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Yang R, Zhao G, Zhang L, Xia Y, Yu H, Yan B, Cheng B. Identification of potential extracellular signal-regulated protein kinase 2 inhibitors based on multiple virtual screening strategies. Front Pharmacol 2022; 13:1077550. [PMID: 36467098 PMCID: PMC9715613 DOI: 10.3389/fphar.2022.1077550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 11/09/2022] [Indexed: 01/08/2024] Open
Abstract
The integration of multiple virtual screening strategies facilitates the balance of computational efficiency and prediction accuracy. In this study, we constructed an efficient and reliable "multi-stage virtual screening-in vitro biological validation" system to identify potential inhibitors targeting extracellular signal-regulated protein kinase 2 (ERK2). Firstly, we rapidly obtained 10 candidate ERK2 inhibitors with desirable pharmacokinetic characteristics from thousands of named natural products in ZINC database based on machine learning classification models and ADME/T prediction. The structure-based molecular docking approach was then used to obtain four further hits with lower binding free energy compared to the positive control molecule Magnolipin. Subsequently, the two compounds were purchased for in vitro biological validation considering commercial availability and economic cost, and the results showed that Dodoviscin A exhibited acceptable inhibitory activity on ERK2 (IC50 = 10.79 μm). Finally, the mechanism of action and binding stability of this natural product inhibitor were investigated by binding mode analysis and molecular dynamics simulation.
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Affiliation(s)
- Ruoqi Yang
- Department of Acupuncture, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Guiping Zhao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lili Zhang
- Department of Ultrasound, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yu Xia
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Huijuan Yu
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Bin Yan
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Bin Cheng
- Department of Acupuncture, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
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Sugimoto S. Searching for constituents from plants in geographically characterized areas, Egypt, Madagascar, and Okinawa. J Nat Med 2022; 76:725-731. [PMID: 35960490 PMCID: PMC9411232 DOI: 10.1007/s11418-022-01638-x] [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: 03/31/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Secondary metabolites may not be produced under some conditions, and in most cases, their function and significance in the producing organisms is unknown. Conversely, there are some that are produced for readily understood reasons, for example, toxic substances as defensive substances against invaders, or volatile substances that attract other species of organisms. These secondary metabolites also contribute to our health. However, there has not been sufficient research to evaluate them from a pharmacological perspective, and much progress is expected in this area in the future. About 90% of the existing plants have not been studied for their chemical components and biological activities (Kazuki Saito in Bunshun shinsho 1119, pp. 119-126. ISBN 978-4-16-661119-5, 2017). On this basis, we have been searching for the constituents of unknown plants, and whose constituents have not been studied extensively. In this paper, the authors have reviewed some of their previous searching for constituents from plants in geographically characterized areas, Egypt, Madagascar, and Okinawa.
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Affiliation(s)
- Sachiko Sugimoto
- Department of Pharmacognosy, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8553, Japan.
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Sagara T, Sugimoto S, Yamano Y, Nehira T, Masuda K, Otsuka H, Matsunami K. Isolation of Three New Diterpenes from Dodonaea viscosa. Chem Pharm Bull (Tokyo) 2021; 69:40-47. [PMID: 33390520 DOI: 10.1248/cpb.c20-00327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
An investigation into the methanol extracts obtained from the stems of Dodonaea viscosa led to the isolation of one nor-clerodane diterpene (1) and two labdane diterpenes (2, 3), as well as 17 known compounds (4-20). The structures of these compounds were elucidated based on chemical and spectral evidence. The stereochemical structure of the nor-clerodane diterpene was confirmed via its circular dichroism spectrum and calculated electronic circular dichroism spectrum. Isolated compounds were evaluated for their inhibitory effects on collagenase and tyrosinase. Since 5,7,4'-trihydroxy-3'-(4-hydroxy-3-methylbutyl)-5'-(3-methylbut-2-enyl)-3,6-dimethoxyflavone (9) showed collagenase inhibitory activity and scopoletin (12) had significant tyrosinase inhibitory activity, they were considered to be good candidates for cosmetic agents.
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Affiliation(s)
- Toshinori Sagara
- Department of Pharmacognosy, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Sachiko Sugimoto
- Department of Pharmacognosy, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Yoshi Yamano
- Department of Pharmacognosy, Graduate School of Biomedical and Health Sciences, Hiroshima University
| | - Tatsuo Nehira
- Graduate School of Integrated Arts and Sciences, Hiroshima University
| | - Kazuma Masuda
- Graduate School of Integrated Arts and Sciences, Hiroshima University
| | - Hideaki Otsuka
- Department of Natural Products Chemistry, Faculty of Pharmacy, Yasuda Women's University
| | - Katsuyoshi Matsunami
- Department of Pharmacognosy, Graduate School of Biomedical and Health Sciences, Hiroshima University
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Dodonaea viscosa Jacq: A Medicinal Plant with Cytotoxic Effect on Colon Cancer Cell Line (HT-29). JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.3.31] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Dodonaea viscosa (Family: Sapindaceae) is a medicinal plant that has been used as anti-rheumatic and bone pain in Peru as a folk remedy. Ethanol extract obtained from D. viscosa leaves was partitioned as n-hexane fraction; chloroform fraction; ethyl acetate fraction; n-butanol fraction and aqueous fraction. Phytoconstituents from D. viscosa leaves were evaluated by using chemical reagents to identify the presence of each phytochemical. In addition, a cytotoxic effect was determined by the Sulforhodamine B (SRB) test. The results showed that the ethanol extract and ethyl acetate fraction of leaves had the highest variety of phytoconstituents. The ethanol extrac of leaves exhibited a major inhibitory effect compared to different fractions in human colon cancer cells (HT-29). From these assays, it is concluded that D. viscosa does not possess any detectable cytotoxic effect on epidermal cells from mouse (3T3), and a slight cytotoxic effect against HT-29 tumor cells compared to 5-FU. This species could appear like a good source of herbal medicine in colorectal cancer disease.
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Zhu JJ, Yan GR, Xu ZJ, Hu X, Wang GH, Wang T, Zhu WL, Hou AJ, Wang HY. Inhibitory Effects of (2'R)-2',3'-dihydro-2'-(1-hydroxy-1-methylethyl)-2,6'-bibenzofuran-6,4'-diol on Mushroom Tyrosinase and Melanogenesis in B16-F10 Melanoma Cells. Phytother Res 2015; 29:1040-5. [PMID: 25826437 DOI: 10.1002/ptr.5344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 02/13/2015] [Accepted: 03/11/2015] [Indexed: 11/08/2022]
Abstract
(2'R)-2',3'-Dihydro-2'-(1-hydroxy-1-methylethyl)-2,6'-bibenzofuran-6,4'-diol (DHMB) is a natural compound extracted from Morus notabilis. It was found that DHMB acts as a competitive inhibitor against mushroom tyrosinase with a Ki value of 14.77 μM. Docking results further indicated that it could form strong interactions with one copper ion with a distance of 2.7 Å, suggesting the mechanism of inhibition might be due to chelating copper ions in the active site. Furthermore, melanin production in B16-F10 murine melanoma cells was significantly inhibited by DHMB in a concentration-dependent manner without cytotoxicity. The results of western blotting also showed that DHMB decreased 3-isobuty-1-methxlzanthine-induced mature tyrosinase expression. Taken together, these findings indicated that DHMB may be a new promising pigmentation-altering agent for agriculture, cosmetic, and therapeutic applications.
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Affiliation(s)
- Jing-Jie Zhu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Gui-Rui Yan
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Zhi-Jian Xu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Xiao Hu
- Department of Pharmacognosy, School of Pharmacy, Fudan University, 826 Zhang Heng Road, Shanghai, 201203, China
| | - Gai-Hong Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Ting Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Wei-Liang Zhu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
| | - Ai-Jun Hou
- Department of Pharmacognosy, School of Pharmacy, Fudan University, 826 Zhang Heng Road, Shanghai, 201203, China
| | - He-Yao Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhang Jiang Hi-Tech Park, Pudong, Shanghai, 201203, China
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