Molecular Dynamics Simulation

Publication Title: 
Journal of Biomolecular Structure & Dynamics

The emergence of bacterial multidrug resistance is an increasing problem in treatment of infectious diseases. An important cause for the multidrug resistance of bacteria is the expression of multidrug efflux transporters. The multidrug and toxic compound extrusion (MATE) transporters are most recently recognized as unique efflux system for extrusion of antimicrobials and therapeutic drugs due to energy stored in either Na(+) or H(+) electrochemical gradient.

Author(s): 
Kesherwani, Manish
Michael Gromiha, M.
Fukui, Kazuhiko
Velmurugan, Devadasan
Publication Title: 
PloS One

In this study, we investigated the influence of single nucleotide polymorphisms on the conformation of mutated cytochrome P450 (CYP) 2B6 proteins using molecular dynamics (MD) simulation. Some of these mutations influence drug metabolism activities, leading to individual variations in drug efficacy and pharmacokinetics. Using computational docking, we predicted the structure of the complex between the antimalarial agent artemether and CYP2B6 whose conformations were obtained by MD simulation.

Author(s): 
Kobayashi, Kana
Takahashi, Ohgi
Hiratsuka, Masahiro
Yamaotsu, Noriyuki
Hirono, Shuichi
Watanabe, Yurie
Oda, Akifumi
Publication Title: 
PLoS computational biology

Overexpression of epidermal growth factor receptor (EGFR) has been associated with cancer. Targeted inhibition of the EGFR pathway has been shown to limit proliferation of cancerous cells. Hence, we employed Traditional Chinese Medicine Database (TCM [email protected]) (http://tcm.cmu.edu.tw) to identify potential EGFR inhibitor.

Author(s): 
Yang, Shun-Chieh
Chang, Su-Sen
Chen, Hsin-Yi
Chen, Calvin Yu-Chian
Publication Title: 
PLoS computational biology

The H1N1 influenza pandemic of 2009 has claimed over 18,000 lives. During this pandemic, development of drug resistance further complicated efforts to control and treat the widespread illness. This research utilizes traditional Chinese medicine [email protected] (TCM [email protected]) to screen for compounds that simultaneously target H1 and N1 to overcome current difficulties with virus mutations. The top three candidates were de novo derivatives of xylopine and rosmaricine.

Author(s): 
Chang, Su-Sen
Huang, Hung-Jin
Chen, Calvin Yu-Chian
Publication Title: 
PloS One

Src kinase is an attractive target for drug development based on its established relationship with cancer and possible link to hypertension. The suitability of traditional Chinese medicine (TCM) compounds as potential drug ligands for further biological evaluation was investigated using structure-based, ligand-based, and molecular dynamics (MD) analysis. Isopraeroside IV, 9alpha-hydroxyfraxinellone-9-O-beta-D-glucoside (9HFG) and aurantiamide were the top three TCM candidates identified from docking.

Author(s): 
Tou, Weng Ieong
Chen, Calvin Yu-Chian
Publication Title: 
PloS One

Compound Danshen Formula (CDF) is a widely used Traditional Chinese Medicine (TCM) which has been extensively applied in clinical treatment of cardiovascular diseases (CVDs). However, the underlying mechanism of clinical administrating CDF on CVDs is not clear. In this study, the pharmacological effect of CDF on CVDs was analyzed at a systemic point of view. A systems-pharmacological model based on chemical, chemogenomics and pharmacological data is developed via network reconstruction approach.

Author(s): 
Li, Xiuxiu
Xu, Xue
Wang, Jinan
Yu, Hua
Wang, Xia
Yang, Hongjun
Xu, Haiyu
Tang, Shihuan
Li, Yan
Yang, Ling
Huang, Luqi
Wang, Yonghua
Yang, Shengli
Publication Title: 
PloS One

Pancreatic triacylglycerol lipase (PNLIP) are primary lipases that are critical for triacylglyceride digestion in human. Since reduced metabolism of triacylglyceride might be a plausible concept for weight loss, we screened for potential PNLIP inhibitors from traditional Chinese medicine (TCM) with the aim to identify weight loss candidate compounds.

Author(s): 
Chen, Kuan-Yu
Chang, Su-Sen
Chen, Calvin Yu-Chian
Publication Title: 
PloS One

Uroporphyrinogen decarboxylase (UROD) has been suggested as a protectant against radiation for head and neck cancer (HNC). In this study, we employed traditional Chinese medicine (TCM) compounds from TCM [email protected] (http://tcm.cmu.edu.tw/) to screen for drug-like candidates with potential UROD inhibition characteristics using virtual screening techniques.

Author(s): 
Tsou, Yung-An
Chen, Kuan-Chung
Lin, Hung-Che
Chang, Su-Sen
Chen, Calvin Yu-Chian
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