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Tian YY, Tong JB, Liu Y, Tian Y. QSAR Study, Molecular Docking and Molecular Dynamic Simulation of Aurora Kinase Inhibitors Derived from Imidazo[4,5- b]pyridine Derivatives. Molecules 2024; 29:1772. [PMID: 38675594 PMCID: PMC11052498 DOI: 10.3390/molecules29081772] [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: 03/09/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer is a serious threat to human life and social development and the use of scientific methods for cancer prevention and control is necessary. In this study, HQSAR, CoMFA, CoMSIA and TopomerCoMFA methods are used to establish models of 65 imidazo[4,5-b]pyridine derivatives to explore the quantitative structure-activity relationship between their anticancer activities and molecular conformations. The results show that the cross-validation coefficients q2 of HQSAR, CoMFA, CoMSIA and TopomerCoMFA are 0.892, 0.866, 0.877 and 0.905, respectively. The non-cross-validation coefficients r2 are 0.948, 0.983, 0.995 and 0.971, respectively. The externally validated complex correlation coefficients r2pred of external validation are 0.814, 0.829, 0.758 and 0.855, respectively. The PLS analysis verifies that the QSAR models have the highest prediction ability and stability. Based on these statistics, virtual screening based on R group is performed using the ZINC database by the Topomer search technology. Finally, 10 new compounds with higher activity are designed with the screened new fragments. In order to explore the binding modes and targets between ligands and protein receptors, these newly designed compounds are conjugated with macromolecular protein (PDB ID: 1MQ4) by molecular docking technology. Furthermore, to study the nature of the newly designed compound in dynamic states and the stability of the protein-ligand complex, molecular dynamics simulation is carried out for N3, N4, N5 and N7 docked with 1MQ4 protease structure for 50 ns. A free energy landscape is computed to search for the most stable conformation. These results prove the efficient and stability of the newly designed compounds. Finally, ADMET is used to predict the pharmacology and toxicity of the 10 designed drug molecules.
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Affiliation(s)
- Yang-Yang Tian
- College of Petroleum Engineering, Xi’an Shiyou University, Xi’an 710065, China;
- Shaanxi Key Laboratory of Advanced Stimulation Technology for Oil & Gas Reservoirs, Xi’an 710065, China
| | - Jian-Bo Tong
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (Y.L.); (Y.T.)
| | - Yuan Liu
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (Y.L.); (Y.T.)
| | - Yu Tian
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China; (Y.L.); (Y.T.)
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El Mouhi R, Daoui O, Fitri A, Benjelloun AT, El Khattabi S, Benzakour M, Mcharfi M, Kurban M. A strategy to enhance VOC of π-conjugated molecules based on thieno[2,3- b] indole for applications in bulk heterojunction organic solar cells using DFT, TD-DFT, and 3D-QSPR modeling studies. NEW J CHEM 2023. [DOI: 10.1039/d2nj04281a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The electronic structure and optical properties of eight novel molecules based on 8-alkyl-8H-thieno[2,3-b] indole was determined using density functional theory DFT, TD-DFT and 3D-QSPR.
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Affiliation(s)
- Rahma El Mouhi
- ECIM, LIMAS, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
| | - Ossama Daoui
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, BP Box 72, Fez, Morocco
| | - Asmae Fitri
- ECIM, LIMAS, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
| | - Adil Touimi Benjelloun
- ECIM, LIMAS, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
| | - Souad El Khattabi
- ECIM, LIMAS, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
- Laboratory of Engineering, Systems and Applications, National School of Applied Sciences, Sidi Mohamed Ben Abdellah-Fez University, BP Box 72, Fez, Morocco
| | - Mohammed Benzakour
- ECIM, LIMAS, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
| | - Mohammed Mcharfi
- ECIM, LIMAS, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
| | - Mustafa Kurban
- Department of Prosthetics & Orthotics, Faculty of Health Science, Ankara University, Ankara, Turkey
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Daoui O, Elkhattabi S, Chtita S. Rational design of novel pyridine-based drugs candidates for lymphoma therapy. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133964] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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3D-QSAR, ADME-Tox, and molecular docking of semisynthetic triterpene derivatives as antibacterial and insecticide agents. Struct Chem 2022; 33:1063-1084. [PMID: 35345415 PMCID: PMC8941842 DOI: 10.1007/s11224-022-01912-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/03/2022] [Indexed: 01/02/2023]
Abstract
In the present work, 27 triterpene derivatives have been subjected to 3D-QSAR, ADME-Tox, and molecular docking for their insecticidal activity. The selected derivatives are previously semi-synthesized based on compounds obtained from Euphorbia resinifera and Euphorbia officinarum latex. The in silico studies were used to predict and to evaluate the antibacterial and insecticidal properties of the 3D structure of triterpene derivatives. The 3D-QSAR models are developed using CoMFA and CoMSIA techniques, and they have showed excellent statistical results (R2 = 0.99; Q2 = 0.672; R2pred = 0.91 for CoMFA and R2 = 0.97; Q2 = 0.61; R2pred = 0.94 for CoMSIA). The results indicate that the built models are able to describe the relationship between the structure of triterpene derivatives and the pLD50 bioactivity. Based on contour maps obtained from CoMFA and CoMSIA models, 38 new molecules are designed and their pLD50 activities are predicted. The drug-like and ADME-Tox properties of the molecule designed are examined and led to the selection of four molecules (55, 56, 59, 64) as promising antibacterial and insecticidal agents. Compounds 55, 56, 59, and 64 are able to inhibit the MurE (PDB code: 1E8C) and EcR (PDB code: 1R20) proteins involved in the process of antibacterial and insecticidal activities. This hypothesis is confirmed by the implementation of a molecular docking test. This test predicted the most important referential interactions that occur between the structure of triterpene derivatives and the targeted receptors. Among the four docked molecules, three molecules (55, 56, and 59) showed greater stability than the reference molecule 16 inside the MurE and EcR receptors pocket. Therefore, the structure of the three new triterpene derivatives can be adopted as reference for the synthesis of antibacterial drugs and also in the development of insecticides.
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Xu J, Chen W, Feng Z, Duan C, Wang B, Zhao Z. Synthesis and effects of ginkgolides and ginkgolide B derivatives on platelet activating factor induced platelet aggregation in rabbits. Med Chem Res 2022. [DOI: 10.1007/s00044-022-02868-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Wang L, Wang J, Zhang A, Huang XA, Lei H. Two binding epitopes modulating specificity of immunoassay for β-agonist detection: Quantitative structure-activity relationship. Food Chem 2022; 371:131071. [PMID: 34537613 DOI: 10.1016/j.foodchem.2021.131071] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 09/03/2021] [Accepted: 09/03/2021] [Indexed: 11/04/2022]
Abstract
A growing number of β-agonists are illegally using for reducing animal fat deposition in animals, but the development of analytical methods always lags behind the emergence of new illegal compounds. Therefore, class specificity antibody-based immunoassays that can detect a great many β-agonists are important for timely supervision. In this study, a competitive inhibition enzyme-linked immunosorbent assay (ciELISA) based on a clenbuterol monoclonal antibody was developed to recognize 23 β-agonists and analogues. Holographic and three-dimensional quantitative structure-activity relationship (HQSAR and 3D QSAR) revealed that there are two critical binding epitopes on β-agonist hapten affecting antibody specificity, and these epitopes have been further validated using a ractopamine antibody with narrow specificity. Tert-butyl at C-2' epitope is needed to generate class specific antibodies, and different characteristics of substituents at benzene ring epitope would adjust antibody specificity. This investigation could provide reference for future design of β-agonist haptens.
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Affiliation(s)
- Lanteng Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Jin Wang
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China
| | - Ang Zhang
- Technology Center of Qinhuangdao Customs, Qinhuangdao 066004, China
| | - Xin-An Huang
- Tropical Medicine Institute & South China Chinese Medicine Collaborative Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Hongtao Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China.
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Qiu L, Zhang X, Tong J. A calculation method for designing new Trypanosoma brucei leucyl-tRNA synthetase inhibitors: combining QSAR and molecular docking technology. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Liu XG, Lu X, Gao W, Li P, Yang H. Structure, synthesis, biosynthesis, and activity of the characteristic compounds from Ginkgo biloba L. Nat Prod Rep 2021; 39:474-511. [PMID: 34581387 DOI: 10.1039/d1np00026h] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Covering: 1928-2021Ginkgo biloba L. is one of the most distinctive plants to have emerged on earth and has no close living relatives. Owing to its phylogenetic divergence from other plants, G. biloba contains many compounds with unique structures that have served to broaden the chemical diversity of herbal medicine. Examples of such compounds include terpene trilactones (ginkgolides), acylated flavonol glycosides (ginkgoghrelins), biflavones (ginkgetin), ginkgotides and ginkgolic acids. The extract of G. biloba leaf is used to prevent and/or treat cardiovascular diseases, while many ginkgo-derived compounds are currently at various stages of preclinical and clinical trials worldwide. The global annual sales of G. biloba products are estimated to total US$10 billion. However, the content and purity of the active compounds isolated by traditional methods are usually low and subject to varying environmental factors, making it difficult to meet the huge demand of the international market. This highlights the need to develop new strategies for the preparation of these characteristic compounds from G. biloba. In this review, we provide a detailed description of the structures and bioactivities of these compounds and summarize the recent research on the development of strategies for the synthesis, biosynthesis, and biotechnological production of the characteristic terpenoids, flavonoids, and alkylphenols/alkylphenolic acids of G. biloba. Our aim is to provide an important point of reference for all scientists who research ginkgo-related compounds for medicinal or other purposes.
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Affiliation(s)
- Xin-Guang Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
| | - Xu Lu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
| | - Wen Gao
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
| | - Ping Li
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
| | - Hua Yang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, #24 Tong Jia Xiang, Nanjing 210009, China.
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Influence of spatial structure on protein damage susceptibility: a bioinformatics approach. Sci Rep 2021; 11:4938. [PMID: 33654113 PMCID: PMC7925522 DOI: 10.1038/s41598-021-84061-8] [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: 03/03/2020] [Accepted: 02/08/2021] [Indexed: 11/08/2022] Open
Abstract
Aging research is a very popular field of research in which the deterioration or decline of various physiological features is studied. Here we consider the molecular level, which can also have effects on the macroscopic level. The proteinogenic amino acids differ in their susceptibilities to non-enzymatic modification. Some of these modifications can lead to protein damage and thus can affect the form and function of proteins. For this, it is important to know the distribution of amino acids between the protein shell/surface and the core. This was investigated in this study for all known structures of peptides and proteins available in the PDB. As a result, it is shown that the shell contains less susceptible amino acids than the core with the exception of thermophilic organisms. Furthermore, proteins could be classified according to their susceptibility. This can then be used in applications such as phylogeny, aging research, molecular medicine, and synthetic biology.
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Wu Z, Xian Z, Ma W, Liu Q, Huang X, Xiong B, He S, Zhang W. Artificial neural network approach for predicting blood brain barrier permeability based on a group contribution method. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2021; 200:105943. [PMID: 33515846 DOI: 10.1016/j.cmpb.2021.105943] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND OBJECTIVE The purpose of this study was to develop a quantitative structure-activity relationship (QSAR) model for the prediction of blood brain barrier (BBB) permeability by using artificial neural networks (ANN) in combination with molecular structure and property descriptors. METHODS Using a database composed of 300 compounds, 52 structure descriptors obtained based on the universal quasichemical functional group activity coefficients (UNIFAC) group contribution method and the selected 8 molecular property descriptors were used as the network inputs, whereas logBB values of compounds constituted its output. RESULTS The correlation coefficient R of the constructed prediction model, the relative error (RE) and the root mean square error (RMSE) was 0.956, 0.857, and 0.171, respectively. These indicators reflected the feasibility, robustness and accuracy of the prediction model. Compared with the previously published results, a significant improvement in the predictions of the proposed ANN model was observed. CONCLUSIONS ANN model based on the group contribution method could achieve a satisfactory performance for logBB prediction.
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Affiliation(s)
- Zeyu Wu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei 230601, China.
| | - Zhaojun Xian
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Wanru Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Qingsong Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Xusheng Huang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Baoyi Xiong
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Shudong He
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Wencheng Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-Process, Ministry of Education, Hefei University of Technology, Hefei 230601, China.
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Tong JB, Luo D, Zhang X, Bian S. Design of novel SHP2 inhibitors using Topomer CoMFA, HQSAR analysis, and molecular docking. Struct Chem 2020. [DOI: 10.1007/s11224-020-01677-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Gupta N, Vyas VK, Patel BD, Ghate M. Design of 2-Nitroimidazooxazine Derivatives as Deazaflavin-Dependent Nitroreductase (Ddn) Activators as Anti-Mycobacterial Agents Based on 3D QSAR, HQSAR, and Docking Study with In Silico Prediction of Activity and Toxicity. Interdiscip Sci 2017; 11:191-205. [PMID: 28895050 DOI: 10.1007/s12539-017-0256-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 07/29/2017] [Accepted: 08/01/2017] [Indexed: 10/18/2022]
Abstract
Deazaflavin-dependent nitroreductase (Ddn) is an emerging target in the field of anti-tuberculosis agents. In the present study, 2-nitroimidazooxazine derivatives as Ddn activators were aligned for CoMFA, CoMSIA and HQSAR analysis. The best CoMFA and CoMSIA model were generated with leave-one-out correlation coefficients (q2) of 0.585 and 0.571, respectively. Both the CoMFA and CoMSIA models were also validated by a test set of 11 compounds with satisfactory [Formula: see text] value of 0.701 and 0.667, respectively. Results of 3D QSAR and HQSAR study were used for the designing of novel and potent nitroimidazooxazine derivatives as Ddn activators. 21 novel compounds were designed, and docked into the Ddn enzyme. In docking study compound ng11 showed interaction with key amino acid residues such as Tyr65 and Tyr133, and also showed better ADMET compatibility. The ADMET prediction, docking study and the predicted activity of novel designed compounds revealed that compound ng11 showed good potential as Ddn activators for the treatment of tuberculosis.
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Affiliation(s)
- Nirzari Gupta
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382 481, Gujarat, India
| | - Vivek K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382 481, Gujarat, India
| | - Bhumika D Patel
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382 481, Gujarat, India
| | - Manjunath Ghate
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad, 382 481, Gujarat, India.
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Gupta N, Vyas VK, Patel B, Ghate M. Predictive 3D-QSAR and HQSAR model generation of isocitrate lyase (ICL) inhibitors by various alignment methods combined with docking study. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0865-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Singh P, Singh IN, Mondal SC, Singh L, Garg VK. Platelet-activating factor (PAF)-antagonists of natural origin. Fitoterapia 2012; 84:180-201. [PMID: 23160091 DOI: 10.1016/j.fitote.2012.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/30/2012] [Accepted: 11/04/2012] [Indexed: 01/06/2023]
Abstract
Presently herbal medicines are being used by about 80% of the world population for primary health care as they stood the test of time for their safety, efficacy, cultural acceptability and lesser side effects. The discovery of platelet activating factor antagonists (PAF antagonists) during these decades are going on with different framework, but the researchers led their efficiency in studying in vitro test models. Since it is assumed that PAF play a central role in etiology of many diseases in humans such as asthma, neuronal damage, migraine, cardiac diseases, inflammatory, headache etc. Present days instinctively occurring PAF antagonist exists as a specific grade of therapeutic agents for the humans against these and different diseases either laid hold of immunological or non-immunological types. Ginkgolide, cedrol and many other natural PAF antagonists such as andrographolide, α-bulnesene, cinchonine, piperine, kadsurenone, different Piper species' natural products and marine origin plants extracts or even crude drugs having PAF antagonist properties are being used currently against different inflammatory pathologies. This review is an attempt to summarize the data on PAF and action of natural PAF antagonists on it, which were evaluated by in vivo and in vitro assays.
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Affiliation(s)
- Preeti Singh
- Department of Pharmacology, R.V.N.I. Dadri, Greater Noida, 201301, Uttar Pradesh, India.
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Ginkgolide B produced endophytic fungus (Fusarium oxysporum) isolated from Ginkgo biloba. Fitoterapia 2012; 83:913-20. [DOI: 10.1016/j.fitote.2012.04.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Revised: 04/04/2012] [Accepted: 04/10/2012] [Indexed: 11/18/2022]
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KONG DEXIN, ZHU WEILIANG, WU DALEI, SHEN XU, JIANG HUALIANG. COMPARISON OF THREE 3D-QSAR METHODS USING A NOVEL CLASS OF MURF INHIBITORS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633607002812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
MurF was considered as an attractive target for new antibacterial discovery. In this paper, three QSAR methods were employed, viz. comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA) and hologram QSAR (HQSAR), to derive highly predictive QSAR models for designing novel MurF inhibitors and comparing different 3D-QSAR/alignment methods. QSAR models with high predictive ability for MurF inhibitors were successfully constructed in terms of cross-validation q2, standard error and predictive coefficient r2, which were around 0.70, 0.55 and 0.99, respectively. All the models from different methods were in good agreement with each other. Compounds with indeterminate activities were used as a test set; results showed that CoMSIA had the best predictive ability, followed by HQSAR and CoMFA. Based on these models, some key features for designing new MurF inhibitors were identified. A virtual database screen process was proposed based on the combination of these models.
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Affiliation(s)
- DE-XIN KONG
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
- Shandong Provincial Research Center for Bioinformatics Engineering and Technique, Shandong University of Technology, Zibo, Shandong 255049, China
| | - WEI-LIANG ZHU
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - DA-LEI WU
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - XU SHEN
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
| | - HUA-LIANG JIANG
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Zhangjiang Hi-Tech Park, Shanghai 201203, China
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2D and 3D QSAR analyses to predict favorable substitution sites in anilino-monoindolylmaleimides acting as PKCβII selective inhibitors. Med Chem Res 2010. [DOI: 10.1007/s00044-010-9439-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Mannock DA, Lewis RN, McMullen TP, McElhaney RN. The effect of variations in phospholipid and sterol structure on the nature of lipid–sterol interactions in lipid bilayer model membranes. Chem Phys Lipids 2010; 163:403-48. [DOI: 10.1016/j.chemphyslip.2010.03.011] [Citation(s) in RCA: 119] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 03/13/2010] [Accepted: 03/27/2010] [Indexed: 01/30/2023]
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Zhao L, Gaudry L, Dunkley S, Brighton T, Guo ZX, Ye ZL, Luo RZ, Chesterman CN. Modulation of platelet and leucocyte function by a Chinese herbal formulation as compared with conventional antiplatelet agents. Platelets 2009; 19:24-31. [DOI: 10.1080/09537100701286123] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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20
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van Beek TA, Montoro P. Chemical analysis and quality control of Ginkgo biloba leaves, extracts, and phytopharmaceuticals. J Chromatogr A 2009; 1216:2002-32. [DOI: 10.1016/j.chroma.2009.01.013] [Citation(s) in RCA: 320] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Revised: 12/31/2008] [Accepted: 01/09/2009] [Indexed: 01/06/2023]
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Salum LDB, Polikarpov I, Andricopulo AD. Structural and chemical basis for enhanced affinity and potency for a large series of estrogen receptor ligands: 2D and 3D QSAR studies. J Mol Graph Model 2007; 26:434-42. [PMID: 17349808 DOI: 10.1016/j.jmgm.2007.02.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 01/31/2007] [Accepted: 02/02/2007] [Indexed: 10/23/2022]
Abstract
The estrogen receptor (ER) is an important drug target for the development of novel therapeutic agents for the treatment of breast cancer. Progress towards the design of more potent and selective ER modulators requires the optimization of multiple ligand-receptor interactions. Comparative molecular field analyses (CoMFA) and hologram quantitative structure-activity relationships (HQSAR) were conducted on a large set of ERalpha modulators. Two training sets containing either 127 or 69 compounds were used to generate QSAR models for in vitro binding affinity and potency, respectively. Significant correlation coefficients (affinity models, CoMFA, r(2)=0.93 and q(2)=0.79; HQSAR, r(2)=0.92 and q(2)=0.71; potency models, CoMFA, r(2)=0.94 and q(2)=0.72; HQSAR, r(2)=0.92 and q(2)=0.74) were obtained, indicating the potential of the models for untested compounds. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. The final QSAR models as well as the information gathered from 3D contour maps should be useful for the design of novel ERalpha modulators having improved affinity and potency.
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Affiliation(s)
- Lívia de B Salum
- Laboratório de Química Medicinal e Computacional, Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, 13560-970 São Carlos, SP, Brazil
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22
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Chang HJ, Kim HJ, Chun HS. Quantitative structure−activity relationship (QSAR) for neuroprotective activity of terpenoids. Life Sci 2007; 80:835-41. [PMID: 17166521 DOI: 10.1016/j.lfs.2006.11.009] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Revised: 10/12/2006] [Accepted: 11/03/2006] [Indexed: 10/23/2022]
Abstract
Neuroprotective activity of thirteen terpenoids on human neuroblastoma SH-SY5Y was evaluated in vitro by using a simulated ischemia model. The protective effects on ischemic damage ranged from 3.0% to 56.5%, and trans-4,11,11-trimethyl-8-methylenebicyclo[7,2,0]undec-4-ene (trans-caryophyllene) showed the highest neuroprotective activity. A quantitative structure-activity relationship (QSAR) model was developed for eleven terpenoids with significant neuroprotective activity using TSAR software. The QSAR study produced two equations with significant predictive values (r(2) and p value) and indicated that the activity was mainly governed by lipophilicity, shape index, and electrostatic property. This QSAR approach can contribute to a better understanding of structural properties of the terpenoids responsible for neuroprotection, and can be useful in predicting the neuroprotective activity of other terpenoids.
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Affiliation(s)
- Hyun-Joo Chang
- Korea Food Research Institute, San 46-1, Backhyun, Bundang-gu, Sungnam, Kyonggi-do 463-746, South Korea
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23
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Zou HB, Dong SY, Zhou CX, Hu LH, Wu YH, Li HB, Gong JX, Sun LL, Wu XM, Bai H, Fan BT, Hao XJ, Stöckigt J, Zhao Y. Design, synthesis, and SAR analysis of cytotoxic sinapyl alcohol derivatives. Bioorg Med Chem 2006; 14:2060-71. [PMID: 16303311 DOI: 10.1016/j.bmc.2005.10.056] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2005] [Revised: 10/30/2005] [Accepted: 10/31/2005] [Indexed: 11/28/2022]
Abstract
Five series totalling 51 of sinapyl alcohol derivatives were designed and synthesized. Their cytotoxicity analyses were performed on six human tumor cell lines such as PC-3, CNE, KB, A549, BEL-7404, and HeLa. Certain sinapyl alcohol derivatives showed significant cytotoxic activities. Compound 14d exhibited especially potent cytotoxicity against the BEL-7404 cell line with an IC50 value of 0.7 microM, which showed more cytotoxic activity than the positive control, cisplatin. The structure-cytotoxicity relationships were discussed and the CoMFA analysis was performed using the cytotoxic data against HeLa cells as a template.
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Affiliation(s)
- Hong Bin Zou
- Department of Traditional Chinese Medicine and Natural Drug Research, College of Pharmaceutical Sciences, Zhejiang University, 353 Yan An Road, Hangzhou 310031, China
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24
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Castilho MS, Postigo MP, de Paula CBV, Montanari CA, Oliva G, Andricopulo AD. Two- and three-dimensional quantitative structure–activity relationships for a series of purine nucleoside phosphorylase inhibitors. Bioorg Med Chem 2006; 14:516-27. [PMID: 16203153 DOI: 10.1016/j.bmc.2005.08.055] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2005] [Revised: 08/16/2005] [Accepted: 08/17/2005] [Indexed: 11/20/2022]
Abstract
Comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis, and hologram quantitative structure-activity relationship (HQSAR) studies were conducted on a series of 52 training set inhibitors of calf spleen purine nucleoside phosphorylase (PNP). Significant cross-validated correlation coefficients (CoMFA, q(2)=0.68; CoMSIA, q(2)=0.66; and HQSAR, q(2)=0.70) were obtained, indicating the potential of the models for untested compounds. The models were then used to predict the inhibitory potency of 16 test set compounds that were not included in the training set, and the predicted values were in good agreement with the experimental results. The final QSAR models along with the information gathered from 3D contour and 2D contribution maps should be useful for the design of novel inhibitors of PNP having improved potency.
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Affiliation(s)
- Marcelo S Castilho
- Laboratório de Química Medicinal e Computacional, Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, 13560-970 São Carlos-SP, Brazil
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25
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van Beek TA. Ginkgolides and bilobalide: Their physical, chromatographic and spectroscopic properties. Bioorg Med Chem 2005; 13:5001-12. [PMID: 15993092 DOI: 10.1016/j.bmc.2005.05.056] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2005] [Accepted: 05/26/2005] [Indexed: 10/25/2022]
Abstract
Ginkgolides A, B, C, J, K, L and M and bilobalide are rare terpene trilactones that have been isolated from leaves and root bark of the Chinese tree Ginkgo biloba. The structures of the highly oxidized ginkgolides were independently elucidated in the 1960s by the groups of Nakanishi and Sakabe. Later these compounds were found to be potent and selective antagonists of platelet activating factor, which fact triggered much new research. During the past 40 years, much physical, chromatographic and spectroscopic data have been published on these compounds in various, sometimes inaccessible, sources. The published melting points, solubility in different solvents, ionization constants, chromatographic behaviour, specific optical rotations, UV, IR, MS and NMR data, and X-ray studies are summarized and, where necessary, discussed. The literature until April 2005 has been reviewed.
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Affiliation(s)
- Teris A van Beek
- Laboratory of Organic Chemistry, Natural Products Chemistry Group, Wageningen University, Dreijenplein 8, 6703 HB Wageningen, The Netherlands.
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Bussey HI, Tapson V, Cannon RO, Nolan PE, Gage B, Penzak SR, Spinler SA, De Smet P, Wittkowsky A, Lee AP, Ernst E, Marder VJ. Opinions and research priorities. Thromb Res 2005; 117:155-69; discussion 170-4. [PMID: 16099491 DOI: 10.1016/j.thromres.2005.05.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2005] [Revised: 05/17/2005] [Accepted: 05/24/2005] [Indexed: 01/30/2023]
Affiliation(s)
- Henry I Bussey
- College of Pharmacy, The University of Texas at Austin, Austin, Texas, USA.
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