proteins, 26 common proteins were obtained. The results of molecular docking showed that anisodamine bound well to all the crucial targets. CONCLUSION: The network pharmacological strategy integrated molecular docking to explore the mechanism of action of AHI against COVID-19. It provides protein targets associated with COVID-19 that may be further tested as therapeutic targets of anisodamine.

COVID-19 was first reported in late December 2019 in Wuhan, China and has rapidly spread to more than a dozen of countries, including the United States, with thousands of infected individuals and hundreds of deaths within a month [1] . As of today (25 Feb 2020) , 77,785 cases have been identified in China, and 25 cases have been cumulatively reported in Taiwan, China. It is of great importance to search for fast and effective therapeutic drugs for COVID-19. Drug reutilization is a common strategy in the search for antiviral treatment. It has been reported that some approved drugs are beneficial to patients. Chinese patent medicine, in particular, plays a key role in the treatment of viral diseases in China [2] . According to the theoretical foundation of plague, it is convinced that Chinese medicine is an effective treatment for COVID-19 [3] .

AHI, an anti-inflammatory agent, can relieve smooth muscle spasm, inhibit gland secretion and improve pulmonary microcirculation, and it is used clinically to treat pneumonia in China and has been reported to improve COVID-19 [4] [5] [6] . e main component of AHI is anisodamine ( Figure 1 ). Anisodamine a tropane alkaloid extracted from the roots of Anisodus tanguticus (Maxim.) Pascher. is an acetylcholine receptor blocker. By blocking the muscarinic acetylcholine receptor, anisodamine can reduce glandular secretion, inhibit the hyperexcitability of cholinergic nerves, eliminate muscarinic symptoms, relax the spasm of smooth muscle, and accelerate the heartbeat etc. [7] . It has been used for many diseases, such as respiratory diseases, various circulatory disorders, septic shock, gastric ulcers, migraine, gastrointestinal colic, acute glomerular nephritis, eclampsia, rheumatoid arthritis, obstructive jaundice, opiate addiction, organophosphorus poisoning, and snake bite, as well as in radiation damage protection, due to its ability to improve microcirculation [8, 9] . Anisodamine had also been used to treat patients of severe acute respiratory syndrome (SARS) with hypoxemia in 2003 [10] . Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause pulmonary inflammatory reactions in patients, leading to pulmonary microcirculation disorder; therefore patients could have symptoms of dyspnea and hypoxia. AHI can improve symptoms of COVID-19 by regulating pulmonary microcirculation. In this study, we explored the mechanism through which AHI improves COVID-19, as it is of great importance to provide a possible therapeutic schedule for COVID-19.

Network pharmacology is considered a promising approach for a cost-effective drug development and it has been widely used to identify the active ingredients of some traditional Chinese medicine and their mechanisms of actions [11, 12] . It has transformed the research approach of "one target, one drug" into a "network target, multicomponent" strategy. Taking anisodamine as an example, a targeting method of natural products based on the PubChem database has been used. e targeting method is rapid and could provide a relatively accurate result without the support of high-performance computing [13] . Based on the principle of structural biology, molecular docking can be applied to perform virtual drug screening via a computer-assisted drug molecular biological design. Hence, molecular docking is an effective way to find and identify drug targets by filtering the docking energy and space matching between molecules and targets [14] . e integration of in silico and experimental results predicted that Qingfei Paidu Decoction could treat pneumonia in COVID-19 patients and Ma Xing Shi Gan Decoction plays an important role in this [15, 16] . erefore, the integration of molecular docking and network pharmacology is helpful in accelerating the progress in target discovery and experimental verification. In this study, a network pharmacological strategy integrated with molecular docking was used to explore the mechanism through which AHI improves COVID-19, so as to provide scientific evidence for clinical medication.

e related targets of anisodamine were extracted from PubChem using the key word "anisodamine." Next, the component targets were imported to the UniProt database (http://www.UniProt.org/) to obtain the UniProt ID.

Topological Feature Analysis. Using String (https://stringdb. org/, ver. 11.0), the revised targets were used to obtain associated protein-protein interactions for the construction of the PIN of AHI. We limited the species to "Homo sapiens" and set the minimum interaction threshold to 0.7. e network construction was visualized using Cytoscape (version 3.7.1). Next, three topological parameters including "Degree," "Betweenness Centrality," and "Closeness Centrality" were calculated by Network Analyzer. Just the nodes with "Degree," "Betweenness Centrality," and "Closeness Centrality" larger than the corresponding median values were recognized as crucial targets of AHI against COVID-19.

e crucial targets were used for GO and KEGG pathway analyses using the String database with the screening criteria of FDR ≤1 × 10 −6 . By using the count score, we selected the top 20 GOs for presentation. e pathway terms with FDR ≤1 × 10 −6 were mapped to the KEGG human diseases in order to obtain the disease pathway.

Coexpression Proteins. ACE2 is the SARS-CoV receptor and has been linked to SARS-CoV-2 infection. ACE2 coexpressed proteins were obtained from colonic epithelial cells in the study conducted by Wang et al. [17] . Hence, the intersection calculation between the AHI targets and ACE2 coexpression proteins was performed to obtain the common protein to explore the moderation effect of AHI on ACE2 coexpression proteins.

e crystal structures of candidate protein targets of anisodamine were downloaded from the RCSB Protein Data Bank (http://www.rcsb.org/). Furthermore, modifications including ligands and water removal, hydrogen subjoining, optimization, and patch of amino acid were conducted with Maestro software (Version 11.1.011), while the ionization parameters remained unchanged. e scale factors and partial charge cutoff values of the van der Waals radius scaling 0.25 1Å were applied to generate grids at the active sites. ChemBioOffice2014 was used to create 3D chemical structures and minimize their energy. e results were saved in MOL.2 format. e docking score between the compound and the target protein was presented as kcal/mol and used as the evaluation criteria to further screen out potential active 2

Evidence-Based Complementary and Alternative Medicine components. Targets with docking scores >4.25 were considered meaningful [18] .

PubMed, a total of 88 targets of anisodamine were obtained, and the target information is shown in Table S1 .

Analysis. e PIN of AHI consisted of 172 nodes and 1454 interactions, as shown in Figure 2 .

ree topological features-"Degree," "Betweenness," and "Closeness"-were calculated for each node in the network to screen the crucial hubs with topological importance (Supplementary Data Table S2 ).

e median values of Degree, Betweenness, and Closeness were 16, 0.00285052, and 0.41707317, respectively. Furthermore, we determined that nodes with "Degree" >16, "Node betweenness" >0.00285052, and "Closeness" >0.41707317 were the crucial targets. As a result, 54 crucial targets were obtained ( Figure 3 ). As shown in Figure 3 , the top five degrees among the crucial targets were TP53, TNF, IL6, CASP3, and CASP8, and their degrees were 60, 59, 53, 46, and 43, respectively. TP53, TNF, and IL6 are closely related to the regulation of inflammation [19] [20] [21] , while CASP3 and CASP8 play an important role in the apoptosis process [22, 23] .

To elucidate the mechanisms of AHI against COVID-19, we conducted GO biological processes and pathway enrichment analysis for crucial targets. e top 30 biological processes involved in AHI against COVID-19 are shown in Figure 4 . e biological processes mainly includes the regulation of cell death, cytokine-mediated signaling pathway, cellular response to chemical stimulus, positive regulation of nitrogen compound metabolic process, response to cytokine, cellular response to cytokine stimulus, positive regulation of cellular metabolic process, cell surface receptor signaling pathway, regulation of immune system process, etc.

KEGG pathway enrichment analysis was executed based on the String database (as shown in Figure 5 ). e results showed that the diseases mainly involved are viral infections, cancer, and immune system diseases, which are associated with inflammation. ey include diseases such as influenza A, HTLV-I infection, small cell lung cancer, inflammatory bowel disease, human papillomavirus, hepatitis B, tuberculosis, hepatitis C, allograft rejection, rheumatoid arthritis, Shigellosis, colorectal cancer, amoebiasis, malaria, viral myocarditis, leishmaniasis, acute myeloid leukemia, pancreatic cancer, and pertussis.

Coexpression Proteins. A total of 5556 proteins coexpressed with ACE2 were obtained. By calculating the intersection between the AHI component proteins and ACE2 coexpression proteins, 26 common proteins were obtained (shown in Table 1 ). Among them, BCL2L1, CASP1, CASP3, CASP8, IL17A, and STAT3 were crucial targets of AHI.

e crucial targets of TP53, UBC, XIAP, and RIPK1 were chosen to further study the accuracy of prediction results by calculating the interaction with anisodamine using molecular docking. e results of molecular docking indicated that all anisodamines entered the active pocket of the enzyme; for example, anisodamine entered the active pocket of TP53. Interestingly, although there was no combination of hydrogen and aromatic bonds with the compound (Figures 6 and 7) , anisodamine combined with an active pocket through van der Waals forces, and the docking scores reached 5.636. Anisodamine bound to the active pockets of UBC and one hydroxyl interacted with GLU34 to form a hydrogen bond, as shown in Figure 6 . However, anisodamine bound to the active pockets of XIAP and two hydroxyl groups interacted with LYS206 and LYS208 to form hydrogen bonds, the carbonyl also interacted with LYS208 to form a hydrogen bond (Figures 8 and  9 ). Similarly, anisodamine was linked to the active pocket of RIPK1, and the carbonyl interacted with LYS648 to form a hydrogen bond. Besides, the hydroxyl interacted with LYS642 to form a hydrogen bond, and the aromatic ring interacted with LYS642 to form aromatic hydrogen bonds ( Figure 8 ).

ere is a worldwide concern about COVID-19 as a global public health threat as SARS-CoV-2 causes severe acute respiratory syndrome [24, 25] , and this has caused the death of many patients. In addition, it has been reported that ACE2 is the main host cell receptor of SARS-CoV-2 and plays a key role in the viral infection [26] . ACE2 could cause various inflammation, it has been proved that AHI can improve microcirculation in the body, and it has been used to treat pneumonia, septic shock, and other diseases [6, 27, 28] . Some studies indicated that AHI combined with Evidence-Based Complementary and Alternative Medicine azithromycin sequential therapy in the treatment of mycoplasma pneumonia infection could improve the clinical curative effect, decrease the serum inflammatory cytokines, and increase immunological markers [29, 30] . AHI can improve COVID-19 by eliminating inflammation and promoting microcirculation.

is study used network pharmacology and molecular docking technology to predict the potential targets of anisodamine as the main active component of AHI in the treatment of COVID-19.

ACE2 is a key negative regulatory factor for the severity of lung edema and acute lung failure; therefore, the mediation of ACE2 downregulation could contribute to the severity of lung pathologies [31] . We screened out some coexpressed targets of anisodamine and ACE2, including  IL17A, STAT3, AOC1, BCL2L1, CASP1, CASP3, CASP8,  CTSD, DNAH8, ICAM2, IL18, IL5, ITGAV, KCNA3, MPO,  MTMR11, NOX4, ODC1, PLAUR, PLGRKT, RSAD2,  SERPINC1, TIMP2, TXN, TXNIP, and VIP. For example, IL17A is a proinflammatory cytokine that critically regulates host defense against multiple pathogens. You et al. used a Pts4 d/d -driven mouse model to confirm that IL17A could regulate tumor latency and metastasis in lung adenocarcinoma and squamous cell carcinoma [32] . Evidence indicated that treatment with anisodamine could markedly reduce the expression of IL17A and IL17F in rats [33] . A study also showed that the levels of MMP2 and TIMP2 mRNA and the protein of MMP2 in livers could be significantly reduced in the anisodamine preventive group and therapeutic groups [34] . STAT3 signaling is linked to multiple pathways and influences both immunity and inflammatory injury. In E. coli pneumonia, STAT3 can promote neutrophil recruitment and limit both infection and lung injury [35] . Choi et al. also reported the antibacterial function of STAT3 in the lung epithelium, which was mediated by the induction of Reg3c [36] . BCL2L1 is an inflammation-protective gene that can regulate apoptosis. Previous studies confirmed that BCL2L1 negatively correlated with the survival of lung cancer patients. Zhang et al. used cell experiments to demonstrate that let-7a-5p could directly target BCL2L1, inhibit BCL2L1 expression, and suppress lung cancer cell proliferation, migration, and invasion [37] . In another study, the antiapoptotic effect of A1AT in alveolar endothelial cells via direct CASP3 inhibition was demonstrated. is result represents a novel antiapoptotic mechanism relevant to disease processes characterized by inflammation, such as pulmonary emphysema [38] . Yuan et al. showed that anisodamine treatment could reduce expression of ER stress markers IRE-1α, CHOP, and ATF4, TXNIP, and NLRP3, as well as ACS, CASP1, IL1α, IL1β, and IL18 [39] . Evidently, anisodamine can indirectly limit the expression of ACE2 by acting on coexpressed targets.

In this study, the biological processes mainly include the regulation of cell death, cytokine-mediated signaling pathway, immune system process, etc. Apoptosis and autophagy are common pathways that regulate cell death and have been extensively studied. It is through the regulation of cell death that the body regulates normal functions. For example, some studies demonstrated that targeting autophagy may be used in the future for the treatment of lung cancer because the disruption of autophagy via the inhibition of Atg5 and Beclin 1 may promote cisplatin-induced apoptotic cell death in A549 human lung cancer cells [40] . e immune depression syndrome caused by spinal cord injury induces pneumonia; however, Tiphaine et al. applied a new model to confirm that the blockade of the negative costimulatory molecule PD-1 decreases the rate of secondary bacterial pneumonia through an increase in IFN-c production by NKT cells [41] . Zou et al. showed that Morf4l1 may be a potential target for the treatment of severe pulmonary infection because, in mice infected with P. aeruginosa, the overexpression of Morf4l1 resulted in lung epithelial cell death, and its depletion restored the vitality of cells [42] . In lung cancer, Baumert et al. used RNA-Seq, mass spectrometry, and linked them with functional cell culture to identify the function of KMT9. e results showed that the depletion of KMT9 inhibited lung cancer cell proliferation by inducing nonapoptotic cell death [43] . Evidence from several clinical studies indicates that a complex network of inflammatory cytokines and chemokines play a major role in mediating, amplifying, and perpetuating the lung injury Evidence-Based Complementary and Alternative Medicine process. Goodman et al. found that the lung-protective ventilatory strategy reduced mortality by 22%, which is related to the concentration of proinflammatory cytokines released into the injured lung airspace [44] . In addition, the cytokine-mediated signaling pathway has potential significance in the treatment of pneumonia. Menna et al. examined Figure 6 : Schematic representation of the molecular docking between TP53, UBC target proteins, and anisodamine (2D). Figure 8 : Schematic representation of the molecular docking between XIAP, RIPK1 target proteins, and anisodamine (2D). lungs. is suggests that T-cell lineage and its cytokines play important roles in skin and mucosal immunity [46] . Komaki et al. used a new bronchoscopic microsampling technique and found that xanthine oxidase (XO) activity is increased in chronic obstructive pulmonary disease (COPD), possibly due to its gene upregulation by proinflammatory cytokines. Consequently, cytokine-XO production pathways might play an important role in the development of inflammation in COPD [47] . e immune system process is also closely linked to the treatment of pneumonia. Roux et al. used a rat model to indicate that C. albicans airway colonization could promote the development of bacterial pneumonia; however, this effect was inhibited in vitro because the inhibition of AM phagocytosis in relation to a 1-17 immune response was triggered by fungal colonization [48] . Alveolar macrophages (AM) are believed to be of central importance to the initial host response to pulmonary cryptococcal infection because they constitute the major resident phagocytic cells in the lungs. e study suggested that the differences in susceptibility to pulmonary cryptococcal infection in rats and mice may result from basic differences in AM [49] . e immune system plays an important role in lung function. Alekseevskikh et al. studied 74 children aged from 1 month to 1 year who died from acute pneumonia and recommended that patients should undergo early immunomodulatory treatment [50] . e immune system process was also closely related to pneumonia. In 76 patients with acute pneumonia, the absolute and relative numbers of T-and B-lymphocytes were determined. Bykova et al. observed that there was a sharp decrease in the number and function of T-and B-lymphocytes in croupous pneumonia and in the prolonged course of local pneumonia [51] . erefore, we found that these signaling pathways are closely related to pneumonia and inflammation and that AHI may improve COVID-19 through the regulation of signaling pathways. e viral infections, bacterial infections, and parasitic infections were analyzed via KEGG enrichment analysis. Novel coronaviruses have been isolated from human airway epithelial cells, and SARS-CoV-2 is the seventh member of the family of coronaviruses [52] . Currently, remdesivir and chloroquine are recognized as promising antiviral drugs. A recent study indicated that remdesivir is an adenosine analog that is incorporated into nascent viral RNA chains and results in premature termination. However, chloroquine blocks viral infection by increasing endosomal pH required for virus/cell fusion and interferes with the glycosylation of cellular receptors of SARS-CoV [53] . Both remdesivir and chloroquine treat COVID-19 by blocking the synthesis of the virus. erefore, AHI may indirectly or directly regulate various inflammatory pathways, immune pathways, and related targets to prevent viral infections.

As Table 2 shows, the higher the docking score, the better the docking effect. According to all the docking results, anisodamine bound well to all targets, and the docking scores of TP53 and XIAP were 5.636 and 4.411, respectively. e results of this study indicate that AHI is a potential therapeutic agent for COVID-19.

In this study, in an attempt to provide a possible therapeutic schedule for COVID-19, a network pharmacology method and molecular docking technology were integrated to predict the mechanism through which AHI improves COVID-19. AHI may regulate cell death, cytokine-mediated signaling pathway, and immune system process to combat viral infections, cancer, and immune system diseases. rough the intersection analysis between the AHI targets and ACE2 coexpression proteins, we observed that AHI may indirectly limit the expression of ACE2 by acting on coexpressed targets. erefore, AHI may be a potential drug for the treatment of COVID-19. Nevertheless, further experiments are needed to support our findings. e present study revealed the mechanisms through which AHI improves COVID-19. It provides an important basis for further study on the mechanisms of AHI and the optimization of experimental designs for more reliable experimental results.

e data used to support the findings of this study are available from the corresponding author upon request.

Qingjiang Wu is the vice president of Chengdu First Pharmaceutical Co., Ltd, and is one of the authors. e authors are authorized by the Chengdu First Pharmaceutical Co., Ltd, to carry out the research work of anisodamine hydrobromide injection. Evidence-Based Complementary and Alternative Medicine 9

Table S1: the detailed information of targets of anisodamine. 

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ACE2 expression by colonic epithelial cells is associated with viral infection, immunity and energy metabolism

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Chronic inflammation initiates multiple forms of K-Ras-independent mouse pancreatic cancer in the absence of TP53

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Two cases of acute pulmonary microcirculation disturbance treated by Anisodamine

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e efficacy of anisodamine injection combined with azithromycin in sequential treatment of children with mycoplasma pneumonia

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IL17A regulates tumor latency and metastasis in lung adeno and squamous SQ.2b and AD.1 cancer

Expression of IL-17A and IL-17F in lipopolysaccharide-induced acute lung injury and the counteraction of anisodamine or methylprednisolone

Antifibrotic activity of anisodamine in vivo is associated with changed intrahepatic levels of matrix metalloproteinase-2 and its inhibitor tissue inhibitors of metalloproteinases-2 and transforming growth factor β1 in rats with carbon tetrachloride-induced liver injury

Alveolar epithelial STAT3, IL-6 family cytokines, and host defense during Escherichia coli pneumonia

Innate Stat3-mediated induction of the antimicrobial protein Reg3c is required for host defense against MRSA pneumonia

Exogenous let-7a-5p induces A549 lung cancer cell death through BCL2L1-mediated PI3Kc signaling pathway

α-1 antitrypsin inhibits caspase-3 activity, preventing lung endothelial cell apoptosis

Anisodamine inhibits endoplasmic reticulum stress-associated TXNIP/ NLRP3 inflammasome activation in rhabdomyolysis-induced acute kidney injury

Inhibition of autophagy promotes cisplatin-induced apoptotic cell death through Atg5 and Beclin 1 in A549 human lung cancer cells

Immunotherapy with antiprogrammed cell death 1 antibody improves outcome in a mouse model of spinal cord injury followed by Staphylococcus aureus pneumonia

Mortality factor 4 like 1 protein mediates epithelial cell death in a mouse model of pneumonia

Depletion of histone methyltransferase KMT9 inhibits lung cancer cell proliferation by inducing non-apoptotic cell death

Cytokine-mediated inflammation in acute lung injury

FccRIIb balances efficient pathogen clearance and the cytokine-mediated consequences of sepsis

Cytokine-mediated regulation of antimicrobial proteins

Cytokine-mediated xanthine oxidase upregulation in chronic obstructive pulmonary disease's airways

Airway fungal colonization compromises the immune system allowing bacterial pneumonia to prevail

An innate immune system cell is a major determinant of species-related susceptibility differences to fungal pneumonia

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A novel coronavirus from patients with pneumonia in China

Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro