• 한국자원식물학회지
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• 제6권1호
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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.

• 약학회지
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• 제40권6호
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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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• 제31권1호
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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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• 제26권1호
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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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• 제30권2호
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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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• 제33권6호
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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.

• 대한화학회지
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• 제29권2호
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• pp.98-103
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• 1985

트리메틸렌 디라디칼의 헤테로원자 유사체에 관한 두 비결합 궤도함수간의 궤도 상호 작용을 MINDO/3 및 STO-3G 방법으로 조사하였다. 그 결과 트리메틸렌 디라디칼에서 알려진 것 처럼 상당한 시그마 방향족성 안정성이 있는 구조는 준위 순서가 뒤바뀌어 $n_-$가$n_+$보다 낮게 나타났다. 고립전자쌍 궤도(LPO)는 vicinal 트란스 $n^{-{\sigma}^*$ 상호작용과 수소결합으로 인한 전하분산에 의해서 안정화 됨을 알았다. 다른 헤테로 원자계인 N과 O에서 O의 LPO기여 $n_O$는 항상 낮은 준위(${\varepsilon}_l$)에 크게 나타나며 N의 LPO기여 $n_N$은 높은 준위(${\varepsilon}_h$)에 크게 나타난다. 즉 다음과 같이 쓸 수 있다.$n_{\pm}$(lower) = $n_O{\pm}{\lambda}_Nn_N.\;n_{\pm}(higher)\;=\;n_N{\pm}{\lambda}_On_O$. 여기서 ${\lambda}_i$< 1.0

• Bulletin of the Korean Chemical Society
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• 제34권7호
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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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• 제31권9호
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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.

• 대한화학회지
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• 제50권4호
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• pp.291-297
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• 2006

Cyclopropyl 링과 할로겐 원소가 결합된 붕소원자 사이의 hyperconjugation 효과를 알아보기 위하여 CPDFB와 CPCFB 분자의 여러 conformation과 transition state 구조들에 대해 DFT와 ab initio 방법을 사용하여 다양한 레벨에서 구조최적화 및 NBO 분석을 수행하였다. 그 결과 주요 상호작용 형태는 화합물에 따라 단일결합 오비탈 (C1-C3, C2-C3) n* (B9) 또는 *(B9-Cl11) 오비탈로 전자를 제공하는 것이었고 이때 안정화 에너지는 CPDFB 분자의 경우 6.63 kcal/mol, CPCFB 분자의 경우는 conformation에 따라 6.97(E-form)/6.79(Z-form) kcal/mol 이었다. 또한, BF2와 BFCl 기의 내부회전에 의한 회전장벽의 크기는 각각 5.3~6.7 kcal/mol과 5.7~6.5 kcal/mol로 기존에 보고된 실험값과 잘 일치함을 보였다. 마지막으로 CPCFB 분자의 conformers 중에서 Z-form이 global minimum으로 확인되었고 E-form 보다 0.2 kcal/mol 정도 안정하였다.