• Bulletin of the Korean Chemical Society
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• v.29 no.5
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• pp.921-927
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• 2008

Discovery of $\alpha$-glucosidase inhibitors has been actively pursued with the aim to develop therapeutics for the treatment of diabetes and the other carbohydrate mediated diseases. As a method for the discovery of new novel inhibitors of $\alpha$-glucosidase, we have addressed the performance of the computer-aided drug design protocol involving the homology modeling of $\alpha$-glucosidase and the structure-based virtual screening with the two docking tools: FlexX and the automated and improved AutoDock implementing the effects of ligand solvation in the scoring function. The homology modeling of $\alpha$-glucosidase from baker’s yeast provides a high-quality 3-D structure enabling the structure-based inhibitor design. Of the two docking programs under consideration, AutoDock is found to be more accurate than FlexX in terms of scoring putative ligands to the extent of 5-fold enhancement of hit rate in database screening when 1% of database coverage is used as a cutoff. A detailed binding mode analysis of the known inhibitors shows that they can be stabilized in the active site of $\alpha$- glucosidase through the simultaneous establishment of the multiple hydrogen bond and hydrophobic interactions. The present study demonstrates the usefulness of the automated AutoDock program with the improved scoring function as a docking tool for virtual screening of new $\alpha$-glucosidase inhibitors as well as for binding mode analysis to elucidate the activities of known inhibitors.

• Molecules and Cells
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• v.39 no.4
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• pp.316-321
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• 2016

The receptor activator of nuclear factor ${\kappa}B$ (RANK) and its ligand RANKL are key regulators of osteoclastogenesis and well-recognized targets in developing treatments for bone disorders associated with excessive bone resorption, such as osteoporosis. Our previous work on the structure of the RANK-RANKL complex revealed that Loop3 of RANK, specifically the non-canonical disulfide bond at the tip, performs a crucial role in specific recognition of RANKL. It also demonstrated that peptide mimics of Loop3 were capable of interfering with the function of RANKL in osteoclastogenesis. Here, we reported the structure-based design of a smaller peptide with enhanced inhibitory efficiency. The kinetic analysis and osteoclast differentiation assay showed that in addition to the sharp turn induced by the disulfide bond, two consecutive arginine residues were also important for binding to RANKL and inhibiting osteoclastogenesis. Docking and molecular dynamics simulations proposed the binding mode of the peptide to the RANKL trimer, showing that the arginine residues provide electrostatic interactions with RANKL and contribute to stabilizing the complex. These findings provided useful information for the rational design of therapeutics for bone diseases associated with RANK/RANKL function.

• Journal of Integrative Natural Science
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• v.8 no.1
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• pp.40-47
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• 2015

Glycogen synthase kinase 3 (GSK-3) is a serine/threonine protein kinase that has recently emerged as a promising target in drug discovery. It is involved in multiple cellular processes and associated with the pathogenesis of several diseases. A three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis was performed on a series of GSK-3 inhibitors to understand the structural basis for inhibitory activity. Comparative molecular field analysis (CoMFA) method was used to derive 3D-QSAR models. A reliable CoMFA model was developed using ligand-based alignment scheme. The model produced statistically acceptable results with a cross-validated correlation coefficient ($q^2$) of 0.594 and a non-cross-validated correlation coefficient ($r^2$) of 0.943. Robustness of the model was checked by bootstrapping and progressive scrambling analysis. This study could assist in the design of novel compounds with enhanced GSK-3 inhibitory activity.

• Journal of Integrative Natural Science
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• v.8 no.1
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• pp.1-12
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• 2015

CRTh2 receptor is an important mediator of the inflammatory effects and act as beneficial target for the treatment of asthma, COPD, allergic rhinitis and atopic dermatitis. In the present work, Hologram QSAR studies were conducted on a series of 50 training set CRTh2 antagonists (2-(2-(benzylthio)-1H-benzo[d]imidazol-1-yl acetic acids). The best HQSAR model was obtained using atoms, bonds, connections and donor/acceptor as fragment distinction parameter using hologram length 257 and 6 components with fragment size of minimum 7 and maximum 10. Significant cross-validated correlation coefficient ($q^2=0.786$) and non cross-validated correlation coefficients ($r^2=0.954$) were obtained. The model was then used to evaluate the 15 external test compounds which are not included in the training set and the predicted values were in good agreement with the experimental results ($r^2_{pred}=0.739$). Contribution map show that presence of C ring and its substituents makes big contributions for activities. The HQSAR model and analysis from the contribution map could be useful for further design of novel structurally related CRTh2 antagonists.

• Bulletin of the Korean Chemical Society
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• v.28 no.7
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• pp.1141-1150
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• 2007

Molecular modeling study has been performed to assist in the design of PTP1B inhibitors using FlexX. FlexX dockings with 19 test ligands, whose structures have been determined by X-ray crystallography, were successful in reproducing the experimental conformations within the protein. An increase in biological activity is observed as hydrophobic character of formylchromone derivatives increases. Most ligands bind to the activesite regions of the protein successfully in two different score runs. The Drug score run gave better results than the FlexX score run based on the score, rank, binding modes and bond distance of docked structures. Consensus values from the CScore scoring function are between 3 and 5, suggesting that the scoring scheme is reliable. All formylchromone inhibitors considered in this work show unidirectional binding modes in the active site pocket, which is contrary to the bidirectional X-ray results by Malamas et al. and amino acid residues responsible for such orientation are identified to help further development of the inhibitors.

• BMB Reports
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• v.41 no.1
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• pp.48-54
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• 2008

PM0188 is a newly identified sialyltransferase from P. multocida which transfers sialic acid from cytidine 5'-monophosphonuraminic acid (CMP-NeuAc) to an acceptor sugar. Although sialyltransferases are involved in important biological functions like cell-cell recognition, cell differentiation and receptor-ligand interactions, little is known about their catalytic mechanism. Here, we report the X-ray crystal structures of PM0188 in the presence of an acceptor sugar and a donor sugar analogue, revealing the precise mechanism of sialic acid transfer. Site-directed mutagenesis, kinetic assays, and structural analysis show that Asp141, His311, Glu338, Ser355 and Ser356 are important catalytic residues; Asp141 is especially crucial as it acts as a general base. These complex structures provide insights into the mechanism of sialyltransferases and the structure-based design of specific inhibitors.

• Bulletin of the Korean Chemical Society
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• v.33 no.12
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• pp.4084-4092
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• 2012

Theoretical calculations based on density functional theory (DFT) were performed to study the substituent effect on the geometric and electronic structures as well as the biological behavior of technetium-99m-labeled diphosphonate complexes. Optimized structures of these complexes are surrounded by six ligands in an octahedral environment with three unpaired 4d electrons ($d^3$ state) and the optimized geometry of $^{99m}Tc$-MDP agrees with experimental data. With the increase of electron-donating substituent or tether between phosphate groups, the energy gap between frontier orbitals increases and the probability of non-radiative deactivation via d-d electron transfer decreases. The charge distribution reflects a significant ligand-to-metal electron donation. Based on the calculated geometric and electronic structures and biologic properties of $^{99m}Tc$-diphosphonate complexes, several structure-activity relationships (SARs) were established. These results may be instructive for the design and synthesis of novel $^{99m}Tc$-diphosphonate bone imaging agent and other $^{99m}Tc$-based radiopharmaceuticals.

• Bulletin of the Korean Chemical Society
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• v.31 no.5
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• pp.1355-1360
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• 2010

In order to search new inhibitors against farnesyl protein transferase (FPTase), a series of 2,3-bis-benzylidenesuccinaldehyde derivatives (1-29) were synthesized and their inhibition activities ($pI_{50}$) against FPTase were measured. From based on the reported results that the inhibitory activities of dimers 2,3-bis-benzylidenesuccinaldehydes were higher than those of monomers cinnamaldehydes, 3D-QSARs on FPTase inhibitory activities of the dimers (1-29) were studied quantitatively using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) methods. The statistical qualities of the optimized CoMFA model II ($r^2{_{cv.}}$= 0.693 and $r^2{_{ncv.}}$= 0.974) was higher than those of the CoMSIA model II ($r^2{_{cv.}}$ = 0.484 and $r^2{_{ncv.}}$ = 0.928). The dependence of CoMFA models on chance correlations was evaluated with progressive scrambling analyses. And the inhibitory activity exhibited a strong correlation with steric factors of the substrate molecules. Therefore, from the results of graphical analyses on the contour maps and of predicted higher inhibitory active compounds, it is suggested that the structural distinctions and descriptors that contribute to inhibitory activities ($pI_{50}$) against FPTase will be able to applied new inhibitor design.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2009.06a
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• pp.223-223
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• 2009

In this paper, designed and simulated Power Splitter (PS) integrated Mach-Zehnder interferometer (MZI) based planar type optical waveguide devices (which is called here a PS-MZI). The PS-MZI optical waveguide sensor was preceded by a Y-junction, which splits the input power between the sensor, and a reference branch, to minimize the effect of optical power variations. The PS-MZI optical waveguide sensor induced changing phases of the incident beam, which had fallen upon the waveguide through computer simulation, according to the small changes in the index of refraction, thus beam intensity was changed. The waveguide were optimized at a wavelength of 1550 nm and fabricated according to the design rule of 0.45 delta%, which is the difference of refractive index between the core and clad. The fabrication of PS-MZI optical waveguide sensor was performed by a conventional planar lightwave circuit (PLC) fabrication process. The PS-MZI optical waveguide that was fabricated to be applied as a biosensor revealed a low insertion loss and a low polarization-dependent loss. After having etched the over-clad at the sensor part in the MZI optical waveguide that was fabricated, Ti deposition was made on the adhesion layer, and then Au thin-film deposition was carried out thereon. In addition, its optical properties were measured by having changed the index of refraction oil at the sensing part of the MZI. To apply the planar type PS-MZI optical waveguide as a biosensor, a detection test for Staphylococcus aureus was conducted according to changes in concentration, having adopted Ti-alkoxide as ligand. The detection result of the S. aureus by the PS-MZI optical waveguide sensor was possible to the level of $10^1$ CFU/ml.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1993.04a
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• pp.73-73
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• 1993

As part of a research program to develope 3rd generation anti tumor platinum complexes, a series of platinum complexes which have 4, 5-bis-(aminomethyl)- 1, 3-dioxolane derivatives as bidenate amine ligands, represented by the general structual formula was prepared. The R$_1$ and/or R$_2$ substituents in this series of platinum complexes can be hydrogen. alkyl, of jointly formed cyclohexane. Two Xs can be a bidenate leaving ligand such as 1, 1-cyclobutanedicarboxylate, malonate, dimethylmalonate, ethylmalonate, glycolate, L-lactate, or N-methyliminodiacetate. From based on the pharmacological and toxicological studies, we have chosen SKI 2053R, cis-malonato[(4R, 5R)-4, 5-bis(aminomethyl)-2-isopropyl-1, 3-dioxolane] platinum(II) complex (NSC D644591) as a candidate for clinical evaluation. The antitumor activity of a new anti tumor platinum complex, cis-malonato [(4R, 5R)-4, 5-bis(aminomethyl)-2-isopropyl-1, 3-dioxolane] platinum(II) (SKI 2053R, NSC D644591), was compared with those of cisplatin and carboplatin using murine tumors. We evaluated three platinum complexes against L1210/CPR, a subline of L1210 leukemia resistant to cisplatin for their abilities to overcome tumor resistance to cisplatin. The in vitro cytotoxicity of SKI 2053R to L1210 cell line was 2.5-fold less potent thann that of cisplatin, and was 10-fold more cytotoxic than that of carboplatin. SKI 2053R retained similar cytotoxic effect and anti tumor activity to L1210/CPR cell line, like the cytotoxicity of SKI 2053R to L1210 cell line, while either cisplatin or carboplatin had not property to overcome the acquired cisplatin-resistance. SKI 2053R exhibited greater or comparable antitumor activity than cisplatin or carboplatin in murine tumor models.