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Hou Y, Bai Y, Lu C, Wang Q, Wang Z, Gao J, Xu H. Applying molecular docking to pesticides. PEST MANAGEMENT SCIENCE 2023; 79:4140-4152. [PMID: 37547967 DOI: 10.1002/ps.7700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/17/2023] [Accepted: 08/05/2023] [Indexed: 08/08/2023]
Abstract
Pesticide creation is related to the development of sustainable agricultural and ecological safety, and molecular docking technology can effectively help in pesticide innovation. This paper introduces the basic theory behind molecular docking, pesticide databases, and docking software. It also summarizes the application of molecular docking in the pesticide field, including the virtual screening of lead compounds, detection of pesticides and their metabolites in the environment, reverse screening of pesticide targets, and the study of resistance mechanisms. Finally, problems with the use of molecular docking technology in pesticide creation are discussed, and prospects for the future use of molecular docking technology in new pesticide development are discussed. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yang Hou
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Yuqian Bai
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Chang Lu
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Qiuchan Wang
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Zishi Wang
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Jinsheng Gao
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Hongliang Xu
- Engineering Research Center of Pesticide of Heilongjiang Province, College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
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Jaradat NJ, Alshaer W, Hatmal M, Taha MO. Discovery of new STAT3 inhibitors as anticancer agents using ligand-receptor contact fingerprints and docking-augmented machine learning. RSC Adv 2023; 13:4623-4640. [PMID: 36760267 PMCID: PMC9896621 DOI: 10.1039/d2ra07007c] [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: 11/04/2022] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
STAT3 belongs to a family of seven vital transcription factors. High levels of STAT3 are detected in several types of cancer. Hence, STAT3 inhibition is considered a promising therapeutic anti-cancer strategy. In this work, we used multiple docked poses of STAT3 inhibitors to augment training data for machine learning QSAR modeling. Ligand-Receptor Contact Fingerprints and scoring values were implemented as descriptor variables. Escalating docking-scoring consensus levels were scanned against orthogonal machine learners, and the best learners (Random Forests and XGBoost) were coupled with genetic algorithm and Shapley additive explanations (SHAP) to identify critical descriptors that determine anti-STAT3 bioactivity to be translated into pharmacophore model(s). Two successful pharmacophores were deduced and subsequently used for in silico screening against the National Cancer Institute (NCI) database. A total of 26 hits were evaluated in vitro for their anti-STAT3 bioactivities. Out of which, three hits of novel chemotypes, showed cytotoxic IC50 values in the nanomolar range (35 nM to 6.7 μM). However, two are potent dihydrofolate reductase (DHFR) inhibitors and therefore should have significant indirect STAT3 inhibitory effects. The third hit (cytotoxic IC50 = 0.44 μM) is purely direct STAT3 inhibitor (devoid of DHFR activity) and caused, at its cytotoxic IC50, more than two-fold reduction in the expression of STAT3 downstream genes (c-Myc and Bcl-xL). The presented work indicates that the concept of data augmentation using multiple docked poses is a promising strategy for generating valid machine learning models capable of discriminating active from inactive compounds.
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Affiliation(s)
- Nour Jamal Jaradat
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan Amman 11492 Jordan +962 6 5339649 +962 6 5355000 ext. 23305
| | - Walhan Alshaer
- Cell Therapy Center, The University of Jordan Amman 11942 Jordan
| | - Mamon Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University P.O. Box 330127 Zarqa 13133 Jordan
| | - Mutasem Omar Taha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan Amman 11492 Jordan +962 6 5339649 +962 6 5355000 ext. 23305
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Wang H, Cheng Y, Zhang X, Wang Y, Zhao H. Comparative analysis of physicochemical properties, ginsenosides content and α-amylase inhibitory effects in white ginseng and red ginseng. FOOD SCIENCE AND HUMAN WELLNESS 2023. [DOI: 10.1016/j.fshw.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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Identification of protein tyrosine phosphatase 1B (PTP1B) inhibitors through De Novo Evoluton, synthesis, biological evaluation and molecular dynamics simulation. Biochem Biophys Res Commun 2020; 526:273-280. [PMID: 32209254 DOI: 10.1016/j.bbrc.2020.03.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 03/12/2020] [Indexed: 02/04/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a widely expressed 50 kDa enzyme and the first intracellular PTP to be purified from human placental tissue. It has been proved that protein tyrosine phosphatase 1B played a significant role in the negative regulation of insulin signaling pathway and overexpression of PTP1B could lead to the decrease of insulin resistance. Therefore PTP1B has emerged as a novel promising therapeutic target for the treatment of type-2 diabetes mellitus. Computer aided drug design (CADD), chemical synthesis and biological activity assay resulted in the identification of a novel potent PTP1B inhibitor, compound 1a, which shared an IC50 value of 4.46 μM. Finally, the analysis of molecular dynamics simulation provided the theoretical basis for favorable activity of compound 1a.
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Paudel P, Park SE, Seong SH, Jung HA, Choi JS. Bromophenols from Symphyocladia latiuscula Target Human Monoamine Oxidase and Dopaminergic Receptors for the Management of Neurodegenerative Diseases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2426-2436. [PMID: 32011134 DOI: 10.1021/acs.jafc.0c00007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Progressive degeneration of dopaminergic neurons in the substantia nigra is the characteristic feature of Parkinson's disease (PD) and the severity accelerates with aging. Therefore, improving dopamine level or dopamine receptor signaling is a standard approach for PD treatment. Herein, our results demonstrate that bromophenols 2,3,6-tribromo-4,5-dihydroxybenzyl alcohol (1), 2,3,6-tribromo-4,5-dihydroxybenzyl methyl ether (2), and bis-(2,3,6-tribromo-4,5-dihydroxybenzyl) ether (3) from red alga Symphyocladia latiuscula are moderate-selective human monoamine oxidase-A inhibitors and good dopamine D3/D4 receptor agonists. Bromophenol 3 showed a promising D4R agonist effect with a low micromole 50% effective concentration (EC50) value. All of the test ligands were docked against a three-dimensional (3D) model of hD3R and hD4R, and the result demonstrated strong binding through interaction with prime interacting residues-Asp110, Cys114, and His349 on hD3R and Asp115 and Cys119 on hD4R. Overall, the results demonstrated natural bromophenols, especially 1 and 3, from Symphyocladia latiuscula as multitarget ligands for neuroprotection, especially in PD and schizophrenia.
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Affiliation(s)
- Pradeep Paudel
- Department of Food and Life Science , Pukyong National University , Busan 48513 , Republic of Korea
| | - Se Eun Park
- Department of Food and Life Science , Pukyong National University , Busan 48513 , Republic of Korea
| | - Su Hui Seong
- Department of Food and Life Science , Pukyong National University , Busan 48513 , Republic of Korea
| | - Hyun Ah Jung
- Department of Food Science and Human Nutrition , Jeonbuk National University , Jeonju 54896 , Republic of Korea
| | - Jae Sue Choi
- Department of Food and Life Science , Pukyong National University , Busan 48513 , Republic of Korea
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Arya R, Gupta SP, Paliwal S, Sharma S, Madan K, Chauhan M. Pharmacophore Modeling and Docking Studies to Investigate Potential Leads for the Development of β -Secretase APP Cleavage Enzyme-1 (BACE-1) Inhibitors. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570180815666181023110736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Alzheimer’s disease is a medical condition with detrimental brain health. It is
majorly diagnosed in aging individuals plaque in β) characterized by accumulated Amyloidal beta (A
1 BACE) 1 secretase APP cleavage enzyme βneurological areas. The ) is the target of choice that can
be exploited to find drugs against Alzheimer’s disease.
Methods:
A series of BACE-1 inhibitors with reported binding constant were considered for the development
of a feature based pharmacophore model.
Results:
The good correlation coefficient (r=0.91) and RMSD of 0.93 was observed with 30 compounds
in training set. The model was validated internally (r2test=0.76) as well as externally by Fischer validation.
The pharmacophore based virtual screening retrieved compounds that were docked and biologically
evaluated.
Conclusion:
The three structurally diverse molecules were tested by in-vitro method. The pyridine
derivative with highest fit value (6.9) exhibited IC50 value of 2.70 µM and thus was found to be the most
promising lead molecule as BACE-1 inhibitor.
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Affiliation(s)
- Richa Arya
- Banasthali University, 304022, Banasthali, (Raj.), India
| | - Satya Prakash Gupta
- Department of Pharmaceutical Technology, Meerut Institute of Engineering and Technology, 250005, Meerut, India
| | | | - Swapnil Sharma
- Banasthali University, 304022, Banasthali, (Raj.), India
| | - Kirtika Madan
- Banasthali University, 304022, Banasthali, (Raj.), India
| | - Monika Chauhan
- Banasthali University, 304022, Banasthali, (Raj.), India
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Chen G, Miao M, Jiang B, Jin J, Campanella OH, Feng B. Effects of high hydrostatic pressure on lipase from Rhizopus chinensis: I. Conformational changes. INNOV FOOD SCI EMERG 2017. [DOI: 10.1016/j.ifset.2017.03.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Srivastav VK, Singh V, Tiwari M. Recent Advancements in Docking Methodologies. Oncology 2017. [DOI: 10.4018/978-1-5225-0549-5.ch033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nowadays molecular docking has become an important methodology in CADD (Computer-Aided Drug Design)-assisted drug discovery process. It is an important computational tool widely used to predict binding mode, binding affinity and binding free energy of a protein-ligand complex. The important factors responsible for accurate results in docking studies are correct binding site prediction, use of suitable small-molecule databases, consistent docking pose, high dock score with good MD (Molecular Dynamics), clarity whether the compound is an inhibitor or agonist, etc. However, still there are several limitations which make it difficult to obtain accurate results from docking studies. In this chapter, the main focus is on recent advancements in various aspects of molecular docking such as ligand sampling, protein flexibility, scoring functions, fragment docking, post-processing, docking into homology models and protein-protein docking.
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Affiliation(s)
| | - Vineet Singh
- Shri Govindram Seksaria Institute of Technology and Science, India
| | - Meena Tiwari
- Shri Govindram Seksaria Institute of Technology and Science, India
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Tang HC, Chen YC. Insight into molecular dynamics simulation of BRAF(V600E) and potent novel inhibitors for malignant melanoma. Int J Nanomedicine 2015; 10:3131-46. [PMID: 25960652 PMCID: PMC4412490 DOI: 10.2147/ijn.s80150] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BRAF inhibitors have changed the standard therapeutic protocol for advanced or metastatic melanoma which harbored notorious BRAF(V600E) single mutation. However, drug resistance to BRAF inhibitors happens just like other cancer treatment. In this study, we constructed the ideal BRAF(V600E)-modeled structure through homology modeling and introduced the method of structure-based docking or virtual screening from the large compound database. Through certain methods of molecular dynamics simulation, we realized that BRAF(V600E) had quite prominent difference of molecular character or structural variation from the wild-type BRAF protein. It might confer the metamorphic character of advanced melanoma for the patients who harbored BRAF(V600E) mutation. By the methods of ligand-based quantitative structure-activity relationship and molecular dynamics simulation, we further recommend that aknadicine and 16beta-hydroxy-19s-vindolinine N-oxide from the traditional Chinese medicine are potent novel inhibitors for the management of malignant melanoma in the future.
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Affiliation(s)
- Hsin-Chieh Tang
- Department of Biomedical Informatics, Asia University, Taichung, Taiwan
| | - Yu-Chian Chen
- Department of Biomedical Informatics, Asia University, Taichung, Taiwan ; Human Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan ; Research Center for Chinese Medicine and Acupuncture, China Medical University Hospital, Taichung, Taiwan
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10
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Chen YC. Beware of docking! Trends Pharmacol Sci 2015; 36:78-95. [DOI: 10.1016/j.tips.2014.12.001] [Citation(s) in RCA: 344] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/23/2014] [Accepted: 12/02/2014] [Indexed: 12/16/2022]
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11
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Tang HC, Chen YC. Molecular insight and resolution for tumors harboring the H-ras(G12V) mutation. RSC Adv 2015. [DOI: 10.1039/c4ra16763e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
GTP-bound H-ras(G12V) provides a convenient condition to phosphorylate the substrate protein.
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Affiliation(s)
- Hsin-Chieh Tang
- Department of Biomedical Informatics
- Asia University
- Taichung
- Taiwan
| | - Yu-Chian Chen
- Department of Biomedical Informatics
- Asia University
- Taichung
- Taiwan
- Human Genetic Center
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12
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Huang HJ, Chen HY, Chang YS, Chen CYC. Insight into two antioxidants binding to the catalase NADPH binding site from traditional Chinese medicines. RSC Adv 2015. [DOI: 10.1039/c4ra14734k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The two TCM compounds, hesperidin and THSG, might help to keep catalase active during the decomposition of hydrogen peroxide.
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Affiliation(s)
- Hung-Jin Huang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources
- College of Pharmacy
- China Medical University
- Taichung 40402
- Taiwan
| | - Hsin-Yi Chen
- Department of Biomedical Informatics
- Asia University
- Taichung
- Taiwan
| | - Yuan-Shiun Chang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources
- College of Pharmacy
- China Medical University
- Taichung 40402
- Taiwan
| | - Calvin Yu-Chian Chen
- Department of Biomedical Informatics
- Asia University
- Taichung
- Taiwan
- Human Genetic Center
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The inhibition of folylpolyglutamate synthetase (folC) in the prevention of drug resistance in Mycobacterium tuberculosis by traditional Chinese medicine. BIOMED RESEARCH INTERNATIONAL 2014; 2014:635152. [PMID: 25050369 PMCID: PMC4090511 DOI: 10.1155/2014/635152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 03/05/2014] [Indexed: 01/11/2023]
Abstract
Tuberculosis (TB) is an infectious disease caused by many strains of mycobacteria, but commonly Mycobacterium tuberculosis. As a possible method of reducing the drug resistance of M. tuberculosis, this research investigates the inhibition of Folylpolyglutamate synthetase, a protein transcript from the resistance association gene folC. After molecular docking to screen the traditional Chinese medicine (TCM) database, the candidate TCM compounds, with Folylpolyglutamate synthetase, were selected by molecular dynamics. The 10,000 ps simulation in association with RMSD analysis and total energy and structural variation defined the protein-ligand interaction. The selected TCM compounds Saussureamine C, methyl 3-O-feruloylquinate, and Labiatic acid have been found to inhibit the activity of bacteria and viruses and to regulate immunity. We also suggest the possible pathway in protein for each ligand. Compared with the control, similar interactions and structural variations indicate that these compounds might have an effect on Folylpolyglutamate synthetase. Finally, we suggest Saussureamine C is the best candidate compound as the complex has a high score, maintains its structural composition, and has a larger variation value than the control, thus inhibiting the drug resistance ability of Mycobacterium tuberculosis.
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Possible inhibitor from traditional Chinese medicine for the β form of calcium-dependent protein kinase type II in the treatment of major depressive disorder. BIOMED RESEARCH INTERNATIONAL 2014; 2014:761849. [PMID: 25045698 PMCID: PMC4086615 DOI: 10.1155/2014/761849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 03/05/2014] [Accepted: 03/05/2014] [Indexed: 11/20/2022]
Abstract
Recently, an important topic of major depressive disorder (MDD) had been published in 2013. MDD is one of the most prevalent and disabling mental disorders. Consequently, much research is being undertaken into the causes and treatment. It has been found that inhibition of the β form of calcium/calmodulin-dependent protein kinase type II (β-CaMKII) can ameliorate the disorder. Upon screening the traditional Chinese medicine (TCM) database by molecular docking, sengesterone, labiatic acid, and methyl 3-O-feruloylquinate were selected for molecular dynamics. After 20 ns simulation, the RMSD, total energy, and structure variation could define the protein-ligand interaction. Furthermore, sengesterone, the principle candidate compound, has been found to have an effect on the regulation of emotions and memory development. In structure variation, we find the sample functional group of important amino acids make the protein stable and have limited variation. Due to similarity of structure variations, we suggest that these compounds may have an effect on β-CaMKII and that sengesterone may have a similar efficacy as the control. However labiatic acid may be a stronger inhibitor of β-CaMKII based on the larger RMSD and variation.
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Hung TC, Lee WY, Chen KB, Chan YC, Lee CC, Chen CYC. In silico investigation of traditional Chinese medicine compounds to inhibit human histone deacetylase 2 for patients with Alzheimer's disease. BIOMED RESEARCH INTERNATIONAL 2014; 2014:769867. [PMID: 25045700 PMCID: PMC4090436 DOI: 10.1155/2014/769867] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 03/05/2014] [Indexed: 11/17/2022]
Abstract
Human histone deacetylase 2 (HDAC2) has been identified as being associated with Alzheimer's disease (AD), a neuropathic degenerative disease. In this study, we screen the world's largest Traditional Chinese Medicine (TCM) database for natural compounds that may be useful as lead compounds in the search for inhibitors of HDAC2 function. The technique of molecular docking was employed to select the ten top TCM candidates. We used three prediction models, multiple linear regression (MLR), support vector machine (SVM), and the Bayes network toolbox (BNT), to predict the bioactivity of the TCM candidates. Molecular dynamics simulation provides the protein-ligand interactions of compounds. The bioactivity predictions of pIC50 values suggest that the TCM candidatesm, (-)-Bontl ferulate, monomethylcurcumin, and ningposides C, have a greater effect on HDAC2 inhibition. The structure variation caused by the hydrogen bonds and hydrophobic interactions between protein-ligand interactions indicates that these compounds have an inhibitory effect on the protein.
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Affiliation(s)
- Tzu-Chieh Hung
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
| | - Wen-Yuan Lee
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
- Department of Neurosurgery, China Medical University Hospital, No. 2, Yude Road, North District, Taichung 40447, Taiwan
| | - Kuen-Bao Chen
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
- Department of Anesthesiology, China Medical University Hospital, Taichung 40447, Taiwan
| | - Yueh-Chiu Chan
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Cheng-Chun Lee
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Calvin Yu-Chian Chen
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
- Research Center for Chinese Medicine & Acupuncture, China Medical University, Taichung 40402, Taiwan
- Human Genetic Center, Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
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Treatment of cardiovascular disease by traditional Chinese medicine against pregnane X receptor. BIOMED RESEARCH INTERNATIONAL 2014; 2014:950191. [PMID: 25050380 PMCID: PMC4090537 DOI: 10.1155/2014/950191] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 03/05/2014] [Indexed: 12/11/2022]
Abstract
Recently, cardiovascular disease, also known as loop circulatory system diseases or disorders, is one of the serious diseases including heart disease, stroke, atherosclerosis, myocardial infarction, hypertension, hypotension, and thrombosis. Human pregnane X receptor, PXR, plays a crucial role in exogenous and endobiotic metabolism for rabbit, rat, mouse, and human. The PXR activation can protect the blood vessels from damage of hazardous substances. In this study we aim to investigate the potent lead compounds as PXR receptor agonist against cardiovascular disease. To improve drug development of TCM compounds, we aim to investigate the potent lead compounds as PXR agonists from the TCM compounds in TCM Database@Taiwan. The top three TCM compounds, bis(4-hydroxybenzyl) ether mono-β-D-glucopyranoside (BEMG), ixerisoside, and tangshenoside II, have displayed higher potent binding affinities than the positive control, PNU-142721, in the docking simulation. After MD simulations, which can optimize the result of docking simulation and validate the stability of H-bonds between each ligand and PXR protein under dynamic conditions, top TCM compounds, BEMG and tangshenoside II, maintain most of interactions with PXR protein, which keep the ligand binding stable in the binding domain. Hence, we propose BEMG and tangshenoside II as potential lead compounds for further study in drug development process with the PXR protein.
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Drug design of cyclin-dependent kinase 2 inhibitor for melanoma from traditional Chinese medicine. BIOMED RESEARCH INTERNATIONAL 2014; 2014:798742. [PMID: 25045703 PMCID: PMC4090515 DOI: 10.1155/2014/798742] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 03/05/2014] [Accepted: 03/05/2014] [Indexed: 02/08/2023]
Abstract
One has found an important cell cycle controller. This guard can decide the cell cycle toward proliferation or quiescence. Cyclin-dependent kinase 2 (CDK2) is a unique target among the CDK family in melanoma therapy. We attempted to find out TCM compounds from TCM Database@Taiwan that have the ability to inhibit the activity of CDK2 by systems biology. We selected Tetrahydropalmatine, Reserpiline, and (+)-Corydaline as the candidates by docking and screening results for further survey. We utilized support vector machine (SVM), multiple linear regression (MLR) models and Bayesian network for validation of predicted activity. By overall analysis of docking results, predicted activity, and molecular dynamics (MD) simulation, we could conclude that Tetrahydropalmatine, Reserpiline, and (+)-Corydaline had better binding affinity than the control. All of them had the ability to inhibit the activity of CDK2 and might have the opportunity to be applied in melanoma therapy.
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Insight into HIV of IFN-induced myxovirus resistance 2 (MX2) expressed by traditional Chinese medicine. BIOMED RESEARCH INTERNATIONAL 2014; 2014:871576. [PMID: 25045710 PMCID: PMC4086518 DOI: 10.1155/2014/871576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/05/2014] [Accepted: 03/05/2014] [Indexed: 11/17/2022]
Abstract
Recently, an important topic of the acquired immunodeficiency syndrome (AIDS) had been published in 2013. In this report, the expression of the IFN-induced myxovirus resistance 2 (MX2) had been defined the function to kill the human immunodeficiency virus (HIV). The screening from the Traditional Chinese Medicine (TCM) database by simulating molecular docking and molecular dynamics could select candidate compounds, which may express MX2 against HIV. Saussureamine C, Crotalaburnine, and Precatorine are selected based on the highest docking score and other TCM compounds. The data from molecular dynamics are helpful in the analysis and detection of protein-ligand interactions. According to the docking poses, hydrophobic interactions, and hydrogen bond with structure variations, this research could assess the interaction between protein and ligand interaction. In addition to the detection of TCM compound efficacy, we suggest that Saussureamine C is better than the others in protein-ligand interaction and the structural variation to express MX2.
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Investigation of potent lead for acquired immunodeficiency syndrome from traditional Chinese medicine. BIOMED RESEARCH INTERNATIONAL 2014; 2014:205890. [PMID: 25013765 PMCID: PMC4075082 DOI: 10.1155/2014/205890] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 03/05/2014] [Accepted: 03/05/2014] [Indexed: 11/18/2022]
Abstract
Acquired immunodeficiency syndrome (AIDS), caused by human immunodeficiency virus (HIV), has become, because of the rapid spread of the disease, a serious global problem and cannot be treated. Recent studies indicate that VIF is a protein of HIV to prevent all of human immunity to attack HIV. Molecular compounds of traditional Chinese medicine (TCM) database filtered through molecular docking and molecular dynamics simulations to inhibit VIF can protect against HIV. Glutamic acid, plantagoguanidinic acid, and Aurantiamide acetate based docking score higher with other TCM compounds selected. Molecular dynamics are useful for analysis and detection ligand interactions. According to the docking position, hydrophobic interactions, hydrogen bonding changes, and structure variation, the study try to select the efficacy of traditional Chinese medicine compound Aurantiamide acetate is better than the other for protein-ligand interactions to maintain the protein composition, based on changes in the structure.
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Lead screening for HIV-1 integrase (IN) inhibited by traditional Chinese medicine. BIOMED RESEARCH INTERNATIONAL 2014; 2014:479367. [PMID: 25013783 PMCID: PMC4071968 DOI: 10.1155/2014/479367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 03/05/2014] [Indexed: 12/25/2022]
Abstract
Human immunodeficiency virus causes the acquired immunodeficiency syndrome (AIDS) and becomes a serious world-wide problem because of this disease's rapid propagation and incurability. Integrase strand transfer inhibitors (INSTIs) supports HIV have rapid drug resistance for antitreatment. Screening the traditional Chinese medicine (TCM) database by simulating molecular docking and molecular dynamics may select molecular compounds to inhibit INSTIs against HIV drug resistance. (S)-cathinone and (1S,2S)-norpseudoephedrine are selected based on structure and ligand-based drugs are designed and then get higher bioactivity predicted score from SVM than Raltegravir and other TCM compounds. The molecular dynamics are helpful in the analysis and detection of protein-ligand interactions. According to the docking poses, hydrophobic interactions and hydrogen bond variations define the main regions of important amino acids in integrase. In addition to the detection of TCM compound efficacy, we suggest (1S,2S)-norpseudoephedrine is better than the others based on the analysis of interaction and the effect on the structural variation.
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In silico design for adenosine monophosphate-activated protein kinase agonist from traditional chinese medicine for treatment of metabolic syndromes. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 2014:928589. [PMID: 24899913 PMCID: PMC4034719 DOI: 10.1155/2014/928589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 01/02/2014] [Accepted: 01/02/2014] [Indexed: 12/25/2022]
Abstract
Adenosine monophosphate-activated protein kinase (AMPK) acts as a master mediator of metabolic homeostasis. It is considered as a significant millstone to treat metabolic syndromes including obesity, diabetes, and fatty liver. It can sense cellular energy or nutrient status by switching on the catabolic pathways. Investigation of AMPK has new findings recently. AMPK can inhibit cell growth by the way of autophagy. Thus AMPK has become a hot target for small molecular drug design of tumor inhibition. Activation of AMPK must undergo certain extent change of the structure. Through the methods of structure-based virtual screening and molecular dynamics simulation, we attempted to find out appropriate small compounds from the world's largest TCM Database@Taiwan that had the ability to activate the function of AMPK. Finally, we found that two TCM compounds, eugenyl_beta-D-glucopyranoside and 6-O-cinnamoyl-D-glucopyranose, had the qualification to be AMPK agonist.
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Huang HJ, Chen HY, Lee CC, Chen CYC. Computational design of apolipoprotein E4 inhibitors for Alzheimer's disease therapy from traditional Chinese medicine. BIOMED RESEARCH INTERNATIONAL 2014; 2014:452625. [PMID: 24967370 PMCID: PMC4055423 DOI: 10.1155/2014/452625] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/05/2014] [Accepted: 03/05/2014] [Indexed: 12/19/2022]
Abstract
Apolipoprotein E4 (Apo E4) is the major genetic risk factor in the causation of Alzheimer's disease (AD). In this study we utilize virtual screening of the world's largest traditional Chinese medicine (TCM) database and investigate potential compounds for the inhibition of ApoE4. We present the top three TCM candidates: Solapalmitine, Isodesacetyluvaricin, and Budmunchiamine L5 for further investigation. Dynamics analysis and molecular dynamics (MD) simulation were used to simulate protein-ligand complexes for observing the interactions and protein variations. Budmunchiamine L5 did not have the highest score from virtual screening; however, the dynamics pose is similar to the initial docking pose after MD simulation. Trajectory analysis reveals that Budmunchiamine L5 was stable over all simulation times. The migration distance of Budmunchiamine L5 illustrates that docked ligands are not variable from the initial docked site. Interestingly, Arg158 was observed to form H-bonds with Budmunchiamine L5 in the docking pose and MD snapshot, which indicates that the TCM compounds could stably bind to ApoE4. Our results show that Budmunchiamine L5 has good absorption, blood brain barrier (BBB) penetration, and less toxicity according to absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction and could, therefore, be safely used for developing novel ApoE4 inhibitors.
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Affiliation(s)
- Hung-Jin Huang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Pharmacy, China Medical University, Taichung 40402, Taiwan
| | - Hsin-Yi Chen
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
| | - Cheng-Chun Lee
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Calvin Yu-Chian Chen
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
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Huang HJ, Chang TT, Chen HY, Chen CYC. Finding inhibitors of mutant superoxide dismutase-1 for amyotrophic lateral sclerosis therapy from traditional chinese medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2014; 2014:156276. [PMID: 24963318 PMCID: PMC4052194 DOI: 10.1155/2014/156276] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 02/06/2014] [Accepted: 02/06/2014] [Indexed: 12/13/2022]
Abstract
Superoxide dismutase type 1 (SOD1) mutations cause protein aggregation and decrease protein stability, which are linked to amyotrophic lateral sclerosis (ALS) disease. This research utilizes the world's largest traditional Chinese medicine (TCM) database to search novel inhibitors of mutant SOD1, and molecular dynamics (MD) simulations were used to analyze the stability of protein that interacted with docked ligands. Docking results show that hesperidin and 2,3,5,4'-tetrahydroxystilbene-2-O- β -D-glucoside (THSG) have high affinity to mutant SOD1 and then dopamine. For MD simulation analysis, hesperidin and THSG displayed similar value of RMSD with dopamine, and the migration analysis reveals stable fluctuation at the end of MD simulation time. Interestingly, distance between the protein and ligand has distinct difference, and hesperidin changes the position from initial binding site to the other place. In flexibility of residues analysis, the secondary structure among all complexes does not change, indicating that the structure are not affect ligand binding. The binding poses of hesperidin and THSG are similar to dopamine after molecular simulation. Our result indicated that hesperidin and THSG might be potential lead compound to design inhibitors of mutant SOD1 for ALS therapy.
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Affiliation(s)
- Hung-Jin Huang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Pharmacy, China Medical University, Taichung 40402, Taiwan
| | - Tung-Ti Chang
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
| | - Hsin-Yi Chen
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
| | - Calvin Yu-Chian Chen
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
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Huang HJ, Lee CC, Chen CYC. In silico design of BACE1 inhibitor for Alzheimer's disease by traditional Chinese medicine. BIOMED RESEARCH INTERNATIONAL 2014; 2014:741703. [PMID: 24900984 PMCID: PMC4034430 DOI: 10.1155/2014/741703] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 02/16/2014] [Indexed: 12/22/2022]
Abstract
The β-site APP cleaving enzyme 1 (BACE1) is an important target for causing Alzheimer's disease (AD), due to the brain deposition peptide amyloid beta (Aβ) require cleavages of amyloid precursor protein (APP) by BACE1 and γ-secretase, but treatments of AD still have side effect in recent therapy. This study utilizes the world largest traditional Chinese medicine (TCM) database and database screening to provide potential BACE1 inhibited compound. Molecular dynamics (MD) simulation was carried out to observe the dynamics structure after ligand binding. We found that Triptofordin B1 has less toxicity than pyrimidine analogue, which has more potent binding affinity with BACE1. For trajectory analysis, all conformations are tending to be stable during 5000 ps simulation time. In dynamic protein validation, the residues of binding region are still stable after MD simulation. For snapshot comparison, we found that Triptofordin B1 could reduce the binding cavity; the results reveal that Triptofordin B1 could bind to BACE1 and better than control, which could be used as potential lead drug to design novel BACE1 inhibitor for AD therapy.
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Affiliation(s)
- Hung-Jin Huang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Pharmacy, China Medical University, Taichung 40402, Taiwan
| | - Cheng-Chun Lee
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Calvin Yu-Chian Chen
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
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Tsou YA, Huang HJ, Lin WWY, Chen CYC. Investigation of anti-infection mechanism of lactoferricin and splunc-1. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2014; 2014:907028. [PMID: 24876880 PMCID: PMC4021689 DOI: 10.1155/2014/907028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 02/08/2014] [Accepted: 02/08/2014] [Indexed: 12/11/2022]
Abstract
The innate immune system is the first line in the defense system and prevents the body from further bacteria, virus, or fungal infections. Most of the innate immune system is relevant to mucosa immunity. Lactotransferrin is secreted from the human mammal breast duct epithelial tissue and strengthens infant immunity to defense with regard to outward pathogens. Splunc-1 is also an innate material secreted from the soft palate, lung, nasal cavity epithelium, and mucosa. It helps with mucosa defense against bacterial, virus, and even fungus. LPS is the main etiology of Gram-negative bacilla infection source. And studies of lactoferricin and slpunc-1 both can combine with LPS and subsequently cause insults to the mucosa. Although, we know that both of them partake in an important role in innate immunity, we do not know the effects when they work together. In this study, we just overview silicon stimulation to examine the combination of Lactoferricin and Splunc-1 and the effect with regard to LPS.
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Affiliation(s)
- Yung An Tsou
- Otolaryngology Head and Neck Surgery, China Medical University Hospital, Taichung 40402, Taiwan
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
| | - Hung-Jin Huang
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, College of Pharmacy, China Medical University, Taichung 40402, Taiwan
| | - Wesley Wen Yang Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan
| | - Calvin Yu-Chian Chen
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan
- Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan
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Chen CYC. WITHDRAWN: DrugPrinter: print any drug instantly. Drug Discov Today 2014:S1359-6446(14)00121-4. [PMID: 24747561 DOI: 10.1016/j.drudis.2014.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 03/12/2014] [Accepted: 03/31/2014] [Indexed: 10/25/2022]
Abstract
This article has been withdrawn at the request of the author. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
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Affiliation(s)
- Calvin Yu-Chian Chen
- School of Medicine, College of Medicine, China Medical University, Taichung 40402, Taiwan; Department of Biomedical Informatics, Asia University, Taichung 41354, Taiwan; Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Investigation of the novel lead of melanocortin 1 receptor for pigmentary disorders. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 2014:254678. [PMID: 24693320 PMCID: PMC3947904 DOI: 10.1155/2014/254678] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 12/15/2013] [Accepted: 12/15/2013] [Indexed: 11/18/2022]
Abstract
Knowing the role of MC1R in skin tanning can provide a brand new idea to resolve pigmentary disorders. α MSH has 13 amino acids and is the most essential pigmentary melanocortin responsible for melanin synthesis. One could utilize the compound library to find lead compounds by virtual screening from peptide database and traditional Chinese medicine (TCM) database@Taiwan. Computational simulation provided a convenient technology to survey potential lead. Ligand-based validation set up the reliable model for molecular dynamics simulation. Molecular dynamics simulation approved the binding affinity and stability of the peptides selected by virtual screening. Thus, we concluded that Glu-Glu-Lys-Glu (EEKE), Glu-Gly-Gly-Ser-Val-Glu-Ser (EGGSVES), and Glu-Glu-Asp-Cys-Lys (EEDCK) were potent lead peptides for MC1R to resolve pigmentary disorders.
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Design of Glucagon-Like Peptide-1 Receptor Agonist for Diabetes Mellitus from Traditional Chinese Medicine. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2014; 2014:385120. [PMID: 24891870 PMCID: PMC4033432 DOI: 10.1155/2014/385120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 01/29/2014] [Indexed: 11/18/2022]
Abstract
Glucagon-like peptide-1 (GLP-1) is a promising target for diabetes mellitus (DM) therapy and reduces the occurrence of diabetes due to obesity. However, GLP-1 will be hydrolyzed soon by the enzyme dipeptidyl peptidase-4 (DPP-4). We tried to design small molecular drugs for GLP-1 receptor agonist from the world's largest traditional Chinese medicine (TCM) Database@Taiwan. According to docking results of virtual screening, we selected 2 TCM compounds, wenyujinoside and 28-deglucosylchikusetsusaponin IV, for further molecular dynamics (MD) simulation. GLP-1 was assigned as the control compound. Based on the results of root mean square deviation (RMSD), solvent accessible surface (SAS), mean square deviation (MSD), Gyrate, total energy, root mean square fluctuation (RMSF), matrices of smallest distance of residues, database of secondary structure assignment (DSSP), cluster analysis, and distance of H-bond, we concluded that all the 3 compounds could bind and activate GLP-1 receptor by computational simulation. Wenyujinoside and 28-deglucosylchikusetsusaponin IV were the TCM compounds that could be GLP-1 receptor agonists.
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Matos KS, da Cunha EF, da Silva Gonçalves A, Wilter A, Kuča K, França TC, Ramalho TC. First principles calculations of thermodynamics and kinetic parameters and molecular dynamics simulations of acetylcholinesterase reactivators: can mouse data provide new insights into humans? J Biomol Struct Dyn 2012; 30:546-58. [DOI: 10.1080/07391102.2012.687521] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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30
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Banappagari S, Corti M, Pincus S, Satyanarayanajois S. Inhibition of protein-protein interaction of HER2-EGFR and HER2-HER3 by a rationally designed peptidomimetic. J Biomol Struct Dyn 2012; 30:594-606. [PMID: 22731912 DOI: 10.1080/07391102.2012.687525] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Protein-protein interactions (PPI) play a crucial role in many biological processes and modulation of PPI using small molecules to target hot spots has therapeutic value. As a model system we will use PPI of human epidermal growth factor receptors (EGFRs). Among the four EGFRs, EGFR-HER2 and HER2-HER3 are well known in cancer. We have designed a small molecule that is targeted to modulate HER2-mediated signaling. Our approach is novel because the small molecule designed disrupts dimerization not only of EGFR-HER2, but also of HER2-HER3. In the present study we have shown, using surface plasmon resonance analysis, that a peptidomimetic, compound 5, binds specifically to HER2 protein extracellular domain and disrupts the dimerization of EGFRs. To evaluate the effect of compound 5 on HER2 signaling in vitro, Western blot and PathHunter assays were used. Results indicated that compound 5 inhibits the phosphorylation of HER2 kinase domain and inhibits the heterodimerization in a dose-dependent manner. Molecular modeling methods were used to model the PPI of HER2-HER3 heterodimer.
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Affiliation(s)
- Sashikanth Banappagari
- Department of Basic Pharmaceutical Sciences, College of Pharmacy, University of Louisiana at Monroe, 1800 Bienville Drive, Monroe, LA 71201, USA
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Divsalar A, Saboury AA, Ahadi L, Zemanatiyar E, Mansouri-Torshizi H, Ajloo D, Sarma RH. Biological evaluation and interaction of a newly designed anti-cancer Pd(II) complex and human serum albumin. J Biomol Struct Dyn 2012; 29:283-96. [PMID: 21875149 DOI: 10.1080/07391102.2011.10507385] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The pharmacokinetics and pharmacodynamics of any drug will depend, largely, on the interaction that has with human serum albumin (HSA), the most abundant plasma protein. The interaction between newly synthesized Pd(II) complexe, 2,2'-bipyridin Butylglycinato Pd(II) nitrate, an anti-tumor component, with HSA was studied at different temperatures by fluorescence, far UV circular dichroism (CD), UV-visible spectrophotometry and theoretical approaches. The Pd(II) complex has a strong ability to quench the intrinsic fluorescence of HSA through a dynamic quenching procedure. The binding parameters and thermodynamic parameters, including δH°, δS° and δG° were calculated by fluorescence quenching method, indicated that hydrophobic forces play a major role in the interaction of Pd(II) complex with HSA. Based on Autodock, FRET (fluorescence resonance energy transfer) and fluorescence quenching data, it may be concluded that one of the binding sites in the complex of HSA is near the only one Trp of HSA (Trp214) in sub domain IIA of the protein. Far-UV-CD results indicated that Pd(II)-complex induced increase in the α-helical content of the protein. The anti-tumor property of the synthesized Pd(II) complex was studied by testing it on human tumor cell line K562. The 50% cytotoxic concentration (Cc₅₀) of complex was determined using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide) assay. Also, fluorescence staining with DAPI (4,6-diamidino-2-phenylindole) revealed some typical nuclear changes that are characteristic of apoptosis which is induced at Cc₅₀ concentration of Pd(II) complex in K562 cell line after 24 h incubation. Our results suggest that Pd(II) complex is a promising anti-proliferative agent and should execute its biological effects by inducing apoptosis.
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Affiliation(s)
- Adeleh Divsalar
- Institute of Biochemistry and Biophysics, University of Tehran. Tehran, Iran.
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Abstract
Cardiac troponin C (cTnC) is the Ca²⁺ dependent switch for contraction in heart muscle making it a potential target for drug research in the therapy of heart failure. Calcium binding on Troponin C (TnC) triggers a series of conformational changes exposing a hydrophobic pocket in the N-domain of TnC (cNTnC), which leads to force generation. Mutations and acidic pH have been related to altering the sensitivity of TnC affecting the efficiency of the heart. Bepridil, identified as a calcium sensitizer to TnC, has been experimentally found to bind to the N-domain pocket of TnC but with negative cooperativity. Screening and de novo design were carried out using LUDI and AUTOLUDI programs in this work to identify and design potential ligands that can bind to the hydrophobic pocket of TnC. Two docking centers and multiple searching radii including 5 Å, 5.5 Å, 6 Å, 6.5 Å, 7.0 Å and 7.5 Å were used in LUDI to screen the ZINC database. Based on the LUDI docking results, 8 molecules were identified from the database with good potential to bind into the binding pocket and they were used as template molecules to generate a series of new molecules by AUTOLUDI design. Out of all the newly-designed molecules, 14 new ligands were recognized to be potential ligands that can bind and fit well into the binding pocket. These molecules can be used as starting molecules to develop TnC ligands. The binding stability and binding affinity of these molecules to the protein was further analyzed by molecular dynamics simulations. The results show that the binding energies, interactions and complex stabilities of 6 ligands are comparable to or better than bepridil.
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Affiliation(s)
- Jayson F Varguhese
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
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Pai S, Das M, Banerjee R, Dasgupta D. Biphasic association of T7 RNA polymerase and a nucleotide analogue, cibacron blue as a model to understand the role of initiating nucleotide in the mechanism of enzyme action. J Biomol Struct Dyn 2011; 29:153-64. [PMID: 21696231 DOI: 10.1080/07391102.2011.10507380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
T7 RNA polymerase (T7 RNAP) is an enzyme that utilizes ribonucleotides to synthesize the nascent RNA chain in a template-dependent manner. Here we have studied the interaction of T7 RNAP with cibacron blue, an anthraquinone monochlorotriazine dye, its effect on the function of the enzyme and the probable mode of binding of the dye. We have used difference absorption spectroscopy and isothermal titration calorimetry to show that the dye binds T7 RNAP in a biphasic manner. The first phase of the binding is characterized by inactivation of the enzyme. The second binding site overlaps with the common substrate-binding site of the enzyme. We have carried out docking experiment to map the binding site of the dye in the promoter bound protein. Competitive displacement of the dye from the high affinity site by labeled GTP and isothermal titration calorimetry of high affinity GTP bound enzyme with the dye suggests a strong correlation between the high affinity dye binding and the high affinity GTP binding in T7 RNAP reported earlier from our laboratory.
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Affiliation(s)
- Sudipta Pai
- Biophysics Division, Saha Institute of Nuclear Physics, 1/AF Bidhan Nagar, Kolkata 700064, India
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Dey R, Chen L. In search of allosteric modulators of a7-nAChR by solvent density guided virtual screening. J Biomol Struct Dyn 2011; 28:695-715. [PMID: 21294583 DOI: 10.1080/07391102.2011.10508600] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nicotinic acetylcholine receptors (nAChR) are pentameric ligand gated ion channels whose activity can be modulated by endogenous neurotransmitters as well as by synthetic ligands that bind the same or distinct sites from the natural ligand. The subtype of α7 nAChR has been considered as a potenial therapeutic target for Alzheimer's disease, schizophrenia and other neurological and psychiatric disorders. Here we have developed a homology model of α7 nAChR based on two high resolution crystal structures with Brookhaven Protein Data Bank (PDB) codes 2QC1 and 2WN9 for threading on one monomer and then for building a pentamer, respectively. A number of small molecule binding sites are identified using Pocket Finder (J. An, M. Tortov, and R. Abagyan, Molecular & Cellular Proteomics, 4.6, 752-761 (2005)) of Internal Coordinate Mechanics (ICM). Remarkably, these computer-identified sites match perfectly with ordered solvent densities found in the high-resolution crystal structure of α1 nAChR, suggesting that the surface cavities in the α7 nAChR model are likely binding sites of small molecules. A high throughput virtual screening by flexible ligand docking of 5008 small molecule compounds was performed at three potential allosteric modulator (AM) binding sites of α7 nAChR using Molsoft ICM software (R. Abagyan, M. Tortov and D. Kuznetsov, J Comput Chem 15, 488-506, (1994)). Some experimentally verified allosteric modulators of α7 like CCMI comp-6, LY 7082101, 5-HI, TQS, PNU-120596, genistein, and NS-1738 ranked among top 100 compounds, while the rest of the compounds in the list could guide further search for new allosteric modulators.
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Affiliation(s)
- Raja Dey
- Molecular and Computational Biology, Department of Biological Sciences,University of Southern California, Los Angeles, CA 90089, USA.
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Chang TT, Sun MF, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Screening from the world's largest TCM database against H1N1 virus. J Biomol Struct Dyn 2011; 28:773-86. [PMID: 21294588 DOI: 10.1080/07391102.2011.10508605] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The swine influenza virus (H1N1) 2009 pandemic highlights the importance of having effective anti-viral strategies. Recently, oseltamivir (Tamiflu) resistant influenza viruses are identified; which further emphasizes the urgency in developing new antiviral agents. In influenza virus replication cycle, viral surface glycoprotein, hemagglutinin, is responsible for viral entry into host cells. Hence, a potentially effective antiviral strategy is to inhibit viral entry mechanism. To develop novel antiviral agent that inhibits viral entry, we analyzed 20,000 traditional Chinese medicine (TCM) ingredients in hemagglutinin subtype H1 sialic acid binding site found on H1N1 virus. We then performed molecular dynamics simulations to investigate receptor-ligand interaction of the candidates obtained from docking. Here, we report three TCM derivatives that have high binding affinities to H1 sialic acid binding site residues based on structure-based calculations. The top three derivatives, xylopine_2, rosmaricine_14 and rosmaricine_15, all have an amine group that interact with Glu83 and a pyridinium group that interact with Asp103. Molecular dynamics simulations show that these derivatives form strong hydrogen bonding with Glu83 but interact transiently with Asp103. We therefore suggest that an enhanced hemagglutinin inhibitor, based on our scaffold, should be designed to bind both Glu83 and Asp103 with high affinity.
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Affiliation(s)
- Tung-Ti Chang
- Laboratory of Computational and Systems Biology, School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
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Li P, Tan JJ, Liu M, Zhang XY, Chen WZ, Wang CX. Insight into the Inhibitory Mechanism and Binding Mode Between D77 and HIV-1 Integrase by Molecular Modeling Methods. J Biomol Struct Dyn 2011; 29:311-23. [DOI: 10.1080/07391102.2011.10507387] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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37
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Oliveira AA, Rennó MN, de Matos CAS, Bertuzzi MD, Ramalho TC, Fraga CA, França TCC. Molecular Modeling Studies ofYersinia pestisDihydrofolate Reductase. J Biomol Struct Dyn 2011; 29:351-67. [DOI: 10.1080/07391102.2011.10507390] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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38
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Sun MF, Yang SC, Chang KW, Tsai TY, Chen HY, Tsai FJ, Lin JG, Chen CYC. Screening from TCM Database@Taiwan and QSAR model for identifying HER2 inhibitors. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.569550] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Sun MF, Chang TT, Chen KC, Yang SC, Chang KW, Tsai TY, Chen HY, Tsai FJ, Lin JG, Chen CYC. Treat Alzheimer's disease by traditional Chinese medicine? MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.577074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Wang Y, Bian F, Deng S, Shi Q, Ge M, Wang S, Zhang X, Xu S. The key residues of active sites on the catalytic fragment for paclitaxel interacting with poly (ADP-ribose) polymerase. J Biomol Struct Dyn 2011; 28:881-93. [PMID: 21469749 DOI: 10.1080/07391102.2011.10508615] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Poly(ADP-ribose) polymerase (PARP) is regarded as a target protein for paclitaxel (PTX) to bind. An important issue is to identify the key residues as active sites for PTX interacting with PARP, which will help to understand the potential drug activity of PTX against cancer cells. Using docking method and MD simulation, we have constructed a refined structure of PTX docked on the catalytic function domain of PARP (PDB code: 1A26). The residues Glu327(988), Tyr246(907), Lys242(903), His165(826), Asp105(766), Gln102(763) and Gln98(759) in PARP are identified as potential sites involved in interaction with PTX according to binding energy (E(b)) between PTX and single residue calculated with B3LYP/6-31G(d,p). These residues form an active binding pocket located on the surface of the catalytic fragment, possibly interacting with the required groups of PTX leading to its activity against cancer cells. It is noted that most of the active sites make conatct with the "southern hemisphere" of PTX except for one residue, Tyr246(907), which interacts with the "northern hemisphere" of PTX. The conformation of PTX in complex with the catalytic fragment is observed as being T-shaped, similar to that complexed with β-tubulin. The total Eb of -269.9 kJ/mol represents the potent interaction between PTX and the catalytic fragment, implying that PTX can readily bind to the active pocket. The tight association of PTX with the catalytic fragment would inhibit PARP activation, suggesting a potential application of PTX as an effective antineoplastic agent.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Education Ministry for Medicinal Chemistry of Natural Resource, College of Chemical Science and Technology, Yunnan University, Kunming 650091, PR China
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Kim DS, Kim CM, Won CI, Kim JK, Ryu J, Cho Y, Lee C, Bhak J. BetaDock: Shape-Priority Docking Method Based on Beta-Complex. J Biomol Struct Dyn 2011; 29:219-42. [DOI: 10.1080/07391102.2011.10507384] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Omidvar Z, Parivar K, Sanee H, Amiri-Tehranizadeh Z, Baratian A, Saberi MR, Asoodeh A, Chamani J. Investigations with Spectroscopy, Zeta Potential and Molecular Modeling of the Non-Cooperative Behaviour Between Cyclophosphamide Hydrochloride and Aspirin upon Interaction with Human Serum Albumin: Binary and Ternary Systems from the View Point of Multi-Drug Therapy. J Biomol Struct Dyn 2011; 29:181-206. [DOI: 10.1080/07391102.2011.10507382] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Xie HZ, Liu LY, Ren JX, Zhou JP, Zheng RL, Li LL, Yang SY. Pharmacophore Modeling and Hybrid Virtual Screening for the Discovery of Novel IκB Kinase 2 (IKK2) Inhibitors. J Biomol Struct Dyn 2011; 29:165-79. [DOI: 10.1080/07391102.2011.10507381] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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Drug design for mPGES-1 from traditional Chinese medicine database: A screening, docking, QSAR, molecular dynamics, and pharmacophore mapping study. J Taiwan Inst Chem Eng 2011. [DOI: 10.1016/j.jtice.2010.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Ramalho TC, Caetano MS, Josa D, Luz GP, Freitas EA, da Cunha EFF. Molecular Modeling ofMycobacterium TuberculosisdUTpase: Docking and Catalytic Mechanism Studies. J Biomol Struct Dyn 2011; 28:907-17. [DOI: 10.1080/07391102.2011.10508617] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Pankratov AN, Tsivileva OM, Drevko BI, Nikitina VE. Compounds of the 1,5-di(4-R-phenyl)-3-selenopentanediones-1,5 series interaction with the BasidiomyceteLentinula edodes, lectins: Computations and Experiment. J Biomol Struct Dyn 2011; 28:969-74. [DOI: 10.1080/07391102.2011.10508622] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Atri MS, Saboury AA, Moosavi-Movahedi AA, Goliaei B, Sefidbakht Y, Alijanvand HH, Sharifzadeh A, Niasari-Naslaji A. Structure and Stability Analysis of Cytotoxic Complex of Camel α-Lactalbumin and Unsaturated Fatty Acids Produced at High Temperature. J Biomol Struct Dyn 2011; 28:919-28. [DOI: 10.1080/07391102.2011.10508618] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Zhuohang M, Ji L, Hongwei Y. Modeling of Transition State by Molecular Dynamics. Prediction of Catalytic Efficiency of the Mutants of Mandelate Racemase. J Biomol Struct Dyn 2011; 28:871-9. [DOI: 10.1080/07391102.2011.10508614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Chang TT, Sun MF, Chang KW, Chen HY, Tsai FJ, Fisher M, Lin JG, Chen CYC. Screening from the world's largest TCM database for inhibiting DNA repair protein XRCC4. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.554550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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