Therapeutic mechanism of Toujie Quwen granules in COVID-19 based on network pharmacology

Discovery of common molecular signatures and drug repurposing for COVID-19/Asthma comorbidity: ACE2 and multi-partite networks

Angiotensin-converting enzyme 2 (ACE2) is identified as the functional receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the ongoing global coronavirus disease-2019 (COVID-19) pandemic. This study aimed to elucidate potential therapeutic avenues by scrutinizing approved drugs through the identification of the genetic signature associated with SARS-CoV-2 infection in individuals with asthma. This exploration was conducted through an integrated analysis, encompassing interaction networks between the ACE2 receptor and common host (co-host) factors implicated in COVID-19/asthma comorbidity. The comprehensive analysis involved the identification of common differentially expressed genes (cDEGs) and hub-cDEGs, functional annotations, interaction networks, gene set variation analysis (GSVA), gene set enrichment analysis (GSEA), and module construction. Interaction networks were used to identify overlapping disease modules and potential drug targets. Computational biology and molecular docking analyzes were utilized to discern functional drug modules. Subsequently, the impact of the identified drugs on the expression of hub-cDEGs was experimentally validated using a mouse model. A total of 153 cDEGs or co-host factors associated with ACE2 were identified in the COVID-19 and asthma comorbidity. Among these, seven significant cDEGs and proteins - namely, HRAS, IFNG, JUN, CDH1, TLR4, ICAM1, and SCD-were recognized as pivotal host factors linked to ACE2. Regulatory network analysis of hub-cDEGs revealed eight top-ranked transcription factors (TFs) proteins and nine microRNAs as key regulatory factors operating at the transcriptional and post-transcriptional levels, respectively. Molecular docking simulations led to the proposal of 10 top-ranked repurposable drug molecules (Rapamycin, Ivermectin, Everolimus, Quercetin, Estradiol, Entrectinib, Nilotinib, Conivaptan, Radotinib, and Venetoclax) as potential treatment options for COVID-19 in individuals with comorbid asthma. Validation analysis demonstrated that Rapamycin effectively inhibited ICAM1 expression in the HDM-stimulated mice group (p < 0.01). This study unveils the common pathogenesis and genetic signature underlying asthma and SARS-CoV-2 infection, delineated by the interaction networks of ACE2-related host factors. These findings provide valuable insights for the design and discovery of drugs aimed at more effective therapeutics within the context of lung disease comorbidities.

Multi-ligand molecular docking, simulation, free energy calculations and wavelet analysis of the synergistic effects between natural compounds baicalein and cubebin for the inhibition of the main protease of SARS-CoV-2

Combination drugs have been used for several diseases for many years since they produce better therapeutic effects. However, it is still a challenge to discover candidates to form a combination drug. This study aimed to investigate whether using a comprehensive in silico approach to identify novel combination drugs from a Chinese herbal formula is an appropriate and creative strategy. We, therefore, used Toujie Quwen Granules for the main protease (M^pro) of SARS-CoV-2 as an example. We first used molecular docking to identify molecular components of the formula which may inhibit M^pro. Baicalein (HQA004) is the most favorable inhibitory ligand. We also identified a ligand from the other component, cubebin (CHA008), which may act to support the proposed HQA004 inhibitor. Molecular dynamics simulations were then performed to further elucidate the possible mechanism of inhibition by HQA004 and synergistic bioactivity conferred by CHA008. HQA004 bound strongly at the active site and that CHA008 enhanced the contacts between HQA004 and M^pro. However, CHA008 also dynamically interacted at multiple sites, and continued to enhance the stability of HQA004 despite diffusion to a distant site. We proposed that HQA004 acted as a possible inhibitor, and CHA008 served to enhance its effects via allosteric effects at two sites. Additionally, our novel wavelet analysis showed that as a result of CHA008 binding, the dynamics and structure of M^pro were observed to have more subtle changes, demonstrating that the inter-residue contacts within M^pro were disrupted by the synergistic ligand. This work highlighted the molecular mechanism of synergistic effects between different herbs as a result of allosteric crosstalk between two ligands at a protein target, as well as revealed that using the multi-ligand molecular docking, simulation, free energy calculations and wavelet analysis to discover novel combination drugs from a Chinese herbal remedy is an innovative pathway.

Kaempferol has potential anti-coronavirus disease 2019 (COVID-19) targets based on bioinformatics analyses and pharmacological effects on endotoxin-induced cytokine storm

COVID-19 has infected 272 million patients and caused 5.33 million deaths around the world, and it remains the main global threat. Previous studies revealed that Chinese traditional medicine is an effective treatment for COVID-19 infection. This study aims to reveal the pharmacological effects of kaempferol, which is the active component of Radix Bupleuri and Tripterygii Radix, and potential mechanisms for the treatment of COVID-19. Here, we employed the bioinformatics methods to filter the anti-COVID-19 candidate genes of kaempferol, which mainly enriched in inflammation (TNF, JUN, etc.) and virus infection (AKT1, JNK, etc.). The Transcription levels of AKT1, JNK and JUN were significantly reduced by kaempferol treatment in the LPS-activated macrophages. In addition, kaempferol reduced the secretion of inflammatory factors by LPS-stimulated macrophages, inhibited MAPK/NF-κB signaling and regulated macrophage polarization to M2 type in vitro, and suppressed endotoxin-induced cytokine storm and improved survival in mice. Molecular docking analysis demonstrated that kaempferol was probable to bind the COVID-19 protein 5R84 and formatted hydrogen bond with the residues, the free binding energy of which was lower than the original ligand. In summary, our current work indicates that kaempferol has anti-COVID-19 potential through the reduction of COVID-19-induced body dysfunction and molecule-protein interaction, and bioinformatics results clarify that some of these key target genes might serve as potential molecular markers for detecting COVID-19.

A bibliometric analysis of research related Chinese Medicine in the prevention and treatment of corona virus disease 2019

Objective

To perform a bibliometric analysis of published research related to the use of traditional Chinese medicine (TCM) for the treatment of Coronavirus Disease 2019 (COVID-19).

Methods

Research documents related to the use of TCM for prevention and treatment of COVID-19 published up to September 19, 2021, were retrieved from the Web of Science database. Bibliometrix R 4.0 software package was used to analyze data, including countries of publication, research institutions, journals, citations, and keywords. Further analysis was conducted to identify co-occurrence of keywords in the documents, including their titles and abstracts. Cooperative network analyses of authors, institutions, and countries of publication were also conducted. The classification types were statistically analyzed and the research progress of key TCMs was reviewed.

Results

A total of 417 documents were included in our analysis. Of these, 85.13% originated in China. Of the 417 documents, 148 (35.5%) were published in journals with impact factors in quartile 1 and 164 (39.3%) in journals in quartile 2. The documents were mainly published in journals categorized as Medicine. The results of network analysis showed close cooperation between institutions and countries. Excluding disease- and drug-related keywords, the top four keywords were ‘Systematic review’, ‘Network pharmacology’, ‘Medicine’ and ‘Molecular docking’. Keyword co-occurrence analysis showed 4 main keywords association groups. Statistical analysis of the TCM studies showed that Lianhua Qingwen capsule, Qingfei Paidu decoction, Shufeng Jiedu capsules and ReDuNing injection were the most studied Chinese medicines. Lianhua Qingwen capsules, Qingfei Paidu decoction, ReDuNing injection, and Shufeng Jiedu capsules were used in clinical, bioinformatics, and basic research. Toujie Quwen granule, Jinhua Qinggan granule, Shuanghuanglian oral liquid, Tanreqing injection, and Xuanfei Baidu decoction were used in clinical and bioinformatics research, although basic research on their mechanisms of action is lacking.

Conclusion

Research intensity and recognition, as well as cooperation, in the field of Chinese medicine for the prevention and treatment of COVID-19 has increased. Research types are generally comprehensive, and investigated several TCM formulations that are specifically recommended by Chinese COVID-19 guidelines. However, comprehensive, in-depth research on their molecular mechanisms of action is still lacking. More basic research is thus needed to identify therapeutic mechanisms to standardize and validate the use of TCM in the prevention and treatment of COVID-19.

The Potential Complementary Role of Using Chinese Herbal Medicine with Western Medicine in Treating COVID-19 Patients: Pharmacology Network Analysis

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic in 2019—coronavirus disease (COVID-19). More and more Western medicine (WM) and Chinese herbal medicine (CHM) treatments have been used to treat COVID-19 patients, especially among Asian populations. However, the interactions between WM and CHM have not been studied. This study aims at using the network pharmacology approach to explore the potential complementary effects among commonly used CHM and WM in a clinical setting from a biomolecular perspective. Three well-published and widely used CHM formulas (National Research Institute of Chinese Medicine 101 (NRICM101), Qing-Fei-Pai-Du-Tang (QFPDT), Hua-Shi-Bai-Du-Formula (HSBDF)) and six categories of WM (Dexamethasone, Janus kinase inhibitors (JAKi), Anti-Interleukin-6 (Anti-IL6), anticoagulants, non-vitamin K antagonist oral anticoagulants (NOAC), and Aspirin) were included in the network pharmacology analysis. The target proteins on which these CHM and WM had direct effects were acquired from the STITCH database, and the potential molecular pathways were found in the REACTOME database. The COVID-19-related target proteins were obtained from the TTD database. For the three CHM formulas, QFPDT covered the most proteins (714), and 27 of them were COVID-19-related, while HSBDF and NRICM101 covered 624 (24 COVID-19-related) and 568 (25 COVID-19-related) proteins, respectively. On the other hand, WM covered COVID-19-related proteins more precisely and seemed different from CHM. The network pharmacology showed CHM formulas affected several inflammation-related proteins for COVID-19, including IL-10, TNF-α, IL-6, TLR3, and IL-8, in which Dexamethasone and Aspirin covered only IL-10 and TNF-α. JAK and IL-6 receptors were only inhibited by WM. The molecular pathways covered by CHM and WM also seemed mutually exclusive. WM had advantages in cytokine signaling, while CHM had an add-on effect on innate and adaptive immunity, including neutrophil regulation. WM and CHM could be used together to strengthen the anti-inflammation effects for COVID-19 from different pathways, and the combination of WM and CHM may achieve more promising results. These findings warrant further clinical studies about CHM and WM use for COVID-19 and other diseases.

Traditional Herbal Medicines, Bioactive Metabolites, and Plant Products Against COVID-19: Update on Clinical Trials and Mechanism of Actions

SARS-CoV-2 is the latest worldwide pandemic declared by the World Health Organization and there is no established anti-COVID-19 drug to combat this notorious situation except some recently approved vaccines. By affecting the global public health sector, this viral infection has created a disastrous situation associated with high morbidity and mortality rates along with remarkable cases of hospitalization because of its tendency to be high infective. These challenges forced researchers and leading pharmaceutical companies to find and develop cures for this novel strain of coronavirus. Besides, plants have a proven history of being notable wellsprings of potential drugs, including antiviral, antibacterial, and anticancer therapies. As a continuation of this approach, plant-based preparations and bioactive metabolites along with a notable number of traditional medicines, bioactive phytochemicals, traditional Chinese medicines, nutraceuticals, Ayurvedic preparations, and other plant-based products are being explored as possible therapeutics against COVID-19. Moreover, the unavailability of effective medicines against COVID-19 has driven researchers and members of the pharmaceutical, herbal, and related industries to conduct extensive investigations of plant-based products, especially those that have already shown antiviral properties. Even the recent invention of several vaccines has not eliminated doubts about safety and efficacy. As a consequence, many limited, unregulated clinical trials involving conventional mono- and poly-herbal therapies are being conducted in various areas of the world. Of the many clinical trials to establish such agents as credentialed sources of anti-COVID-19 medications, only a few have reached the landmark of completion. In this review, we have highlighted and focused on plant-based anti-COVID-19 clinical trials found in several scientific and authenticated databases. The aim is to allow researchers and innovators to identify promising and prospective anti-COVID-19 agents in clinical trials (either completed or recruiting) to establish them as novel therapies to address this unwanted pandemic.

Guangdong's experience in defeating the COVID-19

To provide valuable experience for other countries currently fighting the COVID-19 pandemic by systematically analyzing the effects of control policies on coping with COVID-19 in Guangdong Province of China. Integrating qualitative and quantitative methods to systematically analyze the effects of control policies on fighting COVID-19 with official data in Guangdong Province. Between January 19, 2020 and February 26, 2020, Guangdong Province issued 6 critical control policies to cope with COVID-19 and achieved effects in the following 3-phase. 1. Phase 1: from January 19 to February 7, 2020, Guangdong Province issued the following 4 policies: activating the first-level response to public health emergencies; holding press conferences during the epidemic; carrying out grid investigation; and taking the lead in covering the treatment expenses of suspected patients in basic medical insurance. In this phase, the number of confirmed cases increased rapidly and the number of recovered cases increased gradually. 2. Phase 2: from February 8 to 14, Guangdong Province issued the following 2 polices: applying Toujie Quwen granules to 30 designated hospitals and launching a registration and report system for the sale of fever and cough drugs. In this phase, the growth trend of confirmed cases had slowed down on February 10 and then increased slowly on February 14. The number of recovered cases increased rapidly on February 10 and then increased rapidly on February 14. 3. Phase 3: from February 15 to 26, the increase number of confirmed cases was a small in magnitude on February 20 and then increased slowly on February 26. The number of recovered cases increased rapidly on February 20 and then increased rapidly on February 26. Guangdong Province implemented 6 control policies in 3-phase and finally successfully defeated the COVID-19. In the first phase, the first 4 control policies showed initial effects on COVID-19 epidemic control. In the second phase, the last 2 control policies greatly contributed to containing the COVID-19 epidemic. In the third phase, the 6 control policies completely overcame the COVID-19 in Guangdong Province, China.

Flavonoids against the SARS-CoV-2 induced inflammatory storm

The disease severity of COVID-19, especially in the elderly and patients with co-morbidities, is characterized by hypercytokinemia, an exaggerated immune response associated with an uncontrolled and excessive release of proinflammatory cytokine mediators (cytokine storm). Flavonoids, important secondary metabolites of plants, have long been studied as therapeutic interventions in inflammatory diseases due to their cytokine-modulatory effects. In this review, we discuss the potential role of flavonoids in the modulation of signaling pathways that are crucial for COVID-19 disease, particularly those related to inflammation and immunity. The immunomodulatory ability of flavonoids, carried out by the regulation of inflammatory mediators, the inhibition of endothelial activation, NLRP3 inflammasome, toll-like receptors (TLRs) or bromodomain containing protein 4 (BRD4), and the activation of the nuclear factor erythroid-derived 2-related factor 2 (Nrf2), might be beneficial in regulating the cytokine storm during SARS-CoV-2 infection. Moreover, the ability of flavonoids to inhibit dipeptidyl peptidase 4 (DPP4), neutralize 3-chymotrypsin-like protease (3CL^pro) or to affect gut microbiota to maintain immune response, and the dual action of angiotensin-converting enzyme 2 (ACE-2) may potentially also be applied to the exaggerated inflammatory responses induced by SARS-CoV-2. Based on the previously proven effects of flavonoids in other diseases or on the basis of newly published studies associated with COVID-19 (bioinformatics, molecular docking), it is reasonable to assume positive effects of flavonoids on inflammatory changes associated with COVID-19. This review highlights the current state of knowledge of the utility of flavonoids in the management of COVID-19 and also points to the multiple biological effects of flavonoids on signaling pathways associated with the inflammation processes that are deregulated in the pathology induced by SARS-CoV-2. The identification of agents, including naturally occurring substances such as flavonoids, represents great approach potentially utilizable in the management of COVID-19. Although not clinically investigated yet, the applicability of flavonoids against COVID-19 could be a promising strategy due to a broad spectrum of their biological activities.

Scutellaria baicalensis Flavones as Potent Drugs against Acute Respiratory Injury during SARS-CoV-2 Infection: Structural Biology Approaches

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in severe damage to the respiratory system. With no specific treatment to date, it is crucial to identify potent inhibitors of SARS-CoV-2 Chymotrypsin-like protease (3CLpro) that could also modulate the enzymes involved in the respiratory damage that accompanies SARS-CoV-2 infection. Here, flavones isolated from Scutellaria baicalensis (baicalein, baicalin, wogonin, norwogonin, and oroxylin A) were studied as possible compounds in the treatment of SARS-CoV-2 and SARS-CoV-2-induced acute lung injuries. We used structural bioinformatics and cheminformatics to (i) identify the critical molecular features of flavones for their binding activity at human and SARS-CoV-2 enzymes; (ii) predict their drug-likeness and lead-likeness features; (iii) calculate their pharmacokinetic profile, with an emphasis on toxicology; (iv) predict their pharmacodynamic profiles, with the identification of their human body targets involved in the respiratory system injuries; and (v) dock the ligands to SARS-CoV-2 3CLpro. All flavones presented appropriate drug-like and kinetics features, except for baicalin. Flavones could bind to SARS-CoV-2 3CLpro at a similar site, but interact slightly differently with the protease. Flavones’ pharmacodynamic profiles predict that (i) wogonin strongly binds at the cyclooxygenase2 and nitric oxide synthase; (ii) baicalein and norwogonin could modulate lysine-specific demethylase 4D-like and arachidonate 15-lipoxygenase; and (iii) baicalein, wogonin, norwogonin, and oroxylin A bind to SARS-CoV-2 3CLpro. Our results propose these flavones as possible potent drugs against respiratory damage that occurs during SARS-CoV-2 infections, with a strong recommendation for baicalein.

Analysis of the mechanism of Shufeng Jiedu capsule prevention and treatment for COVID-19 by network pharmacology tools

Introduction

The novel coronavirus pneumonia that broke out in 2019 has become a global epidemic. According to the diagnosis and treatment plan issued in China and the existing clinical data, Shufeng Jiedu (SFJD) Capsule can be effectively used in the treatment of COVID-19 patients. This study aimed to explore its mechanism of action by network pharmacology and molecular docking technology.

Methods

The Chinese Medicine System Pharmacology Analysis Platform (TCMSP), a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine (BATMAN-TCM), the Encyclopedia of Traditional Chinese Medicine (ETCM) and related literature records were used to search the composition and main active compounds of SFJD, and to screen out the targets of drug components. Disease-associated genes were obtained by the Human Gene Database (GeneCards), the Human Online Mendelian Inheritance Platform (OMIM) and the DisGeNET database, and the co-targeted genes/proteins as targets of both SFJD and COVID-19 were selected by the Comparative Toxicogenomics Database (CTD). Co-targeted genes/proteins were analyzed by STRING, the Database for Annotation, Visualization and Integrated Discovery (DAVID) and Reactome for proteins to protein interaction (PPI), pathway and GO (gene ontology) enrichment, and predicted by AutoDock for their high-precision docking simulation. In addition, the therapeutic effect for SFJD treatment on COVID-19 was validated by the Chinese medicine anti-novel coronavirus pneumonia drug effect prediction and analysis platform (TCMCOVID).

Results

Screening resulted in 163 compounds and 463 targeted genes. The PPI core network contains 76 co-targeted proteins. The Reactome pathways were enriched in signaling by interleukins, immune system, etc. Finally, 6 key proteins of TNF, IL-10, IL-2, IL-6, STAT1 and CCL2 were selected and successfully docked with 4 active ingredients of quercetin, luteolin, wogonin and kaempferol.

Conclusion

SFJD may play a role in the prevention and treatment of COVID-19 through multiple active compounds acting on multiple targets and then multiple pathways.