Network pharmacology and RNA-sequencing reveal the molecular mechanism of Xuebijing injection on COVID-19-induced cardiac dysfunction

Therapeutic implications of quercetin and its derived-products in COVID-19 protection and prophylactic

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel human coronavirus, which has triggered a global pandemic of the coronavirus infectious disease 2019 (COVID-19). Outbreaks of emerging infectious diseases continue to challenge human health worldwide. The virus conquers human cells through the angiotensin-converting enzyme 2 receptor-driven pathway by mostly targeting the human respiratory tract. Quercetin is a natural flavonoid widely represented in the plant kingdom. Cumulative evidence has demonstrated that quercetin and its derivatives have various pharmacological properties including anti-cancer, anti-hypertension, anti-hyperlipidemia, anti-hyperglycemia, anti-microbial, antiviral, neuroprotective, and cardio-protective effects, because it is a potential treatment for severe inflammation and acute respiratory distress syndrome. Furthermore, it is the main life-threatening condition in patients with COVID-19. This article provides a comprehensive review of the primary literature on the predictable effectiveness of quercetin and its derivatives docked to multi-target of SARS-CoV-2 and host cells via in silico and some of validation through in vitro, in vivo, and clinically to fight SARS-CoV-2 infections, contribute to the reduction of inflammation, which suggests the preventive and therapeutic latency of quercetin and its derived-products against COVID-19 pandemic, multisystem inflammatory syndromes (MIS), and long-COVID.

Bibliometric analysis and key messages of integrating Chinese and Western Medicine for COVID-19

Background

The coronavirus disease 2019 (COVID-19) has been a global pandemic since it broke out, and integrated Chinese and Western medicine (ICWM) has played an important role in the prevention and treatment of COVID-19. We aimed to analyze the published literature on ICWM for COVID-19 at home and abroad, and compare their differences on hotspots and research fronts.

Methods

Publications before Oct 31, 2022 were retrieved from the Web of Science core database (WOS), PubMed, China National Knowledge Infrastructure database (CNKI), Wanfang Data Knowledge Service Platform (Wanfang), China Science and Technology Journal Database (VIP), China Biology Medicine disc (CBM), CiteSpace and VOSviewer to summarize the basic characteristics of publications, countries, institutions, keywords, and citations.

Results

We included 580 English papers and 1727 Chinese papers in this study. The development trends in China and other countries are relatively asynchronous and show a smooth growth trend for the future. The most productive countries were China, India, and the United States, while the most productive domestic research institution was the Beijing University of Chinese Medicine. The clustering analysis of high-frequency keywords showed that Chinese literature focused on clinical studies of ICWM for COVID-19, such as retrospective studies, clinical features, and traditional Chinese medicine syndrome analysis, while English literature focused on therapeutic mechanism studies and evidence-based medicine studies, such as systematic reviews and meta-analysis, and both of them paid attention to network pharmacological research and Qingfei Paidu Decoction. Sorting out the top 10 highly cited articles, Huang CL's article published in Lancet in 2020 was regarded as a cornerstone in the field.

Conclusion

The treatment of COVID-19 by ICWM has become a worldwide research hotspot. Although there are differences in the specific contents among countries, the development trend of research types to the mechanism of action, and the development trend of research contents to the recovery period treatment and the prevention of COVID-19 by ICWM are consistent.

SinCWIm: An imputation method for single-cell RNA sequence dropouts using weighted alternating least squares

BACKGROUND AND OBJECTIVES

Single-cell RNA sequencing (scRNA-seq) provides a powerful tool for exploring cellular heterogeneity, discovering novel or rare cell types, distinguishing between tissue-specific cellular composition, and understanding cell differentiation during development. However, due to technological limitations, dropout events in scRNA-seq can mistakenly convert some entries in the real data to zero. This is equivalent to introducing noise into the data of cell gene expression entries. The data is contaminated, which affects the performance of downstream analyses, including clustering, cell annotation, differential gene expression analysis, and so on. Therefore, it is a crucial work to accurately determine which zeros are due to dropout events and perform imputation operations on them.

METHODS

Considering the different confidence levels of different zeros in the gene expression matrix, this paper proposes a SinCWIm method for dropout events in scRNA-seq based on weighted alternating least squares (WALS). The method utilizes Pearson correlation coefficient and hierarchical clustering to quantify the confidence of zero entries. It is then combined with WALS for matrix decomposition. And the imputation result is made close to the actual number by outlier removal and data correction operations.

RESULTS

A total of eight single-cell sequencing datasets were used for comparative experiments to demonstrate the overall superiority of SinCWIm over state-of-the-art models. SinCWIm was applied to cluster the data to obtain an adjusted RAND index evaluation, and the Usoskin, Pollen and Bladder datasets scored 94.46%, 96.48% and 76.74%, respectively. In addition, significant improvements were made in the retention of differential expression genes and visualization.

CONCLUSIONS

SinCWIm provides a valuable imputation method for handling dropout events in single-cell sequencing data. In comparison to advanced methods, SinCWIm demonstrates excellent performance in clustering, visualization and other aspects. It is applicable to various single-cell sequencing datasets.

Phenome-wide association study and precision medicine of cardiovascular diseases in the post-COVID-19 era

SARS-CoV-2 infection causes injuries of not only the lungs but also the heart and endothelial cells in vasculature of multiple organs, and induces systemic inflammation and immune over-reactions, which makes COVID-19 a disease phenome that simultaneously affects multiple systems. Cardiovascular diseases (CVD) are intrinsic risk and causative factors for severe COVID-19 comorbidities and death. The wide-spread infection and reinfection of SARS-CoV-2 variants and the long-COVID may become a new common threat to human health and propose unprecedented impact on the risk factors, pathophysiology, and pharmacology of many diseases including CVD for a long time. COVID-19 has highlighted the urgent demand for precision medicine which needs new knowledge network to innovate disease taxonomy for more precise diagnosis, therapy, and prevention of disease. A deeper understanding of CVD in the setting of COVID-19 phenome requires a paradigm shift from the current phenotypic study that focuses on the virus or individual symptoms to phenomics of COVID-19 that addresses the inter-connectedness of clinical phenotypes, i.e., clinical phenome. Here, we summarize the CVD manifestations in the full clinical spectrum of COVID-19, and the phenome-wide association study of CVD interrelated to COVID-19. We discuss the underlying biology for CVD in the COVID-19 phenome and the concept of precision medicine with new phenomic taxonomy that addresses the overall pathophysiological responses of the body to the SARS-CoV-2 infection. We also briefly discuss the unique taxonomy of disease as Zheng-hou patterns in traditional Chinese medicine, and their potential implications in precision medicine of CVD in the post-COVID-19 era.

Xuebijing injection, a Chinese patent medicine, against severe pneumonia: Current research progress and future perspectives

Severe pneumonia is one of the most common infectious diseases and the leading cause of sepsis and septic shock. Preventing infection, balancing the patient's immune status, and anti-coagulation therapy are all important elements in the treatment of severe pneumonia. As multi-target agents, Xuebijing injection (XBJ) has shown unique advantages in targeting complex conditions and saving the lives of patients with severe pneumonia. This review outlines progress in the understanding of XBJ's anti-inflammatory, endotoxin antagonism, and anticoagulation effects. From the hundreds of publications released over the past few years, the key results from representative clinical studies of XBJ in the treatment of severe pneumonia were selected and summarized. XBJ was observed to effectively suppress the release of pro-inflammatory cytokines, counter the effects of endotoxin, and assert an anticoagulation effect in most clinical trials, which are consistent with experimental studies. Collectively, this evidence suggests that XBJ could play an important and expanding role in clinical medicine, especially for sepsis, septic shock and severe pneumonia. Please cite this article as: Zhang M, Zheng R, Liu WJ, Hou JL, Yang YL, Shang HC. Xuebijing injection, a Chinese patent medicine, against severe pneumonia: Current research progress and future perspectives. J Integr Med. 2023; 21(5): 413-422.

Discovering Traditional Chinese Medicine (TCM) Formulas for Complex Diseases Based on a Combination of Reverse Systematic Pharmacology and TCM Meridian Tropism Theory: Taking COVID-19 as an Example

OBJECTIVE

Infections and death have been a part of our daily lives since the COVID-2019 pandemic outbreak in 2019, and the societal and economic consequences have lingered for an unanticipated duration. Novel and effective treatments are still desperately needed around the world to combat the infection. Here, we discovered a novel traditional Chinese medicine formula (TCMF) to potentially combat COVID-19 through reverse systematic pharmacology (disease → targets → TCMF → disease).

METHODS

Combining Integrative network pharmacology and the traditional Chinese medicine (TCM) theory, a TCMF for COVID-19 was identified. In silico physiological interactions between herbs and disease hub targets were validated by molecular docking and dynamics simulation.

RESULTS

Based on disease-related gene/pathway targets and a combination of reverse pharmacology and TCM meridian tropism theory, a COVID-19-associated herb database was constructed. A new TCMF, including Gancao, Baitouweng, Congbai, and Diyu (GBCD), was discovered for anti-COVID-19 therapy. The KEGG and GO analyses of 49 intersecting genes suggested that GBCD could combat COVID-19 through antiviral, antiinflammation, immunoregulation, and cytoprotection activities. Moreover, these possible effects were validated through docking and MD simulation.

CONCLUSIONS

To the best of our knowledge, this study is the first to combine reverse pharmacology and meridian tropism theories for TCMF development, and a novel herbal combination, GBCD, was discovered for anti-COVID-19 therapy.

Potential herb‒drug interactions between anti-COVID-19 drugs and traditional Chinese medicine

Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread worldwide. Effective treatments against COVID-19 remain urgently in need although vaccination significantly reduces the incidence, hospitalization, and mortality. At present, antiviral drugs including Nirmatrelvir/Ritonavir (Paxlovid^TM), Remdesivir, and Molnupiravir have been authorized to treat COVID-19 and become more globally available. On the other hand, traditional Chinese medicine (TCM) has been used for the treatment of epidemic diseases for a long history. Currently, various TCM formulae against COVID-19 such as Qingfei Paidu decoction, Xuanfei Baidu granule, Huashi Baidu granule, Jinhua Qinggan granule, Lianhua Qingwen capsule, and Xuebijing injection have been widely used in clinical practice in China, which may cause potential herb-drug interactions (HDIs) in patients under treatment with antiviral drugs and affect the efficacy and safety of medicines. However, information on potential HDIs between the above anti-COVID-19 drugs and TCM formulae is lacking, and thus this work seeks to summarize and highlight potential HDIs between antiviral drugs and TCM formulae against COVID-19, and especially pharmacokinetic HDIs mediated by metabolizing enzymes and/or transporters. These well-characterized HDIs could provide useful information on clinical concomitant medicine use to maximize clinical outcomes and minimize adverse and toxic effects.

Herbal medicines exhibit a high affinity for ACE2 in treating COVID-19

Coronavirus Disease 2019 (COVID-19) has been an unprecedented disaster for people around the world. A point particularly worth noting is that herbal medicines have made great contributions to the prevention and treatment of COVID-19 in China. Angiotensin converting enzyme 2 (ACE2) has been identified as the critical functional receptor for SARS-CoV-2. It can bind to the receptor-binding domain (RBD) of the spike protein (S protein), which is responsible for the entry of the coronavirus into host cells. Therefore, ACE2 can be regarded as an important intervention target for COVID-19. Recently, many herbal medicines have exhibited a high affinity for ACE2 in treating COVID-19. The current work summarized these herbal medicines including formulas (such as Lianhua Qingwen capsules, Xuebijing injection, Qingfei Paidu Decoction, Huashi Baidu formula, Shufeng Jiedu capsules, and Maxing Shigan decoction), single herbs including Ephedra sinica Stapf (Mahuang), Scutellariae radix (Huangqin), Lonicera japonica (Jinyinhua), and Houttuynia cordata (Yuxingcao), and active ingredients (such as ursodeoxycholic acid, glycyrrhizic acid, glycyrrhizin, salvianolic acid, quercetin, and andrographidine C), which have exhibited a high affinity for ACE2 in treating COVID-19. We hope this work may provide meaningful and useful information on further research to investigate the mechanisms of herbal medicines against SARS-CoV-2 and follow-up drug discovery.

Effects and mechanisms of 6-hydroxykaempferol 3,6-di-O-glucoside-7-O-glucuronide from Safflower on endothelial injury in vitro and on thrombosis in vivo

Background: The florets of Carthamus tinctorius L. (Safflower) is an important traditional medicine for promoting blood circulation and removing blood stasis. However, its bioactive compounds and mechanism of action need further clarification.

Objective: This study aims to investigate the effect and possible mechanism of 6-hydroxykaempferol 3,6-di-O-glucoside-7-O-glucuronide (HGG) from Safflower on endothelial injury in vitro, and to verify its anti-thrombotic activity in vivo.

Methods: The endothelial injury on human umbilical vein endothelial cells (HUVECs) was induced by oxygen-glucose deprivation followed by reoxygenation (OGD/R). The effect of HGG on the proliferation of HUVECs under OGD/R was evaluated by MTT, LDH release, Hoechst-33342 staining, and Annexin V-FITC apoptosis assay. RNA-seq, RT-qPCR, Enzyme-linked immunosorbent assay and Western blot experiments were performed to uncover the molecular mechanism. The anti-thrombotic effect of HGG in vivo was evaluated using phenylhydrazine (PHZ)-induced zebrafish thrombosis model.

Results: HGG significantly protected OGD/R induced endothelial injury, and decreased HUVECs apoptosis by regulating expressions of hypoxia inducible factor-1 alpha (HIF-1α) and nuclear factor kappa B (NF-κB) at both transcriptome and protein levels. Moreover, HGG reversed the mRNA expression of pro-inflammatory cytokines including IL-1β, IL-6, and TNF-α, and reduced the release of IL-6 after OGD/R. In addition, HGG exhibited protective effects against PHZ-induced zebrafish thrombosis and improved blood circulation.

Conclusion: HGG regulates the expression of HIF-1α and NF-κB, protects OGD/R induced endothelial dysfunction in vitro and has anti-thrombotic activity in PHZ-induced thrombosis in vivo.

A review on computational approaches that support the researches on traditional Chinese medicines (TCM) against COVID-19

BACKGROUND

COVID-19 highly caused contagious infections and massive deaths worldwide as well as unprecedentedly disrupting global economies and societies, and the urgent development of new antiviral medications are required. Medicinal herbs are promising resources for the discovery of prophylactic candidate against COVID-19. Considerable amounts of experimental efforts have been made on vaccines and direct-acting antiviral agents (DAAs), but neither of them was fast and fully developed.

PURPOSE

This study examined the computational approaches that have played a significant role in drug discovery and development against COVID-19, and these computational methods and tools will be helpful for the discovery of lead compounds from phytochemicals and understanding the molecular mechanism of action of TCM in the prevention and control of the other diseases.

METHODS

A search conducting in scientific databases (PubMed, Science Direct, ResearchGate, Google Scholar, and Web of Science) found a total of 2172 articles, which were retrieved via web interface of the following websites. After applying some inclusion and exclusion criteria and full-text screening, only 292 articles were collected as eligible articles.

RESULTS

In this review, we highlight three main categories of computational approaches including structure-based, knowledge-mining (artificial intelligence) and network-based approaches. The most commonly used database, molecular docking tool, and MD simulation software include TCMSP, AutoDock Vina, and GROMACS, respectively. Network-based approaches were mainly provided to help readers understanding the complex mechanisms of multiple TCM ingredients, targets, diseases, and networks.

CONCLUSION

Computational approaches have been broadly applied to the research of phytochemicals and TCM against COVID-19, and played a significant role in drug discovery and development in terms of the financial and time saving.

Role of the CCL2-CCR2 axis in cardiovascular disease: Pathogenesis and clinical implications

The CCL2-CCR2 axis is one of the major chemokine signaling pathways that has received special attention because of its function in the development and progression of cardiovascular disease. Numerous investigations have been performed over the past decades to explore the function of the CCL2-CCR2 signaling axis in cardiovascular disease. Laboratory data on the CCL2-CCR2 axis for cardiovascular disease have shown satisfactory outcomes, yet its clinical translation remains challenging. In this article, we describe the mechanisms of action of the CCL2-CCR2 axis in the development and evolution of cardiovascular diseases including heart failure, atherosclerosis and coronary atherosclerotic heart disease, hypertension and myocardial disease. Laboratory and clinical data on the use of the CCL2-CCR2 pathway as a targeted therapy for cardiovascular diseases are summarized. The potential of the CCL2-CCR2 axis in the treatment of cardiovascular diseases is explored.

Revealing the efficacy-toxicity relationship of Fuzi in treating rheumatoid arthritis by systems pharmacology

In recent decades, herbal medicines have played more and more important roles in the healthcare system in the world because of the good efficacy. However, with the increasing use of herbal medicines, the toxicity induced by herbal medicines has become a global issue. Therefore, it is needed to investigate the mechanism behind the efficacy and toxicity of herbal medicines. In this study, using Aconiti Lateralis Radix Praeparata (Fuzi) as an example, we adopted a systems pharmacology approach to investigate the mechanism of Fuzi in treating rheumatoid arthritis and in inducing cardiac toxicity and neurotoxicity. The results showed that Fuzi has 25 bioactive compounds that act holistically on 61 targets and 27 pathways to treat rheumatoid arthritis, and modulation of inflammation state is one of the main mechanisms of Fuzi. In addition, the toxicity of Fuzi is linked to 32 compounds that act on 187 targets and 4 pathways, and the targets and pathways can directly modulate the flow of Na+, Ca2+, and K+. We also found out that non-toxic compounds such as myristic acid can act on targets of toxic compounds and therefore may influence the toxicity. The results not only reveal the efficacy and toxicity mechanism of Fuzi, but also add new concept for understanding the toxicity of herbal medicines, i.e., the compounds that are not directly toxic may influence the toxicity as well.