In silico-based screen synergistic drug combinations from herb medicines: a case using Cistanche tubulosa

Extract of Isatidis Radix Inhibits Lipid Accumulation in In Vitro and In Vivo by Regulating Oxidative Stress

Isatidis Radix (IR), the root of Isatis tinctoria L. belonging to Brassicaceae, has been traditionally used as a fever reducer. Although some pharmacological effects, such as anti-diabetes, anti-virus, and anti-inflammatory, have been reported, there is no study on the anti-obesity effect of IR. This study used 3T3-L1 cells, human mesenchymal adipose stem cells (hAMSCs), and a high-fat diet (HFD)-induced obese mouse model to confirm the anti-adipogenic effect of IR. Intracellular lipid accumulation in 3T3-L1 cells and hAMSCs was decreased by IR treatment.IR extract especially suppressed reactive oxygen species (ROS) production through a cluster of differentiation 36 (CD36)-AMP-activated protein kinase (AMPK) pathway. Consequently, the expressions of peroxisome proliferator-activated receptor gamma (PPARγ), CCAAT-enhancer-binding proteins alpha (C/EBPα), and fatty acid synthesis (FAS) were inhibited by IR extract. In addition, β-oxidation-related genes were also decreased by treatment of IR extract. IR inhibited weight gain through this cascade in the HFD-induced obese mouse model. IR significantly suppressed lipid accumulation in epididymal white adipose tissue (eWAT). Furthermore, the administration of IR extract decreased serum free fatty acid (FFA), total cholesterol (TC), and LDL cholesterol, suggesting that it could be a potential drug for obesity by inhibiting lipid accumulation.

Development of Novel Herbal Compound Formulations Targeting Neuroinflammation: Network Pharmacology, Molecular Docking, and Experimental Verification

Neuroinflammation plays an important role in the onset and progression of neurodegenerative diseases. The multicomponent and multitarget approach may provide a practical strategy to address the complex pathological mechanisms of neuroinflammation. This study aimed to develop synergistic herbal compound formulas to attenuate neuroinflammation using integrated network pharmacology, molecular docking, and experimental bioassays. Eight phytochemicals with anti-neuroinflammatory potential were selected in the present study. A compound-gene target-signaling pathway network was constructed to illustrate the mechanisms of action of each phytochemical and the interactions among them at the molecular level. Molecular docking was performed to verify the binding affinity of each phytochemical and its key gene targets. An experimental study was conducted to identify synergistic interactions among the eight phytochemicals, and the associated molecular mechanisms were examined by immunoblotting based on the findings from the network pharmacology analysis. Two paired combinations, andrographolide and 6-shogaol (AN-SG) (IC50 = 2.85 μg/mL), and baicalein-6-shogaol (BA-SG) (IC50 = 3.28 μg/mL), were found to synergistically (combination index <1) inhibit the lipopolysaccharides (LPS)-induced nitric oxide production in microglia N11 cells. Network pharmacology analysis suggested that MAPK14, MAPK8, and NOS3 were the top three relevant gene targets for the three phytochemicals, and molecular docking demonstrated strong binding affinities of the phytochemicals to their coded proteins. Immunoblotting suggested that the AN-SG and BA-SG both showed prominent effects in inhibiting inducible nitric oxide synthase (iNOS) (p < 0.01 and p < 0.05, respectively) and MAPKp-p38 (both p < 0.05) compared with those induced by the LPS stimulation only. The AN-SG combination exhibited greater inhibitions of the protein expressions of iNOS (p < 0.05 vs. individual components), which may partly explain the mechanisms of the synergy observed. This study established a practical approach to developing novel herbal-compound formulations using integrated network pharmacology analysis, molecular docking, and experimental bioassays. The study provides a scientific basis and new insight into the two synergistic combinations against neuroinflammation.

Natural product-based bioactive agents in combination attenuate neuroinflammation in a tri-culture model

Introduction: Neuroinflammation is an important pathological event contributing to the onset and progression of neurodegenerative diseases. The hyperactivation of microglia triggers the release of excessive proinflammatory mediators that lead to the leaky blood-brain barrier and impaired neuronal survival. Andrographolide (AN), baicalein (BA) and 6-shogaol (6-SG) possess anti-neuroinflammatory properties through diverse mechanisms of action. The present study aims to investigate the effects of the pair-combinations of these bioactive compounds in attenuating neuroinflammation. Methods: A tri-culture model with microglial N11 cells, microvascular endothelial MVEC(B3) cells, and neuroblastoma N2A cells was established in a transwell system. AN, BA and 6-SG used alone (25 µM) or in pair-wised combinations (12.5 + 12.5 µM) were subjected to the tri-culture system. Upon the stimulation of lipopolysaccharides (LPS) at 1 μg/mL, tumor necrosis factor-alpha (TNF-α) and interleukin 6 (IL-6) levels were determined by ELISA assays. Immunofluorescence staining was applied to investigate the nuclear translocation of nuclear factor kappa B p65 (NF-κB p65) on N11 cells, expressions of protein zonula occludens-1 (ZO-1) on MVEC cells and phosphorylated tau (p-tau) on N2A cells, respectively. The endothelial barrier permeability of MVEC cells was assessed by the Evans blue dye, and the resistance from the endothelial barrier was measured by transepithelial/endothelial electrical resistance (TEER) value. Neuronal survival of N2A cells was determined by Alamar blue and MTT assays. Results: Combinations of AN-SG and BA-SG synergistically lowered the TNF and IL-6 levels in LPS-induced N11 cells. Remarkably, the combined anti-neuroinflammatory effects of AN-SG and BA-SG remained significantly greater compared to their individual components at the same concentration level. The molecular mechanism of the attenuated neuroinflammation was likely to be mediated by downregulation of NF-κB p65 translocation (p < 0.0001 vs. LPS stimulation) in N11 cells. In the MVEC cells, both AN-SG and BA-SG restored TEER values, ZO-1 expression and reduced permeability. Furthermore, AN-SG and BA-SG significantly improved neuronal survival and reduced expressions of p-tau on N2A cells. Discussion: The AN-SG and BA-SG combinations showed greater anti-neuroinflammatory potential than those used alone in mono- and tri-cultured N11 cells, thereby further protecting endothelial tight junction and neuronal survival. Taken together, AN-SG and BA-SG may provide improved anti-neuroinflammatory and neuroprotective activities.

Metabolome profiling and molecular docking analysis revealed the metabolic differences and potential pharmacological mechanisms of the inflorescence and succulent stem of Cistanche deserticola

Cistanche deserticola is an endangered plant used for medicine and food. Our purpose is to explore the differences in metabolism between inflorescences in non-medicinal parts and succulent stems in medicinal parts in order to strengthen the application and development of the non-medicinal parts of C. deserticola. We performed metabolomics analysis through LC-ESI-MS/MS on the inflorescences and succulent stems of three ecotypes (saline-alkali land, grassland and sandy land) of C. deserticola. A total of 391 common metabolites in six groups were identified, of which isorhamnetin O-hexoside (inflorescence) and rosinidin O-hexoside (succulent stems) can be used as chemical markers to distinguish succulent stems and inflorescences. Comparing the metabolic differences of three ecotypes, we found that most of the different metabolites related to salt-alkali stress were flavonoids. In particular, we mapped the biosynthetic pathway of phenylethanoid glycosides (PhGs) and showed the metabolic differences in the six groups. To better understand the pharmacodynamic mechanisms and targets of C. deserticola, we screened 88 chemical components and 15 potential disease targets through molecular docking. The active ingredients of C. deserticola have a remarkable docking effect on the targets of aging diseases such as osteoporosis, vascular disease and atherosclerosis. To explore the use value of inflorescence, we analyzed the molecular docking of the unique flavonoid metabolites in inflorescence with inflammation targets. The results showed that chrysoeriol and cynaroside had higher scores for inflammation targets. This study provides a scientific basis for the discovery and industrialization of the resource value of the non-medicinal parts of C. deserticola, and the realization of the sustainable development of C. deserticola. It also provides a novel strategy for exploring indications of Chinese herb.

Flow chart for exploring the metabolic and pharmacological characteristics of different parts of Cistanche deserticola.

Network-based modeling of herb combinations in traditional Chinese medicine

Traditional Chinese medicine (TCM) has been practiced for thousands of years for treating human diseases. In comparison to modern medicine, one of the advantages of TCM is the principle of herb compatibility, known as TCM formulae. A TCM formula usually consists of multiple herbs to achieve the maximum treatment effects, where their interactions are believed to elicit the therapeutic effects. Despite being a fundamental component of TCM, the rationale of combining specific herb combinations remains unclear. In this study, we proposed a network-based method to quantify the interactions in herb pairs. We constructed a protein–protein interaction network for a given herb pair by retrieving the associated ingredients and protein targets, and determined multiple network-based distances including the closest, shortest, center, kernel, and separation, both at the ingredient and at the target levels. We found that the frequently used herb pairs tend to have shorter distances compared to random herb pairs, suggesting that a therapeutic herb pair is more likely to affect neighboring proteins in the human interactome. Furthermore, we found that the center distance determined at the ingredient level improves the discrimination of top-frequent herb pairs from random herb pairs, suggesting the rationale of considering the topologically important ingredients for inferring the mechanisms of action of TCM. Taken together, we have provided a network pharmacology framework to quantify the degree of herb interactions, which shall help explore the space of herb combinations more effectively to identify the synergistic compound interactions based on network topology.

A Network Pharmacology Study on the Molecular Mechanisms of FDY003 for Breast Cancer Treatment

Herbal medicines have drawn considerable attention with regard to their potential applications in breast cancer (BC) treatment, a frequently diagnosed malignant disease, considering their anticancer efficacy with relatively less adverse effects. However, their mechanisms of systemic action have not been understood comprehensively. Based on network pharmacology approaches, we attempted to unveil the mechanisms of FDY003, an herbal drug comprised of Lonicera japonica Thunberg, Artemisia capillaris Thunberg, and Cordyceps militaris, against BC at a systemic level. We found that FDY003 exhibited pharmacological effects on human BC cells. Subsequently, detailed data regarding the biochemical components contained in FDY003 were obtained from comprehensive herbal medicine-related databases, including TCMSP and CancerHSP. By evaluating their pharmacokinetic properties, 18 chemical compounds in FDY003 were shown to be potentially active constituents interacting with 140 BC-associated therapeutic targets to produce the pharmacological activity. Gene ontology enrichment analysis using g:Profiler indicated that the FDY003 targets were involved in the modulation of cellular processes, involving the cell proliferation, cell cycle process, and cell apoptosis. Based on a KEGG pathway enrichment analysis, we further revealed that a variety of oncogenic pathways that play key roles in the pathology of BC were significantly enriched with the therapeutic targets of FDY003; these included PI3K-Akt, MAPK, focal adhesion, FoxO, TNF, and estrogen signaling pathways. Here, we present a network-perspective of the molecular mechanisms via which herbal drugs treat BC.

Systems Pharmacology Study of the Anticervical Cancer Mechanisms of FDY003

Increasing data support that herbal medicines are beneficial in the treatment of cervical cancer; however, their mechanisms of action remain to be elucidated. In the current study, we used a systems pharmacology approach to explore the pharmacological mechanisms of FDY003, an anticancer herbal formula comprising Lonicera japonica Thunberg, Artemisia capillaris Thunberg, and Cordyceps militaris (Linn.) Link, in the treatment of cervical cancer. Through the pharmacokinetic assessment of absorption-distribution-metabolism-excretion characteristics, we found 18 active compounds that might interact with 106 cervical cancer-related targets responsible for the pharmacological effects. FDY003 targets were significantly associated with gene ontology terms related to the regulation of cellular behaviors, including cell proliferation, cell cycle processes, cell migration, cell apoptosis, cell death, and angiogenesis. The therapeutic targets of the herbal drug were further enriched in various oncogenic pathways that are implicated in the tumorigenesis and progression of cervical cancer, including the phosphatidylinositol 3-kinase, mitogen-activated protein kinase, focal adhesion, human papillomavirus infection, and tumor necrosis factor signaling pathways. Our study provides a systematic approach to explore the anticancer properties of herbal medicines against cervical cancer.

Systems Pharmacology Dissection of Mechanisms of Dengzhan Xixin Injection against Cardiovascular Diseases

Dengzhan Xixin injection (DZXXI), a herbal product prepared from a Chinese herb called Erigeron breviscapus, is a classical and traditional therapeutic for cadiovascular diseases (CVDs), including coronary heart disease (CHD), angina, and stroke, etc. However, its potential pharmacology mechanism against CVDs remains unclear. In this paper, a systems pharmacology-based strategy is presented for predicting drug targets and understanding therapeutic mechanisms of DZXXI against CVDs. The main ingredients were identified by HPLC-diode array detector (DAD). The target fishing was performed on the PharmMapper Server (http://lilab-ecust.cn/pharmmapper/). Potential targets were confirmed by two molecular docking tools, Sybyl-X 1.3 and Ledock to ensure the accuracy. The resulting target proteins were applied as baits to fish their related diseases and pathways from the molecular annotation system (MAS 3.0, http://bioinfo.capitalbio.com/mas3/) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database (http://www.genome.jp/kegg/). Network generation and topological analysis were performed in Cytoscape 3.6.0. 15 main ingredients from DZXXI were identified. Forty five putative drug targets and 50 KEGG pathways, which have highly relevance to the therapeutic effects of DZXXI against CVDs, were then obtained. The systems analysis suggested that DZXXI could attenuate cardiac fibrosis, regulate cardiac contractility, and preserve heart function in adverse cardiac remodeling; meanwhile DZXXI also could have the function of activating blood circulation and dilating blood vessels. DZXXI exerts its therapeutic effects on CVDs possibly through multi-targets including CMA1, epidermal growth factor receptor (EGFR), phenylalanine-4-hydroxylase (PAH), SRC, F7, etc., and multi-pathways including Focal adhesion, mitogen-activated protein kinase (MAPK) signaling pathway, complement and coagulation cascades, Wnt signaling pathway, vascular endothelial growth factor (VEGF) signaling pathway, Renin-angiotensin system, etc.

Integrated network pharmacology and zebrafish model to investigate dual-effects components of Cistanche tubulosa for treating both Osteoporosis and Alzheimer's Disease

ETHNOPHARMACOLOGICAL RELEVANCE

Osteoporosis (OP) and Alzheimer's disease (AD) are common geriatric concurrent diseases, and many studies indicate the connection of their pathogenesis. Cistanche tubulosa (Schenk) Wight (CT) is a widely used traditional Chinese medicine and has been extensively applied to treat OP and AD, respectively. However, the active ingredients for both concurrent diseases simultaneously and underlying mechanisms are limited.

AIM OF STUDY

This work aimed at establishing an effective and reliable network screening method to find dual-effects compounds in CT that can protect AD and OP concurrently. And it will provide new perspectives of the link between OP and AD on molecular mechanisms.

MATERIAL AND METHODS

The dual-effects of CT were systematically analyzed with integrating multiple databases and extensive analysis at a network pharmacology level. Classified drug-target interaction network was constructed to reveal differences in effects between different types of compounds. To prove the effectiveness of this network, some compounds were selected to verify in Pre-induced OP model and AlCl₃-induced AD model of zebrafish according to the topological parameters.

RESULTS

22 dual-effects active ingredients in CT were initially screened out via network pharmacology with a closely connection with 81 OP and AD-related targets. Classified network analysis found the better bioactivities of phenylethanoid glycosides and flavonoids. The dual-effects of four selected compounds demonstrated that the network is reasonable and effective, suggesting the dual-effects of the remaining 18 compounds. Moreover, we identified 9 putative targets and two pathways that were significantly related to OP and AD.

CONCLUSIONS

We successfully identified 22 dual-effects active components in CT. This systematic screening strategy provided a new protocol to objectively discover multi-effects compounds of traditional Chinese medicine, and even a macroscopic perspective that will improve our understanding of the link between OP and AD on molecular mechanisms.

Systems Pharmacology-Dissection of the Molecular Mechanisms of Dragon's Blood in Improving Ischemic Stroke Prognosis

Materials and Methods

(1) Based on system-pharmacology platform, the potential active compounds of DB are screened out according to ADME. (2) The ischemic stroke-related targets are predicted by utilizing these active compounds as probes, mapping the targets to the CTD database to establish a molecular-target-disease network. (3) To analyze the mechanism of DB treatment for the prognosis of ischemic stroke, we used the Metascape and DAVID databases to construct "ischemic stroke pathways". (4) PC12 cells were used to explore the protective effect of loureirin B on oxygen-glucose deprivation/reperfusion (OGD/R) injury, and BV-2 cells were used to determine the anti-inflammation effect of 4',7-dihydroxyflavone.

Results

Finally, we obtained 38 active compounds and 58 stroke-related targets. Network and pathway analysis indicate that DB is effective in the treatment of ischemic stroke by enhancing cell survival and inhibiting inflammatory and antiplatelet activation. In in vitro experiments, the main component loureirin B promoted the expression of HO-1 and Bcl-2 via positive regulation of PI3K/AKT/CREB and Nrf2 signaling pathways in PC12 cells against OGD/R damage. And the anti-inflammatory activity of 4',7-dihydroxyflavone was related to the inhibition of COX-2, TNF-α, and IL-6 in LPS-induced BV-2 cells.

Conclusions

In our study, the results illustrated that DB in improving ischemic stroke prognosis may involve enhancing cell survival and antioxidant, anti-inflammation, and antiplatelet activities.

A Systems Biological Approach to Understanding the Mechanisms Underlying the Therapeutic Potential of Red Ginseng Supplements against Metabolic Diseases

Red ginseng has been widely used in health-promoting supplements in Asia and is becoming increasingly popular in Western countries. However, its therapeutic mechanisms against most diseases have not been clearly elucidated. The aim of the present study was to provide the biological mechanisms of red ginseng against various metabolic diseases. We used a systems biological approach to comprehensively identify the component-target and target-pathway networks in order to explore the mechanisms underlying the therapeutic potential of red ginseng against metabolic diseases. Of the 23 components of red ginseng with target, 5 components were linked with 37 target molecules. Systematic analysis of the constructed networks revealed that these 37 targets were mainly involved in 9 signaling pathways relating to immune cell differentiation and vascular health. These results successfully explained the mechanisms underlying the efficiency of red ginseng for metabolic diseases, such as menopausal symptoms in women, blood circulation, diabetes mellitus, and hyperlipidemia.

Applications of Network Pharmacology in Traditional Chinese Medicine Research

Human diseases, especially infectious ones, have been evolving constantly. However, their treatment strategies are not developing quickly. Some diseases are caused by a variety of factors with very complex pathologies, and the use of a single drug cannot solve these problems. Traditional Chinese Medicine (TCM) medication is a unique treatment method in China. TCM formulae contain multiple herbs with multitarget, multichannel, and multilink characteristics. In recent years, with the flourishing development of network pharmacology, a new method for searching therapeutic drugs has emerged. The multitarget action in network pharmacology is consistent with the complex mechanisms of disease and drug action. Using network pharmacology to understand TCM is an emerging trend.

Network Pharmacology-Based Investigation of the System-Level Molecular Mechanisms of the Hematopoietic Activity of Samul-Tang, a Traditional Korean Herbal Formula

Hematopoiesis is a dynamic process of the continuous production of diverse blood cell types to meet the body's physiological demands and involves complex regulation of multiple cellular mechanisms in hematopoietic stem cells, including proliferation, self-renewal, differentiation, and apoptosis. Disruption of the hematopoietic system is known to cause various hematological disorders such as myelosuppression. There is growing evidence on the beneficial effects of herbal medicines on hematopoiesis; however, their mechanism of action remains unclear. In this study, we conducted a network pharmacological-based investigation of the system-level mechanisms underlying the hematopoietic activity of Samul-tang, which is an herbal formula consisting of four herbal medicines, including Angelicae Gigantis Radix, Rehmanniae Radix Preparata, Paeoniae Radix Alba, and Cnidii Rhizoma. In silico analysis of the absorption-distribution-metabolism-excretion model identified 16 active phytochemical compounds contained in Samul-tang that may target 158 genes/proteins associated with myelosuppression to exert pharmacological effects. Functional enrichment analysis suggested that the targets of Samul-tang were significantly enriched in multiple pathways closely related to the hematopoiesis and myelosuppression development, including the PI3K-Akt, MAPK, IL-17, TNF, FoxO, HIF-1, NF-kappa B, and p53 signaling pathways. Our study provides novel evidence regarding the system-level mechanisms underlying the hematopoiesis-promoting effect of herbal medicines for hematological disorder treatment.

A Review of Biologically Active Natural Products from a Desert Plant Cistanche tubulosa

An Orobanchaceae plant Cistanche tubulosa (SCHENK) WIGHT (Kanka-nikujuyou in Japanese), which is one of the authorized plant resources as Cistanches Herba in both Japanese and Chinese Pharmacopoeias, is a perennial parasitic plant growing on roots of sand-fixing plants. The stems of C. tubulosa have traditionally been used for treatment of impotence, sterility, lumbago, and body weakness as well as a promoting agent of blood circulation. In recent years, Cistanches Herba has also been widely used as a health food supplement in Japan, China, and Southeast Asian countries. Here we review our recent studies on chemical constituents from the stems of C. tubulosa as well as their bioactivities such as vasorelaxtant, hepatoprotective, and glucose tolerance improving effects.

A Novel Systems Pharmacology Method to Investigate Molecular Mechanisms of Scutellaria barbata D. Don for Non-small Cell Lung Cancer

Non-small cell lung cancer (NSCLC) is the most ordinary type of lung cancer which leads to 1/3 of all cancer deaths. At present, cytotoxic chemotherapy, surgical resection, radiation, and photodynamic therapy are the main strategies for NSCLC treatment. However, NSCLC is relatively resistant to the above therapeutic strategies, resulting in a rather low (20%) 5-year survival rate. Therefore, there is imperative to identify or develop efficient lead compounds for the treatment of NSCLC. Here, we report that the herb Scutellaria barbata D. Don (SBD) can effectively treat NSCLC by anti-inflammatory, promoting apoptosis, cell cycle arrest, and angiogenesis. In this work, we analyze the molecular mechanism of SBD for NSCLC treatment by applying the systems pharmacology strategy. This method combines pharmacokinetics analysis with pharmacodynamics evaluation to screen out the active compounds, predict the targets and assess the networks and pathways. Results show that 33 compounds were identified with potential anti-cancer effects. Utilizing these active compounds as probes, we predicted that 145 NSCLC related targets mainly involved four aspects: apoptosis, inflammation, cell cycle, and angiogenesis. And in vitro experiments were managed to evaluate the reliability of some vital active compounds and targets. Overall, a complete overview of the integrated systems pharmacology method provides a precise probe to elucidate the molecular mechanisms of SBD for NSCLC. Moreover, baicalein from SBD effectively inhibited tumor growth in an LLC tumor-bearing mice models, demonstrating the anti-tumor effects of SBD. Our findings further provided experimental evidence for the application in the treatment of NSCLC.

From 1H NMR-based non-targeted to LC-MS-based targeted metabolomics strategy for in-depth chemome comparisons among four Cistanche species

The great orthogonality between ¹H NMR spectroscopy and LC-MS implies that their deployments in series could offer an opportunity to gain the qualified molecular markers via comparative metabolomics, and an attempt was made here to propose an integrated strategy namely "from ¹H NMR-based non-targeted to LC-MS-based targeted metabolomics". In-depth chemome comparisons of Cistanche plants, such as C. deserticola, C. salsa, C. tubulosa, and C. sinensis, that possess dramatic economic and ecological benefits for the arid regions in the northwest China attributing to their dramatic medicinal and edible values, were employed to verify the applicability. ¹H NMR-based non-targeted matabolomics acted as the survey experiment to find those signals offering decisive contributions towards the species discrimination, and the signals were translated to a set of putative identities, eighteen ones in total, through matching with authentic compounds and referring to some accessible databases. Afterwards, an advanced LC-MS platform assembling reversed phase liquid chromatography, hydrophilic interaction liquid chromatography, and tailored multiple reaction monitoring, was introduced to simultaneously quantify those eighteen potential markers in a single analytical run, because those candidates exhibited great polarity span as well as wide content range. Significant species differences occurred amongst their chemome patterns. Echinacoside, acteoside, betaine, mannitol, 6-deoxycatalpol, sucrose, and 8-epi-loganic acid were disclosed as the markers enabling the discrimination of those four species. The findings offered an alternative tool to differentiate Cistanche plants. More importantly, the strategy namely "from ¹H NMR-based non-targeted to LC-MS-based targeted metabolomics" facilitates the pursuit of molecular markers among analogue plants, and thereby provides a promising choice for in-depth chemome comparison.