1
|
El Aissouq A, Bouachrine M, Bouayyadi L, Ouammou A, Khalil F. Structure-based virtual screening of novel natural products as chalcone derivatives against SARS-CoV-2 M pro. J Biomol Struct Dyn 2023; 41:13235-13249. [PMID: 36752320 DOI: 10.1080/07391102.2023.2172456] [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: 07/04/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has spread quickly around the world, causing a global pandemic. It has infected more than 500 million people as of April 28, 2022. Much research has been reported to stop the virus from spreading, but there are currently no approved medicines to treat COVID-19. In this work, a dataset of 142 natural products collected from various medicinal plants was used to perform structure-based virtual screening (SBVS) through the combined application of molecular docking and molecular dynamics (MD) simulation methods. First, the dataset of compounds was optimized using the density functional theory (DFT) approach. The optimized compounds were then submitted to the first screening, which was done by the pKCM web server to look for drug-likeness and the PyRx to look for binding affinity. Among the 142 natural substances, 10 compounds were selected for docking validation. Compounds that interact with CYS145 and LEU141, the essential catalytic residues, as well as compounds with binding affinities less than -8.0 kcal/mol, are considered promising anti-SARS-CoV-2 drug candidates. The top-ranked compounds were then evaluated by MD simulations and MM-GBSA method. These results could help researchers come up with new natural compounds that could be used to treat SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Abdellah El Aissouq
- Laboratory of Processes, Materials, and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Mohammed Bouachrine
- MCNS Laboratory, Faculty of Sciences, Moulay Ismail University, Meknes, Morocco
| | | | - Abdelkrim Ouammou
- LIMOME Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| | - Fouad Khalil
- Laboratory of Processes, Materials, and Environment (LPME), Faculty of Science and Technology, Sidi Mohamed Ben Abdellah University, Fez, Morocco
| |
Collapse
|
2
|
Wang M, Yang TT, Rao Y, Wang ZM, Dong X, Zhang LH, Han L, Zhang Y, Wang T, Zhu Y, Gao XM, Li TX, Wang HY, Xu YT, Wu HH. A review on traditional uses, phytochemistry, pharmacology, toxicology and the analytical methods of the genus Nardostachys. JOURNAL OF ETHNOPHARMACOLOGY 2021; 280:114446. [PMID: 34339792 DOI: 10.1016/j.jep.2021.114446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/22/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The plants of the genus Nardostachys (Caprifoliaceae) have been used for a long history in different cultural systems of medicine, including Chinese, Ayurvedic, Korean folk medicine and Islamic, for treatments of disorders in nervous, digestive, cardiovascular and integumentary systems. AIM OF THE REVIEW This review aims to provide comprehensive information on Nardostachys plants including botany update, traditional uses, data mining of uses in traditional Chinese medicine (TCM) and current Chinese medicinal patents, chemical constituents, pharmacological effects, toxicity and analytical method studies. MATERIALS AND METHODS Studies of the genus Nardostachys were collected via Google Scholar and Baidu Scholar, ScienceDirect, SciFinder, Wiley Online Library, ACS Publications, NLM/NCBI, Web of Science, CNKI, WANFANG DATA, EMBASE, Huabeing database and Traditional Chinese Medicine Resource Network and libraries. Some local books, PhD or MS's dissertations were also included. The literatures cited in this review covered the period from 1962 to March 2021. The Plant List and Kew Herbarium Catalogue databases were used to authenticate the scientific name. RESULTS Botany description of Nardostachys genus is updated. Analysis of the literatures indicates that Nardostachys species are valuable herbs with therapeutic potentials for various disorders. Data mining on ancient TCM prescriptions and current Chinese medicinal patents containing Nardostachys revealed its common compatibility with other herbs in China. Phytochemical studies identified terpenoids and phenolic compounds as the main constituents in the genus Nardostachys and sesquiterpenoids as the major bioactive components. Experimental studies demonstrated that crude extracts, major fractions and the main constituents from Nardostachys species mainly exhibited pharmacological activities on nervous, digestive, cardiovascular and skin systems. Further, in vivo and in vitro toxicological studies demonstrated that Nardostachys plants showed either no or low toxicities, except at high doses. Finally, methods of qualitative and quantitative analyses on chemical constituents of genus Nardostachys were summarized, including TLC/HPTLC, GC and HPLC/UPLC methods, combined with common detectors including PDA, DAD and MS. CONCLUSIONS This review summarizes the progress on phytochemistry, pharmacology, toxicology and analytical methods of the genus Nardostachys. Studies demonstrate traditional uses of the genus Nardostachys, and reveal novel bioactive effects for clinical uses. These achievements expand our knowledge on the genus Nardostachys and its clinical value.
Collapse
Affiliation(s)
- Miao Wang
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Tian-Tian Yang
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Yao Rao
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Zhi-Mei Wang
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Xueqi Dong
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Li-Hua Zhang
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Lifeng Han
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Yi Zhang
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Tao Wang
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Yan Zhu
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Xiu-Mei Gao
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Tian-Xiang Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Hai-Ying Wang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China
| | - Yan-Tong Xu
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China; Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, PR China
| | - Hong-Hua Wu
- State Key Laboratory of Component-based Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, West Area, Tuanbo New Town, Jinghai District, Tianjin, 301617, PR China.
| |
Collapse
|
3
|
Wang Z, Dong X, Zheng HH, Zhang H, Deng X, Chen YP, Zhu Y, Wu HH, Xu YT. Two isonardosinane-type sesquiterpenoids from Nardostachys jatamansi DC. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.06.052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
4
|
Liu X, Yang J, Yao XJ, Yang X, Fu J, Bai LP, Liu L, Jiang ZH, Zhu GY. Linderalides A–D, Disesquiterpenoid–Geranylbenzofuranone Conjugates from Lindera aggregata. J Org Chem 2019; 84:8242-8247. [DOI: 10.1021/acs.joc.9b00522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xin Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China
| | - Ji Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Xiao-Jun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Xing Yang
- Department of Chemistry, Lanzhou University, Lanzhou 730000, China
| | - Jing Fu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Li-Ping Bai
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| | - Guo-Yuan Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, China
| |
Collapse
|
5
|
Deng X, Wang Y, Wu HH, Zhang W, Dong X, Wang Z, Zhu Y, Gao XM, Li L, Wang YN, Xu YT. Six kanshone C-derived sesquiterpenoid hybrids nardochalaristolones A–D, nardoflavaristolone A and dinardokanshone F from Nardostachys jatamansi DC. Bioorg Chem 2018; 81:35-43. [DOI: 10.1016/j.bioorg.2018.07.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/29/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
|
6
|
Wu HH, Deng X, Zhang H, Chen YP, Ying SS, Wu YJ, Liu YT, Zhu Y, Gao XM, Xu YT, Li L. Dinardokanshones C-E, isonardoeudesmols A-D and nardoeudesmol D from Nardostachys jatamansi DC. PHYTOCHEMISTRY 2018; 150:50-59. [PMID: 29544214 DOI: 10.1016/j.phytochem.2018.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/28/2018] [Accepted: 03/05/2018] [Indexed: 06/08/2023]
Abstract
Dinardokanshones C-E, three sesquiterpenoid dimers comprising an unusual nornardosinane-type sesquiterpenoid core and an aristolane-type sesquiterpenoid unit conjugated by an extra pyran or furan ring, together with monomeric sesquiterpenoids isonardoeudesmols A-D and nardoeudesmol D, were isolated from the underground parts of Nardostachys jatamansi DC. Structures of the eight compounds were elucidated by analysis of the extensive spectroscopic data, and their absolute configurations were established by analysis of NOESY and X-ray diffraction data, combined with computational electronic circular dichroism (ECD) calculations. The results of SERT activity assay revealed that isonardoeudesmol D and nardoeudesmol D significantly inhibited SERT activity, while dinardokanshones D-E and isonardoeudesmols B-C significantly enhanced SERT activity, among which dinardokanshone D exhibited the strongest effect.
Collapse
Affiliation(s)
- Hong-Hua Wu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China
| | - Xu Deng
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China
| | - Hu Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China
| | - Ying-Peng Chen
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China
| | - Shu-Song Ying
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China
| | - Yi-Jing Wu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China
| | - Yan-Ting Liu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China
| | - Yan Zhu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China
| | - Xiu-Mei Gao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China
| | - Yan-Tong Xu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of Chemistry and Analysis of Traditional Chinese Medicine, Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 312 Anshan Xidao Road, Nankai District, Tianjin 300193, PR China.
| | - Li Li
- Institute of Materia Medica, Chinese Academy of Medical Science Peking Union Medical College, 1 Xian Nong Tan Street, Xicheng District, Beijing 100050, PR China
| |
Collapse
|
7
|
Fang Y, Lu Y, Zang X, Wu T, Qi X, Pan S, Xu X. 3D-QSAR and docking studies of flavonoids as potent Escherichia coli inhibitors. Sci Rep 2016; 6:23634. [PMID: 27049530 PMCID: PMC4822154 DOI: 10.1038/srep23634] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 03/10/2016] [Indexed: 02/08/2023] Open
Abstract
Flavonoids are potential antibacterial agents. However, key substituents and mechanism for their antibacterial activity have not been fully investigated. The quantitative structure-activity relationship (QSAR) and molecular docking of flavonoids relating to potent anti-Escherichia coli agents were investigated. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were developed by using the pIC50 values of flavonoids. The cross-validated coefficient (q(2)) values for CoMFA (0.743) and for CoMSIA (0.708) were achieved, illustrating high predictive capabilities. Selected descriptors for the CoMFA model were ClogP (logarithm of the octanol/water partition coefficient), steric and electrostatic fields, while, ClogP, electrostatic and hydrogen bond donor fields were used for the CoMSIA model. Molecular docking results confirmed that half of the tested flavonoids inhibited DNA gyrase B (GyrB) by interacting with adenosine-triphosphate (ATP) pocket in a same orientation. Polymethoxyl flavones, flavonoid glycosides, isoflavonoids changed their orientation, resulting in a decrease of inhibitory activity. Moreover, docking results showed that 3-hydroxyl, 5-hydroxyl, 7-hydroxyl and 4-carbonyl groups were found to be crucial active substituents of flavonoids by interacting with key residues of GyrB, which were in agreement with the QSAR study results. These results provide valuable information for structure requirements of flavonoids as antibacterial agents.
Collapse
Affiliation(s)
- Yajing Fang
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, P.R. China
| | - Yulin Lu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xixi Zang
- Oilcrops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, P.R. China
| | - Ting Wu
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, P.R. China
| | - XiaoJuan Qi
- College of Science, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Siyi Pan
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, P.R. China
| | - Xiaoyun Xu
- Key Laboratory of Environment Correlative Dietology (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, P.R. China
| |
Collapse
|
8
|
Wu HH, Chen YP, Ying SS, Zhang P, Xu YT, Gao XM, Zhu Y. Dinardokanshones A and B, two unique sesquiterpene dimers from the roots and rhizomes of Nardostachys chinensis. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.08.079] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
9
|
Lu Z, Zhou P, Zhan Y, Su J, Yi D. Quantification of Nardosinone in Rat Plasma Using Liquid Chromatography–Tandem Mass Spectrometry and Its Pharmacokinetics Application. J Chromatogr Sci 2015; 53:1725-9. [DOI: 10.1093/chromsci/bmv081] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 11/13/2022]
|
10
|
Hu J, Liu D, Xu W, Zhang F, Zheng H. One-pot reaction for the concise synthesis of spiro[benzofuran-2,2′-naphthalen]-1′-one derivatives. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.08.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
|