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Abstract
B-family DNA polymerases (PolBs) of different groups are widespread in Archaea, and different PolBs often coexist in the same organism. Many of these PolB enzymes remain to be investigated. One of the main groups that is poorly characterized is PolB2, whose members occur in many archaea but are predicted to be inactivated forms of DNA polymerase. Here, Sulfolobus islandicus DNA polymerase 2 (Dpo2), a PolB2 enzyme, was expressed in its native host and purified. Characterization of the purified enzyme revealed that the polymerase possesses a robust nucleotide incorporation activity but is devoid of the 3'-5' exonuclease activity. Enzyme kinetics analyses showed that Dpo2 replicates undamaged DNA templates with high fidelity, which is consistent with its inefficient nucleotide insertion activity opposite different DNA lesions. Strikingly, the polymerase is highly efficient in extending mismatches and mispaired primer termini once a nucleotide is placed opposite a damaged site. This extender polymerase represents a novel type of prokaryotic PolB specialized for DNA damage repair in Archaea. IMPORTANCE In this work, we report that Sulfolobus islandicus Dpo2, a B-family DNA polymerase once predicted to be an inactive form, is a bona fide DNA polymerase functioning in translesion synthesis. S. islandicus Dpo2 is a member of a large group of B-family DNA polymerases (PolB2) that are present in many archaea and some bacteria, and they carry variations in well-conserved amino acids in the functional domains responsible for polymerization and proofreading. However, we found that this prokaryotic B-family DNA polymerase not only replicates undamaged DNA with high fidelity but also extends mismatch and DNA lesion-containing substrates with high efficiencies. With these data, we propose this enzyme functions as an extender polymerase, the first prokaryotic enzyme of this type. Our data also suggest this PolB2 enzyme represents a functional counterpart of the eukaryotic DNA polymerase Pol zeta, an enzyme that is devoted to DNA damage repair.
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Wang Y, Chang J, Wang J, Zhong P, Zhang Y, Lai CC, He Y. 3D-QSAR Studies of S-DABO Derivatives as Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666180810112321] [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:
S-dihydro-alkyloxy-benzyl-oxopyrimidines (S-DABOs) as non-nucleoside
reverse transcriptase inhibitors have received considerable attention during the last decade due to
their high potency against HIV-1.
Methods:
In this study, three-dimensional quantitative structure-activity relationship (3D-QSAR) of
a series of 38 S-DABO analogues developed in our lab was studied using Comparative Molecular
Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA). The
Docking/MMFF94s computational protocol based on the co-crystallized complex (PDB ID: 1RT2)
was used to determine the most probable binding mode and to obtain reliable conformations for
molecular alignment. Statistically significant CoMFA (q2=0.766 and r2=0.949) and CoMSIA
(q2=0.827 and r2=0.974) models were generated using the training set of 30 compounds on the basis
of hybrid docking-based and ligand-based alignment.
Results:
The predictive ability of CoMFA and CoMSIA models was further validated using a test
set of eight compounds with predictive r2
pred values of 0.843 and 0.723, respectively.
Conclusion:
The information obtained from the 3D contour maps can be used in designing new SDABO
derivatives with improved HIV-1 inhibitory activity.
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Affiliation(s)
- Yueping Wang
- Department of Applied Chemistry, Faculty of Science, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Jie Chang
- Department of Applied Chemistry, Faculty of Science, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Jiangyuan Wang
- Key Laboratory of Medicinal Chemistry for Natural Resource, (Ministry of Education), School of Chemical Science and Technology, Yunnan University, Kunming Yunnan, 650091, China
| | - Peng Zhong
- Department of Applied Chemistry, Faculty of Science, Kunming University of Science and Technology, Kunming, Yunnan, 650500, China
| | - Yufang Zhang
- Key Laboratory of Medicinal Chemistry for Natural Resource, (Ministry of Education), School of Chemical Science and Technology, Yunnan University, Kunming Yunnan, 650091, China
| | - Christopher Cong Lai
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, United States
| | - Yanping He
- Key Laboratory of Medicinal Chemistry for Natural Resource, (Ministry of Education), School of Chemical Science and Technology, Yunnan University, Kunming Yunnan, 650091, China
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Zhang S, Zhang L, Wang Y, Yang J, Liao M, Bi S, Xie Z, Ho CT, Wan X. TBC2target: A Resource of Predicted Target Genes of Tea Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2018; 9:211. [PMID: 29520288 PMCID: PMC5827417 DOI: 10.3389/fpls.2018.00211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/05/2018] [Indexed: 05/29/2023]
Abstract
Tea is one of the most popular non-alcoholic beverages consumed worldwide. Numerous bioactive constituents of tea were confirmed to possess healthy benefits via the mechanisms of regulating gene expressions or protein activities. However, a complete interacting profile between tea bioactive compounds (TBCs) and their target genes is lacking, which put an obstacle in the study of healthy function of tea. To fill this gap, we developed a database of target genes of TBCs (TBC2target, http://camellia.ahau.edu.cn/TBC2target) based on a pharmacophore mapping approach. In TBC2target, 6,226 interactions between 240 TBCs and 673 target genes were documented. TBC2target contains detailed information about each interacting entry, such as TBC, CAS number, PubChem CID, source of compound (e.g., green, black), compound type, target gene(s) of TBC, gene symbol, gene ID, ENSEMBL ID, PDB ID, TBC bioactivity and the reference. Using the TBC-target associations, we constructed a bipartite network and provided users the global network and local sub-network visualization and topological analyses. The entire database is free for online browsing, searching and downloading. In addition, TBC2target provides a BLAST search function to facilitate use of the database. The particular strengths of TBC2target are the inclusion of the comprehensive TBC-target interactions, and the capacity to visualize and analyze the interacting networks, which may help uncovering the beneficial effects of tea on human health as a central resource in tea health community.
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Affiliation(s)
- Shihua Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
- Department of Genetics, University of Georgia, Athens, GA, United States
| | - Liang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| | - Yijun Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| | - Jian Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| | - Mingzhi Liao
- College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Shoudong Bi
- State Key Laboratory of Tea Plant Biology and Utilization, Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| | - Zhongwen Xie
- State Key Laboratory of Tea Plant Biology and Utilization, Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
| | - Chi-Tang Ho
- Department of Food Science, Rutgers University, New Brunswick, NJ, United States
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Institute of Applied Mathematics, Anhui Agricultural University, Hefei, China
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Zhang S, Xuan H, Zhang L, Fu S, Wang Y, Yang H, Tai Y, Song Y, Zhang J, Ho CT, Li S, Wan X. TBC2health: a database of experimentally validated health-beneficial effects of tea bioactive compounds. Brief Bioinform 2017; 18:830-836. [PMID: 27387194 PMCID: PMC5862282 DOI: 10.1093/bib/bbw055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 11/14/2022] Open
Abstract
Tea is one of the most consumed beverages in the world. Considerable studies show the exceptional health benefits (e.g. antioxidation, cancer prevention) of tea owing to its various bioactive components. However, data from these extensively published papers had not been made available in a central database. To lay a foundation in improving the understanding of healthy tea functions, we established a TBC2health database that currently documents 1338 relationships between 497 tea bioactive compounds and 206 diseases (or phenotypes) manually culled from over 300 published articles. Each entry in TBC2health contains comprehensive information about a bioactive relationship that can be accessed in three aspects: (i) compound information, (ii) disease (or phenotype) information and (iii) evidence and reference. Using the curated bioactive relationships, a bipartite network was reconstructed and the corresponding network (or sub-network) visualization and topological analyses are provided for users. This database has a user-friendly interface for entry browse, search and download. In addition, TBC2health provides a submission page and several useful tools (e.g. BLAST, molecular docking) to facilitate use of the database. Consequently, TBC2health can serve as a valuable bioinformatics platform for the exploration of beneficial effects of tea on human health. TBC2health is freely available at http://camellia.ahau.edu.cn/TBC2health.
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Affiliation(s)
- Shihua Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Hongdong Xuan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Liang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Sicong Fu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Yijun Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Hua Yang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Yuling Tai
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Youhong Song
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Jinsong Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Chi-Tang Ho
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Shaowen Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- College of Information and Computer science, Anhui Agricultural University, Hefei, China
- Corresponding authors. Xiaochun Wan, State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China. Tel.: +86-551-65786468, Fax.: +86-551-65786765; E-mail: ; Shaowen Li, College of Information and Computer science, Anhui Agricultural University, Hefei 230036, China. Tel.: +86-551-65786146; Fax.: +86-551-65786183; E-mail:
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Wang S, Liu Q, Li X, Zhao X, Qiu L, Lin J. Possible binding sites and interactions of propanidid and AZD3043 within the γ-aminobutyric acid type A receptor (GABAAR). J Biomol Struct Dyn 2017; 36:3926-3937. [DOI: 10.1080/07391102.2017.1403959] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Shanshan Wang
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, P.R China
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Qingzhu Liu
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Xi Li
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, P.R China
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Xueyu Zhao
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, P.R China
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Ling Qiu
- School of Chemical and Material Engineering, Jiangnan University, Wuxi 214122, P.R China
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
| | - Jianguo Lin
- Key Laboratory of Nuclear Medicine, Ministry of Health & Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi 214063, P.R. China
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Cheng P, Li J, Wang J, Zhang X, Zhai H. Investigations of FAK inhibitors: a combination of 3D-QSAR, docking, and molecular dynamics simulations studies. J Biomol Struct Dyn 2017; 36:1529-1549. [PMID: 28490269 DOI: 10.1080/07391102.2017.1329095] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Focal adhesion kinase (FAK) is one kind of tyrosine kinases that modulates integrin and growth factor signaling pathways, which is a promising therapeutic target because of involving in cancer cell migration, proliferation, and survival. To investigate the mechanism between FAK and triazinic inhibitors and design high activity inhibitors, a molecular modeling integrated with 3D-QSAR, molecular docking, molecular dynamics simulations, and binding free energy calculations was performed. The optimum CoMFA and CoMSIA models showed good reliability and satisfactory predictability (with Q2 = 0.663, R2 = 0.987, [Formula: see text] = 0.921 and Q2 = 0.670, R2 = 0.981, [Formula: see text] = 0.953). Its contour maps could provide structural features to improve inhibitory activity. Furthermore, a good consistency between contour maps, docking, and molecular dynamics simulations strongly demonstrates that the molecular modeling is reliable. Based on it, we designed several new compounds and their inhibitory activities were validated by the molecular models. We expect our studies could bring new ideas to promote the development of novel inhibitors with higher inhibitory activity for FAK.
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Affiliation(s)
- Peng Cheng
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
| | - Jiaojiao Li
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
| | - Juan Wang
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
| | - Xiaoyun Zhang
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
| | - Honglin Zhai
- a College of Chemistry and Chemical Engineering , Lanzhou University , No.222, Tianshui Road (South), Lanzhou , Gansu , 730000 , People's Republic of China
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Therese PJ, Manvar D, Kondepudi S, Battu MB, Sriram D, Basu A, Yogeeswari P, Kaushik-Basu N. Multiple e-pharmacophore modeling, 3D-QSAR, and high-throughput virtual screening of hepatitis C virus NS5B polymerase inhibitors. J Chem Inf Model 2014; 54:539-52. [PMID: 24460140 DOI: 10.1021/ci400644r] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRP) is a crucial and unique component of the HCV RNA replication machinery and a validated target for drug discovery. Multiple crystal structures of NS5B inhibitor complexes have facilitated the identification of novel compound scaffolds through in silico analysis. With the goal of discovering new NS5B inhibitor leads, HCV NS5B crystal structures bound with inhibitors in the palm and thumb allosteric pockets in combination with ligands with known inhibitory potential were explored for a comparative pharmacophore analyses. The energy-based and 3D-QSAR-based pharmacophore models were validated using enrichment analysis, and the six models thus developed were employed for high-throughput virtual screening and docking to identify nonpeptidic leads. The hits derived at each stage were analyzed for diversity based on the six pharmacophore models, followed by molecular docking and filtering based on their interaction with amino acids in the NS5B allosteric pocket and 3D-QSAR predictions. The resulting 10 hits displaying diverse scaffold were then screened employing biochemical and cell-based NS5B and anti-HCV inhibition assays. Of these, two molecules H-5 and H-6 were the most promising, exhibiting IC50 values of 28.8 and 47.3 μM against NS5B polymerase and anti-HCV inhibition of 96% and 86% at 50 μM, respectively. The identified leads comprised of benzimidazole (H-5) and pyridine (H-6) scaffolds thus constitute prototypical molecules for further optimization and development as NS5B inhibitors.
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Affiliation(s)
- Patrisha Joseph Therese
- Computer-Aided Drug Design Lab, Department of Pharmacy, Birla Institute of Technology & Science-Pilani , Hyderabad campus, Jawahar Nagar, Hyderabad-500078, Andhra Pradesh, India
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Li Y, Han C, Wang J, Xiao W, Wang Z, Zhang J, Yang Y, Zhang S, Ai C. Investigation into the mechanism of Eucommia ulmoides Oliv. based on a systems pharmacology approach. JOURNAL OF ETHNOPHARMACOLOGY 2013; 151:452-460. [PMID: 24239601 DOI: 10.1016/j.jep.2013.10.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 10/30/2013] [Accepted: 10/30/2013] [Indexed: 06/02/2023]
Abstract
ETHNOPHARMACOLOGY RELEVANCE Though Traditional Chinese Medicine (TCM) has long been playing a significant role in the maintenance of health for people in Asia as well as many other places, the mechanism of its action still remains ambiguous for most of the plants used in TCM, such as Eucommia ulmoides Oliv., a kind of herb that is widely used to help regulate hypertension and the immune system nowadays. However, its functioning mechanism is still unknown. Thus it is necessary to exploit the mechanism of Eucommia ulmoides Oliv. METHODS A systems pharmacology approach combining drug-likeness evaluation, oral bioavailability prediction, multiple drug targets prediction as well as network pharmacology techniques has been used. RESULTS This comprehensive systematic approach helps successfully to identify 41 candidate compounds contained in Eucommia ulmoides Oliv. while 39 potential targets hit by these ingredients and helps to uncover the synergistic mechanism of action on a systematic level. CONCLUSIONS Our work successfully explains the mechanism of the efficiency of Eucommia ulmoides Oliv. for the treatment of hypertension and enhancing immune. These results not only provide a new insight for the understanding of the chemical and pharmacological basis of Eucommia ulmoides Oliv., but also provide an efficient way for drug discovery from herbal medicine.
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Affiliation(s)
- Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China.
| | - Chunxiao Han
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Jinghui Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Wei Xiao
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Jiangsu Kanion Parmaceutical Co. Ltd., Lianyungang 222001, Jiangsu, China
| | - Zhenzhong Wang
- State Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Jiangsu Kanion Parmaceutical Co. Ltd., Lianyungang 222001, Jiangsu, China
| | - Jingxiao Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Yinfeng Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Shuwei Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Chemical Engineering, Dalian University of Technology, Dalian 116024, Liaoning, China
| | - Chunzhi Ai
- Lab of Pharmaceutical Resource Discovery, Dalian Institute of Chemical Physics, Graduate School of the Chinese Academy of Sciences, Dalian 116023, Liaoning, China
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Insight into the binding mode and the structural features of the pyrimidine derivatives as human A2A adenosine receptor antagonists. Biosystems 2013; 115:13-22. [PMID: 23665268 DOI: 10.1016/j.biosystems.2013.04.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/07/2013] [Accepted: 04/24/2013] [Indexed: 12/12/2022]
Abstract
The interaction of 278 monocyclic and bicyclic pyrimidine derivatives with human A2A adenosine receptor (AR) was investigated by employing molecular dynamics, thermodynamic analysis and three-dimensional quantitative structure-activity relationship (3D-QSAR) approaches. The binding analysis reveals that the pyrimidine derivatives are anchored in TM2, 3, 5, 6 and 7 of A2A AR by the aromatic stacking and hydrogen bonding interactions. The key residues involving Phe168, Glu169, and Asn253 stabilize the monocyclic and bicyclic cores of inhibitors. The thermodynamic analysis by molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) approach also confirms the reasonableness of the binding modes. In addition, the ligand-/receptor-based comparative molecular similarity indices analysis (CoMSIA) models of high statistical significance were generated and the resulting contour maps correlate well with the structural features of the antagonists essential for high A2A AR affinity. A minor/bulky group with negative charge at C2/C6 of pyrimidine ring respectively enhances the activity for all these pyrimidine derivatives. Particularly, the higher electron density of the ring in the bicyclic derivatives, the more potent the antagonists. The obatined results might be helpful in rational design of novel candidate of A2A adenosine receptor antagonist for treatment of Parkinson's disease.
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A system-level investigation into the mechanisms of Chinese Traditional Medicine: Compound Danshen Formula for cardiovascular disease treatment. PLoS One 2012; 7:e43918. [PMID: 22962593 PMCID: PMC3433480 DOI: 10.1371/journal.pone.0043918] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 07/27/2012] [Indexed: 11/19/2022] Open
Abstract
Compound Danshen Formula (CDF) is a widely used Traditional Chinese Medicine (TCM) which has been extensively applied in clinical treatment of cardiovascular diseases (CVDs). However, the underlying mechanism of clinical administrating CDF on CVDs is not clear. In this study, the pharmacological effect of CDF on CVDs was analyzed at a systemic point of view. A systems-pharmacological model based on chemical, chemogenomics and pharmacological data is developed via network reconstruction approach. By using this model, we performed a high-throughput in silico screen and obtained a group of compounds from CDF which possess desirable pharmacodynamical and pharmacological characteristics. These compounds and the corresponding protein targets are further used to search against biological databases, such as the compound-target associations, compound-pathway connections and disease-target interactions for reconstructing the biologically meaningful networks for a TCM formula. This study not only made a contribution to a better understanding of the mechanisms of CDF, but also proposed a strategy to develop novel TCM candidates at a network pharmacology level.
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