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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>
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>
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>