Citation: Jian-Bo TONG, Tian-Hao WANG, Ying-Ji WU, Yi FENG. QSAR and Docking Studies of Thiazolidine-4-carboxylic Acid Derivatives as Neuraminidase Inhibitors[J]. Chinese Journal of Structural Chemistry, ;2020, 39(4): 651-661. doi: 10.14102/j.cnki.0254-5861.2011-2508 shu

QSAR and Docking Studies of Thiazolidine-4-carboxylic Acid Derivatives as Neuraminidase Inhibitors

Jian-Bo TONG ^{a, b,,} ,
Tian-Hao WANG ^{a, b} ,
Ying-Ji WU ^{a, b} ,
Yi FENG ^{a, b}

a.
College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an 710021, China
b.
Shaanxi Key Laboratory of Chemical Additives for Industry, Xi'an 710021, China

Corresponding author: Jian-Bo TONG, jianbotong@aliyun.com
Received Date: 21 June 2019
Accepted Date: 20 November 2019

Fund Project: the National Natural Science Funds of China 21475081the Natural Science Foundation of Shaanxi Province 2019JM-237

Figures(3)

In order to understand the chemical-biological interactions governing their activities toward neuraminidase (NA), QSAR models of 28 thiazolidine-4-carboxylic acid derivatives with inhibitory influenza A virus were developed. Here a quantitative structure activity relationship (QSAR) model was built by three-dimensional holographic atomic vector field (3D-HoVAIF) and multiple linear regression (MLR). The estimation stability and prediction ability of the model were strictly analyzed by both internal and external validations. The correlation coefficient (R²) of established MLR model was 0.984, and the cross-validated correlation coefficient (Q²) of MLR model was 0.947. Furthermore, the cross-validated correlation coefficient for the test set (Q_ext²) was 0.967. The binding mode pattern of the compounds to the binding site of integrase enzyme was confirmed by docking studies. The results of present study indicated that this model can aid in designing more potent neuraminidase inhibitors.
- 3D-QSAR,
- thiazolidine-4-carboxylic acid derivatives,
- 3D-HoVAIF,
- molecular designing,
- molecular docking
1. [1]
  Chen, Y. Q.; Wohlbold, T. J.; Zheng, N. Y. Influenza infection in humans induces broadly cross-reactive and protective neuraminidase-reactive antibodies. Cell 2018, 173, 417−429. doi: 10.1016/j.cell.2018.03.030
2. [2]
  Wang, X. L.; Jiang, H.; Wu, P. Epidemiology of avian influenza A H7N9 virus in human beings across five epidemics in mainland China, 2013-17: an epidemiological study of laboratory-confirmed case series. Lancet Infect Dis. 2017, 17, 822−832. doi: 10.1016/S1473-3099(17)30323-7
3. [3]
  Zhao, H. Y.; Chen, Z. L. Screening of neuraminidase inhibitors from traditional Chinese medicines by integrating capillary electrophoresis with immobilized enzyme microreactor. J. Chromatogr. A 2014, 1340, 139−145. doi: 10.1016/j.chroma.2014.03.028
4. [4]
  Anne Moscona, M. D. Neuraminidase inhibitors for influenza. New Engl. J. Med. 2005, 353, 1363−1373. doi: 10.1056/NEJMra050740
5. [5]
  Chen, B. Y.; Zhang, T.; Bond, T. Development of quantitative structure activity relationship (QSAR) model for disinfection byproduct (DBP) research: a review of methods and resources. J. Hazard. Mater. 2015, 299, 260−279. doi: 10.1016/j.jhazmat.2015.06.054
6. [6]
  Bhole, R. P.; Bhusari, K. P. Synthesis, antihypertensive activity, and 3D-QSAR studies of some new p-hydroxybenzohydrazide derivatives. Arch. Pharm. 2011, 344, 119−134. doi: 10.1002/ardp.201000008
7. [7]
  Sun, J. Y.; Wang, J. C.; Mei, H. QSAR and pharmacophore studies of thiazolidine-4-carboxylic acid derivatives as novel influenza neuraminidase inhibitors using HQSAR, Topomer CoMFA and CoMSIA. Chin. J. Struc. Chem. 2013, 32, 744−750.
8. [8]
  Van Damme, S.; Bultinck, P. 3D QSAR based on conceptual DFT molecular fields: antituberculotic activity. J. Mol. Struc.-Theochem. 2010, 943, 83−89. doi: 10.1016/j.theochem.2009.10.031
9. [9]
  Tong, J. B.; Liu, S. L. Three-dimensional holographic vector of atomic interaction field applied in QSAR of anti-HIV HEPT analogues. QSAR Comb. Sci. 2008, 27, 330−337. doi: 10.1002/qsar.200710076
10. [10]
  Tong, J. B.; Chen, Y.; Liu, S. L. QSAR studies of antituberculosis drug using three-dimensional structure descriptors. Med. Chem. Res. 2013, 22, 4946−4952. doi: 10.1007/s00044-013-0502-y
11. [11]
  Tong, J. B.; Che, T.; Li, Y. F. A descriptor of amino acids: SVRG and its application to peptide quantitative structure-activity relationship. SAR QSAR Environ. Res. 2011, 22, 611−620. doi: 10.1080/1062936X.2011.604099
12. [12]
  Levitt, M. Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 1983, 170, 723−764. doi: 10.1016/S0022-2836(83)80129-6
13. [13]
  Levitt, M.; Perutz, M. F. Aromatic rings act as hydrogen bond acceptors. J. Mol. Biol. 1988, 201, 751−754. doi: 10.1016/0022-2836(88)90471-8
14. [14]
  Hahn, M. Receptor surface models. 1. Definition and construction. J. Med. Chem. 1995, 38, 2080−2090. doi: 10.1021/jm00012a007
15. [15]
  Kellogg, G. E.; Semus, S. F.; Abraham, D. J. HINT: a new method of empirical hydrophobic field calculation for CoMFA. J. Comput. Aid. Mol. Des. 1991, 5, 545−552. doi: 10.1007/BF00135313
16. [16]
  Wireko, F. C.; Kellogg, G. E.; Abraham, D. J. Allosteric modifiers of hemoglobin. 2. Crystallographically determined binding sites and hydrophobic binding/interaction analysis of novel hemoglobin oxygen effectors. J. Med. Chem. 1991, 34, 758−767. doi: 10.1021/jm00106a042
17. [17]
  Tong, J. B.; Zhong, L.; Zhao, X. Quantitative structure-activity relationship studies of diarylpyrimidine derivatives as anti-HIV drugs using new three-dimensional structure descriptors. Med. Chem. Res. 2014, 23, 1634−1642. doi: 10.1007/s00044-013-0770-6
18. [18]
  Kellogg, G. E.; Abraham, D. J. Key, lock, and locksmith: complementary hydropathic map predictions of drug structure from a known receptor-receptor structure from known drugs. J. Mol. Graph. 1992, 10, 212−217. doi: 10.1016/0263-7855(92)80070-T
19. [19]
  Tong, J. B.; Chen, Y.; Liu, S. L. A novel 3D molecular structural characterization method applied in QSAR study. Rev. Chim.-Bucharest. 2013, 64, 707−712.
20. [20]
  Li, Z. H.; Chen, G.; Chen, Z. T. Three-dimensional holographic vector of atomic interaction field (3D-HoVAIF) for the QSPR/QSAR of polychlorinated naphthalenes. Chin. J. Struct. Chem. 2012, 31, 345−352.
21. [21]
  Shu, M.; Zhang, Y. R.; Tian, F. F. Molecular docking and 3D-QSAR research of biphenyl carboxylic acid MMP-3 inhibitors. Chin. J. Struct. Chem. 2012, 31, 443−451.
22. [22]
  Liao, L. M.; Huang, X.; Li, J. F. Structural characterization and acute toxicity simulation for nitroaromatic compounds. Chin. J. Struct. Chem. 2016, 35, 449−456.
23. [23]
  Huey, R.; Morris, G. M.; Olson, A. J. A semiempirical free energy force field with charge-based desolvation. J. Comput. Chem. 2007, 28, 1145−1152. doi: 10.1002/jcc.20634
24. [24]
  Liu, Y.; Jing, F. B.; Xu, Y. Y. Design, synthesis and biological activity of thiazolidine-4-carboxylic acid derivatives as novel influenza neuraminidase inhibitors. Bioorgan. Med. Chem. 2011, 19, 2342−2348. doi: 10.1016/j.bmc.2011.02.019
25. [25]
  Golbraikh, Alexander; Tropsha, Alexander. Beware of q²! J. Mol. Graph. Model. 2002, 20, 269−276. doi: 10.1016/S1093-3263(01)00123-1
26. [26]
  Tong, J. B.; Wang, Y.; Lei, S. 3D-QSAR and docking studies of 1,3,4-thiazolidinone derivatives using R-group search and surflex-dock. Chin. J. Struct. Chem. 2019, 38, 464−475.
1. [1]
  Yan Cheng , Hua-Peng Ruan , Yan Peng , Longhe Li , Zhenqiang Xie , Lang Liu , Shiyong Zhang , Hengyun Ye , Zhao-Bo Hu . Magnetic, dielectric and luminescence synergetic switchable effects in molecular material [Et₃NCH₂Cl]₂[MnBr₄]. Chinese Chemical Letters, 2024, 35(4): 108554-. doi: 10.1016/j.cclet.2023.108554
2. [2]
  Yi Zhu , Jingyan Zhang , Yuchao Zhang , Ying Chen , Guanghui An , Ren Liu . Designing unimolecular photoinitiator by installing NHPI esters along the TX backbone for acrylate photopolymerization and their applications in coatings and 3D printing. Chinese Chemical Letters, 2024, 35(7): 109573-. doi: 10.1016/j.cclet.2024.109573
3. [3]
  Ao Sun , Zipeng Li , Shuchun Li , Xiangbao Meng , Zhongtang Li , Zhongjun Li . Stereoselective synthesis of α-3-deoxy-D-manno-oct-2-ulosonic acid (α-Kdo) derivatives using a C3-p-tolylthio-substituted Kdo fluoride donor. Chinese Chemical Letters, 2025, 36(3): 109972-. doi: 10.1016/j.cclet.2024.109972
4. [4]
  Fang-Yuan Chen , Wen-Chao Geng , Kang Cai , Dong-Sheng Guo . Molecular recognition of cyclophanes in water. Chinese Chemical Letters, 2024, 35(5): 109161-. doi: 10.1016/j.cclet.2023.109161
5. [5]
  Yutong Xiong , Ting Meng , Wendi Luo , Bin Tu , Shuai Wang , Qingdao Zeng . Molecular conformational effects on co-assembly systems of low-symmetric carboxylic acids investigated by scanning tunneling microscopy. Chinese Journal of Structural Chemistry, 2025, 44(2): 100511-100511. doi: 10.1016/j.cjsc.2025.100511
6. [6]
  Hualin Jiang , Wenxi Ye , Huitao Zhen , Xubiao Luo , Vyacheslav Fominski , Long Ye , Pinghua Chen . Novel 3D-on-2D g-C₃N₄/AgI._x._y heterojunction photocatalyst for simultaneous and stoichiometric production of H₂ and H₂O₂ from water splitting under visible light. Chinese Chemical Letters, 2025, 36(2): 109984-. doi: 10.1016/j.cclet.2024.109984
7. [7]
  Yuexi Guo , Zhaoyang Li , Jingwei Dai . Charlie and the 3D Printing Chocolate Factory. University Chemistry, 2024, 39(9): 235-242. doi: 10.3866/PKU.DXHX202309067
8. [8]
  Caili Yang , Tao Long , Ruotong Li , Chunyang Wu , Yuan-Li Ding . Pseudocapacitance dominated Li₃VO₄ encapsulated in N-doped graphene via 2D nanospace confined synthesis for superior lithium ion capacitors. Chinese Chemical Letters, 2025, 36(2): 109675-. doi: 10.1016/j.cclet.2024.109675
9. [9]
  Caihong Mao , Yanfeng He , Xiaohan Wang , Yan Cai , Xiaobo Hu . Synthesis and molecular recognition characteristics of a tetrapodal benzene cage. Chinese Chemical Letters, 2024, 35(8): 109362-. doi: 10.1016/j.cclet.2023.109362
10. [10]
  Cheng-Da Zhao , Huan Yao , Shi-Yao Li , Fangfang Du , Li-Li Wang , Liu-Pan Yang . Amide naphthotubes: Biomimetic macrocycles for selective molecular recognition. Chinese Chemical Letters, 2024, 35(4): 108879-. doi: 10.1016/j.cclet.2023.108879
11. [11]
  Yanwei Duan , Qing Yang . Molecular targets and their application examples for interrupting chitin biosynthesis. Chinese Chemical Letters, 2025, 36(4): 109905-. doi: 10.1016/j.cclet.2024.109905
12. [12]
  Keke Han , Wenjun Rao , Xiuli You , Haina Zhang , Xing Ye , Zhenhong Wei , Hu Cai . Two new high-temperature molecular ferroelectrics [1,5-3.2.2-Hdabcni]X (X = ClO₄⁻, ReO₄⁻). Chinese Chemical Letters, 2024, 35(6): 108809-. doi: 10.1016/j.cclet.2023.108809
13. [13]
  Hualei Xu , Manman Han , Haiqiang Liu , Liang Qin , Lulu Chen , Hao Hu , Ran Wu , Chenyu Yang , Hua Guo , Jinrong Li , Jinxiang Fu , Qichen Hao , Yijun Zhou , Jinchao Feng , Xiaodong Wang . 4-Nitrocatechol as a novel matrix for low-molecular-weight compounds in situ detection and imaging in biological tissues by MALDI-MSI. Chinese Chemical Letters, 2024, 35(6): 109095-. doi: 10.1016/j.cclet.2023.109095
14. [14]
  Bairu Meng , Zongji Zhuo , Han Yu , Sining Tao , Zixuan Chen , Erik De Clercq , Christophe Pannecouque , Dongwei Kang , Peng Zhan , Xinyong Liu . Design, synthesis, and biological evaluation of benzo[4,5]thieno[2,3-d]pyrimidine derivatives as novel HIV-1 NNRTIs. Chinese Chemical Letters, 2024, 35(6): 108827-. doi: 10.1016/j.cclet.2023.108827
15. [15]
  Jie XIE , Hongnan XU , Jianfeng LIAO , Ruoyu CHEN , Lin SUN , Zhong JIN . Nitrogen-doped 3D graphene-carbon nanotube network for efficient lithium storage. Chinese Journal of Inorganic Chemistry, 2024, 40(10): 1840-1849. doi: 10.11862/CJIC.20240216
16. [16]
  Xi Xu , Chaokai Zhu , Leiqing Cao , Zhuozhao Wu , Cao Guan . Experiential Education and 3D-Printed Alloys: Innovative Exploration and Student Development. University Chemistry, 2024, 39(2): 347-357. doi: 10.3866/PKU.DXHX202308039
17. [17]
  Qiang Zhou , Pingping Zhu , Wei Shao , Wanqun Hu , Xuan Lei , Haiyang Yang . Innovative Experimental Teaching Design for 3D Printing High-Strength Hydrogel Experiments. University Chemistry, 2024, 39(6): 264-270. doi: 10.3866/PKU.DXHX202310064
18. [18]
  Changyuan Bao , Yunpeng Jiang , Haoyin Zhong , Huaizheng Ren , Junhui Wang , Binbin Liu , Qi Zhao , Fan Jin , Yan Meng Chong , Jianguo Sun , Fei Wang , Bo Wang , Ximeng Liu , Dianlong Wang , John Wang . Synergizing 3D-printed structure and sodiophilic interface enables highly efficient sodium metal anodes. Chinese Chemical Letters, 2024, 35(11): 109353-. doi: 10.1016/j.cclet.2023.109353
19. [19]
  Chengmin Hu , Pingxuan Liu , Ziyang Song , Yaokang Lv , Hui Duan , Li Xie , Ling Miao , Mingxian Liu , Lihua Gan . Tailor-made overstable 3D carbon superstructures towards efficient zinc-ion storage. Chinese Chemical Letters, 2025, 36(4): 110381-. doi: 10.1016/j.cclet.2024.110381
20. [20]
  Zhimin Sun , Xin-Hui Guo , Yue Zhao , Qing-Yu Meng , Li-Juan Xing , He-Lue Sun . Dynamically switchable porphyrin-based molecular tweezer for on−off fullerene recognition. Chinese Chemical Letters, 2024, 35(6): 109162-. doi: 10.1016/j.cclet.2023.109162

Get Citation

PDF

XML

Metrics

PDF Downloads(2)
Abstract views(279)
HTML views(12)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142