• Korean Journal of Plant Resources
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• v.6 no.1
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• pp.13-23
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• 1993

To data, many types of compounds having antineoplastic activity have been isolated from higher plants, that is, alkalodids, terpenes, lignans, steroids and so on. Some of ther were isolated from Indonesian plants, Curcuma xanthorrhiza and Eurycoma longifolia. Bisaborane type compounds were compounds were isolated as antimeoplastic compounds againest Sarcoma 180A from C. xanthorrhiza, and quassinoids and euryrene type triterpenes from triterpenes from El longifolia. Casearines, a kind of diterpene, had been isolated as cytotxic components from Casearia sylvestris distributed in South America. RA series Cyclic hexapeptides isolated from Rubia akane and R. cordifolia also have strong antineoplastic activity against various types of tumors. Till now, 16 kinds of RA series compounds were isolated and named as RA-I~XVI. Moreover, monoglucoside of RA-V newly isolated from same plant. Many kinds of derivatives including natural RA compounds were tested for QSAR, and one of them, RA-VII was screened up as a most suitable substance as an antitumor agent. RA-VII(=RA 700) has strong cytotoxic activity against KB cells, P388 lymphocytic leukemia and MM2 mammary carcinoma cells. In some solution, three conformers of RA-VII were observed by NMR. It was discussed the relationship between conformation and activity. Total synthesis was already completed, but there is left room for improvement. Phase I clinical trials for RA-VII has been finished, then Phase II trials will be started before long.

• YAKHAK HOEJI
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• v.40 no.6
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• pp.632-639
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• 1996

Most stable conformers of some antiinflammatory fenamates were obtained by conformational free energy change calculations. Conformational energies for the molecules as unhydrate d state were estimated first, and those as hydrated state were calculated then to simulate the molecules in aqueous solution using a hydration shell model. The initial geometries of the molecules were obtained either from X-ray crystallographic data or from homologous molecular fragments. The bond lengths and angles were not varied, but all the torsion angles were varied step by step during the conformational free energy surface searching. The results show that there are several feasible conformations for a compound. And the molecules are somewhat stabilized by hydration (-${\delta}G_{hyd}{\cong}$13 to 16kcal/mole), but the conformations were not changed significantly by the hydration itself. There seems to be a strong tendency of intramolecular hydrogen bonding between imino hydrogen and carboxyl oxygen of the compounds. As a result, the carboxyl group cannot be rotated freely, and the rotation of the second aromatic ring is the main reason for the conformational variations of the compounds. The ECEPP force fields via the program CONBIO were used throughout this study.

• Bulletin of the Korean Chemical Society
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• v.31 no.1
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• pp.59-63
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• 2010

Calculations are presented for the $\gamma$-aminobutyric acid-$(H_2O)_n$ (n = 0-5) clusters in both canonical and zwitterionic forms. We examine the effects of microsolvation on the structures and transformation between the canonical and zwitterionic forms. The canonical forms are predicted to be more stable for n = 0-4. With five microsolvating water molecules, the two forms of $\gamma$-aminobutyric acid become quasidegenerate, with the energies of zwitterionic forms slightly (by 1 - 3 kcal/mol) higher. The lowest energy zwitterionic conformer of $\gamma$-aminobutyric acid-$(H_2O)_5$ cluster is calculated to isomerize to canonical form through a barrier-less proton transfer process and is thus predicted to be kinetically unstable. Therefore, we predict that the canonical conformers of $\gamma$-aminobutyric acid should be observed predominantly in the gas phase at low temperature in presence of up to five water molecules.

• Journal of Pharmaceutical Investigation
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• v.26 no.1
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• pp.55-59
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• 1996

The crystal structure of diflunisal, 2',4'-difluoro-4-hydroxy-3-biphenyl-carboxylic acid, was determined by single crystal X-ray diffraction technique. The compound was recrystallized from a mixture of acetone and water in monoclinic, space group C2/c, with $a\;=\;34.666(6),\;b\;=\;3.743(1),\;c\;=\;20.737(4)\;{\AA},\;{\beta}=\;110.57(2)^{\circ}$, and Z = 8. The calculated density is $1.324\;g/cm^3$. The structure was solved by the direct method and refined by full matrix least-squares procedure to the final R value of 0.045 for 1299 observed reflections. It was found that the molecules in the crystal are partially disordered, that is, the two equivalent conformers $(180^{\circ}$ rotated ones through C(1)-C(7)) are packed alternatively without regular symmetry or sequence. The two phenyl rings of the biphenyl group is tilted to each other by the dihedral angle of $43.3^{\circ}$. The carboxyl group at the salicylic moiety is just coplanar to the phenyl ring, and the planarity of this salicylic moiety is stabilized by an intramolecular hydrogen bond of O(3)-H(O3) O(2). The molecules are dimerized through the intermolecular hydrogen bonds at the carboxyl group in the crystal.

• Bulletin of the Korean Chemical Society
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• v.30 no.2
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• pp.423-428
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• 2009

The comparative study of three calix[4]heterocycles (calix[4]pyrrole, calix[4]furan, and calix[4]thiophene) has been theoretically performed by using high-level density functional theory (DFT) at the MPWB1K/6-311G$^{**}$//B3LYP/6- 311G$^{**}$ level. The effect of different hetero-atoms (nitrogen, oxygen, and sulfur) placed in the heterocycles on the conformational flexibility, thermodynamic stability order, cavity sizes, charge distributions, and binding propensities are examined. The thermodynamic stability differences between the conformers are found to be much greater in calix[4]pyrrole compared to those in calix[4]furan and calix[4]thiophene. Relatively larger NH group and higher dipole of a pyrrole ring in calix[4]pyrrole contribute to the higher energy barrier for the conformational conversions and relatively rigid potential energy surface compared to the case of calix[4]furan and calix[4]thiophene. The computational results herein provide theoretical understanding of the conformational flexibility and the thermodynamic nature which can be applied to understand the complexation behavior of the three calix[4]heterocycles.

• Bulletin of the Korean Chemical Society
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• v.33 no.6
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• pp.1998-2004
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• 2012

We carried out DFT calculations for monohydrated sulfuric and phosphoric acids. We are interested in clusters which differ in orientation of hydrogen atoms only. Such molecular complexes are close in energy, since they lie in the vicinity of the global minimum energy structure on the flat potential energy surface. For monohydrated sulfuric acid we identified four different isomers. The monohydrated phosphoric acid forms five different conformers. These systems are difficult to study from the theoretical point of view, since binding energy differences in several cases are very small. For each structure, we calculated harmonic vibrational frequencies to be sure that if the optimized structures are at the local or global minima on the potential energy surface. The analysis of calculated -OH vibrational frequencies is useful in interpretation of infrared photodissociation spectroscopy experiments. We employed four different DFT functionals in our calculations. For each structure, we calculated binding energies, thermodynamic properties, and harmonic vibrational frequencies. Our analysis clearly shows that DFT approach is suitable for studying monohydrated inorganic acids with different hydrogen atom orientations. We carried out MP2 calculations with aug-cc-pVDZ basis set for both monohydrated acids. MP2 results serve as a benchmark for DFT calculations.

• Journal of the Korean Chemical Society
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• v.29 no.2
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• pp.98-103
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• 1985

Orbital interactions between two nonbonding orbitals have been investigated for heteroatom analogues of trimethylene diradical using MINDO/3 and STO-3G methods. The results showed that the conformers in which significant ${\sigma}$-aromatic stabilization is involved exhibited level order reversal to $n_-$ below $n_+$ as it was found for trimethylene diradical. Lone pair orbitals (LPO) were found to be stabilized by charge dispersion accompanying vicinal trans $n-{\sigma}^*$ interaction and hydrogen bonding. In systems with different heteroatoms, N and O, the contribution of the LPO of oxygen, $n_O$ was always greater in the lower level whereas that of nitrogen, nN, was greater in the higher level as can be expressed as : $n_{\pm}$(lower) = $n_O{\pm}{\lambda}_Nn_N.\;n_{\pm}(higher)\;=\;n_N{\pm}{\lambda}_On_O$. where ${\lambda}_i$< 1.0

• Bulletin of the Korean Chemical Society
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• v.34 no.7
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• pp.1972-1984
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• 2013

Microtubules play an important role in intracellular transport, mobility, and particularly mitosis. Paclitaxel (Taxol$^{TM}$) and paclitaxel-like compounds have been shown to be anti-tumor agents useful for various human tumors. Paclitaxel-like compounds operate by stabilizing microtubules through interface binding at the interface between two ${\beta}$-tubulin monomers in adjacent protofilaments. In this paper we present the elucidation of the structural features of paclitaxel and paclitaxel-like compounds (e.g., epothilones) with microtubule stabilizing activities, and relate their activities to spatial and chemical features of the molecules. CATALYST program was used to generate three-dimensional quantitative structure activity relationships (3D-QSARs) resulting in 3D pharmacophore models of epothilone- and paclitaxel-derivatives. Pharmacophore models were generated from diverse conformers of these compounds resulting in a high correlation between experimental and predicted biological activities (r = 0.83 and 0.91 for epothilone and paclitaxel derivatives, respectively). On the basis of biological activities of the training sets, five- and four-feature pharmacophore hypotheses were generated in the epothilone and paclitaxel series. The validation of generated hypotheses was achieved by using twelve epothilones and ten paclitaxels, respectively, which are not in the training sets. The clustering (grouping) and merging techniques were used in order to supplement spatial restrictions of each of hypothesis and to develop more comprehensive models. This approach may be of use in developing novel inhibitor candidates as well as contributing a better understanding of structural characters of many compounds useful as anticancer agents targeting microtubules.

• Bulletin of the Korean Chemical Society
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• v.31 no.9
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• pp.2581-2587
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• 2010

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both $\alpha$- and $\beta$-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.

• Journal of the Korean Chemical Society
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• v.50 no.4
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• pp.291-297
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• 2006

The equilibrium structures, relative energies and NBO analyses for the possible conformations and transition states which can exist on the internal rotation of CPDFB and CPCFB molecules have been investigated using DFT and ab initio methods with various basis sets. The interaction between bonding orbital ((C1-C3, C2-C3)) and antibonding orbital (n*(B9) and *(B9-Cl11)) was the main characteristic hyperconjugation in both molecules. In addition, the stabilization energy of CPDFB was 6.63kcal/mol and that of CPCFB was 6.97(E-form)/6.79(Z-form) kcal/mol for each conformation. The rotational barriers by internal rotation of BF2- and BFCl- functional groups were evaluated to be 5.3~6.7kcal/mol and 5.7~6.5kcal/mol respectively, which showed good agreement with the experimental values reported by previous dynamic NMR study. Finally, Z-form was more stable than E-form by 0.2 kcal/mol in CPCFB molecule and therefore Z-form was confirmed as global minimum.