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Zhang Y, Chen L, Wang Z, Zhu Y, Jiang H, Xu J, Xiong F. Design of novel DABO derivatives as HIV-1 RT inhibitors using molecular docking, molecular dynamics simulations and ADMET properties. J Biomol Struct Dyn 2024; 42:4196-4213. [PMID: 37272892 DOI: 10.1080/07391102.2023.2219331] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/23/2023] [Indexed: 06/06/2023]
Abstract
HIV-1 reverse transcriptase is an important target for developing effective anti-HIV-1 inhibitors. Different types of small molecules have been designed based on this target, showing different levels of inhibitory activity against various types of HIV-1 strains. The relationship between structure and activity of DABO derivatives was investigated by means of 3D-QSAR molecular model, molecular docking, molecular dynamics and ADMET properties. The statistical results of molecular models show that the CoMFA and CoMSIA models have good internal stability (CoMFA: q2 = 0.623, r2 = 0.946; CoMSIA: q2 = 0.668, r2 = 0.983) and external prediction ability (CoMFA: rpred2 = 0.961; CoMSIA: rpred2 = 0.961). In addition, molecular docking has explored the mechanism of action between small molecules and receptor proteins, and the results show that hydrogen bonding between amino acid Lys101 and small molecules can improve the affinity of ligands to receptor binding. A total of 12 novel molecules were designed and their activities were predicted based on the 3D-QSAR model and molecular docking results. The results showed that the designed molecules had higher predictive activity. Subsequently, 100 ns MD simulation and binding free energy verified the stability of molecular docking results. Finally, the pharmacokinetic properties of the novel designed molecule were verified by using ADMET to predict its properties. These results can provide reference for the design and development of novel and effective HIV-1 RT inhibitors, and provide new ideas for the design of subsequent drugs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yanjun Zhang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Lu Chen
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Zhonghua Wang
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, P. R. China
| | - Yiren Zhu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Huifang Jiang
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Jie Xu
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Fei Xiong
- Department of Chemistry, University of Shanghai for Science and Technology, Shanghai, P. R. China
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Liu M, Wang B, Liu H, Xia H, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of benzimidazole Pin1 inhibitors. Phys Chem Chem Phys 2024; 26:4643-4656. [PMID: 38251755 DOI: 10.1039/d3cp05658a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Pin1 (protein interacting with never-in-mitosis akinase-1) is a member of the family of peptidylprolyl cis-trans isomerases (PPIases) that specifically recognize and isomerize substrates containing phosphorylated Ser/Thr-Pro sequences. Pin1 is involved in many cellular processes and plays a key role in the cell cycle, transcriptional regulation, cell metabolism, proliferation and differentiation, and its abnormalities lead to degenerative and neoplastic diseases. Pin1 is highly expressed in human cancers and promotes the development of tumors by activating multiple oncogenes and inactivating multiple tumor suppressor genes, making it an attractive target for cancer therapy. In this study, we investigated the binding mechanism and conformational relationship between benzimidazole Pin1 inhibitors and Pin1 proteins by molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling, binding free energy calculations and decomposition, and molecular dynamics simulations. Molecular docking and molecular dynamics simulations disclosed the most likely binding pose of benzimidazoles with the Pin1 protein. The results of 3D-QSAR modeling indicated that electrostatic fields, hydrophobic fields and hydrogen bonding play important roles in the binding process of inhibitors to proteins. The binding free energy calculations and energy decomposition indicated that Lys63, Arg69, Cys113, Leu122, Met130, and Ser154 may be key residues in the binding of benzimidazole-based inhibitors to the Pin1 protein. This study provides an important theoretical basis for the design and optimization of benzimidazole compounds.
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Affiliation(s)
- Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
| | - Bingli Wang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
| | - Huan Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
| | - Haolun Xia
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
| | - Lina Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality and Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, P.R. China.
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Wu J, Li P, Chen X, Liu R, Mu Y, Shen Y, Cheng X, Shu M, Bai Y. Structural optimization of pyrrolopyrimidine BTK inhibitors based on molecular simulation. J Mol Model 2023; 29:367. [PMID: 37950076 DOI: 10.1007/s00894-023-05744-9] [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: 08/06/2023] [Accepted: 10/02/2023] [Indexed: 11/12/2023]
Abstract
CONTEXT BTK is a critical regulator involved in the proliferation, differentiation, and apoptosis of B cells. BTK inhibitors can effectively alleviate various diseases such as tumors, leukemia, and asthma. During this study, a range of novel BTK inhibitors were designed using 3D-QSAR, molecular docking, and molecular dynamics (MD) simulation. METHODS We selected 41 pyrrolopyrimidine derivatives as BTK inhibitors to structure a 3D-QSAR model. Comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA) were adopted to research the connection between the pharmacological activities and chemical structures of the compounds. The CoMFA model (q2 = 0.519, R2 = 0.971), CoMSIA model (q2 = 0.512, R2 = 0.990), and external validation demonstrated excellent predictive performance and reliability of the 3D-QSAR model. We designed eight novel molecules with higher inhibitory activities according to the three-dimensional equipotential fields and explored the interactions between the compounds and BTK by molecular docking, which showed that the novel molecules had higher binding affinities with BTK than the template molecule 18. Then, the results of molecular docking were further verified by MD simulation, which showed that amino acid residues such as Leu528, Val416, and Met477 played vital parts in the interaction, and the binding free energy analysis showed that the novel molecules had higher stability with BTK. Finally, the ADME/T properties were predicted for all of the novel compounds, and the results showed that the majority of them had favorable pharmacokinetic properties. Therefore, this study provides strong support for the development of novel BTK inhibitors.
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Affiliation(s)
- Jinping Wu
- Pharmacy Department, Langzhong People's Hospital, Nanchong, China
| | - Peng Li
- Pharmacy Department, Langzhong People's Hospital, Nanchong, China
| | - Xiaodie Chen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Screening and Activity Evaluation of Targeted Drugs, Chongqing, China
| | - Rong Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Screening and Activity Evaluation of Targeted Drugs, Chongqing, China
| | - Yucheng Mu
- Pharmacy Department, Langzhong People's Hospital, Nanchong, China
| | - Yan Shen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Screening and Activity Evaluation of Targeted Drugs, Chongqing, China
| | - Xilan Cheng
- Pharmacy Department, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Mao Shu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
- Chongqing Key Laboratory of Screening and Activity Evaluation of Targeted Drugs, Chongqing, China
| | - Yixiao Bai
- Pharmacy Department, Langzhong People's Hospital, Nanchong, China.
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Mousavi SL, Sajjadi SM. Predicting rejection of emerging contaminants through RO membrane filtration based on ANN-QSAR modeling approach: trends in molecular descriptors and structures towards rejections. RSC Adv 2023; 13:23754-23771. [PMID: 37560620 PMCID: PMC10407621 DOI: 10.1039/d3ra03177b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/24/2023] [Indexed: 08/11/2023] Open
Abstract
In this work, a quantitative structure-activity relationship (QSAR) study was performed on a set of emerging contaminants (ECs) to predict their rejections by reverse osmosis membrane (RO). A wide range of molecular descriptors was calculated by Dragon software for 72 ECs. The QSAR data was analyzed by an artificial neural network method (ANN), in which four out of 3000 theoretical molecular descriptors were chosen and their significance was computed based on the Garson method. The significance trends of descriptors were as follows in descending order: ESpm14u > R2e > SIC1 > EEig03d. The selected descriptors were ranked based on their importance and then an explorative study was conducted on the QSAR data to show the trends in molecular descriptors and structures toward the rejections values of ECs. The MLR algorithm was used to make a linear model and the results were compared with those of the nonlinear ANN algorithm. The comparison results revealed it is necessary to apply the ANN model to this data with non-linear properties. For the whole dataset, the correlation coefficient (R2) and residual mean squared error (RMSE) of the ANN and MLR methods were 0.9528, 6.4224; and 0.8753, 11.3400, respectively. The comparison results showed the superiority of ANN modeling in the analysis of ECs' QSAR data.
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Affiliation(s)
- Setare Loh Mousavi
- Faculty of Chemistry, Semnan University Semnan Iran +98 23 33384110 +98 23 31533192
| | - S Maryam Sajjadi
- Faculty of Chemistry, Semnan University Semnan Iran +98 23 33384110 +98 23 31533192
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QSAR, molecular docking, and molecular dynamics simulation–based design of novel anti-cancer drugs targeting thioredoxin reductase enzyme. Struct Chem 2023. [DOI: 10.1007/s11224-022-02111-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Zhao J, Liu M, Zang J, Yang S, Chen R, Zhao X, Ding L. Molecular docking, 3D-QASR and molecular dynamics simulations of thiazoles Pin1 inhibitors. J Biomol Struct Dyn 2022; 40:12699-12713. [PMID: 34499020 DOI: 10.1080/07391102.2021.1975568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pin1 (protein interacting with never-in-mitosis akinase-1) is a member of the PPIase (peptidylprolyl cis-trans isomerase) family. It can interact with a variety of carcinogenic or tumor suppressive phosphorylated proteins. The interaction results in the conformational changes of target proteins, and ultimately regulates the activity of these proteins. These activity changes play a key role in tumorigenesis. Pin1 is an attractive target for cancer therapy due to its over-expression and/or activation in various types of cancer and the disorder of Proline directed phosphorylation. In this study, molecular docking, three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular dynamics (MD) simulations were performed to investigate the structure-activity relationship and binding mechanism of 45 thiazole-class Pin1 inhibitors. Molecular docking studies predict the binding mode and the interactions between the ligand and the receptor protein. The results of the 3 D-QSAR model show that electrostatic field, hydrophobic field and hydrogen bond play important roles in the binding process of inhibitors to protein. Molecular dynamics simulation results reveal that the complex of the ligand and the receptor protein are stable at 300 K. The binding free energy calculation and energy decomposition results show that His59, Cys113, Ser114, Ser115, Leu122, Met130, Gln131, Phe134, Ser154 and His157 may be the key to the inhibitor binding to Pin1 protein. This study provides an important theoretical basis for further development of the new Pin1 inhibitor design. These results can provide more useful information for our further drug design. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jiangheng Zhao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Min Liu
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Jieying Zang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Shuangshuang Yang
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Ruiyou Chen
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Xin Zhao
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
| | - Lina Ding
- Collaborative Innovation Center of New Drug Research and Safety Evaluation, Henan Province, Key Laboratory of Technology of Drug Preparation (Zhengzhou University), Ministry of Education of China, Key Laboratory of Henan Province for Drug Quality & Evaluation, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, PR China
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Sun S, Zuo Q, Du M, Li Y. Molecular Design and Mechanism Analysis of Phthalic Acid Ester Substitutes: Improved Biodegradability in Processes of Sewage Treatment and Soil Remediation. TOXICS 2022; 10:783. [PMID: 36548616 PMCID: PMC9781866 DOI: 10.3390/toxics10120783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/10/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Phthalic acid esters (PAEs) have the characteristics of environmental persistence. Therefore, improving the biodegradability of PAEs is the key to reducing the extent of ecological harm realized. Firstly, the scoring function values of PAEs docking with various degrading enzymes in sewage treatment were calculated. Based on this, a 3D-quantitative structure-activity relationship (3D-QSAR) model for PAE biodegradability was built, and 38 PAE substitutes were created. By predicting the endocrine-disrupting toxicity and functions of PAE substitutes, two types of PAE substitutes that are easily degraded by microorganisms, have low toxicity, and remain functional were successfully screened. Meanwhile, the differences in the mechanism of molecular degradation difference before and after PAE modification were analyzed based on the distribution characteristics of amino acid residues in the molecular docking complex. Finally, the photodegradability and microbial degradability of the PAE substitutes in the soil environment was evaluated. From the 3D-QSAR model design perspective, the modification mechanism of PAE substitutes suitable for sewage treatment and soil environment degradation was analyzed. We aim to improve the biodegradability of PAEs at the source and provide theoretical support for alleviating the environmental hazards of using PAEs.
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Affiliation(s)
- Shuhai Sun
- School of Hydraulic and Environmental Engineering, Changchun Institute of Technology, Changchun 130012, China
| | - Qilin Zuo
- School of Hydraulic and Environmental Engineering, Changchun Institute of Technology, Changchun 130012, China
| | - Meijin Du
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
| | - Yu Li
- MOE Key Laboratory of Resources and Environmental Systems Optimization, North China Electric Power University, Beijing 102206, China
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QSAR study, molecular docking, and ADMET prediction of vinyl sulfone-containing Nrf2 activator derivatives for treating Parkinson disease. Struct Chem 2022. [DOI: 10.1007/s11224-022-01909-z] [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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9
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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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Jian-Bo T, Xing Z, Shuai B, Ding L, Tian-Hao W. Topomer CoMFA and HQSAR Study on Benzimidazole Derivative as NS5B Polymerase Inhibitor. LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180818666210804125607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
In recent years, the number of people infected with the hepatitis C virus
(HCV) is increasing rapidly. This has become a major threat to global health, therefore, new anti-
HCV drugs are urgently needed. HCV NS5B polymerase is an RNA-dependent RNA polymerase
(RdRp), which plays an important role in virus replication, and can effectively prevent the replication
of HCV sub-genomic RNA in daughter cells. It is considered a very promising HCV therapeutic
target for the design of anti-HCV drugs.
Methods:
In order to explore the relationship between the structure of benzimidazole derivative and
its inhibitory activity on NS5B polymerase, holographic quantitative structure-activity relationship
(HQSAR) and Topomer comparative molecular field analysis (CoMFA) were used to establish benzimidazole
QSAR model of derivative inhibitors.
Results:
The results show that for the Topomer CoMFA model, the cross-validation coefficient q2
value is 0.883, and the non-cross-validation coefficient r2 value is 0.975. The model is reasonable,
reliable, and has a good predictive ability. For the HQSAR model, the cross-validated q2 value is
0.922, and the uncross-validated r2 value is 0.971, indicating that the model data fit well and has a
high predictive ability. Through the analysis of the contour map and color code diagram, 40 new
benzimidazole inhibitor molecules were designed, and all of them have higher activity than template
molecules, and the new molecules have significant interaction sites with protein 3SKE.
Conclusion:
The 3D-QSAR model established by Topomer CoMFA and HQSAR has good prediction
results and the statistical verification is valid. The newly designed molecules and docking results
provide theoretical guidance for the synthesis of new NS5B polymerase inhibitors and for the identification
of key residues that the inhibitors bind to NS5B, which helps to better understand their inhibitory
mechanism. These findings are helpful for the development of new anti-HCV drugs.
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Affiliation(s)
- Tong Jian-Bo
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Zhang Xing
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Bian Shuai
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Luo Ding
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
| | - Wang Tian-Hao
- College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi\'an 710021, China
- Shaanxi Key Laboratory of Chemical Additives for Industry, Xi\'an, 710021, China
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Tong JB, Luo D, Bian S, Zhang X. Structural investigation of tetrahydropteridin analogues as selective PLK1 inhibitors for treating cancer through combined QSAR techniques, molecular docking, and molecular dynamics simulations. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116235] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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A selectivity study of polysubstituted pyridinylimidazoles as dual inhibitors of JNK3 and p38α MAPK based on 3D-QSAR, molecular docking, and molecular dynamics simulation. Struct Chem 2020. [DOI: 10.1007/s11224-020-01668-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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