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

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
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.

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

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
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 ◽  
Small Gtpases ◽  
Ligand Interaction ◽  
Protein Ligand Interactions ◽  
Ligand Interactions ◽  
Protein Ligand Interaction ◽  
Better Than

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.

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

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):  
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.

scholarly journals Ligand-Based and Structure-Based Investigation for Alzheimer’s Disease from Traditional Chinese Medicine

2014 ◽  
Vol 2014 ◽  
pp. 1-16 ◽  
Author(s):  
Kai Hsin Liao ◽  
Kuen-Bao Chen ◽  
Wen-Yuan Lee ◽  
Mao-Feng Sun ◽  
Cheng-Chun Lee ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Amyloid Beta ◽  
Complex Structure ◽  
Hydrocarbon Chain ◽  
Tau Proteins ◽  
Structure Stability ◽  
Ligand Interaction

Alzheimer’s disease is a neurodegenerative disease that was conventionally thought to be related to the sedimentation of beta-amyloids, but drugs designed according to this hypothesis have generally failed. That FKBP52 can reduce the accumulation of tau proteins, and that Tacrolimus can reduce the pathological changes of tau proteins are new directions away from the long held amyloid-beta-centric concept. Therefore, the screening of traditional Chinese medicine compounds for those with higher affinity towards FKBP52 than Tacrolimus may be a new direction for treating Alzheimer’s disease. This study utilizes ligand-based and structure-based methods as the foundation. By utilizing dock scores and the predicted pIC50 from SVM, MLR, and Bayesian Network, several TCM compounds were selected for further analysis of their protein-ligand interactions. Daphnetoxin has higher affinity and complex structure stability than Tacrolimus; Lythrancine II exhibits the most identical trends in FKBP52 interactions as Tacrolimus, and 20-O-(2′E,4′E-decadienoyl)ingenol may be further modified at its hydrocarbon chain to promote interaction with FKBP52. In addition, we observed the residue Tyr113 of FKBP52 may play a key role in protein-ligand interaction. Our results indicate that Daphnetoxin, 20-O-(2′E,4′E-decadienoyl)ingenol, and Lythrancine II may be starting points for further modification as a new type of non-amyloid-beta-centric drug for Alzheimer’s disease.

scholarly journals Lead Discovery for Alzheimer’s Disease Related Target Protein RbAp48 from Traditional Chinese Medicine

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Hung-Jin Huang ◽  
Cheng-Chun Lee ◽  
Calvin Yu-Chian Chen
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Protein Structure ◽  
Chinese Medicine ◽  
Traditional Chinese Medicine ◽  
Md Simulation ◽  
Loss Of Function ◽  
Lead Discovery ◽  
Ligand Interaction ◽  
Age Related

Deficiency or loss of function of Retinoblastoma-associated proteins (RbAp48) is related with Alzheimer’s disease (AD), and AD disease is associated with age-related memory loss. During normal function, RbAp48 forms a complex with the peptide FOG-1 (friend of GATA-1) and has a role in gene transcription, but an unstable complex may affect the function of RbAp48. This study utilizes the world’s largest traditional Chinese medicine (TCM) database and virtual screening to provide potential compounds for RbAp48 binding. A molecular dynamics (MD) simulation was employed to understand the variations after protein-ligand interaction. FOG1 was found to exhibit low stability after RbAp48 binding; the peptide displayed significant movement from the initial docking position, a phenomenon which matched the docking results. The protein structure of the other TCM candidates was not variable during MD simulation and had a greater stable affinity for RbAp48 binding than FOG1. Our results reveal that the protein structure does not affect ligand binding, and the top three TCM candidates Bittersweet alkaloid II, Eicosandioic acid, and Perivine might resolve the instability of the RbAp48-FOG1 complex and thus be used in AD therapy.

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

2014 ◽  
Vol 2014 ◽  
pp. 1-16 ◽  
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.

scholarly journals The Use of Functional Genomics in Conjunction with Metabolomics forMycobacterium tuberculosisResearch

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Conrad C. Swanepoel ◽  
Du Toit Loots
Keyword(s):  
Infectious Disease ◽  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Systems Biology ◽  
Functional Genomics ◽  
The Past ◽  
Holistic Understanding ◽  
Transcriptomics Data ◽  
Genomic Studies ◽  
Complex Genome

Tuberculosis (TB), caused byMycobacterium tuberculosis, is a fatal infectious disease, resulting in 1.4 million deaths globally per annum. Over the past three decades, genomic studies have been conducted in an attempt to elucidate the functionality of the genome of the pathogen. However, many aspects of this complex genome remain largely unexplored, as approaches like genomics, proteomics, and transcriptomics have failed to characterize them successfully. In turn, metabolomics, which is relatively new to the “omics” revolution, has shown great potential for investigating biological systems or their modifications. Furthermore, when these data are interpreted in combination with previously acquired genomics, proteomics and transcriptomics data, using what is termed a systems biology approach, a more holistic understanding of these systems can be achieved. In this review we discuss how metabolomics has contributed so far to characterizing TB, with emphasis on the resulting improved elucidation ofM. tuberculosisin terms of (1) metabolism, (2) growth and replication, (3) pathogenicity, and (4) drug resistance, from the perspective of systems biology.

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

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
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.

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

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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