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Yao Y, Li X, Yang X, Mou H, Wei L. Indirubin, an Active Component of Indigo Naturalis, Exhibits Inhibitory Effects on Leukemia Cells via Targeting HSP90AA1 and PI3K/Akt Pathway. Anticancer Agents Med Chem 2024; 24:718-727. [PMID: 38347773 DOI: 10.2174/0118715206258293231017063340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/10/2023] [Accepted: 09/14/2023] [Indexed: 06/04/2024]
Abstract
BACKGROUND This research intended to predict the active ingredients and key target genes of Indigo Naturalis in treating human chronic myeloid leukemia (CML) using network pharmacology and conduct the invitro verification. METHODS The active components of Indigo Naturalis and the corresponding targets and leukemia-associated genes were gathered through public databases. The core targets and pathways of Indigo Naturalis were predicted through protein-protein interaction (PPI) network, gene ontology (GO) function, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Next, after intersecting with leukemia-related genes, the direct core target gene of Indigo Naturalis active components was identified. Subsequently, HL-60 cells were stimulated with indirubin (IND) and then examined for cell proliferation using CCK-8 assay and cell cycle, cell apoptosis, and mitochondrial membrane potential using flow cytometry. The content of apoptosis-associated proteins (Cleaved Caspase 9, Cleaved Caspase 7, Cleaved Caspase 3, and Cleaved parp) were detected using Western blot, HSP90AA1 protein, and PI3K/Akt signaling (PI3K, p-PI3K, Akt, and p-Akt) within HL-60 cells. RESULTS A total of 9 active components of Indigo Naturalis were screened. The top 10 core target genes (TNF, PTGS2, RELA, MAPK14, IFNG, PPARG, NOS2, IKBKB, HSP90AA1, and NOS3) of Indigo Naturalis active components within the PPI network were identified. According to the KEGG enrichment analysis, these targets were associated with leukemia-related pathways (such as acute myeloid leukemia and CML). After intersecting with leukemia-related genes, it was found that IND participated in the most pairs of target information and was at the core of the target network; HSP90AA1 was the direct core gene of IND. Furthermore, the in-vitro cell experiments verified that IND could inhibit the proliferation, elicit G2/M-phase cell cycle arrest, enhance the apoptosis of HL-60 cells, reduce mitochondrial membrane potential, and promote apoptosis-related protein levels. Under IND treatment, HSP90AA1 overexpression notably promoted cell proliferation and inhibited apoptosis. Additionally, IND exerted tumor suppressor effects on leukemia cells by inhibiting HSP90AA1 expression. CONCLUSION IND, an active component of Indigo Naturalis, could inhibit CML progression, which may be achieved via inhibiting HSP90AA1 and PI3K/Akt signaling expression levels.
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MESH Headings
- Humans
- Cell Proliferation/drug effects
- Proto-Oncogene Proteins c-akt/metabolism
- Proto-Oncogene Proteins c-akt/antagonists & inhibitors
- Apoptosis/drug effects
- Phosphatidylinositol 3-Kinases/metabolism
- Indoles/pharmacology
- Indoles/chemistry
- HSP90 Heat-Shock Proteins/antagonists & inhibitors
- HSP90 Heat-Shock Proteins/metabolism
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/chemical synthesis
- Drug Screening Assays, Antitumor
- HL-60 Cells
- Molecular Structure
- Dose-Response Relationship, Drug
- Structure-Activity Relationship
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia/drug therapy
- Leukemia/pathology
- Leukemia/metabolism
- Signal Transduction/drug effects
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Affiliation(s)
- Yuanzhi Yao
- College of Biology and Food Engineering, Huaihua University, Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua 418000, China
| | - Xiaoying Li
- College of Biology and Food Engineering, Huaihua University, Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua 418000, China
| | - Xiaoqin Yang
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Hai Mou
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Lin Wei
- College of Biology and Food Engineering, Huaihua University, Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua 418000, China
- College of Basic Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
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2
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Challenges and Perspectives in Target Identification and Mechanism Illustration for Chinese Medicine. Chin J Integr Med 2023:10.1007/s11655-023-3629-9. [PMID: 36809500 DOI: 10.1007/s11655-023-3629-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2023] [Indexed: 02/23/2023]
Abstract
Chinese medicine (CM) is an important resource for human life understanding and discovery of drugs. However, due to the unclear pharmacological mechanism caused by unclear target, research and international promotion of many active components have made little progress in the past decades of years. CM is mainly composed of multi-ingredients with multi-targets. The identification of targets of multiple active components and the weight analysis of multiple targets in a specific pathological environment, that is, the determination of the most important target is the main obstacle to the mechanism clarification and thus hinders its internationalization. In this review, the main approach to target identification and network pharmacology were summarized. And BIBm (Bayesian inference modeling), a powerful method for drug target identification and key pathway determination was introduced. We aim to provide a new scientific basis and ideas for the development and international promotion of new drugs based on CM.
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An Updated Review on Efficiency of Penthorum chinense Pursh in Traditional Uses, Toxicology, and Clinical Trials. BIOMED RESEARCH INTERNATIONAL 2023; 2023:4254051. [PMID: 36852294 PMCID: PMC9966574 DOI: 10.1155/2023/4254051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/02/2023] [Accepted: 01/06/2023] [Indexed: 02/20/2023]
Abstract
Traditional Chinese medicines (TCM) play an important role in the control and treatment of several animal diseases. Penthorum chinense Pursh (PCP) is a famous plant for its use in traditional medication practice and therapeutic effects in numerous pathological conditions. In China, PCP is utilized for both food and medication due to numerous bioactivities. PCP is widely administered in prevention and treatment of traumatic injury, edema, and liver diseases with functions of reducing swelling, support diuresis, blood stasis, and mitigation symptoms of excessive alcohol intake. Recently, PCP highlighted for research trials in various fields including pharmacology, pharmacognosy, cosmeceuticals, nutraceuticals, and pharmaceuticals due to medicinal significance with less toxicity and an effective ethnomedicine in veterinary practice. PCP contains diverse important ingredients such as flavonoids, organic acids, coumarins, lignans, polyphenols, and sterols that are important bioactive constituents of PCP exerting the therapeutic benefits and organ-protecting effects. In veterinary, PCP extract, compound, and phytochemicals/biomolecules significantly reversed the liver and kidney injuries, via antioxidation, oxidative stress, apoptosis, mitochondrial signaling pathways, and related genes. PCP water extract and compounds also proved in animal and humans' clinical trial for their hepatoprotective, antiaging, nephroprotective, anti-inflammatory, antidiabetic, antibacterial, antiapoptotic, immune regulation, and antioxidative stress pathways. This updated review spotlighted the current information on efficiency and application of PCP by compiling and reviewing recent publications on animal research. In addition, this review discussed the toxicology, traditional use, comparative, and clinical application of PCP in veterinary practices to authenticate and find out new perspectives on the research and development of this herbal medicine.
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Xu W, Ren B, Zhang Z, Chen C, Xu T, Liu S, Ma C, Wang X, Wang Q, Cheng F. Network pharmacology analysis reveals neuroprotective effects of the Qin-Zhi-Zhu-Dan Formula in Alzheimer’s disease. Front Neurosci 2022; 16:943400. [DOI: 10.3389/fnins.2022.943400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
There is yet no effective drug for Alzheimer’s disease (AD) which is one of the world’s most common neurodegenerative diseases. The Qin-Zhi-Zhu-Dan Formula (QZZD) is derived from a widely used Chinese patent drug–Qing-Kai-Ling Injection. It consists of Radix Scutellariae, Fructus Gardeniae, and Pulvis Fellis Suis. Recent study showed that QZZD and its effective components played important roles in anti-inflammation, antioxidative stress and preventing brain injury. It was noted that QZZD had protective effects on the brain, but the mechanism remained unclear. This study aims to investigate the mechanism of QZZD in the treatment of AD combining network pharmacology approach with experimental validation. In the network pharmacology analysis, a total of 15 active compounds of QZZD and 135 putative targets against AD were first obtained. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were then applied to clarify the biological mechanism. The anti-inflammatory mechanism of QZZD was proved, and a synthetic pathway–TNFR1-ERK1/2-NF-κBp65 signaling pathway was obtained. On the basis of the above discoveries, we further validated the protective effects QZZD on neurons with an APP/PS1 double transgenic mouse model. Weight change of the mice was monitored to assess QZZD’s influence on the digestive system; water maze experiment was used for evaluating the effects on spatial learning and memory; Western blotting and immunohistochemistry analysis were used to detect the predicted key proteins in network pharmacology analysis, including Aβ, IL-6, NF-κBp65, TNFR1, p-ERK1/2, and ERK1/2. We proved that QZZD could improve neuroinflammation and attenuate neuronal death without influencing the digestive system in APP/PS1 double transgenic mice with dementia. Combining animal pharmacodynamic experiments with network pharmacology analysis, we confirmed the importance of inflammation in pathogenesis of AD, clarified the pharmacodynamic characteristics of QZZD in treating AD, and proved its neuroprotective effects through the regulation of TNFR1-ERK1/2-NF-κBp65 signaling pathway, which might provide reference for studies on treatment of AD in the future.
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Zhang SS, Hou YF, Liu SJ, Guo S, Ho CT, Bai NS. Exploring Active Ingredients, Beneficial Effects, and Potential Mechanism of Allium tenuissimum L. Flower for Treating T2DM Mice Based on Network Pharmacology and Gut Microbiota. Nutrients 2022; 14:nu14193980. [PMID: 36235633 PMCID: PMC9571170 DOI: 10.3390/nu14193980] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Forty compounds were isolated and characterized from A. tenuissimum flower. Among them, twelve flavonoids showed higher α−glucosidase inhibition activities in vitro than acarbose, especially kaempferol. The molecular docking results showed that the binding of kaempferol to α−glucosidase (GAA) could reduce the hydrolysis of substrates by GAA and reduce the glucose produced by hydrolysis, thus exhibiting α−glucosidase inhibition activities. The in vivo experiment results showed that flavonoids−rich A. tenuissimum flower could decrease blood glucose and reduce lipid accumulation. The protein expression levels of RAC−alpha serine/threonine−protein kinase (AKT1), peroxisome proliferator activated receptor gamma (PPARG), and prostaglandin G/H synthase 2 (PTGS2) in liver tissue were increased. In addition, the Firmicutes/Bacteroidetes (F/B) ratio was increased, the level of gut probiotics Bifidobacterium was increased, and the levels of Enterobacteriaceae and Staphylococcus were decreased. The carbohydrate metabolism, lipid metabolism, and other pathways related to type 2 diabetes mellitus were activated. This study indicating flavonoids−rich A. tenuissimum flower could improve glycolipid metabolic disorders and inflammation in diabetic mice by modulating the protein expression and gut microbiota.
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Affiliation(s)
- Shan-Shan Zhang
- Department of Pharmaceutical Engineering, College of Chemical Engineering, Northwest University, Xi’an 710069, China
| | - Yu-Fei Hou
- Department of Food Science, College of Food Science and Technology, Northwest University, Xi’an 710069, China
| | - Shao-Jing Liu
- Department of Medicinal Chemistry, College of Pharmacy, Xi’an Medical University, Xi’an 710021, China
| | - Sen Guo
- Department of Food Science, College of Food Science and Technology, Northwest University, Xi’an 710069, China
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, NJ 08901, USA
| | - Nai-Sheng Bai
- Department of Food Science, College of Food Science and Technology, Northwest University, Xi’an 710069, China
- Correspondence: ; Tel.: +029-88305208
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Du Z, Huang D, Shi P, Dong Z, Wang X, Li M, Chen W, Zhang F, Sun L. Integrated Chemical Interpretation and Network Pharmacology Analysis to Reveal the Anti-Liver Fibrosis Effect of Penthorum chinense. Front Pharmacol 2022; 13:788388. [PMID: 35721129 PMCID: PMC9201443 DOI: 10.3389/fphar.2022.788388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 03/23/2022] [Indexed: 11/24/2022] Open
Abstract
Liver fibrosis is a disease with complex pathological mechanisms. Penthorum chinense Pursh (P. chinense) is a traditional Chinese medicine (TCM) for liver injury treatment. However, the pharmacological mechanisms of P. chinense on liver fibrosis have not been investigated and clarified clearly. This study was designed to investigate the chemicals in P. chinense and explore its effect on liver fibrosis. First, we developed a highly efficient method, called DDA-assisted DIA, which can both broaden mass spectrometry (MS) coverage and MS2 quality. In DDA-assisted DIA, data-dependent acquisition (DDA) and data-independent acquisition (DIA) were merged to construct a molecular network, in which 1,094 mass features were retained in Penthorum chinense Pursh (P. chinense). Out of these, 169 compounds were identified based on both MS1 and MS2 analysis. After that, based on a network pharmacology study, 94 bioactive compounds and 440 targets of P. chinense associated with liver fibrosis were obtained, forming a tight compound–target network. Meanwhile, the network pharmacology experimental results showed that multiple pathways interacted with the HIF-1 pathway, which was first identified involved in P. chinense. It could be observed that some proteins, such as TNF-α, Timp1, and HO-1, were involved in the HIF-1 pathway. Furthermore, the pharmacological effects of P. chinense on these proteins were verified by CCl4-induced rat liver fibrosis, and P. chinense was found to improve liver functions through regulating TNF-α, Timp1, and HO-1 expressions. In summary, DDA-assisted DIA could provide more detailed compound information, which will help us to annotate the ingredients of TCM, and combination with computerized network pharmacology provided a theoretical basis for revealing the mechanism of P. chinense.
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Affiliation(s)
- Zenan Du
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China.,Institute of Chinese Materia Madica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Doudou Huang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China.,Institute of Chinese Materia Madica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Pengjie Shi
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China.,Institute of Chinese Materia Madica, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhiying Dong
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China
| | - Xiujuan Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China
| | - Mengshuang Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China
| | - Wansheng Chen
- Institute of Chinese Materia Madica, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Feng Zhang
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Lianna Sun
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine (SHUTCM), Shanghai, China
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7
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A Network Pharmacology Approach for Uncovering the Antitumor Effects and Potential Mechanisms of the Sijunzi Decoction for the Treatment of Gastric Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:9364313. [PMID: 35463069 PMCID: PMC9019414 DOI: 10.1155/2022/9364313] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/11/2022] [Accepted: 03/15/2022] [Indexed: 12/15/2022]
Abstract
Background Sijunzi decoction (SJZD), a classic Chinese formula, has been clinically used for the treatment of gastrointestinal disorders. However, few studies have uncovered its antitumor effects and its potential mechanisms against gastric cancer (GC). Therefore, this work aimed to identify the active compounds and putative targets of the SJZD and to further explore the potential mechanisms involved in the treatment of GC. Materials and Methods The active compounds and potential targets of the SJZD and related genes for GC treatment were collected from a public database. Traditional Chinese medicine (TCM)-compound-target-disease networks, Venn diagrams, protein–protein interactions (PPIs), gene ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to obtain the bioactive compounds, key targets, and potential pathways. Next, the human gastric adenocarcinoma cell line NUGC-4 was inoculated subcutaneously into the right flank of NCG mice to build a tumor-bearing mouse model to further verify the findings. Results There were 117 compounds in the SJZD in total. The SJZD and GC had 161 and 3288 potential targets, respectively, among which 123 targets overlapped. The network analysis showed that quercetin, kaempferol formononetin, ginsenoside, atractylenolide III, etc., were bioactive molecules. The tumor necrosis factor (TNF), interleukin-6 (IL-6), cellular tumor antigen p53 (TP53), transcription factor AP-1 (JUN), and vascular endothelial growth factor A (VEGFA) were potential targets. A KEGG pathway enrichment analysis revealed 110 pathways involved in the pathways for cancer, including the PI3K-AKT signaling pathway. Validation experiments showed that the SJZD inhibited tumor growth and induced apoptosis in tumor cells. In addition, the SJZD downregulated expressions of VEGFA, iNOS, COX-2, and Bax/Bcl2 and inhibited the expressions of p-PI3K and p-AKT. Conclusion The SJZD treats GC by inhibiting blood vessel hyperplasia and inducing cell apoptosis by regulating the PI3K/AKT pathway.
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Guo S, Tan Y, Huang Z, Li Y, Liu W, Fan X, Zhang J, Stalin A, Fu C, Wu Z, Wang P, Zhou W, Liu X, Wu C, Jia S, Zhang J, Duan X, Wu J. Revealing Calcium Signaling Pathway as Novel Mechanism of Danhong Injection for Treating Acute Myocardial Infarction by Systems Pharmacology and Experiment Validation. Front Pharmacol 2022; 13:839936. [PMID: 35281886 PMCID: PMC8905633 DOI: 10.3389/fphar.2022.839936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/07/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction: Danhong injection (DHI) is a traditional Chinese medicine preparation commonly used in the clinical treatment of acute myocardial infarction (AMI). In this study, the active components of DHI and its mechanism in the treatment of AMI were investigated. Methods: The chemical components of DHI were detected by the ultra-high-performance liquid chromatography-linear trap quadrupole-orbitrap-tandem mass spectrometry (UHPLC-LTQ-Orbitrap-MS/MS), and the targets and pathways of DHI in the treatment of AMI were analyzed by systems pharmacology, which was verified by molecular docking and animal experiments. Results: A total of 12 active components of DHI were obtained, and 158 common targets of component and disease were identified by systems pharmacology. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis results showed that DHI is closely related to the calcium signaling pathway in the treatment of AMI. Molecular docking showed that the key target protein has good binding affinity to related compounds. The experimental results showed that compared with the model group, LVAWs, EF, and FS significantly (p < 0.05) increased in the DHI group. The percentage of myocardial infarction significantly (p < 0.01) decreased, both in the ventricular and total cardiac regions, and the pathological damage of myocardial tissue also decreased. In addition, the expression of the protein CaMK II decreased (p < 0.01) and the expression of SERCA significantly increased (p < 0.01). Conclusion: This study revealed that ferulic acid, caffeic acid and rosmarinic acid could inhibit AMI by regulating PLB, CaMK II, SERCA, etc. And mechanistically, calcium signaling pathway was critically involved. Combination of systems pharmacology prediction with experimental validation may provide a scientific basis for in-depth clinical investigation of the material basis of DHI.
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Affiliation(s)
- Siyu Guo
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yingying Tan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhihong Huang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yikui Li
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Weiyu Liu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaotian Fan
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jingyuan Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Antony Stalin
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Changgeng Fu
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhishan Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Penglong Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Wei Zhou
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China.,China-Japan Friendship Hospital, Beijing, China
| | - Xinkui Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chao Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shanshan Jia
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jinyan Zhang
- Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoxia Duan
- Beijing Zest Bridge Medical Technology Inc., Beijing, China
| | - Jiarui Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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Wu J, Wang K, Liu Q, Li Y, Huang Y, Liu Y, Cai J, Yin C, Li X, Yu H, Meng W, Wang H, Lu A, Li Y, Guan D. An Integrative Pharmacology Model for Decoding the Underlying Therapeutic Mechanisms of Ermiao Powder for Rheumatoid Arthritis. Front Pharmacol 2022; 13:801350. [PMID: 35281924 PMCID: PMC8905663 DOI: 10.3389/fphar.2022.801350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/04/2022] [Indexed: 12/17/2022] Open
Abstract
As a systemic inflammatory arthritis disease, rheumatoid arthritis (RA) is complex and hereditary. Traditional Chinese medicine (TCM) has evident advantages in treating complex diseases, and a variety of TCM formulas have been reported that have effective treatment on RA. Clinical and pharmacological studies showed that Ermiao Powder, which consists of Phellodendron amurense Rupr. (PAR) and Atractylodes lancea (Thunb.) DC. (ALD), can be used in the treatment of RA. Currently, most studies focus on the anti-inflammatory mechanism of PAR and ALD and are less focused on their coordinated molecular mechanism. In this research, we established an integrative pharmacological strategy to explore the coordinated molecular mechanism of the two herbs of Ermiao Powder in treating RA. To explore the potential coordinated mechanism of PAR and ALD, we firstly developed a novel mathematical model to calculate the contribution score of 126 active components and 85 active components, which contributed 90% of the total contribution scores that were retained to construct the coordinated functional space. Then, the knapsack algorithm was applied to identify the core coordinated functional components from the 85 active components. Finally, we obtained the potential coordinated functional components group (CFCG) with 37 components, including wogonin, paeonol, ethyl caffeate, and magnoflorine. Also, functional enrichment analysis was performed on the targets of CFCG to explore the potential coordinated molecular mechanisms of PAR and ALD. The results indicated that the CFCG could treat RA by coordinated targeting to the genes involved in immunity and inflammation-related signal pathways, such as phosphatidylinositol 3‑kinase/protein kinase B signaling pathway, mitogen-activated protein kinase signaling pathway, tumor necrosis factor signaling pathway, and nuclear factor-kappa B signaling pathway. The docking and in vitro experiments were used to predict the affinity and validate the effect of CFCG and further confirm the reliability of our method. Our integrative pharmacological strategy, including CFCG identification and verification, can provide the methodological references for exploring the coordinated mechanism of TCM in treating complex diseases and contribute to improving our understanding of the coordinated mechanism.
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Affiliation(s)
- Jie Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Kexin Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Neurosurgery Institute, Department of Neurosurgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Qinwen Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Yi Li
- Department of Radiology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yingying Huang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yujie Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Jieqi Cai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Chuanhui Yin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Xiaowei Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Hailang Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Wei Meng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Handuo Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Aiping Lu
- Institute of Integrated Bioinformedicine and Translational Science, Hong Kong Baptist University, Hong Kong, China
- Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
| | - Yazi Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Daogang Guan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
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Network Pharmacology-Based Study of the Underlying Mechanisms of Huangqi Sijunzi Decoction for Alzheimer's Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:6480381. [PMID: 34650613 PMCID: PMC8510793 DOI: 10.1155/2021/6480381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/22/2021] [Accepted: 09/21/2021] [Indexed: 12/14/2022]
Abstract
Background Huangqi Sijunzi decoction (HQSJZD) is a commonly used conventional Chinese herbal medicine prescription for invigorating Qi, tonifying Yang, and removing dampness. Modern pharmacology and clinical applications of HQSJZD have shown that it has a certain curative effect on Alzheimer's disease (AD). Methods The active components and targets of HQSJZD were searched in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP). The genes corresponding to the targets were retrieved using UniProt and GeneCard database. The herb-compound-target network and protein-protein interaction (PPI) network were constructed by Cytoscape. The core targets of HQSJZD were analysed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The main active compounds of HQSJZD were docked with acetylcholinesterase (AChE). In vitro experiments were conducted to detect the inhibitory and neuroprotective effects of AChE. Results Compound-target network mainly contained 132 compounds and 255 corresponding targets. The main compounds contained quercetin, kaempferol, formononetin, isorhamnetin, hederagenin, and calycosin. Key targets contained AChE, PTGS2, PPARG, IL-1B, GSK3B, etc. There were 1708 GO items in GO enrichment analysis and 310 signalling pathways in KEGG, mainly including the cAMP signalling pathway, the vascular endothelial growth factor (VEGF) signalling pathway, serotonergic synapses, the calcium signalling pathway, type II diabetes mellitus, arginine and proline metabolism, and the longevity regulating pathway. Molecular docking showed that hederagenin and formononetin were the top 2 compounds of HQSJZD, which had a high affinity with AChE. And formononetin has a good neuroprotective effect, which can improve the oxidative damage of nerve cells. Conclusion HQSJZD was found to have the potential to treat AD by targeting multiple AD-related targets. Formononetin and hederagenin in HQSJZD may regulate multiple signalling pathways through AChE, which might play a therapeutic role in AD.
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Zheng L, Wen XL, Dai YC. Mechanism of Jianpi Qingchang Huashi Recipe in treating ulcerative colitis: A study based on network pharmacology and molecular docking. World J Clin Cases 2021; 9:7653-7670. [PMID: 34621817 PMCID: PMC8462257 DOI: 10.12998/wjcc.v9.i26.7653] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/28/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ulcerative colitis (UC) is a refractory intestinal disease with alternating onset and remission and a long disease course, which seriously affects the health and quality of life of patients. The goal of treatment is to control clinical symptoms, induce and maintain remission, promote mucosal healing, and reduce recurrence. Clinical trials have shown unsatisfactory clinical response rates. As a supplementary alternative medicine, traditional Chinese medicine has a rich history and has shown good results in the treatment of UC. Because of the quality of herbal medicine and other factors, the curative effect of traditional Chinese medicine is not stable enough. The mechanism underlying the effect of Jianpi Qingchang Huashi Recipe (JPQCHSR) on inducing UC mucosal healing is not clear. AIM To investigate the potential mechanism of JPQCHSR for the treatment of UC based on network pharmacology and molecular docking. METHODS Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform was used to extract the active components and action targets of JPQCHSR, and the target names were standardized and corrected through UniProt database. The related targets of UC were obtained through GeneCards database, and the intersection targets of drugs and diseases were screened by jvenn online analysis tool. The visual regulatory network of "Traditional Chinese medicine-active components-target-disease" was constructed using Cytoscape software, the protein interaction network was constructed using STRING database, and enrichment analysis of gene ontology and Kyoto Encyclopedia of Genes and Genomes pathways was conducted through R software. At last, the active components were docked with the core target through SYBYL-X 2.1.1 software. RESULTS Through database analysis, a total of 181 active components, 302 targets and 205 therapeutic targets were obtained for JPQCHSR. The key compounds include quercetin, luteolin, kaempferol, etc. The core targets involved STAT3, AKT1, TP53, MAPK1, MAPK3, JUN, TNF, etc. A total of 2861 items were obtained by GO enrichment analysis, and 171 items were obtained by KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway enrichment analysis. The results of molecular docking showed that the key active components in JPQCHSR had certain affinity with the core target. CONCLUSION The treatment of UC with JPQCHSR is a complex process of multi-component, multi-target and multi-pathway regulation. The mechanism of this Recipe in the treatment of UC can be predicted through network pharmacology and molecular docking, so as to provide theoretical reference for it to better play its therapeutic role.
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Affiliation(s)
- Lie Zheng
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an 730000, Shaanxi Province, China
| | - Xin-Li Wen
- Department of Gastroenterology, Shaanxi Hospital of Traditional Chinese Medicine, Shaanxi Provincial Hospital of Traditional Chinese Medicine, Xi’an 730000, Shaanxi Province, China
| | - Yan-Cheng Dai
- Department of Gastroenterology, Shanghai Traditional Chinese Medicine Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200082, China
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Singh H, Bharadvaja N. Treasuring the computational approach in medicinal plant research. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 164:19-32. [PMID: 34004233 DOI: 10.1016/j.pbiomolbio.2021.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 05/11/2021] [Indexed: 01/24/2023]
Abstract
Medicinal plants serve as a valuable source of secondary metabolites since time immemorial. Computational Research in 21st century is giving more attention to medicinal plants for new drug design as pharmacological screening of bioactive compound was time consuming and expensive. Computational methods such as Molecular Docking, Molecular Dynamic Simulation and Artificial intelligence are significant Insilico tools in medicinal plant research. Molecular docking approach exploits the mechanism of potential phytochemicals into the target active site to elucidate its interactions and biological therapeutic properties. MD simulation illuminates the dynamic behavior of biomolecules at atomic level with fine quality representation of biomolecules. Dramatical advancement in computer science is illustrating the biological mechanism via these tools in different diseases treatment. The advancement comprises speed, the system configuration, and other software upgradation to insights into the structural explanation and optimization of biomolecules. A probable shift from simulation to artificial intelligence has in fact accelerated the art of scientific study to a sky high. The most upgraded algorithm in artificial intelligence such as Artificial Neural Networks, Deep Neural Networks, Neuro-fuzzy Logic has provided a wide opportunity in easing the time required in classical experimental strategy. The notable progress in computer science technology has paved a pathway for understanding the pharmacological functions and creating a roadmap for drug design and development and other achievement in the field of medicinal plants research. This review focus on the development and overview in computational research moving from static molecular docking method to a range of dynamic simulation and an advanced artificial intelligence such as machine learning.
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Affiliation(s)
- Harshita Singh
- Plant Biotechnology Laboratory, Delhi Technological University, Delhi, 110042, India
| | - Navneeta Bharadvaja
- Plant Biotechnology Laboratory, Delhi Technological University, Delhi, 110042, India.
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Yi J, Tian M, Hu L, Kang N, Ma W, Zhi J, Zheng X, Ruan X, Gao M. The mechanisms of celastrol in treating papillary thyroid carcinoma based on network pharmacology and experiment verification. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:866. [PMID: 34164500 PMCID: PMC8184492 DOI: 10.21037/atm-21-1854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background Celastrol, a triterpene present in the traditional Chinese medicine (TCM) Triptergium wilfordii, has been demonstrated to have remarkable anticancer activity. However, its specific mechanism on papillary thyroid carcinoma (PTC) remains to be elucidated. Methods Potential targets of celastrol were screened from public databases. Through the Gene Expression Omnibus (GEO) online database, we obtained the bioinformatics analysis profile of PTC, GSE33630, and analyzed the differentially expressed genes (DEGs). Then, a protein-protein interaction (PPI) network was constructed by utilizing the STRING database. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were conducted. Finally, drug interactions between hub genes and celastrol were verified by molecular docking. Results Four core nodes (MMP9, JUN, ICAM1, and VCAM1) were discerned via constructing a PPI network of 47 common targets. Through functional enrichment analysis, it was confirmed that the above target genes were basically enriched in the interleukin-17 (IL-17), nuclear factor kappa-B (NF-κB), and tumor necrosis factor (TNF) signaling pathways, which are involved in the inflammatory microenvironment to inhibit the development and progression of tumors. Molecular docking results demonstrated that celastrol has a strong binding efficiency with the 4 key proteins. Conclusions In this research, it was demonstrated that celastrol can regulate a variety of proteins and signaling pathways against PTC, providing a theoretical basis for future clinical applications.
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Affiliation(s)
- Jiaoyu Yi
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Mengran Tian
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Linfei Hu
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ning Kang
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Weike Ma
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Jingtai Zhi
- Department of Otolaryngology-Head and Neck Surgery, Tianjin First Center Hospital, Tianjin, China
| | - Xiangqian Zheng
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Xianhui Ruan
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Ming Gao
- Department of Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, China.,Department of Thyroid and Breast Surgery, Tianjin Union Medical Center, Tianjin, China
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Chen J, Zhang Y, Wang Y, Jiang P, Zhou G, Li Z, Yang J, Li X. Potential mechanisms of Guizhi decoction against hypertension based on network pharmacology and Dahl salt-sensitive rat model. Chin Med 2021; 16:34. [PMID: 33906674 PMCID: PMC8077739 DOI: 10.1186/s13020-021-00446-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 04/20/2021] [Indexed: 12/11/2022] Open
Abstract
Background Guizhi decoction (GZD), a classical Chinese herbal formula, has been widely used to treat hypertension, but its underlying mechanisms remain elusive. The present study aimed to explore the potential mechanisms and therapeutic effects of GZD on hypertension by integrating network pharmacology and experimental validation. Methods The active ingredients and corresponding targets were collected from the Traditional Chinese Medicine Systems Pharmacology database and Analysis Platform (TCMSP). The targets related to hypertension were identified from the CTD, GeneCards, OMIM and Drugbank databases. Multiple networks were constructed to identify the key compounds, hub targets, and main biological processes and pathways of GZD against hypertension. The Surflex-Dock software was used to validate the binding affinity between key targets and their corresponding active compounds. The Dahl salt-sensitive rat model was used to evaluate the therapeutic effects of GZD against hypertension. Results A total of 112 active ingredients, 222 targets of GZD and 341 hypertension-related targets were obtained. Furthermore, 56 overlapping targets were identified, five of which were determined as the hub targets for experimental verification, including interleukin 6 (IL-6), C–C motif chemokine 2 (CCL2), IL-1β, matrix metalloproteinase 2 (MMP-2), and MMP-9. Pathway enrichment analysis results indicated that 56 overlapping targets were mainly enriched in several inflammation pathways such as the tumor necrosis factor (TNF) signaling pathway, Toll-like receptor (TLR) signaling pathway and nuclear factor kappa-B (NF-κB) signaling pathway. Molecular docking confirmed that most active compounds of GZD could bind tightly to the key targets. Experimental studies revealed that the administration of GZD improved blood pressure, reduced the area of cardiac fibrosis, and inhibited the expression of IL-6, CCL2, IL-1β, MMP-2 and MMP-9 in rats. Conclusion The potential mechanisms and therapeutic effects of GZD on hypertension may be attributed to the regulation of cardiac inflammation and fibrosis. Supplementary Information The online version contains supplementary material available at 10.1186/s13020-021-00446-x.
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Affiliation(s)
- Jiye Chen
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Yongjian Zhang
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Yongcheng Wang
- Department of Cardiovascular, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, China
| | - Ping Jiang
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Guofeng Zhou
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Zhaoyu Li
- First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, 250014, China
| | - Jinlong Yang
- Department of Cardiovascular, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, China
| | - Xiao Li
- Department of Cardiovascular, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, 250011, China.
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Li L, Jin XJ, Li JW, Li CH, Zhou SY, Li JJ, Feng CQ, Liu DL, Liu YQ. Systematic insight into the active constituents and mechanism of Guiqi Baizhu for the treatment of gastric cancer. Cancer Sci 2021; 112:1772-1784. [PMID: 33682294 PMCID: PMC8088928 DOI: 10.1111/cas.14851] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/29/2021] [Accepted: 02/07/2021] [Indexed: 12/12/2022] Open
Abstract
Traditional Chinese medicine treatment of diseases has been recognized, but the material basis and mechanisms are not clear. In this study, target prediction of the antigastric cancer (GC) effect of Guiqi Baizhu (GQBZP) and the analysis of potential key compounds, key targets, and key pathways for the therapeutic effects against GC were carried out based on the method of network analysis and Kyoto Encyclopedia of Genes and Genomes enrichment. There were 33 proteins shared between GQBZP and GC, and 131 compounds of GQBZP had a high correlation with these proteins, indicating that the PI3K‐AKT signaling pathway might play a key role in GC. From these studies, we selected human epidermal growth factor receptor 2 (HER2) and programmed cell death 1‐ligand 1 (PD‐L1) for docking; the results showed that 385 and 189 compounds had high docking scores with HER2 and PD‐L1, respectively. Six compounds were selected for microscale thermophoresis (MST). Daidzein/quercetin and isorhamnetin/formononetin had the highest binding affinity for HER2 and PD‐L1, with Kd values of 3.7 μmol/L and 490, 667, and 355 nmol/L, respectively. Molecular dynamics simulation studies based on the docking complex structures as the initial conformation yielded the binding free energy between daidzein/quercetin with HER2 and isorhamnetin/formononetin with PD‐L1, calculated by molecular mechanics Poisson‐Boltzmann surface area, of −26.55, −14.18, −19.41, and −11.86 kcal/mol, respectively, and were consistent with the MST results. In vitro experiments showed that quercetin, daidzein, and isorhamnetin had potential antiproliferative effects in MKN‐45 cells. Enzyme activity assays showed that quercetin could inhibit the activity of HER2 with an IC50 of 570.07 nmol/L. Our study provides a systematic investigation to explain the material basis and molecular mechanism of traditional Chinese medicine in treating diseases.
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Affiliation(s)
- Ling Li
- Gansu University Key Laboratory for Molecular Medicine & Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China
| | - Xiao-Jie Jin
- Gansu University Key Laboratory for Molecular Medicine & Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China.,College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China
| | - Jia-Wei Li
- Gansu University Key Laboratory for Molecular Medicine & Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China.,School of basic medical sciences, Gansu University of Chinese Medicine, Lanzhou, China
| | - Cheng-Hao Li
- Gansu University Key Laboratory for Molecular Medicine & Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China
| | - Shuang-Yan Zhou
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Jun-Jie Li
- Gansu University Key Laboratory for Molecular Medicine & Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China
| | - Cai-Qin Feng
- Affiliated Hospital of Gansu University of Chinese Medicine, Lanzhou, China
| | - Dong-Ling Liu
- Gansu University Key Laboratory for Molecular Medicine & Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China.,College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou, China
| | - Yong-Qi Liu
- Gansu University Key Laboratory for Molecular Medicine & Chinese Medicine Prevention and Treatment of Major Diseases, Gansu University of Chinese Medicine, Lanzhou, China.,Key Laboratory of Dun huang Medical and Transformation, Ministry of Education of The People's Republic of China, Gansu University of Chinese Medicine, Lanzhou, China
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Unraveling the Molecular Mechanisms of Fructus Anisi Stellati as a Remedy for Infantile Colic by Network Pharmacology. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:9210304. [PMID: 33381218 PMCID: PMC7762657 DOI: 10.1155/2020/9210304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 12/04/2020] [Accepted: 12/10/2020] [Indexed: 11/18/2022]
Abstract
Fructus anisi stellati (FAS) is an anise-scented star-shaped fruit from Illicium verum tree. It is commonly consumed in many cultures as food and medicine, particularly as a remedy for infantile colic (IC). The elucidation of molecular mechanisms of action would contribute to the understanding of the traditional therapy of FAS and help to guide the preclinical and clinical study of this herb. The aim is to investigate the key therapeutic compounds of FAS and to explore the underlying molecular mechanisms of FAS therapy. The chemical compounds of FAS were obtained through data mining on TCMSP and ADME screening, and the common targets of the FAS compounds and the IC-correlated diseases were obtained from PharmMapper, GeneCards, and OMIM databases. GO and KEGG databases were used for molecular function and pathway enrichment. Cytoscape was used for network construction and analysis. SystemsDock was used for molecular docking. Three key compounds (i.e., quercetin, luteolin, and kaempferol), 19 targets, 7 molecular pathways, and 12 IC-correlated diseases were identified to be involved in the molecular mechanisms of FAS for the treatment of IC. This work showed that three therapeutic modules were primarily engaged in the molecular mechanisms of FAS for IC therapy, including the inhibition of inflammatory reactions, stimulating immunoglobulin A (IgA) production in the gastrointestinal tract, and enhancing the secretion of digestive enzymes.
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Huang Y, Lin J, Yi W, Liu Q, Cao L, Yan Y, Fu A, Huang T, Lyu Y, Huang Q, Wang J. Research on the Potential Mechanism of Gentiopicroside Against Gastric Cancer Based on Network Pharmacology. Drug Des Devel Ther 2020; 14:5109-5118. [PMID: 33262572 PMCID: PMC7700081 DOI: 10.2147/dddt.s270757] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 09/24/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Gastric cancer was still one of the commonly diagnosed cancer types and the third-most common cause of cancer-related death in the world. Gentiopicroside, which is extracted from the Gentianella acuta, is commonly used in both traditional treatment and modern clinical care; therefore, its anticancer effects have been attracted more attention. However, the systematic analysis of action mechanism of Gentiopicroside on gastric cancer (GC) has not yet been carried out. AIM A network pharmacology-based strategy combined with molecular docking studies and in vitro validation was employed to investigate potential targets and molecular mechanism of Gentiopicroside against GC. MATERIALS AND METHODS Potential targets of Gentiopicroside, as well as related genes of GC, were acquired from public databases. Potential targets, and signaling pathways were determined through bioinformatic analysis, including protein-protein interaction (PPI), the Gene Ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Subsequently, molecular docking and cell experiments were performed to further verify the above findings. RESULTS Our findings revealed that the anticancer activity of Gentiopicroside potentially involves 53 putative identified target genes. In addition, GO, KEGG, and network analyses revealed that these targets were associated with cell proliferation, metabolic process, and other physiological processes. Furthermore, we have proved that critical compound affected the expression of CCND1, CCNE1, p-AKT and p-P38 at protein levels. These findings provide an overview of the anticancer action of Gentiopicroside from a network perspective; meanwhile, it might also set an example for future studies of other materials used in traditional Chinese medicine (TCM). CONCLUSION This study comprehensively illuminated the potential targets and molecular mechanism of Gentiopicroside against GC. It also provided a promising approach to uncover the scientific basis and therapeutic mechanism of TCM treating for disease.
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Affiliation(s)
- Yanxia Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Department of Traditional Chinese Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jiatong Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Weimin Yi
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Department of Traditional Chinese Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Qinghua Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Linhui Cao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Department of Traditional Chinese Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Yongcong Yan
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Anqi Fu
- Sun Yat-Sen University Zhongshan School of Medicine, Guangzhou, People’s Republic of China
| | - Tingxuan Huang
- Sun Yat-Sen University Zhongshan School of Medicine, Guangzhou, People’s Republic of China
| | - Yingcheng Lyu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
| | - Qihui Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Department of Traditional Chinese Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People’s Republic of China
| | - Jie Wang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, People's Republic of China
- Department of Hepatobiliary Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People’s Republic of China
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Integrated Analysis of the Mechanisms of Da-Chai-Hu Decoction in Type 2 Diabetes Mellitus by a Network Pharmacology Approach. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2020; 2020:9768414. [PMID: 32419835 PMCID: PMC7204321 DOI: 10.1155/2020/9768414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 01/31/2020] [Accepted: 02/26/2020] [Indexed: 12/12/2022]
Abstract
Background The incidence of type 2 diabetes mellitus (T2DM) has increased year by year, which not only seriously affects people's quality of life, but also imposes a heavy economic burden on the family, society, and country. Currently, the pathogenesis, diagnosis, and treatment of T2DM are still unclear. Therefore, exploration of a precise multitarget treatment strategy is urgent. Here, we attempt to screen out the active components, effective targets, and functional pathways of therapeutic drugs through network pharmacology with taking advantages of traditional Chinese medicine (TCM) formulas for multitarget holistic treatment of diseases to clarify the potential therapeutic mechanism of TCM formulas and provide a systematic and clear thought for T2DM treatment. Methods First, we screened the active components of Da-Chai-Hu Decoction (DCHD) by absorption, distribution, metabolism, excretion, and toxicity (ADME/T) calculation. Second, we predicted and screened the active components of DCHD and its therapeutic targets for T2DM relying on the Traditional Chinese Medicine Systems Pharmacology Analysis Platform (TCMSP database) and Text Mining Tool (GoPubMed database), while using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to obtain T2DM targets. Third, we constructed a network of the active component-target, target-pathway of DCHD using Cytoscape software (http://cytoscape.org/,ver.3.5.1) and then analyzed gene function, related biological processes, and signal pathways through the DAVID database. Results We screened 77 active components from 1278 DCHD components and 116 effective targets from 253 ones. After matching the targets of T2DM, we obtained 38 important targets and 7 core targets were selected through further analysis. Through enrichment analysis, we found that these important targets were mainly involved in many biological processes such as oxidative stress, inflammatory reaction, and apoptosis. After analyzing the relevant pathways, the synthetic pathway for the treatment of T2DM was obtained, which provided a diagnosis-treatment idea for DCHD in the treatment of T2DM. Conclusions This article reveals the mechanism of DCHD in the treatment of T2DM related to inflammatory response and apoptosis through network pharmacology, which lays a foundation for further elucidation of drugs effective targets.
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Zhou Z, Chen B, Chen S, Lin M, Chen Y, Jin S, Chen W, Zhang Y. Applications of Network Pharmacology in Traditional Chinese Medicine Research. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2020; 2020:1646905. [PMID: 32148533 PMCID: PMC7042531 DOI: 10.1155/2020/1646905] [Citation(s) in RCA: 169] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 01/01/2023]
Abstract
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.
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Affiliation(s)
- Zhuchen Zhou
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Bing Chen
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Simiao Chen
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Minqiu Lin
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Ying Chen
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Shan Jin
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Weiyan Chen
- School of Basic Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
| | - Yuyan Zhang
- School of Life Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, China
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Newman DJ. Modern traditional Chinese medicine: Identifying, defining and usage of TCM components. PHARMACOLOGICAL ADVANCES IN NATURAL PRODUCT DRUG DISCOVERY 2020; 87:113-158. [DOI: 10.1016/bs.apha.2019.07.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Pan Y, Jia LP, Liu Y, Han Y, Deng Q. Alteration of tumor associated neutrophils by PIK3CA expression in endometrial carcinoma from TCGA data. J Ovarian Res 2019; 12:81. [PMID: 31472672 PMCID: PMC6717327 DOI: 10.1186/s13048-019-0557-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/20/2019] [Indexed: 12/26/2022] Open
Abstract
Uterine corpus endometrial carcinoma (UCEC) is one of the most common cancer in female worldwide. PIK3CA has been proven to be a strong prognostic biomarker in UCEC. Nevertheless, current studies have not investigated what effects PIK3CA had on tumor associated neutrophils (TANss). Kaplan-Meier methods were used to compute the survival time of TCGA UCEC patients. GO and KEGG enrichment analysis unveiled relevant pathways PIK3CA affected using DEGs between PIK3CA high expression group and PIK3CA low expression group in TCGA UCEC, as well as GSEA. immune infiltration status was calculated using TIMER. We found that PIK3CA influenced a number of pathways including immune related pathways. The fraction of TANs was certainly altered by PIK3CA expression in UCEC. Our findings suggest that PIK3CA expression may play an important role in tumor immune microenvironment and could alter fraction of TANs in UCEC.
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Affiliation(s)
- Yinglian Pan
- Department of Medical Oncology, Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570102, People's Republic of China
| | - Li Ping Jia
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570102, People's Republic of China
| | - Yuzhu Liu
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570102, People's Republic of China
| | - Yixu Han
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570102, People's Republic of China
| | - Qingchun Deng
- Department of Gynecology, The Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, 570102, People's Republic of China.
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Shi XQ, Yue SJ, Tang YP, Chen YY, Zhou GS, Zhang J, Zhu ZH, Liu P, Duan JA. A network pharmacology approach to investigate the blood enriching mechanism of Danggui buxue Decoction. JOURNAL OF ETHNOPHARMACOLOGY 2019; 235:227-242. [PMID: 30703496 DOI: 10.1016/j.jep.2019.01.027] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/21/2019] [Accepted: 01/26/2019] [Indexed: 06/09/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Danggui buxue Decoction (DBD) has been frequently used to treat with blood deficiency, which consisted of Danggui (DG) and Huangqi (HQ) at a ratio of 1:5. Accumulating evidence showed that blood deficiency in traditional Chinese medicine (TCM) was similar to anemia in modern medicine. AIM OF THE STUDY The purpose of this study was to explore its therapeutic mechanism of with network pharmacology approach. MATERIALS AND METHODS We explored the chemical compounds of DBD and used compound ADME screening to identify the potential compounds. Targets for the therapeutic actions of DBD were obtained from the PharmMapper, Swiss, SEA and STITCH. GO analysis and pathway enrichment analysis was performed using the DAVID webserver. Cytoscape was used to visualize the compound-target-pathway network for DBD. The pharmacodynamics and crucial targets were also validated. RESULTS Thirty-six potential active components in DBD and 49 targets which the active components acted on were identified. 47 KEGG pathways which DBD acted on were also come to light. And then, according to KEGG pathway annotation analysis, only 16 pathways seemed to be related to the blood nourishing effect of DBD, such as PI3K-AKT pathway, and so on. Only 32 targets participated in these 16 pathways and they were acted on by 29 of the 36 active compounds. Whole pharmacodynamic experiments showed that DBD had significant effects to blood loss rats. Furthermore, DBD could promote the up-regulation of hematopoietic and immune related targets and the down-regulation of inflammatory related targets. Significantly, with the results of effective rate, molecular docking and experimental validation, we predicted astragaloside IV in HQ, senkyunolide A and senkyunolide K in DG might be the major contributing compounds to DBD's blood enriching effect. CONCLUSION In this study, a systematical network pharmacology approach was built. Our results provided a basis for the future study of senkyunolide A and senkyunolide K as the blood enriching compounds in DBD. Furthermore, combined network pharmacology with validation experimental results, the nourishing blood effect of DBD might be manifested by the dual mechanism of enhancing immunity and promoting hematopoiesis.
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Affiliation(s)
- Xu-Qin Shi
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and Jiangsu Key Laboratory for High Technology Research of Traditional Chinese Medicine Formulae and Key Laboratory of Chinese Medicinal Resources Recycling Utilization, State Administration of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Shi-Jun Yue
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and Jiangsu Key Laboratory for High Technology Research of Traditional Chinese Medicine Formulae and Key Laboratory of Chinese Medicinal Resources Recycling Utilization, State Administration of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China; Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xi'an 712046, Shaanxi Province, China
| | - Yu-Ping Tang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and Jiangsu Key Laboratory for High Technology Research of Traditional Chinese Medicine Formulae and Key Laboratory of Chinese Medicinal Resources Recycling Utilization, State Administration of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China; Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xi'an 712046, Shaanxi Province, China.
| | - Yan-Yan Chen
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and Jiangsu Key Laboratory for High Technology Research of Traditional Chinese Medicine Formulae and Key Laboratory of Chinese Medicinal Resources Recycling Utilization, State Administration of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China; Key Laboratory of Shaanxi Administration of Traditional Chinese Medicine for TCM Compatibility, Shaanxi University of Chinese Medicine, Xi'an 712046, Shaanxi Province, China
| | - Gui-Sheng Zhou
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and Jiangsu Key Laboratory for High Technology Research of Traditional Chinese Medicine Formulae and Key Laboratory of Chinese Medicinal Resources Recycling Utilization, State Administration of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Jing Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and Jiangsu Key Laboratory for High Technology Research of Traditional Chinese Medicine Formulae and Key Laboratory of Chinese Medicinal Resources Recycling Utilization, State Administration of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Zhen-Hua Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and Jiangsu Key Laboratory for High Technology Research of Traditional Chinese Medicine Formulae and Key Laboratory of Chinese Medicinal Resources Recycling Utilization, State Administration of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Pei Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and Jiangsu Key Laboratory for High Technology Research of Traditional Chinese Medicine Formulae and Key Laboratory of Chinese Medicinal Resources Recycling Utilization, State Administration of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization and Jiangsu Key Laboratory for High Technology Research of Traditional Chinese Medicine Formulae and Key Laboratory of Chinese Medicinal Resources Recycling Utilization, State Administration of Traditional Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, Jiangsu Province, China
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Ning J, Ahmed S, Cheng G, Chen T, Wang Y, Peng D, Yuan Z. Analysis of the stability and affinity of BlaR-CTD protein to β-lactam antibiotics based on docking and mutagenesis studies. J Biol Eng 2019; 13:27. [PMID: 30976316 PMCID: PMC6441189 DOI: 10.1186/s13036-019-0157-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/14/2019] [Indexed: 12/20/2022] Open
Abstract
Owing to the thermal instability and low affinity of BlaR-CTD to some β-lactams, the receptor assay based on BlaR-CTD is limited in the detection of abundant variety of drugs and the result is often unstable. In this study, the three-dimensional structure of BlaR-CTD from Bacillus licheniformis ATCC14580 was constructed by homologous modeling based on the crystal structure of BlaR-CTD from B. licheniformis 749/I, and the binding sites of this protein to 40 β-lactams were also obtained by molecular docking. To improve the stability and affinity of the protein, 23 mutant proteins were designed based on docking and homologous alignment results as well as by inserting disulfide bond and building the salt bridge. The mutation was rationality evaluated by SIFT and PloyPhen2 software. The heterologous expressed and purified mutant proteins were then subjected to the activity and stability assay. It was shown that among all mutant proteins, I188K/S19C/G24C, A138E/R50C/Q147C and S190Y/E183C/I188K respectively exhibited a higher affinity to 33, 22 and 21 β-lactams than the wild-type protein, while I188K/S19C/G24C exhibited the best stability. This may due to that the conformation of the active site in mutant protein I188K/S19C/G24C changed, and the random coli in the surface of protein activity increased. Our study suggests a possible structure-function relationship on the stability and affinity of BlaR-CTD, which provides new insights into protein rational design study and lays a solid foundation for establishing the receptor-based screening assay for the detection of β-lactam residues.
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Affiliation(s)
- Jianan Ning
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Saeed Ahmed
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Guyue Cheng
- 2MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
| | - Ting Chen
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yulian Wang
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Dapeng Peng
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zonghui Yuan
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070 China.,2MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070 China
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