• Journal of Integrative Natural Science
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• v.6 no.2
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• pp.100-103
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• 2013

Using computational approaches we can dock small molecules into the structures of Macromolecular targets and then score their potential complementarity to binding sites is widely used in hit identification and lead optimization techniques. This review seeks to provide the application of docking in structure-based drug design (binding mode prediction, Lead Identification and Lead optimization), and also discussed how to manage errors in docking methodology in order to overcome certain limitations of docking and scoring algorithm.

• Proceedings of the Korean Magnetic Resonance Society Conference
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• 1999.02a
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• pp.6-6
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• 1999

• Journal of Integrative Natural Science
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• v.7 no.2
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• pp.75-78
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• 2014

Computer-aided drug design uses computational chemistry to discover, enhance, or study drugs and related biologically active molecules. It is now proved to be effective in reducing costs and speeding up drug discovery. In this short review, we discussed on the importance of combining molecular docking and molecular dynamics simulation methodologies. We also reviewed the importance of protein flexibility, refinement of docked complexes using molecular dynamics and the use of free energy calculations for the calculation of accurate binding energies has been reviewed.

• Journal of Microbiology and Biotechnology
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• v.10 no.5
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• pp.733-736
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• 2000

Since pathogens resistant against vancomycin occur rapidly, the development of a new drug is needed. To make a new drug based on a rational drug design, the structural study of vancomycin is necessary. Accordingly, this study reports on a comparison of the solution structure of vancomycin determined by NMR spectroscopy, which was performed in the present work, with the X-ray crystallographic structure previously deposited in the Protein Data Bank (PDB).

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.2
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• pp.797-802
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• 2014

We screened a small molecular library that was designed and independently synthesized in vitro and found a new drug (MY-03-01) that is active against ovarian cancer. We established that MY-03-01 effectively inhibited SKOV-3 cell survival in a dose-dependent manner, based on cell viability rates, and that it not only induced SKOV-3 apoptosis by itself, but also did so synergistically with paclitaxel. Secondly, when MY-03-01 was applied at $40{\mu}M$, its hemolytic activity was less than 10%, compared with the control, and there was almost no damage to nor mal cells at this concentration. In addition, we used DAPI staining and flow cytometry to show that MY-03-01 could significantly induce apoptosis of SKOV-3 cells. Finally, we found that MY-03-01 likely induced SKOV-3 apoptosis by activating caspase3 and caspase9 through the mitochondrial pathway.

• Journal of Microbiology and Biotechnology
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• v.27 no.5
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• pp.878-895
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• 2017

Phosphorylation, a critical mechanism in biological systems, is estimated to be indispensable for about 30% of key biological activities, such as cell cycle progression, migration, and division. It is synergistically balanced by kinases and phosphatases, and any deviation from this balance leads to disease conditions. Pathway or biological activity-based abnormalities in phosphorylation and the type of involved phosphatase influence the outcome, and cause diverse diseases ranging from diabetes, rheumatoid arthritis, and numerous cancers. Protein tyrosine phosphatases (PTPs) are of prime importance in the process of dephosphorylation and catalyze several biological functions. Abnormal PTP activities are reported to result in several human diseases. Consequently, there is an increased demand for potential PTP inhibitory small molecules. Several strategies in structure-based drug designing techniques for potential inhibitory small molecules of PTPs have been explored along with traditional drug designing methods in order to overcome the hurdles in PTP inhibitor discovery. In this review, we discuss druggable PTPs and structure-based virtual screening efforts for successful PTP inhibitor design.

• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.2006-2010
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• 2013

Leukocyte common antigen-related phosphatase (LAR) has been considered a promising target for the development of therapeutics for neurological diseases. Here, we report the first example for a successful application of the structure-based virtual screening to identify the novel small-molecule LAR inhibitors. Five of these inhibitors revealed micromolar inhibitory activities with the associated $IC_{50}$ values ranging from 2 to 6 ${\mu}M$. Because the newly identified inhibitors were also screened for having desirable physicochemical properties as a drug candidate, they may serve as a starting point of the structure-activity relationship study to optimize the medical efficacy. Structural features relevant to the stabilization of the new inhibitors in the active site of LAR are discussed in detail.

• Bulletin of the Korean Chemical Society
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• v.30 no.6
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• pp.1313-1316
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• 2009

Cdc25 phosphatases have been considered as attractive drug targets for anticancer therapy due to the correlation of their overexpression with a wide variety of cancers. We have been able to identify five novel Cdc25 phosphatase inhibitors with micromolar activity by means of a structure-based de novo design method with a known inhibitor scaffold. Because the newly discovered inhibitors are structurally diverse and have desirable physicochemical properties as a drug candidate, they deserve further investigation as anticancer drugs. The differences in binding modes of the identified inhibitors in the active sites of Cdc25A and B are addressed in detail.

• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4397-4402
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• 2011

The NF-${\kappa}B$ system of transcription factors plays a crucial role in inflammatory diseases, making it an important drug target. We combined quantitative structure activity relationships for predicting the activity of new compounds and quantitative dynamic models for the NF-${\kappa}B$ network with intracellular concentration models. GFA-MLR QSAR analysis was employed to determine the optimal QSAR equation. To validate the predictability of the $IKK{\beta}$ QSAR model for an external set of inhibitors, a set of ordinary differential equations and mass action kinetics were used for modeling the NF-${\kappa}B$ dynamic system. The reaction parameters were obtained from previously reported research. In the IKKb QSAR model, good cross-validated $q^2$ (0.782) and conventional $r^2$ (0.808) values demonstrated the correlation between the descriptors and each of their activities and reliably predicted the $IKK{\beta}$ activities. Using a developed simulation model of the NF-${\kappa}B$ signaling pathway, we demonstrated differences in $I{\kappa}B$ mRNA expression between normal and different inhibitory states. When the inhibition efficiency increased, inhibitor 1 (PS-1145) led to long-term oscillations. The combined computational modeling and NF-${\kappa}B$ dynamic simulations can be used to understand the inhibition mechanisms and thereby result in the design of mechanism-based inhibitors.

• Archives of Pharmacal Research
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• v.28 no.2
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• pp.142-150
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• 2005

The synthesis and structure-activity relationships of a novel series of substituted quercetins that activates peroxisome proliferator-activated receptor gamma ($PPAR{\gamma}$) are reported. The $PPAR{\gamma}$ agonistic activity of the most potent compound in this series is comparable to that of the thiazolidinedione-based antidiabetic drugs currently in clinical use.