An Investigation of Small GTPases in relation to Liver Tumorigenesis Using Traditional Chinese Medicine

Recently, an important topic of liver tumorigenesis had been published in 2013. In this report, Ras and Rho had defined the relation of liver tumorigenesis. The traditional Chinese medicine (TCM) database has been screened for molecular compounds by simulating molecular docking and molecular dynamics to regulate Ras and liver tumorigenesis. Saussureamine C, S-allylmercaptocysteine, and Tryptophan are selected based on the highest docking score than other TCM compounds. The molecular dynamics are helpful in the analysis and detection of protein-ligand interactions. Based on the docking poses, hydrophobic interactions, and hydrogen bond variations, this research surmises are the main regions of important amino acids in Ras. In addition to the detection of TCM compound efficacy, we suggest Saussureamine C is better than the others for protein-ligand interaction.

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Investigation of Estrogen Receptor (ESR1) for Breast Cancer from Traditional Chinese Medicine

BioMed Research International ◽

10.1155/2014/321486 ◽

2014 ◽

Vol 2014 ◽

pp. 1-12 ◽

Cited By ~ 3

Author(s):

Tzu-Chieh Hung ◽

Wen-Yuan Lee ◽

Kuen-Bao Chen ◽

Yueh-Chiu Chan ◽

Calvin Yu-Chian Chen

Keyword(s):

Breast Cancer ◽

Molecular Dynamics ◽

Estrogen Receptor ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Hydrophobic Interactions ◽

Ligand Interaction ◽

Protein Ligand Interactions ◽

Ligand Interactions ◽

Protein Ligand Interaction

Recently, an important topic of breast cancer had been published in 2013. In this report, estrogen receptor (ESR1) had defined the relation of hormone-cause breast cancer. The screening of traditional Chinese medicine (TCM) database has found the molecular compounds by simulating molecular docking and molecular dynamics to regulate ESR1. S-Allylmercaptocysteine and 5-hydroxy-L-tryptophan are selected according to the highest docking score than that of other TCM compounds and Raloxifene (control). The simulation from molecular dynamics is helpful in analyzing and detecting the protein-ligand interactions. After a comparing the control and the Apo form, then based on the docking poses, hydrophobic interactions, hydrogen bond and structure variations, this research postulates that S-allylmercaptocysteine may be more appropriate than other compounds for protein-ligand interaction.

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Insight into HIV of IFN-Induced Myxovirus Resistance 2 (MX2) Expressed by Traditional Chinese Medicine

BioMed Research International ◽

10.1155/2014/871576 ◽

2014 ◽

Vol 2014 ◽

pp. 1-14

Author(s):

Tzu-Chieh Hung ◽

Wen-Yuan Lee ◽

Kuen-Bao Chen ◽

Yueh-Chiu Chan ◽

Calvin Yu-Chian Chen

Keyword(s):

Molecular Dynamics ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Hydrophobic Interactions ◽

Ligand Interaction ◽

Protein Ligand Interactions ◽

Immunodeficiency Virus ◽

Ligand Interactions ◽

Acquired Immunodeficiency ◽

Immunodeficiency Syndrome

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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Lead Screening for CXCR4 of the Human HIV Infection Receptor Inhibited by Traditional Chinese Medicine

BioMed Research International ◽

10.1155/2014/809816 ◽

2014 ◽

Vol 2014 ◽

pp. 1-13

Author(s):

Tzu-Chieh Hung ◽

Wen-Yuan Lee ◽

Kuen-Bao Chen ◽

Calvin Yu-Chian Chen

Keyword(s):

Molecular Dynamics ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Hiv Infection ◽

Chemokine Receptor ◽

Hydrophobic Interactions ◽

Protein Ligand Interactions ◽

Ligand Interactions ◽

Acquired Immunodeficiency ◽

Immunodeficiency Syndrome

The acquired immunodeficiency syndrome (AIDS) is a serious worldwide disease caused by the human immunodeficiency virus (HIV) infection. Recent research has pointed out that the G protein-coupled chemokine receptor CXCR4 and the coreceptor C-C chemokine receptor type 5 (CCR5) are important targets for HIV infection. The traditional Chinese medicine (TCM) database has been screened for candidate compounds by simulating molecular docking and molecular dynamics against HIV. Saussureamine C, 5-hydroxy-L-tryptophan, and diiodotyrosine are selected based on the highest docking score. The molecular dynamics is helpful in the analysis and detection of protein-ligand interactions. According to the analysis of docking poses, hydrophobic interactions, hydrogen bond variations, and the comparison of the effect on CXCR4 and CCR5, these results indicate Saussureamine C may have better effect on these two receptors. But for some considerations, diiodotyrosine could make the largest variation and may have some efficacy contrary to expectations.

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Lead Screening for HIV of C-C Chemokine Receptor Type 5 Receptor Inhibited by Traditional Chinese Medicine

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2014/313094 ◽

2014 ◽

Vol 2014 ◽

pp. 1-10 ◽

Cited By ~ 1

Author(s):

Tzu-Chieh Hung ◽

Kuen-Bao Chen ◽

Hung-Jin Huang ◽

Calvin Yu-Chian Chen

Keyword(s):

Molecular Dynamics ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Chemokine Receptor ◽

Hydrophobic Interactions ◽

Protein Composition ◽

Receptor Type ◽

Ligand Interaction ◽

Ligand Interactions ◽

Immunodeficiency Syndrome

The acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV), has become a serious world-wide problem because of this disease's rapid propagation and incurability. Recent research has pointed out that the C-C chemokine receptor type 5 (CCR5) is an important target for HIV infection. The traditional Chinese medicine (TCM) database (http://tcm.cmu.edu.tw/) has been screened for molecular compounds that, by simulating molecular docking and molecular dynamics, may protect CCR5 against HIV. Saussureamine C, 5-hydroxy-L-tryptophan, and abrine are selected based on the docking score being higher than Maraviroc 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, this research surmises TRP86, TYR108, GLN194, TYR251, and GLU283 are the main regions of important amino acids in CCR5. In addition to the detection of TCM compound efficacy, we suggest saussureamine C is better than the others for maintaining protein composition during protein-ligand interaction, based on the structural variation.

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Lead Screening for HIV-1 Integrase (IN) Inhibited by Traditional Chinese Medicine

BioMed Research International ◽

10.1155/2014/479367 ◽

2014 ◽

Vol 2014 ◽

pp. 1-12

Author(s):

Tzu-Chieh Hung ◽

Wen-Yuan Lee ◽

Kuen-Bao Chen ◽

Yueh-Chiu Chan ◽

Calvin Yu-Chian Chen

Keyword(s):

Molecular Dynamics ◽

Drug Resistance ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Hydrophobic Interactions ◽

Strand Transfer ◽

Protein Ligand Interactions ◽

Ligand Interactions ◽

Acquired Immunodeficiency ◽

Immunodeficiency Syndrome

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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Investigation of Potent Lead for Acquired Immunodeficiency Syndrome from Traditional Chinese Medicine

BioMed Research International ◽

10.1155/2014/205890 ◽

2014 ◽

Vol 2014 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Tzu-Chieh Hung ◽

Wen-Yuan Lee ◽

Kuen-Bao Chen ◽

Yueh-Chiu Chan ◽

Calvin Yu-Chian Chen

Keyword(s):

Molecular Dynamics ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Acquired Immunodeficiency Syndrome ◽

Hydrophobic Interactions ◽

Structure Variation ◽

Ligand Interactions ◽

Acquired Immunodeficiency ◽

Immunodeficiency Syndrome ◽

Aurantiamide Acetate

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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Identification of Interactions of ABT-341 to Dipeptidyl Peptidase IV during Molecular Dynamics Simulations

Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) ◽

10.22487/j24428744.2021.v7.i2.15516 ◽

2021 ◽

Vol 7 (2) ◽

pp. 91-98

Author(s):

Enade Istyastono ◽

Michael Gani

Keyword(s):

Molecular Dynamics ◽

Design Research ◽

Hydrophobic Interactions ◽

Md Simulations ◽

Dipeptidyl Peptidase ◽

Dipeptidyl Peptidase Iv ◽

Structure Based Drug Design ◽

Protein Ligand Interactions ◽

Dpp Iv ◽

Ligand Interactions

Background: Dipeptidyl Peptidase IV (DPP-IV) is an established drug discovery target for type 2 diabetes mellitus (T2DM) therapy. On the other hand, molecular dynamics (MD) simulations have been widely employed to obtain insights of the protein-ligand interactions in structure-based drug design research projects. Moreover, a software to identify protein-ligand interactions called PyPLIF HIPPOS was made publicly available recently. Employing PyPLIF HIPPOS to identify the interactions of DPP-IV and its ligand ABT-341 during MD simulations was then of considerable interest. Objectives: The main aim of this study was to identify protein-ligand interactions of ABT-341 to DPP-IV during MD simulations. Material and Methods: The crystal structure of DPP-IV co-crystallized with ABT-341 obtained from the Protein Data Bank with code of 2I78 was used as the main material. YASARA-Structure was employed for performing 10 ns prodution run MD simulations with snapshots in every 100 ps and PyPLIF HIPPOS was used to identify the protein-ligand interactions. Results: There were 23 interactions involving 13 residues identified by employing PyPLIF HIPPOS during the MD simulations. Two of them identified in all snapshots, i.e., hydrophobic interactions to PHE357 and TYR666. Conclusions: PyPLIF HIPPOS was succesfully employed to identify the interactions of ABT-341 to DPP-IV during MD simulations.

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Lead Screening for Chronic Obstructive Pulmonary Disease of IKK2 Inhibited by Traditional Chinese Medicine

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2014/465025 ◽

2014 ◽

Vol 2014 ◽

pp. 1-16 ◽

Cited By ~ 2

Author(s):

Yung-An Tsou ◽

Hung-Jin Huang ◽

Wesley Wen-Yang Lin ◽

Calvin Yu-Chian Chen

Keyword(s):

Chronic Obstructive Pulmonary Disease ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Pulmonary Disease ◽

Hydrophobic Interactions ◽

Sinapic Acid ◽

Developed Countries ◽

Chronic Obstructive ◽

Ligand Interaction ◽

Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is a chronic obstructive lung disease and is frequently found in well-developed countries due to the issue of aging populations. Not all forms of medical treatment are unable to return a patient's limited pulmonary function back to normal and eventually they could require a lung transplant. At this time, COPD is the leading cause of death in the world. Studies surveying I-kappa-B-kinase beta (IKK2) are very relevant to the occurrence and deterioration of the condition COPD. The sinapic acid-4-O-sulfate, kaempferol, and alpha-terpineol were found to be IKK2 inhibitors and helped prevent COPD occurrence and worsening according to a screening of the traditional Chinese medicine (TCM) database. The protein-ligand interaction of these three compounds with regard to IKK2 was also done by molecular dynamics. The docking poses, hydrogen bond variation, and hydrophobic interactions found Asp103 and Lys106 are crucial to IKK2 binding areas for IKK2 inhibition. Finally, we found the three compounds that have an equally strong effect in terms of IKK2 binding proven by the TCM database and perhaps these may be an alternative treatment for COPD in the future.

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The Inhibition of Folylpolyglutamate Synthetase (folC) in the Prevention of Drug Resistance inMycobacterium tuberculosisby Traditional Chinese Medicine

BioMed Research International ◽

10.1155/2014/635152 ◽

2014 ◽

Vol 2014 ◽

pp. 1-14 ◽

Cited By ~ 1

Author(s):

Tzu-Chieh Hung ◽

Kuen-Bao Chen ◽

Wen-Yuan Lee ◽

Calvin Yu-Chian Chen

Keyword(s):

Infectious Disease ◽

Drug Resistance ◽

Mycobacterium Tuberculosis ◽

Chinese Medicine ◽

Traditional Chinese Medicine ◽

Structural Variation ◽

Structural Variations ◽

Ligand Interaction ◽

Folylpolyglutamate Synthetase ◽

Protein Ligand Interaction

Tuberculosis (TB) is an infectious disease caused by many strains of mycobacteria, but commonlyMycobacterium tuberculosis. As a possible method of reducing the drug resistance ofM. 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 ofMycobacterium tuberculosis.

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