key: cord-0993877-mfenlbcl authors: Wang, Linyan; Du, Zhongyan; Guan, Yang; Wang, Bo; Pei, Yanling; Zhang, Lizong; Fang, Mingsun title: Identifying absorbable bioactive constituents of yupingfeng powder acting on COVID-19 through integration of UPLC-Q/TOF-MS and network pharmacology analysis date: 2022-02-09 journal: Chin Herb Med DOI: 10.1016/j.chmed.2022.02.001 sha: 47ca653e4688aa863e052c61a159d7d9921f3ee7 doc_id: 993877 cord_uid: mfenlbcl OBJECTIVE: Yupingfeng Powder (YPF), a kind of preventative patent medicine, is chosen for treatment of coronavirus disease 2019 (COVID-19) due to its high frequency application in respiratory tract diseases, such as chronic obstructive pulmonary disease, asthma, respiratory tract infections, and pneumonia, with the advantage of reducing the relapse rate and the severity. However, the active components of YPF and the mechanisms of components affecting COVID-19 are unclear. This study aimed to determine active constituents and elucidate its potential mechanisms. METHODS: Ultra performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC-Q/TOF-MS) and liquid chromatography-triple quadrupole mass spectrometry (LC-QQQ-MS) were used to determine the components and absorbable constituents of YPF. Secondly, TCMSP, Drugbank, Swiss and PharmMapper were used to search the targets of absorbable bioactive constituents of YPF, and the targets of COVID-19 were identified based on GeneCards and OMIM databases. STRING database was used to filter the possible inter-protein interactions. Thirdly, Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis were performed to identify molecular function and systemic involvement of target genes. RESULTS: A total of 61 components of YPF and 36 absorbable constituents were identified through UPLC-Q/TOF-MS. Wogonin, prim-O-glucosylcimifugin, 5-O-methylvisamminol, astragaloside IV and 5-O-methylvisamminol (hydroxylation) were vital constituents for the treatment of COVID-19, and RELA, TNF, IL-6, MAPK14 and MAPK8ere recognized as key targets of YPF. The major metabolic reactions of the absorbed constituents of YPF were demethylation, hydroxylation, sulfation and glucuronidation. GO and KEGG pathway analysis further showed that the most important functions of YPF were T cell activation, response to molecule of bacterial origin, cytokine receptor binding, receptor ligand activity, cytokine activity, IL-17 signaling pathway, Chagas disease, lipid and atherosclerosis, etc. CONCLUSION: The approach of combining UPLC-Q/TOF-MS with network pharmacology is an effective tool to identify potentially bioactive constituents of YPF and its key targets on treatment of COVID-19. Corona Virus Disease 2019 , which is caused by a newly identified coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has spread to about 215 countries and regions around the world, with about seven million confirmed cases, endangering the health of people all over the world and causing a global health crisis. In the theory of traditional Chinese medicine (TCM), 2019-new coronavirus (2019-nCoV) infected pneumonia was deemed to the category of "Pestilence", and the characteristics of its pathogenesis was "dampness, toxin, stasis and closure", which consumes Qi and Yin and leads to a deficiency (Jing et al., 2020; Wang et al., 2020; You Yannan et al., 2020; Zhang et al., 2020) . Chinese medicine had been used to treat and prevent viral infection pneumonia diseases for thousands of years and had accumulated a large number of clinical experience and effective prescriptions . As recommended in the Guideline on Diagnosis and Treatment of Coronavirus Disease 2019 (Revised 7th version), which was officially released by National Health Commission of the People's Republic of China, TCM had achieved good clinical effects in treatment of COVID-19, because of its unique therapeutic principles including syndrome differentiation and treatment, boosting the individual's endogenous healing ability, balancing Yin and Yang Yang et al., 2020) . Yupingfeng Powder (YPF), a kind of preventative patent medicine, is chosen due to its high frequency application in respiratory tract diseases, such as chronic obstructive pulmonary disease (Ma et al., 2018) , asthma Wang et al., 2016b) , respiratory tract infections (Song et al., 2016) , and pneumonia (Yan et al., 2010) , with the advantage of reducing the relapse rate and the severity. Its recipe contains three herbal medicines including Astragali Radix, Atractylodis Macrocephalae Rhizoma and Saposhnikoviae Radix. In which, Astragali Radix act as the monarch herbs due to the flavonoids and saponins have the effects of boosting energy, strengthening the immune system, and promoting healthy activities (Oh et al., 2014; Shi et al., 2015) . The main constituents in Saposhnikoviae Radix are chromones and coumarins, such as cimifugin, prim-O-glucosylcimifugin, sec-O-glucosylhamaudol and so on, which concentrate in the antipyretic, analgesic, anti-inflammatory effects (Han et al., 2016; Nikles et al., 2017; Yang et al., 2017) ; And the major bioactive constituents in Atractylodis Macrocephalae Rhizoma are amino acids, polysaccharides and lactones which show anti-inflammatory and immune regulation (Sun et al., 2015; Zhao et al., 2016) . Recently, many researchers poured attention into the pharmacology and pharmacological mechanisms of YPF acting on respiratory tract diseases Li et al., 2017c) integrated with network pharmacology (Shen et al., 2019; Zuo et al., 2018) . However, the studies gathering compounds from various databases to generate compound-target maps may produce false-positive results, for some substances with plenty of targets but possess low bioavailability are also taken into account. In this context, we focused on the absorbable constituents as selected target constituents, then integrated the target constituents and corresponding target proteins by network pharmacology. The absorbed substances were identified by UPLC-Q/TOF-MS method, and a network pharmacology investigation was conducted to determine the potential key constituents and targets (Fig.1) . YPF composes of Astragali Radix, Atractylodis Macrocephalae Rhizoma and Saposhnikoviae Radix in a dry weight ratio of 2:2:1. The pieces (150 g) were weighed and double extracted by refluxing with boiling water (1:10, mass to volume ratio) for 1.5 h. Thereafter the water decoction was concentrated to 1.0 g/mL (crude drugs) and centrifuged at 12000 rpm for 15 min, and the supernatant was stored at 4 °C before analysis. Six male Wistar rats (200−220 g) were applied in the study. Rats were obtained from Laboratory Animal Research Center of Zhejiang Chinese Medical University (Hangzhou, China). All experimental protocols were in accordance with the guidelines approved by The Animal Ethical Committee of Zhejiang Chinese Medical University (approval number : SYXK(Zhe) 2018-0012). Before the day of last administration, the rats were fasted for 12 h but allowed water. Six rats were intragastrically administrated with YPF (12 g/kg). Blood samples were collected in heparinized tubes via the orbital venous plexus from each rat before drug administration and at 10, 20, 40, 60 min after drug administration. Pharmacokinetics studies have proved that the peak time (Tmax) of flavonoids after oral administration of Astragali Radix were ranged from 10.8 min to 50.0 min (Shi et al., 2015) , the main components of Tmax of Saposhnikoviae Radix were ranged from 12.0 min to 70 min Li et al., 2012) . Based on above parameters, 10, 20, 40, 60 min were chosen as four time points to obtain the dosed plasma and mixed for later analysis. The blood samples were then immediately centrifuged at 5000 rpm for 5 min to collect the plasma and the plasma of different time points were mixed. The plasma (100 µL) was mixed with 400 µL of methanol at 4 °C, vortexed 1 min and centrifuged at 13500 rpm for 10 min. The supernatant was dried with nitrogen gas at 40 °C, added 100 µL 50% methanol to reconstitute the residue and centrifuged at 12000 rpm for 15 min, transferred to a vial and injected 2 µL and 5µL for UPLC-Q/TOF-MS analysis and liquid chromatography-triple quadrupole mass spectrometry (LC-QQQ-MS) analysis, respectively. The electrospray ionization (ESI) was used as the ionization source by Q-TOF SYNAPT G2-Si High Definition Mass Spectrometer (Waters, UK). The separation was performed by a Waters ACQUITY UPLC BEH C18 Column (2.1× 50 mm, 1.7µm) with BEH C18 Van Guard (2.1 mm × 50 mm, 1.7 μm) at 40 °C. Briefly, in ESI-MS analysis, the capillary voltage was set as 3.0 kV. The MS E continuum mode was carried out over the range of m/z 50−1200. Each sample was injected 2 µL into the column and employed with a gradient elution. The column and autosampler temperature were maintained at 40 °C and 4 °C. The gradient elution consisted of A (methanol) and B (0.1% formic acid in water), the flow rate was controlled at 0.25 mL/min. The gradient program was set as follows: 0−0.5 min, 5% A; 0.8−10 min, 5%−55% A; 10−15 min, 55%−70% A; 15−19 min, 70%−95% A; 19−20 min, 95% A. The LC-QQQ-MS procedure was performed by using SHIMADZU LC-20A system and SHIMADZU 8050 Triple Quadrupole mass spectrometer equipped with an ESI source. Chromatographic separation was achieved on an InertSustain C18 column (4.6 mm ×150 mm, 5μm) at 40 °C. The mobile phases consisted of A (methanol) and B (0.1% formic acid in water). The gradient program was set as follows: 0−0.5 min, 5% A; 0.5−7 min, 5%−40% A; 7−30 min, 40%−85% A; 30−35 min, 85−95% A; 35−38 min, 95% A; The flow rate was 0.6 mL/min, and the injection volume was 5 μL. The mass spectrometer was operated in positive ion mode. Analysis was performed by multiple reactions monitoring (MRM), the parameters were summarized in Table 1 . (Gfeller et al., 2013) and PharmMapper (http://www.lilab-ecust.cn/pharmmapper/) (Liu et al., 2010; Wang et al., 2016a; Wang et al., 2017b) . The molecular files of the prototype compounds were downloaded from PubChem (https://pubchem.ncbi.nlm.nih.gov/) and the metabolites were drawn by Chem3D. All the structures were saved in sdf format. Then the targets of these compounds were obtained from PharmMapper. To improve the reliability of the target prediction results, the top 30 matches (Z-Score > 0.3). STRING database (http://string-db.org/) was used to filter the possible inter-protein interactions (PPIs) (von Mering et al., 2003) . The attained PPIs with high confidence (combine score > 0.90) were kept for network construction and analysis. Cytoscape software (version 3.7.1) was applied to create a network compounds-target network and PPIs network. The parameters of average shortest pathway length (ASPL) and betweeness centrality (BC) were calculated by Network Analyzer (Arrell et al., 2009 ). To identify the hub targets, Cytohubba was applied to further analyze the PPIs network (Zhai et al., 2020) . Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis were performed to identify molecular function and systemic involvement of target genes. GO classification and enrichment analysis of potential target genes were performed using the STRING database (https://string-db.org/). The top 10 results of molecular function, biological process, and cell component analysis were selected, and R software (R version 3.6.0) was used for plotting. The top 10 pathway information was selected with P < 0.05, Omicshare database (http://www.omicshare.com), and the histogram was drawn using R software. In total, 61 compounds in YPF were successfully characterized through comparison with the UNIFI software (version 1.7) and literatures. Eleven of these compounds were further confirmed by the reference standards. All YPF component information was summarized in Table S1 . The total ion chromatograms of YPF extracts obtained in positive and negative modes were shown in Fig. S1 . Diverse components, seven amino acids, 14 chromogens, 13 flavonoids, 14 saponins, 11 lactones and two others were identified in YPF. Among these components, chromogens, flavonoids and saponins were the major components of YPF. By analyzing their structural features, fragmentation patterns, and typical peak ions in MS e high spectra, the components and their fragmentation patterns were identified. It could be summarized as follows and some specific compounds were taken as examples. Thirteen flavonoids mainly originated from Astragali Radix, including calycosin, formononetin, To characterize the absorbable constituents of YPF, a UPLC-Q/TOF-MS method with UNIFI software was utilized to screen the constituents. The absorbed constituents were shown in Table 2 , and a total of nine prototype constituents were found in the dosed plasma. Of note, the mass errors of the identified constituents were less than 10×10 -6 , and the numbers of constituents identified from Astragali Radix and Saposhnikoviae Radix were one and eight, respectively. The vast majority of prototype constituents were chromones of Saposhnikoviae Radix. Based on this situation, and according to the literatures, MRM mode of LC-QQQ-MS with high sensitivity was utilized. Calycosin, formononetin, atractylenolide II and astragaloside IV were detected by MRM mode (Fig. 4) . Totally, the numbers of prototype constituents identified from Astragali Radix, Atractylodis Macrocephalae Rhizoma and Saposhnikoviae Radix were four, one and eight. The MS spectrums were shown as supplement Figs. S2−S10. The peaks detectable in dosed rat plasma and not in blank rat plasma were considered as probable metabolites. The metabolites of the absorbed substances in rat plasma were further analyzed by UNIFI software. Furthermore, the ion of MS e high energy mode was analyzed to further identify the structures. Finally, a total of 23 metabolites were observed (Table 3 ). The MS spectrums were shown as supplement Figs. S11−S33. and glucuronide conjugation or sulfate conjugation after oral administration in phase I/II reactions. As shown in Fig. 5 , the metabolic pathways of some major flavonoids after oral administration of YPF were proposed. The biotransformation between the main flavonoids and their glucuronides could be a fundamental factor of the pharmacological effects of Astragali Radix (Shi et al., 2015) . M8 [M+H] + ions at m/z 461.1077, which corresponded with the formula of C22H20O11. It was apt to experience the neutral loss of 176 Da (C6H8O6), and yield product ions at m/z 285, 270, 253 and 225 in MS E spectrum. We presumed that they might be the glucuronide conjugates of calycosin at C7 or C3' positions. However, the position of glucuronide conjugates could hardly be located, due to the same product ions in MS E spectrum. M10 and M11, the components metabolized from formononetin phase II reactions, were tentatively characterized as the glucuronide and sulfate conjugated metabolites, respectively. Moreover, M9 metabolized from formononetin through both of phase I and phase II reactions, were tentatively characterized as the successive hydroxyl and glucuronide conjugated metabolites. A total of 394 putative targets of the YPF components and 251 COVID-19 related targets were identified. Among all targets, 41 overlapped genes were identified, and were kept for network construction (Fig. 7) . By operating network analyzer, topological parameters such as degree, ASPL and BC were attained (Table S2 ). The five components with largest BC and smallest ASPL were identified as the key components of YPF, including wogonin, prim-O-glucosylcimifugin, 5-O-methylvisamminol, astragaloside IV and 5-O-methylvisamminol (hydroxylation) ( Table 4 ). Among the five ingredients, wogonin was found with the smallest ASPL (2.38) and largest BC (0.27). or target (in green arrow) Among the overlapped 41 targets, a total of 346 protein-protein interactions (PPIs) were obtained from STRING Database. By comparing the combine scores of the PPIs, 91 PPIs (P-value > 0.9, high confidence) were kept for PPIs network construction using Cytoscape software (Fig. 8 , Table S3 ). With the analysis using Cytohubba, RELA, TNF, IL-4, IL-6, CXCL8, IL-2, CCL2, MAPK14, MAPK8 and LCK were found with the highest average scores (Table 5 -Cytohubba). Among the ten top ranked hub targets, RELA, TNF, IL-6, MAPK14 and MAPK8 were also recognized as key targets by network analyzer (Table 5-network analyzer) , and therefore were identified as key targets for the treatment of COVID-19 of YPF. Among five key components of YPF, wogonin, astragaloside IV and 5-O-methylvisamminol (hydroxylation) interacted with four, two, and one hub targets respectively, were considered active constituents with activity against COVID-19 in this study. The details were summarized in Table 6 . The results of GO and KEGG analysis were shown in Fig. 9 . The T cell activation, response to lipopolysaccharide, response to molecule of bacterial origin, response to oxidative stress and positive regulation of establishment of protein localization ranked first in BP (Fig. 9A ). Molecular functions of these proteins include cytokine receptor binding, phosphatase binding, receptor ligand activity, protein phosphatase binding and cytokine activity (Fig. 9B ). Membrane raft, membrane microdomain, membrane region, vesicle lumen and secretory granule lumen were the top ones in CC (Fig. 9C) . KEGG pathway analysis further showed that YPF targeted proteins are involved in IL-17 signaling pathway, AGE-RAGE signaling pathway in diabetic complications, Chagas disease, lipid and atherosclerosis and Kaposi sarcoma-associated herpesvirus infection (Fig. 9D ). This study systematically explored the pharmacological mechanisms of YPF in the treatment of COVID-19 through UPLC-Q/TOF-MS and network pharmacology analysis. Network pharmacology can identify potentially active compounds, targets, and pharmacological mechanisms of complex compounds in Chinese herbal formulas . However, abound of network pharmacology research, the compounds were collected from databases, however, some compounds related to plenty of targets but have lower bioavailability, which may produce false positive results. Our study, which is constructed by the absorbable constituents and the corresponding targets, provided a better understanding of the metabolic and therapeutic pathways of TCM in vivo. For example, 5-O-methylvisamminol (3' hydroxylation), a metabolite of 5-O-methylvisamminol, played a vital role in the regulation of target of COVID-19, which could not be collected from databases directly. However, the research of the absorbed ingredients is based on the theory of that only some components absorbed in the body possess therapeutic effects, or produced from several reactions in the body ignoring components that play a regulatory role in intestinal flora to possess therapeutic effects, just like polysaccharides of YPF (Yin et al., 2019) . So, we will explore the effect of YPF on intestinal flora in the future research. Via network pharmacology analysis, three key active components were regarded to be effective on COVID-19, and five targets were screened to be effective on COVID-19. Multiple studies have indicated that two of these components are effective against COVID-19 Ye et al., 2020) . Wogonin, a flavonoid compound was considered to be the most important ingredient in YPF which has been studied thoroughly by many researchers for its anti-viral, anti-oxidant, anti-cancerous and anti-inflammatory activities (Wang et al., 2017a; Wu et al., 2019) . It regulated the production of inflammatory cytokines, including IL-6, TNF-α and GMCSF (Li et al., 2017a) , and is the main active ingredients of Chinese medicines for the management of COVID-19 by inhibiting inflammatory mediators, regulating immunity, and eliminating free radicals through COX-2, CASP3, IL-6, MAPK1, MAPK14, MAPK8, and REAL in the signaling pathways of IL-17, arachidonic acid, HIF-1, NF-κB, Ras, and TNF , which are consistent with our study. It was found that the second-important component astragaloside IV may possess good efficacy on COVID-19. Astragaloside IV is one of the major and main active substances of Astragali Radix, demonstrated potential cardioprotective and immunological enhancement activities through experimentation in vitro and in vivo. It appeared to have powerful antagonistic effects on inflammatory, via regulating IL-1β, TNF-α, ICAM and chemokine (Li et al., 2017b; Ren et al., 2013) . , without relevant studies, may act on MAPK14 according to our study, suggesting have effects on COVID-19. Even so, the targets could be further analyzed and validated to deeply understand the mechanism of 5-O-methylvisamminol (3' hydroxylation). The results of network pharmacology and PPI analysis showed that the top targets involved RELA, TNF, IL-6, MAPK14 and MAPK8,which are the potential targets of the compounds of YPF. Elevated levels of tumor necrosis factor (TNF), a key pro-inflammatory cytokine, have been shown to be associated with increased COVID-19 mortality. In addition, anti-TNF therapies have a well-demonstrated ability to reduce inflammation and specifically reduce levels of pro-inflammatory cytokines associated with poor COVID-19 outcomes . IL-6 was proven to be a key driver of the inflammation associated with COVID-19 infection . As such, it has been hypothesized that monoclonal antibodies blocking IL-6 could help improve clinical outcomes in COVID-19 patients with severe pneumonia. GO and KEGG pathway analysis further showed that the most important of YPF were T cell activation, response to molecule of bacterial origin, cytokine receptor binding, receptor ligand activity, cytokine activity, IL-17 signaling pathway, Chagas disease, lipid and atherosclerosis. This result indicated that these pathways might be critical biological processes through which YPF achieves its therapeutic effect. Therefore, we speculated that the multiple active compounds in YPF may play an important role in COVID-19 therapy by multiple signal pathways. Though some results have been attained in this research, there are still limitations. The absorbable constituents of YPF were not identified thoroughly, and the targets of components should be further investigated to prove the speculation. In this study, 61 components of YPF and 36 absorbable constituents were identified through UPLC-Q/TOF-MS, and five absorbable bioactive constituents were shown by network pharmacology analysis to have potential anti-COVID-19 effects. The major metabolic reactions of the absorbed constituents were demethylation, hydroxylation, sulfation and glucuronidation. All in all, the results clearly presented the metabolic pathways of YPF in vivo that not only provided the absorbable constituents but also, and more importantly, discovered potential targets and biological processing mechanisms of YPF, which will open up a new approach in the study of YPF in future. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. 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The Lancet A network pharmacology-based approach to analyse potential targets of traditional herbal formulas: An example of Yu Ping Feng decoction The research was supported by the Natural Science Foundation of Zhejiang Province (No. LQ20H270008) and Natural Science Foundation of Zhejiang Chinese Medical University (No. 2018ZZ13). Supplementary materials associated with this article can be found, in the online version, at doi: