• Journal of Integrative Natural Science
• /
• v.3 no.1
• /
• pp.49-53
• /
• 2010

Molecular docking is a critical event which mostly forms Van der waals complex in molecular recognition. Since the majority of developed drugs are small molecules, docking them into proteins has been a prime concern in drug discovery community. Since the binding pose space is too vast to cover completely, many search algorithms such as genetic algorithm, Monte Carlo, simulated annealing, distance geometry have been developed. Proper evaluation of the quality of binding is an essential problem. Scoring functions derived from force fields handle the ligand binding prediction with the use of potential energies and sometimes in combination with solvation and entropy contributions. Knowledge-based scoring functions are based on atom pair potentials derived from structural databases. Forces and potentials are collected from known protein-ligand complexes to get a score for their binding affinities (e.g. PME). Empirical scoring functions are derived from training sets of protein-ligand complexes with determined affinity data. Because non of any single scoring function performs generally better than others, some other approaches have been tried. Although numerous scoring functions have been developed to locate the correct binding poses, it still remains a major hurdle to derive an accurate scoring function for general targets. Recently, consensus scoring functions and target specific scoring functions have been studied to overcome the current limitations.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.25 no.6
• /
• pp.474-484
• /
• 1992

The stock identification of small yellow croaker. Pseudosciaena Polyactis from Mokpo area was carried out using molecular biological methods such as mt-DNA restriction fragment length polymorphism(RFLP) and the N-terminal fragment polymorphism of muscle actin obtained after protease digestion. The entire mt-DNA genomic size from the small yellow croaker at Mokpo area was estimated to be about $16\pm0.2$ Kb. Furthermore, fourteen restriction endonucleases revealed a total of 37 restriction sites to the mt-DNA molecule, however, eight of the fourteen enzymes showed a significant restriction site variation. Six of the enzymes examined produced a single restriction profile for all individuals surveyed, indicating that they don't react on the same mt-DNA obtained from small yellow croaker. The Staphylococcus aureus $V_8$ protease is able to cleave the muscle actin of small yellow croaker and to yield a N-terminal peptide of 26 and 16 KDa, respectively.

• Tuberculosis and Respiratory Diseases
• /
• v.85 no.2
• /
• pp.147-154
• /
• 2022

Background: The expression of calcium signaling pathway molecules is altered in various carcinomas, which are related to the proliferation and altered characteristics of cancer cells. However, changes in calcium signaling in anti-cancer drug-resistant cells (bearing a T790M mutation in epidermal growth factor receptor [EGFR]) remain unclear. Methods: Afatinib-mediated changes in the level of store-operated Ca²⁺ entry (SOCE)-related proteins and intracellular Ca²⁺ level in non-small cell lung cancer cells with T790M mutation in the EGFR gene were analyzed using western blot and ratiometric assays, respectively. Afatinib-mediated autophagic flux was evaluated by measuring the cleavage of LC3B-II. Flow cytometry and cell proliferation assays were conducted to assess cell apoptosis and proliferation. Results: The levels of SOCE-mediating proteins (ORAI calcium release-activated calcium modulator 1 [ORAI1], stromal interaction molecule 1 [STIM1], and sarco/endoplasmic reticulum Ca²⁺ ATPase [SERCA2]) decreased after afatinib treatment in non-small cell lung cancer cells, whereas the levels of SOCE-related proteins did not change in gefitinib-resistant non-small cell lung cancer cells (PC-9/GR; bearing a T790M mutation in EGFR). Notably, the expression level of SOCE-related proteins in PC-9/GR cells was reduced also responding to afatinib in the absence of extracellular Ca²⁺. Moreover, extracellular Ca²⁺ influx through the SOCE was significantly reduced in PC-9 cells pre-treated with afatinib than in the control group. Additionally, afatinib was found to decrease the level of SOCE-related proteins through autophagic degradation, and the proliferation of PC-9GR cells was significantly inhibited by a lack of extracellular Ca²⁺. Conclusion: Extracellular Ca²⁺ plays important role in afatinib-mediated autophagic degradation of SOCE-related proteins in cells with T790M mutation in the EGFR gene and extracellular Ca²⁺ is essential for determining anti-cancer drug efficacy.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2016.02a
• /
• pp.432.2-432.2
• /
• 2016

A new A-D-A type (Acceptor-Donor-Acceptor) conjugated based on pyridine-borane complex (Donor), non-boron fluorine (Donor) and 2,5-bis(alkyl)-3,6-di(thiophen-2-yl)pyrrolo[3,4-c]pyrrole-1,4(2H,5H)-dione (DPP) (Acceptor) were designed and synthesized via Pd-catalyzed Suzuki cross-coupling reaction. The synthesized boron based complex exhibited high electron affinity, which indicates deep HOMO energy levels and good visible absorption led to their use as donors in BHJ (bulk heterojunction) solar cells. Inverted devices were fabricated, reaching open-circuit voltage as high as 0.91eV. To probe structure-property relationship and search for design principle, we have synthesized pyridine-boron based electron donating small molecules. In this study, we report a new synthetic approach, molecular structure, charge carrier mobility and morphology of blended film and their correlation with the photovoltaic J-V characteristics in details.

• Parasites, Hosts and Diseases
• /
• v.52 no.4
• /
• pp.439-441
• /
• 2014

Toxoplasma gondii is the causative agent of toxoplasmosis with symptoms of congenital neurological and ocular diseases and acquired lymphadenitis, retinochoroiditis, and meningoencephalitis. Small molecules which block the activity of protein kinases were tested in in vitro culture of T. gondii to find new therapeutic drugs of safer and more effective than the combined administration of pyrimethamine and sulfadoxine that sometimes provoke lethal Stevens-Johnson syndrome. Among them, Gefitinib and Crizotinib inhibited intracellular growth of T. gondii in HeLa cells by counting the number of T. gondii per parasitophorous vacuolar membrane whereas Sunitinib did not. Gefitinib inhibited the growth of T. gondii in a dose-dependent manner over $5{\mu}M$ up to the tolerable concentration of HeLa cells and halted the division of the parasite immediately from the time point of treatment. Gefitinib inhibition suggests that tyrosine kinases of EGFR family or other homologous kinases of the parasite itself may be the target to cause the block of T. gondii growth.

• Mass Spectrometry Letters
• /
• v.6 no.3
• /
• pp.65-70
• /
• 2015

N-Alkyl/benzyl substituted isatin derivatives are intermediates and synthetic precursors for the preparation of biological active heterocycles. N-alkyl/benzyl isatins have showed various biological activities, such as cytotoxicity, antiviral, caspase inhibition, cannabinoid receptor 2 agonists for the treatment of neuropathic pain, etc. In this study, N-alkyl/benzyl isatin derivatives were synthesized from isatin and alkyl/benzyl halides in presence of K₂CO₃ in DMF and excellent to quantitative yields (~95%) were obtained. Isatins and benzyl-isatins were condensed with fluorescein hydrazide to form fluorescein hydrazone. All the compounds were subjected to their fragmentation behavior study using LC/MSⁿ. N-Alkyl substituted isatin derivatives fragmented at nitrogen-carbon (N-C) bond, hence gave daughter ion as [RN+H]⁺. Whereas, N-benzyl substituted isatin derivatives fragmented at carbon-carbon (C-C) bond of alkyl chain which linked with nitrogen molecules, therefore gave N-methyl fragments [RNCH₂]⁺. This study demonstrated that, isatin moiety present in a small/large molecule or in a matrix of reaction mixture with/without N-alkyl/benzyl substituents can be identified by mass spectroscopic fragmentation behavior study.

• YAKHAK HOEJI
• /
• v.60 no.3
• /
• pp.135-140
• /
• 2016

Heat shock protein 90 (Hsp90) is a ubiquitous molecular chaperone, which is associated with stabilization of many oncogenic proteins for cancer cell survival. Hsp90 is overexpressed 2-10 fold higher in cancer cells than normal cells. Due to its potential to simultaneously disable multiple signaling pathway, Hsp90 has been identified as a validated target for cancer therapy. Accordingly, we designed and synthesized 2',4'-dimethoxychalcone derivatives to inhibit Hsp90 chaperone function. Among 2',4'-dimethoxychalcone derivatives, we found that compound 1g disrupted Hsp90 chaperoning function and impaired the growth of cancer cells. These findings indicated that 1g could serve a potential lead compound to target Hsp90 in cancer chemotherapy.

• Journal of Integrative Natural Science
• /
• v.5 no.1
• /
• pp.32-37
• /
• 2012

Chemokine receptor antagonists have potential applications in field of drug discovery. Although the chemokine receptors are G-protein-coupled receptors, their cognate ligands are small proteins (8 to 12 kDa), and so inhibiting the ligand/receptor interaction has been challenging. The application of structure-based in-silico methods to drug discovery is still considered a major challenge, especially when the x-ray structure of the target protein is unknown. Such is the case with human CCR2 and CCR5, the most important members of the chemokine receptor family and also a potential drug target. Herein, we review the success stories of combined receptor modeling/mutagenesis approach to probe the allosteric nature of chemokine receptor binding by small molecule antagonists for CCR2 and CCR5 using Rhodopsin as template. We also urged the importance of recently available ${\beta}2$-andrenergic receptor as an alternate template to guide mutagenesis. The results demonstrate the usefulness and robustness of in-silico 3D models. These models could also be useful for the design of novel and potent CCR2 and CCR5 antagonists using structure based drug design.

• Journal of Powder Materials
• /
• v.30 no.2
• /
• pp.156-168
• /
• 2023

The semiconductor industry faces physical limitations due to its top-down manufacturing processes. High cost of EUV equipment, time loss during tens or hundreds of photolithography steps, overlay, etch process errors, and contamination issues owing to photolithography still exist and may become more serious with the miniaturization of semiconductor devices. Therefore, a bottom-up approach is required to overcome these issues. The key technology that enables bottom-up semiconductor manufacturing is area-selective atomic layer deposition (ASALD). Here, various ASALD processes for elemental metals, such as Co, Cu, Ir, Ni, Pt, and Ru, are reviewed. Surface treatments using chemical species, such as self-assembled monolayers and small-molecule inhibitors, to control the hydrophilicity of the surface have been introduced. Finally, we discuss the future applications of metal ASALD processes.

• IMMUNE NETWORK
• /
• v.16 no.3
• /
• pp.183-188
• /
• 2016

Sirtuin family members with lysine deacetylase activity are known to play an important role in anti-aging and longevity. Cellular senescence is one of the hallmarks of aging, and downregulation of sirtuin is reported to induce premature senescence. In this study, we investigated the effects of small-molecule sirtuin inhibitors on cellular senescence. Various small molecules such as tenovin-1 and EX527 were employed for direct sirtuin activity inhibition. U251, SNB-75, and U87MG glioblastoma cells treated with sirtuin inhibitors exhibited phenotypes with nuclear enlargement. Furthermore, treatment of rat primary astrocytes with tenovin-1 also increased the size of the nucleus. The activity of senescence-associated β-galactosidase, a marker of cellular senescence, was induced by tenovin-1 and EX527 treatment in U87MG glioblastoma cells. Consistent with the senescent phenotype, treatment with tenovin-1 increased p53 expression in U87MG cells. This study demonstrated the senescence-inducing effect of sirtuin inhibitors, which are potentially useful tools for senescence research.