• Bulletin of the Korean Chemical Society
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• 제21권11호
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• pp.1119-1124
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• 2000

$\beta-Cyclodextrin$ derivatives connected with diaza-18-crown-6 through flexible bridges (R) at the secondary face 1a-c (1a: R = $-(CH_2)4-;$ 1b: R = $-CH_2CH_2OCH_2CH2-;$ 1c: R = $-(CH_2)8-)$ have been prepared. The associa tion constants of 1 with (2-naphthoxy)alkylammonium ions (2a: alkyl = butyl; 2b: alkyl = octyl) were determined by induced circular dichroism (ICD) spectroscopy and it was found that the derivatization of $\beta-CD$ with the diazacrown resulted in enhanced binding with 2, compared to the native $\beta-CD.$ ICD Characteristics of the host-guest complexes indicate that a part of the alkylammonium moiety of 2 is protruded from the secondary side of the $\beta-CD$ cavity, and the guest molecules 2a and 2b move to the secondary and primary side, respectively, to make the binding of the ammonium group with the diaza-18-crown-6 moiety more feasible. The energy accompanied by the relocation of the guest molecules inside $\beta-CD$ moiety is compensated by the interaction energy between the ammonium ion and diazacrown ether.

• Bulletin of the Korean Chemical Society
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• 제26권4호
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• pp.537-542
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• 2005

It was proposed that Ru(II)[(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine ([Ru(phen)$_2$DPPZ]$^{2+}$)complexes and 4',6-diamidino-2-phenylindole (DAPI) simultaneously bind to poly[d(A-T)$_2$] (Biophysics. J. 2003, 85, 3865). Förster type resonance energy transfer from excited DAPI to [Ru(phen)2DPPZ]$^{2+}$ complexes was observed. In this study, we synthesized $\Delta$- and $\wedge$-[Ru(phenanthroline)$_2$dipyrido[3,2-a:2’3’c]6-azaphenazine] ([Ru(phen)$_2$DPAPZ]$^{2+}$) at which the DNA intercalating ligand DPPZ was replaced and we studied its binding properties to poly[d(A-T)$_2$] in the presence and absence of DAPI using polarized spectroscopy and fluorescence techniques. All the spectroscopic properties of the [Ru(phen)$_2$DPAPZ]$^{2+}$-poly[d(A-T)$_2$] complex were the same in the presence and absence of DAPI that blocks the minor groove of polynucleotide, suggesting both $\Delta$- and $\wedge$-[Ru(phen)$_2$DPAPZ]$^{2+}$ complexes are located at the major groove of poly[d(A-T)2]. On the other hand, in contrast with [Ru(phen)$_2$DPPZ]$^{2+}$, both $\Delta$- and $\wedge$-[Ru(phen)$_2$DPAPZ]$^{2+}$ exhibited almost twice the efficiency in the fluorescence quenching of DAPI that binds at the minor groove of poly[d(A-T)$_2$]. This observation indicates that the efficiency of the Förster type resonance energy transfer can be controlled by a small change in the chemical structure of the intercalated ligand.

• Bulletin of the Korean Chemical Society
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• 제34권11호
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• pp.3327-3334
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• 2013

Infrared multiphoton dissociation (IRMPD) spectra of various protonated 1,2-diaminoethane-water clusters DAE-$H^+-(H_2O)_n$ (n = 1-6) were measured in the wavelength range of 3000-3800 $cm^{-1}$. The IRMPD spectra of the well separated ionic clusters were simulated by the MP2 method employing various basis sets. Comparison of the IRMPD spectra with the theory indicates that each cluster may exist as several low-lying conformers, and the sum spectra of the various conformers reveal almost one to one correspondence between theory and experiment. Free N-H and O-H stretches are observed in the ranges of 3400-3500 and 3600-3800 $cm^{-1}$, respectively. The $O-H{\cdots}N$ and $N-H{\cdots}O$ stretches are, however, observed in the broad region of 3000-3600 $cm^{-1}$. The theoretical calculations on DAE-$H^+-(H_2O)_n$ (n = 1-4) show gradual decrease of the average binding energy between DAE-$H^+$ and $H_2O$ as the cluster size increases, attaining the lowest value of 55 kJ/mol when n = 4. We found a low energy barrier of 21 kJ/mol to the isomerization converting the lowest energy cluster of DAE-$H^+-(H_2O)_n$ to the second lowest one.

• 방사선산업학회지
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• 제9권4호
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• pp.187-192
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• 2015

CD44 is a particular adhesion molecule and facilitates both cell-cell and cell-matrix interactions. In particular, splice variants of CD44 are particularly overexpressed in a large number of malignancies and carcinomas. In this study, the $^{177}Lu$-labelled CD44 targeting antibody was prepared and bioevaluated in vitro and in vivo. Anti-CD44 was immunoconjugated with the equivalent molar ratio of cysteine-based DTPA-NCS and radioimmunoconjugated with $^{177}Lu$ at room temperature within 15 minutes. The stability was tested in human serum. An in vitro study was carried out in HT-29 human colon cancer cell lines. For the biodistribution study $^{177}Lu$-labelled anti-CD44 was injected in xenograft mice. Anti-CD44 was immunoconjugated with cysteine-based DTPA-NCS and purified by a centricon filter system having a molecular cut-off of 50 kDa. Radioimmunoconjugation with $^{177}Lu$ was reacted for 15 min at room temperature. The radiolabeling yield was >99%, and it was stable in human serum without any fragmentation or degradation. The radioimmunoconjugate showed a high binding affinity on HT-29 colon cancer cell surfaces. In a biodistribution study, the tumor-to-blood ratio of the radioimmunoconjugate was 43 : 1 at 1 day post injection (p.i) in human colon cancer bearing mice. The anti-CD44 monoclonal antibody for the targeting of colon cancer was effectively radioimmunoconjugated with $^{177}Lu$. The in vitro high immunoactivity of this radioimmunoconjugate was determined by a cell binding assay. In addition, the antibody's tumor targeting ability was demonstrated with very high uptake in tumors. This radioimmunoconjugate is applicable to therapy in human colon cancer with highly expressed CD44.

• 방사선산업학회지
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• 제7권2_3호
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• pp.127-134
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• 2013

Bombesin receptors are overexpressed in many kinds of human tumors. In particular, the gastrin releasing peptide receptor (GRPR) which is also called bombesin receptor subtype 2, has been identified in prostate cancer. In the present study, we developed a bombesin antagonist-based $^{177}Lu$-labeled peptide, $^{177}Lu$-DOTA-$Ala(SO_3H)$-Aminooctanoyl-Gln-Trp-Ala-Val-N methyl Gly-His-Statine-Leu-$NH_2$ (DOTA-sBBNA). DOTA-sBBNA was prepared using a solid phase synthesis method. It was labeled with $^{177}Lu$ by a high radiolabeling yield (>98%), and its Log P value was -2.05. The radiolabeled peptide was highly stable in serum incubation at $37^{\circ}C$ for 48 hr. A competitive displacement of $^{125}I-[Tyr^4]$-Bombesin on the PC-3 human prostate carcinoma cells revealed that the $IC_{50}$ value of the peptide was 6.76 nM indicating a highly nanomolar binding affinity for GRPR. These results suggest that $^{177}Lu$-DOTA-sBBNA can be a potential candidate for targeting prostate cancer, and further studies to evaluate its biological characteristics are needed.

• 대한화학회지
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• 제56권1호
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• pp.34-46
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• 2012

Dopants and defects can be introduced as well as the intercalation of metals into single wall carbon nanotubes (SWCNTs) to modify their electronic and magnetic properties, thus significantly widening their application areas. Through spinpolarized density functional theory (DFT) calculations, we have systemically studied the following: (i) (10,0) and (5,5) SWCNT doped with nitrogen ($CN_xNT$), (ii) (10,0) and (5,5) SWCNT with pyridine-like defects (3NV-$CN_xNT$), and (iii) chemical functionalization of (10,0) and (5,5) 3NV-$CN_xNT$ with 12 different transition metals (TMs) (Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Pd, and Pt). Attention was done in searching for the most stable configurations, deformation, calculating the formation energies, and exploring the effects of the doping concentration of nitrogen and pyridine-like nitrogenated defects on the electronic properties of the nanotubes. Also, calculating the corresponding binding energies and effects of chemical functionalization of TMs on the electronic and magnetic properties of the nanotubes has been made. We found out that the electronic properties of SWCNT can be effectively modified in various ways, which are strongly dependent not only on the concentration of the adsorbed nitrogen but also to the configuration of the adsorbed nitrogen impurities, the pyridine-like nitrogenated defects, and the TMs absorbed; due to the strong interaction between the d orbitals of TMs and the p orbitals of N atoms, the binding strengths of TMs with the two 3NV-$CN_xNT$ are significantly enhanced when compared to the pure SWCNTs.

• 통합자연과학논문집
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• 제8권3호
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• pp.209-213
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• 2015

Influenza A virus (H1N1) causes and spreads infectious diseases and becomes a major health threat in humans. Among the subtypes of influenza virus, neuraminidase (NA) plays an important role in viral life cycle and becomes an attractive therapeutic target. Currently two NA inhibitors namely Zanamivir and Oseltamivir are available for treating infectious diseases. Recently five naturally derived polyphenols extracted from Phellinus baumii was reported as inhibitors against NA. Molecular docking is powerful tool in computer aided drug designing which aids in exploring and elucidating the properties of the molecules from their 3D structure. Hence, in the present study, molecular docking was carried out on reported polyphenols isolated from ethanolic extract of fruiting bodies of Phellinus baumii. The objective of this work was to study the interaction and to propose the binding mode of these compounds within the binding site of H1N1 neuraminidase. The results showed these compounds had better binding energy and H-bond interactions with the important active site residues of the receptor which authenticate these compounds contributes to inhibitory activity of neuraminidase to treat influenza infection.

• Bulletin of the Korean Chemical Society
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• 제35권4호
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• pp.1005-1010
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• 2014

We have performed DFT calculations to devise some possible fullerene dimers (from $C_{60}$ and $C_{80}$) connected through $C_{24}$ and $C_{36}$ bridge cages with the face-to-face linking model. The fullerene dimers with $C_{36}$ bridges have lower binding energies and greater HOMO-LUMO gaps than those of the fullerene dimers with $C_{24}$ bridges. Also, the replacement of $C_{60}$ cages with $C_{80}$ ones always leads to an increase in binding energies and HOMO-LUMO gaps in these systems. Dimerization of $C_{60}$ and $C_{80}$ fullerenes with $C_{24}$ and $C_{36}$ results in a significant decrease in antiaromaticity of the antiaromatic cages $C_{24}$ and $C_{80}$, and an increase in the aromaticity of the aromatic cages $C_{36}$ and $C_{60}$. Therefore, DFT results indicate that those fullerene dimers involving the initially harshly antiaromatic $C_{24}$ or $C_{80}$ cages are more energetically favorable configuration than the fullerene dimers involving the aromatic $C_{36}$ and $C_{60}$ cages.

• 통합자연과학논문집
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• 제15권4호
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• pp.179-186
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• 2022

The c-Jun N-terminal kinase (JNK3) play major role in neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, cerebral ischemia and other Central Nervous System disorders. Since JNK3 is primarily stated in the brain and stimulated by stress-stimuli, this situation is conceivable that inhibiting JNK3 could be a possible treatment for the mechanisms underlying neurodegenerative diseases. In this study drugs from Zinc15 database were screened to identify the JNK3 inhibitors by Molecular docking and Density functional theory approach. Molecular docking was done by Autodock vina and the ligands were selected based on the binding affinity. Our results identified top ten novel ligands as potential inhibitors against JNK3. Molecular docking revealed that Venetoclax, Fosaprepitant and Avapritinib exhibited better binding affinity and interacting with proposed binding site residues of JNK3. Density functional theory was used to compute the values for energy gap, lowest unoccupied molecular orbital (LUMO), and highest occupied molecular orbital (HOMO). The results of Density functional theory study showed that Venetoclax, Fosaprepitant and Avapritinib serves as a lead compound for the development of JNK3 small molecule inhibitors.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2020년도 추계국제학술대회
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• pp.14-14
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• 2020

In December 2019, the COVID-19 epidemic was discovered in Wuhan, China, and since has disseminated around the world impacting human health for millions. Herein, in-silico drug discovery approaches were utilized to identify potential candidates as Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) main protease (M^pro) inhibitors. We investigated several databases including natural and natural-like products (>100,000 molecules), DrugBank database (10,036 drugs), major metabolites isolated from daily used spices (32 molecules), and current clinical drug candidates for the treatment of COVID-19 (18 drugs). All tested compounds were prepared and screened using molecular docking techniques. Based on the calculated docking scores, the top ones from each project under investigation were selected and subjected to molecular dynamics (MD) simulations followed by molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations. Combined long MD simulations and MM-GBSA calculations revealed the potent compounds with prospective binding affinities against M^pro. Structural and energetic analyses over the simulated time demonstrated the high stabilities of the selected compounds. Our results showed that 4-bis([1,3]dioxolo)pyran-5-carboxamide derivatives (natural and natural-like products database), DB02388 and Cobicistat (DB09065) (DrugBank database), salvianolic acid A (spices secondary metabolites) and TMC-310911 (clinical-trial drugs database) exhibited high binding affinities with SARS-CoV-2 M^pro. In conclusion, these compounds are up-and-coming anti-COVID-19 drug candidates that warrant further detailed in vitro and in vivo experimental estimations.