• Journal of Microbiology and Biotechnology
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• v.16 no.5
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• pp.651-660
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• 2006

Natural products are a rich source of biologically active small molecules and a fertile area for lead discovery of new drugs [10, 52]. For instance, 5% of the 1,031 new chemical entities approved as drugs by the US Food and Drug Administration (FDA) were natural products between 1981 and 2002, and another 23% were natural product-derived molecules [53]. These molecules have evolved through millions of years of natural selection to interact with biomolecules in the cells or organisms and offer unrivaled chemical and structural diversity [14, 37]. Nonetheless, a large percentage of nature remains unexplored, in particular, in the marine and microbial environments. Therefore, natural products are still major valuable sources of innovative therapeutic agents for human diseases. However, even when a natural product is found to exhibit biological activity, the cellular target and mode of action of the compound are mostly mysterious. This is also true of many natural products that are currently under clinical trials or have already been approved as clinical drugs [11]. The lack of information on a definitive cellular target for a biologically active natural product prevents the rational design and development of more potent therapeutics. Therefore, there is a great need for new techniques to expedite the rapid identification and validation of cellular targets for biologically active natural products. Chemical genomics is a new integrated research engine toward functional studies of genome and drug discovery [40, 69]. The identification and validation of cellular receptors of biologically active small molecules is one of the key goals of the discipline. This eventually facilitates subsequent rational drug design, and provides valuable information on the receptors in cellular processes. Indeed, several biologically crucial proteins have already been identified as targets for natural products using chemical genomics approach (Table 1). Herein, the representative case studies of chemical genomics using natural products derived from microbes, marine sources, and plants will be introduced.

• Korean Journal of Clinical Pharmacy
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• v.22 no.1
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• pp.21-29
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• 2012

Modern biologics are biotechnology-derived therapeutics, including recombinant therapeutic proteins like monoclonal antibodies, cytokines and tissue growth factors. Although the pharmacokinetics of therapeutic biologics should be evaluated based on the same general principles as small molecules, careful considerations should be given to bioanalytics and pharmacokinetics when designing pharmacokinetic studies of biologics during their drug development, due to their different physicochemical properties compared with small molecules. The aim of this study was to develop a draft guidance on pharmacokinetic studies of therapeutic biologics in clinical studies. All the elements outlined in the current Food and Drug Administration (FDA), European Medicinal Agency (EMEA), and International Conference on Harmonisation (ICH) guidelines and regulations, and the related literatures previously published were searched and evaluated. In this draft guidance, the specific problems related to the pharmacokinetics of therapeutic biologics that need special consideration during drug development process were addressed, and differences in pharmacokinetic characteristics between biologics and small molecules affecting the content of the development programme were presented.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.9
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• pp.3759-3765
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• 2015

Background: Approaches in disruption of MDM2-p53 interactions have now emerged as an important therapeutic strategy in resurrecting wild type p53 functional status. The present study highlights virtual screening strategies in identification of high affinity small molecule non-peptidic inhibitors. Nutlin3A and RG7112 belonging to compound class of Cis-imidazoline, MI219 of Spiro-oxindole class and Benzodiazepine derived TDP 665759 served as query small molecules for similarity search with a threshold of 95%. The query molecules and the similar molecules corresponding to each query were docked at the transactivation binding cleft of MDM2 protein. Aided by MolDock algorithm, high affinity compound against MDM2 was retrieved. Patch Dock supervised Protein-Protein interactions were established between MDM2 and ligand (query and similar) bound and free states of p53. Compounds with PubCid 68870345, 77819398, 71132874, and 11952782 respectively structurally similar to Nutlin3A, RG7112, Mi219 and TDP 665759 demonstrated higher affinity to MDM2 in comparison to their parent compounds. Evident from the protein-protein interaction studies, all the similar compounds except for 77819398 (similar to RG 7112) showed appreciable inhibitory potential. Of particular relevance, compound 68870345 akin to Nutlin 3A had highest inhibitory potential that respectively showed 1.3, 1.2, 1.16 and 1.26 folds higher inhibitory potential than Nutilin 3A, MI 219, RG 7112 and TDP 1665759. Compound 68870345 was further mapped for structure based pharamacophoric features. In the study, we report Cis-imidazoline derivative compound; Pubcid: 68870345 to have highest inhibitory potential in blocking MDM2-p53 interactions hitherto discovered.

• Molecules and Cells
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• v.43 no.6
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• pp.517-529
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• 2020

Carboxyl-terminal binding proteins (CtBPs) are transcription regulators that control gene expression in multiple cellular processes. Our recent findings indicated that overexpression of CtBP2 caused the repression of multiple bone development and differentiation genes, resulting in atrophic nonunion. Therefore, disrupting the CtBP2-associated transcriptional complex with small molecules may be an effective strategy to prevent nonunion. In the present study, we developed an in vitro screening system in yeast cells to identify small molecules capable of disrupting the CtBP2-p300 interaction. Herein, we focus our studies on revealing the in vitro and in vivo effects of a small molecule NSM00158, which showed the strongest inhibition of the CtBP2-p300 interaction in vitro. Our results indicated that NSM00158 could specifically disrupt CtBP2 function and cause the disassociation of the CtBP2-p300-Runx2 complex. The impairment of this complex led to failed binding of Runx2 to its downstream targets, causing their upregulation. Using a mouse fracture model, we evaluated the in vivo effect of NSM00158 on preventing nonunion. Consistent with the in vitro results, the NSM00158 treatment resulted in the upregulation of Runx2 downstream targets. Importantly, we found that the administration of NSM00158 could prevent the occurrence of nonunion. Our results suggest that NSM00158 represents a new potential compound to prevent the occurrence of nonunion by disrupting CtBP2 function and impairing the assembly of the CtBP2-p300-Runx2 transcriptional complex.

• Proceedings of the Korean Vacuum Society Conference
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• 2013.08a
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• pp.245.2-245.2
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• 2013

Solution processed organic photovoltaic devices have relatively less attention compared to polymer photovoltaic devices even though they have high possibility to be developed because they have both advantages of polymer and organic, such as solution processable, no synthetic batch dependence of photovoltaic performance, high purity and high charge carrier mobility as well as relatively high efficiency (~7%). In addition, solution processed organic photovoltaic devices have an advantage of easiness to study the relationship between the molecular structure and photovoltaic performance due to its simple structure. In this work, five isoindigo based low band gap donor-acceptor-donor (D-A-D) small molecules with different electron donating strength were synthesized for investigating the relationship between the molecular structure and photovoltaic performance, especially, investigating the effects of different electron donating effect of donor group in isoindigo backbone to photovoltaic device performance. The variation of electron donating strength of donor group strongly affected the optical, thermal, electrochemical and photovoltaic device performances of isoindigo organic materials. The highest power conversion efficiency of ~3.2% was realized in bulk heterojuction photovoltaic device consisted of the ID3T as donor and PC70BM as acceptor. This work demonstrates the great potential of isoindigo moieties as electron deficient units as well as guideline for synthesis of donor-acceptor-donor (D-A-D) small molecules for realizing highly efficient solution processed organic photovoltaic devices.

• Journal of Life Science
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• v.12 no.1
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• pp.14-18
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• 2002

Subpopulations of nucleotides that bind specifically to a variety of proteins have been isolated from a population of random sequence RNA/DNA molecules. Roughly one in $10^{13}$ random sequence RNA/DNA molecules folds in such a way as to create a specific binding site for small ligands. Since the development of in vitro selection procedure, more than 50 nucleic acid ligands (aptamers) have been isolated. These molecules are very useful for the study of molecular recognition between nucleic acid and protein/organic compound. In addition to these basic studies this method gives us a dream to produce new drugs against several diseases. We focused on several aptamers which specifically binds to trypsin-like serine proteases (thrombin, human neutrophil elastase, activated protein C and NS3 protease of human hepatitis C virus) and want to introduce their structural characteristics and some functions.

• Journal of Integrative Natural Science
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• v.3 no.3
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• pp.162-167
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• 2010

A pseudoreceptor combines structure-based and ligand-based techniques to represent a unifying concept for both receptor mapping and ligand matching. In this molecular modeling approach, there are opportunities to construct the pseudoreceptor models using a set of small molecules. To build a reliable pseudoreceptor model, we need a set of ligand molecules with known affinity (biological activity) to generate 3D bioactive conformation for each of these ligand molecules. Several software packages are available to generate a pseudoreceptor model and this can provide an entry point for structure based drug discovery in cases where receptor structure information is not available. In this review, we presented the concept of pseudoreceptor, as well as discussed about various software packages available to generate a pseudoreceptor model.

• Bulletin of the Korean Chemical Society
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• v.24 no.11
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• pp.1671-1674
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• 2003

The effects of amine donors ($a:NH_2,\;b:NMe_2,\;c:NMePh,\;d:NPh_2$) and conjugation length on the molecular hyperpolarizabilities of a series of dipolar molecules have been theoretically investigated by using CPHF/6-31G method. The first hyperpolarizabilities (${\beta}$) of p-nitrobenzene derivatives increase with the donor in the order, $NH_2\;<\;NMe_2\;<\;NMePh\;<\;NPh_2$, whereas slightly different order is observed in more conjugated derivatives, i.e., $NH_2\;<\;NPh_2\;<\;NMe_2\;<\;NMePh$. The result has been attributed to the extent of charge transfer and torsion angle. Moreover, the results show that "non-traditional" ${\pi}$-conjugation effect exists in small compounds and decreases as the conjugation length between donor and acceptor increases.

• Bulletin of the Korean Chemical Society
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• v.16 no.9
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• pp.850-858
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• 1995

Golden-rule like formulas have been used without theoretical basis to calculate the resonance lifetimes and final state distributions in the predissociation of van der Waals molecules. Here we present their theoretical basis by extending Fano's configuration interaction theory. Such extensions were independently done by Farnonux [Phys. Rev. 1985, 25, 287] but his work, unfortunately, was not well known outside some small group of people in the field of Auger spectroscopy. Since my extension is easier to understand than his, it is presented here. Theoretical basis of Golden rule like formulas used in the predissociation of van der Waals molecules was obtained by using such extensions. Factors responsible for several aspects of predissociation dynamics, such as variations of dynamics as functions of resonance lifetimes, or variations in shapes of final quantum state distributions of photofragments around resonances, were identified. Parameters, or dynamical information that could be obtained from the measurement of partial cross section spectra were accordingly determined. The theory was applied to the vibrational predissociation of triatomic van der Waals molecules and its result was compared with those calculated by close-coupling method. An example where Golden-rule like expression fails and branching ratios vary greatly around a resonance was considered.

• Journal of Embryo Transfer
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• v.27 no.3
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• pp.171-174
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• 2012

Various small molecules can be used to control major signaling pathways to enhance stemness and inhibit differentiation in murine embryonic stem cell (mESC) culture. Small molecules inhibiting the fibroblast growth factor (FGF)/ERK pathway can preserve pluripotent cells from stimulation of differentiation. In this study, we aimed to evaluate the effect of pluripotin (SC-1), an inhibitor of the FGF/ERK pathway, on the colony formation of outgrowing presumptive mESCs. After plating the zona pellucida-free blastocyst on the feeder layer, attached cell clumps was cultured with SC-1 until the endpoint of the experiment at passage 10. In this experiment, when the number of colonies was counted at passage 3, SC-1-treated group showed 3.4 fold more mESC colonies when compared with control group. However, after passage 4, there was no stimulating effect of SC-1 on the colony formation. In conclusion, SC-1 treatment can be used to promote mESC generation by increasing the number of early mESC colonies.