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Binding mode analysis between membrane dipeptidase and its substrates
Kim, M.,Kim, J.,Jung, E.,Choi, K.,Shin, J. -M.,Kang, S. -K.,Kim, M. -K.,Choi, Y. -J.,Choi, S. -H. GORDON & BREACH SCIENCE PUBLISHERS 2007 MOLECULAR SIMULATION Vol.33 No.6
<P> Membrane dipeptidase (MDP) is a membrane-bound glycoprotein involved in the hydrolysis of dipeptides, showing specific activity for dipeptides. Recent study showed that membrane dipeptidase was the receptor for a lung-targeting peptide identified by in vivo phage display and the crystal structure of the cilastatin-liganded human renal dipeptidase was determined. We performed a pharmacophore-based virtual screening and molecular docking in order to characterize MDP binding interactions with its substrates. A ligand-based pharmacophore model represented only a slight enrichment because of a lacked variety and centralization of ligand features. Molecular docking study was used to incorporate ligand conformational changes in the binding sites and the performance was much better than pharmacophore model; only 10% of compound library needed to be screened in order to detect all included active compounds. In addition, we found that one of the crystallographically observed water molecules plays an important role in the binding modes between MDP and its substrate.</P>
Docking and 3-D QSAR studies of dual PDE4-PDE7 inhibitors
Kang, N. S.,Jhon, D. J.,Song, J. H.,Yoo, S. -E. GORDON & BREACH SCIENCE PUBLISHERS 2007 MOLECULAR SIMULATION Vol.33 No.14
<P> Small dual-specificity molecules inhibiting PDE4 and PDE7 can be used to treat inflammatory diseases. To design and synthesize dual PDE4 and PDE7 inhibitors, we carried out the target-based docking and the 3D QSAR study using CoMFA. Three compounds were synthesized. We predicted their inhibitory activities using our 3D QSAR model and tested their activities against PDE4 and PDE7 in vitro.</P>
Study on the hydrolysis mechanism of phosphodiesterase 4 using molecular dynamics simulations
Kang, N. S.,Chae, C. H.,Yoo, S.-E. GORDON & BREACH SCIENCE PUBLISHERS 2006 MOLECULAR SIMULATION Vol.32 No.5
<P>We carried out NPT molecular dynamics simulations in an explicit solvent to better understand the mechanism of cyclic adenosine monophosphates (cAMP) hydrolysis by phosphodiesterase 4 (PDE4) enzyme on atomic details and to obtain information on the dynamics characteristic of the catalytic domains of PDE4. In analyzing the water hydrogen-bond network around the active site, we also showed the importance of water in drug–protein interactions. In addition, we reported the characteristics of the hydration pattern and the dynamic distance distribution around the interesting residues. The results indicated that Asp318 plays the role of a general base that can activate water molecule for nucleophilic attack on cAMP. As expected, His160 plays the role of a proton donor for cAMP.</P>
FlexE ensemble docking approach to virtual screening for CDK2 inhibitors
Kim, J.,Park, J. G.,Chong, Y. GORDON & BREACH SCIENCE PUBLISHERS 2007 MOLECULAR SIMULATION Vol.33 No.8
<P> In spite of a proven potential and effectiveness of FlexE in docking flexible ligands into an ensemble of protein structures, FlexE has rarely been successful in virtual screening situations. In this study, we constructed cyclin-dependent kinase 2 (CDK2) ensemble structures which have exactly the same backbone conformations as 1AQ1 but differ only at the side chain torsion angles of the key amino acid (Lys33, Phe80, Lys89 and Asp145) residues: the torsion angles observed in the 17 CDK2 crystal structures were adapted to represent conformational flexibility. FlexE ensemble docking protocol then completely samples the full conformational fields generated by combination of torsions of the four amino acids in the ATP binding site. Virtual screening for CDK2 inhibitors by using the FlexE ensemble docking of a database composed of 48,703 inactives and 82 actives showed significant enrichment factor (EF = 18.5), and successfully identified 71 actives among the top 132 ligands (53.8%) ranked by total energy scores. Moreover, total energy scoring followed by visual inspection filtered-off non-specific binders among the highly-ranked ligands to increase the ratio of actives-to-inactives to 71:13 at the top 5% of the virtual screening solutions.</P>
A study of direct moxibustion using mathematical methods.
Liu, Miao,Kauh, Sang Ken,Lim, Sabina Gordon and Breach Science Publishers 2012 Computer methods in biomechanics and biomedical en Vol.15 No.4
<P>Direct moxibustion is an important and widely used treatment method in traditional medical science. The use of a mathematical method to analyse direct moxibustion treatment is necessary and helpful in exploring the new direct moxibustion instruments and their standardisation. Thus, this paper aims to use a mathematical method to study direct moxibustion in skin to demonstrate a direct relationship between direct moxibustion and skin stimuli. In this paper, the transient thermal response of skin layers is analysed to study direct moxibustion using the data got from standardised method to measure the temperature of a burning moxa cone. Numerical simulations based on an appropriate finite element model are developed to predict the heat transfer, thermal damage and thermal stress distribution of barley moxa cones and jujube moxa cones in the skin tissue. The results are verified by the ancient literatures of traditional Chinese medicine and clinical application, and showed that mathematical method can be a good interface between moxa cone and skin tissue providing the numerical value basis for moxibustion.</P>
Dynamic simulation of tibial tuberosity realignment: model evaluation.
Purevsuren, Tserenchimed,Elias, John J,Kim, Kyungsoo,Kim, Yoon Hyuk Gordon and Breach Science Publishers 2015 Computer methods in biomechanics and biomedical en Vol.18 No.14
<P>This study was performed to evaluate a dynamic multibody model developed to characterize the influence of tibial tuberosity realignment procedures on patellofemoral motion and loading. Computational models were created to represent four knees previously tested at 40, 60, and 80 of flexion with the tibial tuberosity in a lateral, medial and anteromedial positions. The experimentally loaded muscles, major ligaments of the knee, and patellar tendon were represented. A repeated measures ANOVA with post-hoc testing was performed at each flexion angle to compare data between the three positions of the tibial tuberosity. Significant experimental trends for decreased patella flexion due to tuberosity anteriorization and a decrease in the lateral contact force due to tuberosity medialization were reproduced computationally. The dynamic multibody modeling technique will allow simulation of function for symptomatic knees to identify optimal surgical treatment methods based on parameters related to knee pathology and pre-operative kinematics.</P>