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Zhao Z, Ma R, Ma Y, Zhao L, Wang L, Fang Y, Zhang Y, Wu X, Wang X. Discovery of Nine Dipeptidyl Peptidase-4 Inhibitors from Coptis chinensis Using Virtual Screening, Bioactivity Evaluation, and Binding Studies. Molecules 2024; 29:2304. [PMID: 38792165 PMCID: PMC11123979 DOI: 10.3390/molecules29102304] [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: 04/07/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The objective of this study was to identify multiple alkaloids in Coptis chinensis that demonstrate inhibitory activity against DPP-4 and systematically evaluate their activity and binding characteristics. A combined strategy that included molecular docking, a DPP-4 inhibition assay, surface plasmon resonance (SPR), and a molecular dynamics simulation technique was employed. The results showed that nine alkaloids in Coptis chinensis directly inhibited DPP-4, with IC50 values of 3.44-53.73 μM. SPR-based binding studies revealed that these alkaloids display rapid binding and dissociation characteristics when interacting with DPP-4, with KD values ranging from 8.11 to 29.97 μM. A molecular dynamics analysis revealed that equilibrium was rapidly reached by nine DPP-4-ligand systems with minimal fluctuations, while binding free energy calculations showed that the ∆Gbind values for the nine test compounds ranged from -31.84 to -16.06 kcal/mol. The most important forces for the binding of these alkaloids with DPP-4 are electrostatic interactions and van der Waals forces. Various important amino acid residues, such as Arg125, His126, Phe357, Arg358, and Tyr547, were involved in the inhibition of DPP-4 by the compounds, revealing a mechanistic basis for the further optimization of these alkaloids as DPP-4 inhibitors. This study confirmed nine alkaloids as direct inhibitors of DPP-4 and characterized their binding features, thereby providing a basis for further research and development on novel DPP-4 inhibitors.
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Affiliation(s)
- Zixi Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Ruonan Ma
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Yuqing Ma
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Liqiang Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Lele Wang
- School of Pharmacy, Minzu University of China, Haidian District, Beijing 100081, China; (L.W.); (Y.F.)
| | - Yuzhen Fang
- School of Pharmacy, Minzu University of China, Haidian District, Beijing 100081, China; (L.W.); (Y.F.)
| | - Yuxin Zhang
- School of Pharmacy, Minzu University of China, Haidian District, Beijing 100081, China; (L.W.); (Y.F.)
| | - Xia Wu
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; (Z.Z.); (R.M.); (Y.M.); (L.Z.)
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Bhattacharya S, Sadhukhan D, Saraswathy R. Role of sex in immune response and epigenetic mechanisms. Epigenetics Chromatin 2024; 17:1. [PMID: 38247002 PMCID: PMC10802034 DOI: 10.1186/s13072-024-00525-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
The functioning of the human immune system is highly dependent on the sex of the individual, which comes by virtue of sex chromosomes and hormonal differences. Epigenetic mechanisms such as X chromosome inactivation, mosaicism, skewing, and dimorphism in X chromosome genes and Y chromosome regulatory genes create a sex-based variance in the immune response between males and females. This leads to differential susceptibility in immune-related disorders like infections, autoimmunity, and malignancies. Various naturally available immunomodulators are also available which target immune pathways containing X chromosome genes.
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Affiliation(s)
- Sombodhi Bhattacharya
- Biomedical Genetics Research Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Debasmita Sadhukhan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Radha Saraswathy
- Biomedical Genetics Research Lab, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
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Wang C, Liu P, Sun Y, Liu T, Xu X, Guo J, Gong Z, Sun H, Xu R. Prognostic biomarker SYK and its correlation with immune infiltrates in glioma. Exp Ther Med 2023; 26:499. [PMID: 37810632 PMCID: PMC10557046 DOI: 10.3892/etm.2023.12198] [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: 10/29/2022] [Accepted: 03/24/2023] [Indexed: 10/10/2023] Open
Abstract
The tumor microenvironment (TME) provides excellent conditions for the development of glioma. The present study sought to identify the prognostic factors of glioma that could be used to improve the prognosis of patients with this disease. In the present study, Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) and Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data calculations were employed to estimate the ratio of tumor-infiltrating immune cells and the quantity of immune and stromal components in 698 glioma cases from the Cancer Genome Atlas database. In addition, certain differentially expressed genes were studied by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses and single genes associated with prognosis were identified by protein-protein interaction (PPI) network and Cox combined analysis. The immune and stromal scores of the TME were significantly associated with glioma patient survival. By using the PPI network and Cox regression analyses, spleen tyrosine kinase (SYK) was eventually identified as the best prognostic factor for patients with glioma. In addition, Gene Set Enrichment Analysis and CIBERSORT analyses were employed. The former indicated that the high-expression SYK group genes were mainly enriched in immune-related activities. The latter revealed that SYK expression was positively associated with T cell cluster of differentiation 4 memory resting and monocytes. The aforementioned experimental analyses provided the theoretical basis for the biological prediction of SYK. The data indicated that SYK contributed to immune predictors in patients with glioma by facilitating the shift of the TME from immune dominance to metabolic activity. Finally, reverse transcription-quantitative PCR and western blotting were used to verify the single gene expression in glioma cells. This may provide prognostic value for the treatment of glioma.
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Affiliation(s)
- Changxin Wang
- School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Pei Liu
- College of Life Sciences, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Yu Sun
- Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Ting Liu
- Medical College, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Xiaoxiao Xu
- College of Life Sciences, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Jiamin Guo
- College of Life Sciences, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Zheng Gong
- College of Life Sciences, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Haixin Sun
- College of Life Sciences, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Rui Xu
- Department of Interventional Radiology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266000, P.R. China
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Muthumanickam S, Ramachandran B, Boomi P, Jeyakanthan J, Prabu HG, Jegatheswaran S, Premkumar K. Combination of bendamustine-azacitidine against Syk target of breast cancer: an in silico study. J Biomol Struct Dyn 2023; 41:13950-13962. [PMID: 37098715 DOI: 10.1080/07391102.2023.2203259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/28/2023] [Indexed: 04/27/2023]
Abstract
Breast cancer (BC) is the most serious and second leading cause of death in women worldwide. When breast cancer is diagnosed and treated early, the chance of long-term survival is up to 90%. On the other hand, 90% of BC patient deaths are due to metastasis and a lack of effective early diagnosis. The existing conventional chemotherapy provides negative feedback due to transportation barriers towards the action sites, multidrug resistance, poor bio-availability, non-specific delivery and systemic side effects on the healthy tissue. Syk protein Kinase has been reported in BC, as a tumor modulator, providing a pro-survival signal and also by restricting epithelial-mesenchymal transition, enhancing cell-cell interactions and inhibiting migration. In the present study, we explored the possibility of targeting BC by attenuating Syk protein Kinase. Hence, we have conjugated the hydrophobic Bendamustine (BEN) and hydrophilic Azacitidine (AZA) anticancer drugs to evaluate their efficacy against BC. The native drugs (BEN and AZA) and designed drug-drug conjugate (BEN-AZA) were docked with Syk protein. Then, the docked complex was performed for Binding Free Energy and Molecular Dynamics Simulations. Furthermore, DFT and ADME properties were carried out. The results revealed that the designed drug-drug conjugate has a better docking score, ΔGbind and admirable stability throughout the simulation when compared with native drugs. In DFT and ADME analyses, the designed drug-drug conjugate has shown good stereo electronic features and pharmaceutical relevant parameters than that of native drugs. The overall results suggested that the designed drug-drug conjugate may be a suitable candidate for BC treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Pandi Boomi
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - Halliah Gurumallesh Prabu
- Department of Industrial Chemistry, School of Chemical Sciences, Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - Kumpati Premkumar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
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Screening assays for tyrosine kinase inhibitors:A review. J Pharm Biomed Anal 2022; 223:115166. [DOI: 10.1016/j.jpba.2022.115166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/16/2022]
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Asai H, Kato K, Suzuki M, Takahashi M, Miyata E, Aoi M, Kumazawa R, Nagashima F, Kurosaki H, Aoyagi Y, Fukuishi N. Potential Anti-allergic Effects of Bibenzyl Derivatives from Liverworts, Radula perrottetii. PLANTA MEDICA 2022; 88:1069-1077. [PMID: 35081628 DOI: 10.1055/a-1750-3765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The liverwort Radula perrottetii contains various bibenzyl derivatives which are known to possess various biological activities, such as anti-inflammatory effects. Mast cells (MC) play crucial roles in allergic and inflammatory diseases; thus, inhibition of MC activation is pivotal for the treatment of allergic and inflammatory disorders. We investigated the effects of perrottetin D (perD), isolated from Radula perrottetii, and perD diacetate (Ac-perD) on antigen-induced activation of MCs. Bone marrow-derived MCs (BMMCs) were generated from C57BL/6 mice. The degranulation ratio, histamine release, and the interleukin (IL)-4 and leukotriene B4 productions on antigen-triggered BMMC were investigated. Additionally, the effects of the bibenzyls on binding of IgE to FcεRI were observed by flow cytometry, and signal transduction proteins was examined by Western blot. Furthermore, binding of the bibenzyls to the Fyn kinase domain was calculated. At 10 µM, perD decreased the degranulation ratio (p < 0.01), whereas 10 µM Ac-perD down-regulated IL-4 production (p < 0.05) in addition to decreasing the degranulation ratio (p < 0.01). Both compounds tended to decrease histamine release at a concentration of 10 µM. Although 10 µM perD reduced only Syk phosphorylation, 10 µM Ac-perD diminished phosphorylation of Syk, Gab2, PLC-γ, and p38. PerD appeared to selectively bind Fyn, whereas Ac-perD appeared to act as a weak but broad-spectrum inhibitor of kinases, including Fyn. In conclusion, perD and Ac-perD suppressed the phosphorylation of signal transduction molecules downstream of the FcεRI and consequently inhibited degranulation, and/or IL-4 production. These may be beneficial potential lead compounds for the development of novel anti-allergic and anti-inflammatory drugs.
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Affiliation(s)
- Haruka Asai
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | - Koichi Kato
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | - Moe Suzuki
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | - Misato Takahashi
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | - Erika Miyata
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | - Moeka Aoi
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | - Reika Kumazawa
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | | | - Hiromasa Kurosaki
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | - Yutaka Aoyagi
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
| | - Nobuyuki Fukuishi
- Department of Pharmacology, College of Pharmacy, Kinjo Gakuin University, Aichi, Japan
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Kumar V, Parate S, Danishuddin, Zeb A, Singh P, Lee G, Jung TS, Lee KW, Ha MW. 3D-QSAR-Based Pharmacophore Modeling, Virtual Screening, and Molecular Dynamics Simulations for the Identification of Spleen Tyrosine Kinase Inhibitors. Front Cell Infect Microbiol 2022; 12:909111. [PMID: 35846777 PMCID: PMC9280624 DOI: 10.3389/fcimb.2022.909111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Spleen tyrosine kinase (SYK) is an essential mediator of immune cell signaling and has been anticipated as a therapeutic target for autoimmune diseases, notably rheumatoid arthritis, allergic rhinitis, asthma, and cancers. Significant attempts have been undertaken in recent years to develop SYK inhibitors; however, limited success has been achieved due to poor pharmacokinetics and adverse effects of inhibitors. The primary goal of this research was to identify potential inhibitors having high affinity, selectivity based on key molecular interactions, and good drug-like properties than the available inhibitor, fostamatinib. In this study, a 3D-QSAR model was built for SYK based on known inhibitor IC50 values. The best pharmacophore model was then used as a 3D query to screen a drug-like database to retrieve hits with novel chemical scaffolds. The obtained compounds were subjected to binding affinity prediction using the molecular docking approach, and the results were subsequently validated using molecular dynamics (MD) simulations. The simulated compounds were ranked according to binding free energy (ΔG), and the binding affinity was compared with fostamatinib. The binding mode analysis of selected compounds revealed that the hit compounds form hydrogen bond interactions with hinge region residue Ala451, glycine-rich loop residue Lys375, Ser379, and DFG motif Asp512. Identified hits were also observed to form a desirable interaction with Pro455 and Asn457, the rare feature observed in SYK inhibitors. Therefore, we argue that identified hit compounds ZINC98363745, ZINC98365358, ZINC98364133, and ZINC08789982 may help in drug design against SYK.
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Li Y, Zhang Y, Wu X, Gao Y, Guo J, Tian Y, Lin Z, Wang X. Discovery of natural 15-LOX small molecule inhibitors from Chinese herbal medicine using virtual Screening, biological evaluation and molecular dynamics studies. Bioorg Chem 2021; 115:105197. [PMID: 34426159 DOI: 10.1016/j.bioorg.2021.105197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/15/2021] [Accepted: 07/18/2021] [Indexed: 11/19/2022]
Abstract
Chinese herbal medicines (CHM) are frequently used to treat different types of inflammatory diseases and 15-Lipoxygenase (15-LOX) is a critical target enzyme for treating various inflammatory diseases. In this study, natural 15-LOX inhibitors were identified in CHM using an approach of virtual screening combined with the biological assays. First, an in-house Chinese medicine database containing 360 compounds was screened using a virtual screening approach based on pharmacophore and molecular docking to uncover several novel potential 15-LOX inhibitors. Secondly, the inhibitory effect of virtual screening hits against the 15-LOX enzyme was validated in an in vitro enzyme inhibition assay. Then, a tumor necrosis factor-α (TNF-α) release assay was carried out to explore the anti-inflammatory response of the active compounds. Furthermore, molecular dynamics (MD) simulation and binding free energy calculation were applied to analyze the process of inhibitors binding and also compared the mode of binding of the inhibitors by using the Molecular Mechanics-Generalized Born Surface Area (MM/GBSA) method. Finally, licochalcone B and eriodictyol were confirmed as inhibitors of the 15-LOX enzyme with IC50 values of 9.67 and 18.99 μM, respectively. In vitro cell-based assay showed that licochalcone B and eriodictyol inhibited the release of TNF-α factor in RAW264.7 cells stimulated by lipopolysaccharides (LPS) in a dose-dependent manner. Molecular dynamics and binding free energy analysis showed that the two 15-LOX-ligand systems immediately attained equilibrium with almost 1 Å fluctuation, the calculated binding free energies were found around -18.89 and -12.96 kcal/mol for licochalcone B and eriodictyol, respectively. Thr412, Arg415, Val420, Thr429, Ile602 and Trp606 were the main amino acid residues for the inhibition of 15-LOX enzyme activity. The current study confirms that licochalcone B and eriodictyol are 15-LOX inhibitors and can suppress the release of the TNF-α factor in RAW264.7 cells stimulated by LPS, thus providing a basis for the follow-up research and development for 15-LOX inhibitors.
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Affiliation(s)
- Yatong Li
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yuxin Zhang
- Key Laboratory of Ethnomedicine, School of Pharmacy, Ministry of Education, Minzu University of China, Haidian District, Beijing 100081, China
| | - Xia Wu
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yanbin Gao
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Junfang Guo
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Yulang Tian
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Ziyue Lin
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China
| | - Xing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Fengtai District, Beijing 100069, China; Beijing Key Lab of Traditional Chinese Medicine Collateral Disease Theory Research, Capital Medical University, Fengtai District, Beijing 100069, China.
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Lai Z, He J, Zhou C, Zhao H, Cui S. Tanshinones: An Update in the Medicinal Chemistry in Recent 5 Years. Curr Med Chem 2021; 28:2807-2827. [PMID: 32436817 DOI: 10.2174/0929867327666200521124850] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/02/2020] [Accepted: 04/04/2020] [Indexed: 11/22/2022]
Abstract
Tanshinones are an important type of natural products isolated from Salvia miltiorrhiza Bunge with various bioactivities. Tanshinone IIa, cryptotanshinone and tanshinone I are three kinds of tanshinones which have been widely investigated. Particularly, sodium tanshinone IIa sulfonate is a water-soluble derivative of tanshinone IIa and it is used in clinical in China for treating cardiovascular diseases. In recent years, there are increasing interests in the investigation of tanshinones derivatives in various diseases. This article presents a review of the anti-atherosclerotic effects, cardioprotective effects, anticancer activities, antibacterial activities and antiviral activities of tanshinones and structural modification work in recent years.
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Affiliation(s)
- Zhencheng Lai
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jixiao He
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Changxin Zhou
- Institute of Modern Chinese Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Huajun Zhao
- College of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Sunliang Cui
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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