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Wu Y, Li M, Shen J, Pu X, Guo Y. A consensual machine-learning-assisted QSAR model for effective bioactivity prediction of xanthine oxidase inhibitors using molecular fingerprints. Mol Divers 2023:10.1007/s11030-023-10649-z. [PMID: 37043162 DOI: 10.1007/s11030-023-10649-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/06/2023] [Indexed: 04/13/2023]
Abstract
Xanthine oxidase inhibitors (XOIs) have been widely studied due to the promising potential as safe and effective therapeutics in hyperuricemia and gout. Currently, available XOI molecules have been developed from different experiments but they are with the wide structure diversity and significant varying bioactivities. So it is of great practical significance to present a consensual QSAR model for effective bioactivity prediction of XOIs based on a systematic compiling of these XOIs across different experiments. In this work, 249 XOIs belonging to 16 scaffolds were collected and were integrated into a consensual dataset by introducing the concept of IC50 values relative to allopurinol (RIC50). Here, extended connectivity fingerprints (ECFPs) were employed to represent XOI molecules. By performing effective feature selection by machine-learning method, 54 crucial fingerprints were indicated to be valuable for predicting the inhibitory potency (IP) of XOIs. The optimal predictor yields the promising performance by different cross-validation tests. Besides, an external validation of 43 XOIs and a case study on febuxostat also provide satisfactory results, indicating the powerful generalization of our predictor. Here, the predictor was interpreted by shapely additive explanation (SHAP) method which revealed several important substructures by mapping the featured fingerprints to molecular structures. Then, 15 new molecules were designed and predicted by our predictor to show superior IP than febuxostat. Finally, molecular docking simulation was performed to gain a deep insight into molecular binding mode with xanthine oxidase (XO) enzyme, showing that molecules with selenazole moiety, cyano group and isopropyl group tended to yield higher IP. The absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction results further enhanced the potential of these novel XOIs as drug candidates. Overall, this work presents a QSAR model for accurate prediction of IP of XOIs, and is expected to provide new insights for further structure-guided design of novel XOIs.
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Affiliation(s)
- Yanling Wu
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Jinru Shen
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
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Unraveling the mystery of efficacy in Chinese medicine formula: New approaches and technologies for research on pharmacodynamic substances. ARAB J CHEM 2022; 15:104302. [PMID: 36189434 PMCID: PMC9514000 DOI: 10.1016/j.arabjc.2022.104302] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/21/2022] [Indexed: 12/25/2022] Open
Abstract
Traditional Chinese medicine (TCM) is the key to unlock treasures of Chinese civilization. TCM and its compound play a beneficial role in medical activities to cure diseases, especially in major public health events such as novel coronavirus epidemics across the globe. The chemical composition in Chinese medicine formula is complex and diverse, but their effective substances resemble "mystery boxes". Revealing their active ingredients and their mechanisms of action has become focal point and difficulty of research for herbalists. Although the existing research methods are numerous and constantly updated iteratively, there is remain a lack of prospective reviews. Hence, this paper provides a comprehensive account of existing new approaches and technologies based on previous studies with an in vitro to in vivo perspective. In addition, the bottlenecks of studies on Chinese medicine formula effective substances are also revealed. Especially, we look ahead to new perspectives, technologies and applications for its future development. This work reviews based on new perspectives to open horizons for the future research. Consequently, herbal compounding pharmaceutical substances study should carry on the essence of TCM while pursuing innovations in the field.
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Key Words
- 2D, Two Dimensional
- 3D, Three Dimensional
- ADME, Absorption, Distribution, Metabolism, and Excretion
- AFA DESI-MSI, Air flow-assisted desorption electrospray ionization mass spectrometry imaging
- AI, Artificial Intelligence
- Active ingredient
- CDE, Center for Drug Evaluation
- COX-2, Cyclooxygenase 2
- Chemical components
- Chinese medicine formula
- Compound
- Disease Targets
- GC-MS, Gas chromatography-mass spectrometry
- HPLC, High Performance Liquid Chromatography
- HR-MS, High Resolution Mass Spectrometry
- HTS, High Throughput Screening
- HUA, hyperuricemia
- ICPMS, inductively coupled plasma mass spectrometry
- MALDI MS, Matrix for surface-assisted laser desorption/ionization mass spectrometry
- MD, Microdialysis
- MI, Molecular imprinting
- MSI, Mass spectrometry imaging
- Mass Spectrometry
- NL/PR, Neutral loss/precursor ion
- NMPA, National Medical Products Administration
- OPLS-DA, Orthogonal partial least squares discriminant analysis
- PD, Pharmacodynamic
- PK, Pharmacokinetic
- Q-TOF/MS, Quadrupole time-of-flight mass spectrometry
- QSAR, Quantitative structure-activity relationship
- QqQ-MS, Triple quadruple mass spectrometry
- R-strategy, Reduce strategy
- TCM, Traditional Chinese medicine
- UF, Affinity ultrafiltration
- UPLC, Ultra Performance Liquid Chromatography
- XO, Xanthine oxidase
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Zhao Y, Yang H, Wu F, Luo X, Sun Q, Feng W, Ju X, Liu G. Exploration of N-Arylsulfonyl-indole-2-carboxamide Derivatives as Novel Fructose-1,6-bisphosphatase Inhibitors by Molecular Simulation. Int J Mol Sci 2022; 23:ijms231810259. [PMID: 36142164 PMCID: PMC9499002 DOI: 10.3390/ijms231810259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 11/18/2022] Open
Abstract
A series of N-arylsulfonyl-indole-2-carboxamide derivatives have been identified as potent fructose-1,6-bisphosphatase (FBPase) inhibitors (FBPIs) with excellent selectivity for the potential therapy of type II diabetes mellitus. To explore the structure–activity relationships (SARs) and the mechanisms of action of these FBPIs, a systematic computational study was performed in the present study, including three-dimensional quantitative structure–activity relationship (3D-QSAR) modeling, pharmacophore modeling, molecular dynamics (MD), and virtual screening. The constructed 3D-QSAR models exhibited good predictive ability with reasonable parameters using comparative molecular field analysis (q2 = 0.709, R2 = 0.979, rpre2 = 0.932) and comparative molecular similarity indices analysis (q2 = 0.716, R2 = 0.978, rpre2 = 0.890). Twelve hit compounds were obtained by virtual screening using the best pharmacophore model in combination with molecular dockings. Three compounds with relatively higher docking scores and better ADME properties were then selected for further studies by docking and MD analyses. The docking results revealed that the amino acid residues Met18, Gly21, Gly26, Leu30, and Thr31 at the binding site were of great importance for the effective bindings of these FBPIs. The MD results indicated that the screened compounds VS01 and VS02 could bind with FBPase stably as its cognate ligand in dynamic conditions. This work identified several potential FBPIs by modeling studies and might provide important insights into developing novel FBPIs.
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Affiliation(s)
- Yilan Zhao
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Honghao Yang
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Fengshou Wu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xiaogang Luo
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
- School of Materials Science and Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Wuhan Institute of Technology, Wuhan 430205, China
| | - Qi Sun
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Wuhan Institute of Technology, Wuhan 430205, China
| | - Weiliang Feng
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
- Correspondence: (W.F.); (G.L.)
| | - Xiulian Ju
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Genyan Liu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, Key Laboratory for Green Chemical Process of Ministry of Education, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
- Key Laboratory of Novel Biomass-Based Environmental and Energy Materials in Petroleum and Chemical Industry, Wuhan Institute of Technology, Wuhan 430205, China
- Correspondence: (W.F.); (G.L.)
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Zhai N, Chen Y, Wang C, Wu F, Luo X, Ju X, Liu H, Liu G. A multiscale screening strategy for the identification of novel xanthine oxidase inhibitors based on the pharmacological features of febuxostat analogues. NEW J CHEM 2022. [DOI: 10.1039/d2nj00115b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two compounds as potential XOI hits were identified by a novel screening strategy based on the pharmacophores of well-known scaffolds.
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Affiliation(s)
- Na Zhai
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Yanming Chen
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Chenchen Wang
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Fengshou Wu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Xiaogang Luo
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
- School of Materials Science and Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou City, 450001, Henan Province, P. R. China
| | - Xiulian Ju
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
| | - Hui Liu
- Department of Hematology, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, P. R. China
| | - Genyan Liu
- Key Laboratory for Green Chemical Process of Ministry of Education, Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, P. R. China
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Wang C, Zhai N, Zhao Y, Wu F, Luo X, Ju X, Liu G, Liu H. Exploration of Novel Hepatitis B Virus Capsid Assembly Modulators by Integrated Molecular Simulations. ChemistrySelect 2021. [DOI: 10.1002/slct.202102965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chenchen Wang
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology Key Laboratory for Green Chemical Process of Ministry of Education School of Chemical Engineering and Pharmacy Wuhan Institute of Technology Wuhan 430205 Hubei P. R. China
| | - Na Zhai
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology Key Laboratory for Green Chemical Process of Ministry of Education School of Chemical Engineering and Pharmacy Wuhan Institute of Technology Wuhan 430205 Hubei P. R. China
| | - Yilan Zhao
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology Key Laboratory for Green Chemical Process of Ministry of Education School of Chemical Engineering and Pharmacy Wuhan Institute of Technology Wuhan 430205 Hubei P. R. China
| | - Fengshou Wu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology Key Laboratory for Green Chemical Process of Ministry of Education School of Chemical Engineering and Pharmacy Wuhan Institute of Technology Wuhan 430205 Hubei P. R. China
| | - Xiaogang Luo
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology Key Laboratory for Green Chemical Process of Ministry of Education School of Chemical Engineering and Pharmacy Wuhan Institute of Technology Wuhan 430205 Hubei P. R. China
- School of Materials Science and Engineering Zhengzhou University No.100 Science Avenue Zhengzhou 450001 Henan P. R. China
| | - Xiulian Ju
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology Key Laboratory for Green Chemical Process of Ministry of Education School of Chemical Engineering and Pharmacy Wuhan Institute of Technology Wuhan 430205 Hubei P. R. China
| | - Genyan Liu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology Key Laboratory for Green Chemical Process of Ministry of Education School of Chemical Engineering and Pharmacy Wuhan Institute of Technology Wuhan 430205 Hubei P. R. China
| | - Hui Liu
- Department of Hematology Renmin Hospital of Wuhan University Wuhan 430060 Hubei P. R. China
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Zheng X, Wang C, Zhai N, Luo X, Liu G, Ju X. In Silico Screening of Novel α1-GABA A Receptor PAMs towards Schizophrenia Based on Combined Modeling Studies of Imidazo [1,2-a]-Pyridines. Int J Mol Sci 2021; 22:9645. [PMID: 34502550 PMCID: PMC8431797 DOI: 10.3390/ijms22179645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 02/01/2023] Open
Abstract
The ionotropic GABAA receptor (GABAAR) has been proven to be an important target of atypical antipsychotics. A novel series of imidazo [1,2-a]-pyridine derivatives, as selective positive allosteric modulators (PAMs) of α1-containing GABAARs with potent antipsychotic activities, have been reported recently. To better clarify the pharmacological essentiality of these PAMs and explore novel antipsychotics hits, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking, pharmacophore modeling, and molecular dynamics (MD) were performed on 33 imidazo [1,2-a]-pyridines. The constructed 3D-QSAR models exhibited good predictive abilities. The dockings results and MD simulations demonstrated that hydrogen bonds, π-π stackings, and hydrophobic interactions play essential roles in the binding of these novel PAMs in the GABAAR binding pocket. Four hit compounds (DS01-04) were then screened out by the combination of the constructed models and computations, including the pharmacophore model, Topomer Search, molecular dockings, ADME/T predictions, and MD simulations. The compounds DS03 and DS04, with higher docking scores and better predicted activities, were also found to be relatively stable in the binding pocket by MD simulations. These results might provide a significant theoretical direction or information for the rational design and development of novel α1-GABAAR PAMs with antipsychotic activities.
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Affiliation(s)
- Xiaojiao Zheng
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (X.Z.); (C.W.); (N.Z.); (X.L.)
| | - Chenchen Wang
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (X.Z.); (C.W.); (N.Z.); (X.L.)
| | - Na Zhai
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (X.Z.); (C.W.); (N.Z.); (X.L.)
| | - Xiaogang Luo
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (X.Z.); (C.W.); (N.Z.); (X.L.)
- School of Materials Science and Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Genyan Liu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (X.Z.); (C.W.); (N.Z.); (X.L.)
| | - Xiulian Ju
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (X.Z.); (C.W.); (N.Z.); (X.L.)
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Zhai N, Wang C, Wu F, Xiong L, Luo X, Ju X, Liu G. Exploration of Novel Xanthine Oxidase Inhibitors Based on 1,6-Dihydropyrimidine-5-Carboxylic Acids by an Integrated in Silico Study. Int J Mol Sci 2021; 22:8122. [PMID: 34360886 PMCID: PMC8348919 DOI: 10.3390/ijms22158122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/19/2021] [Accepted: 07/22/2021] [Indexed: 02/07/2023] Open
Abstract
Xanthine oxidase (XO) is an important target for the effective treatment of hyperuricemia-associated diseases. A series of novel 2-substituted 6-oxo-1,6-dihydropyrimidine-5-carboxylic acids (ODCs) as XO inhibitors (XOIs) with remarkable activities have been reported recently. To better understand the key pharmacological characteristics of these XOIs and explore more hit compounds, in the present study, the three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, pharmacophore modeling, and molecular dynamics (MD) studies were performed on 46 ODCs. The constructed 3D-QSAR models exhibited reliable predictability with satisfactory validation parameters, including q2 = 0.897, R2 = 0.983, rpred2 = 0.948 in a CoMFA model, and q2 = 0.922, R2 = 0.990, rpred2 = 0.840 in a CoMSIA model. Docking and MD simulations further gave insights into the binding modes of these ODCs with the XO protein. The results indicated that key residues Glu802, Arg880, Asn768, Thr1010, Phe914, and Phe1009 could interact with ODCs by hydrogen bonds, π-π stackings, or hydrophobic interactions, which might be significant for the activity of these XOIs. Four potential hits were virtually screened out using the constructed pharmacophore model in combination with molecular dockings and ADME predictions. The four hits were also found to be relatively stable in the binding pocket by MD simulations. The results in this study might provide effective information for the design and development of novel XOIs.
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Affiliation(s)
- Na Zhai
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
| | - Chenchen Wang
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
| | - Fengshou Wu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
| | - Liwei Xiong
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
- Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, Wuhan Institute of Technology, Wuhan 430205, China
| | - Xiaogang Luo
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
- School of Materials Science and Engineering, Zhengzhou University, No. 100 Science Avenue, Zhengzhou 450001, China
| | - Xiulian Ju
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
| | - Genyan Liu
- Hubei Key Laboratory of Novel Reactor and Green Chemical Technology, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China; (N.Z.); (C.W.); (F.W.); (X.L.); (X.J.)
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