• 대한화학회지
• /
• 제49권5호
• /
• pp.461-469
• /
• 2005

• Bulletin of the Korean Chemical Society
• /
• 제28권12호
• /
• pp.2203-2208
• /
• 2007

Three possible binding modes of cationic meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to d[(GCATATATGC)2] duplex were investigated by the molecular dynamics (MD) simulation. Among the three binding modes namely, “along the groove”, “across the groove” and “face on the groove”, the “across the groove” model exhibited the largest negative binding free energy and the DNA backbone remained as the B form. In this model, the molecular plain of the TMPyP tilts 45o with respect to the DNA helix axis and is largely exposed to the solvent. TMPyP was stabilized mainly by the interaction between the positively charged neighboring pyridinium moieties of TMPyP and negatively charged phosphate groups of DNA. The result obtained in this work by MD and the report (Jin, B. et al., J. Am. Chem. Soc. 2005, 127, 2417.) that the spectral properties of poly[d(A-T)2] bound TMPyP in the presence and absence of the minor groove binding drug 4',6- diamidino-2-phenylindole are similar, we propose that TMPyP bind across the minor groove of the AT rich- DNA.

• Bulletin of the Korean Chemical Society
• /
• 제21권8호
• /
• pp.779-784
• /
• 2000

Comparing the adsorption properties and dissociation on a Pt(111) iththat ona Fe(111) surface, we have con-sidered seven coordination modes of the adsorbed binding site: $di-${\sigma}$${\Delta}$\mu\pi/\mu$, 1-fbld,2-fold, and 3-fbld sites. On the Pt(111) surface, t he adsorbed binding site of carbon dioxide was strongestat the1-fold site and weakest at the $\pi/\mu-site.$ The adsorbed binding site on the Fe(111) surface was strongest at the di-бsite and weakest at the 3-fold site. We have found that the binding energy at each site that excepted 3-fold on the Fe(111) surface was stronger than the binding energy on the Pt(111) surface and that chemisorbed $CO_2bends$ because of metal mixing with $2\piu${\rightarrow}$6a_1CO_2orbital.$, The dissociation reaction occured in two steps, with an intermediate com-plex composed of atomic oxygen and ${\pi}bonding$ CO forming. The OCO angles of reaction intermediate com-plex structure for the dissociation reaction $were115^{\circ}Con$ the Pt(111), and $117^{\circ}C$ on the Fe(111) surface. We have found that the $CO_2dissociation$ rea11) surface proceeds easily,with an activationenergy about 0.2 eV lower than that on the Pt(111) surface.

• 대한약학회:학술대회논문집
• /
• 대한약학회 2002년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.1
• /
• pp.189.1-189.1
• /
• 2002

• 한국자기공명학회논문지
• /
• 제2권1호
• /
• pp.50-58
• /
• 1998

The systematic chirality investigations were made on the basic of the fact that zinc-binding tallysomycin (ZnTLMA) could have chiral centers (Zn, NC3, C6) at possible 4-, 5-, and 6-coordination models. Although our NMR data exhibit that the ligation sites are ${\beta}$-aminoalanine, ${\beta}$-hydroxyhistidine, and pyrimidine moiety, all possible coordination modes were tested out to see what kind of chiralities on NC3-C6 are favorable to each coordination mode. Tests were also made that take into account the specific configuration of functional groups, including ${\beta}$-aminoalanine, sugar ring, and ${\beta}$-hydroxyhistidine. Tests were finally extended to zinc-water binding and specific conformational studies by introducing various hydrogen bonding networks associated with the propionamide side chain and the carbamide group of mannose. Results of systematic chirality investigations exhibit that the S-S configuration of NC3-C6 is favorable to all of coordination models, but the R-S configuration, if exists at all, should have internal strain on C6 chiral center.

• Bulletin of the Korean Chemical Society
• /
• 제30권8호
• /
• pp.1743-1748
• /
• 2009

Novel 2-aminothiazolinium based tripodal receptors were designed and synthesized. The binding property of these receptors toward various anions was investigated by the isothermal titration calorimetry (ITC) method. Receptor 4 recognized the acetate anion with 1:1 stoichiometry, whereas it bound the other oxoanions such as sulfate and phosphate in complex modes. By modifying the phenyl groups at the 4-position of the thiazoline rings of the tripodal receptor 4 to induce a mutual aromatic stacking interaction among the three ligands, receptor 10 showed totally different binding behavior, which gave rise to the 1:1 binding mode for the sulfate anion. This result was confirmed by ESI MS spectrometry.

• 약학회지
• /
• 제33권2호
• /
• pp.87-100
• /
• 1989

Salicylic acids as anti-inflammatory agents were analyzed by ab initio, quantum chemical methods to study the possible modes of binding to the receptor. As the result of multiple regression analysis of reactivity indices and interpretation of normalized frontier orbital charges of drugs, potency seems to be related to energy of HOMO and LUMO at the 5 position of benzene ring, and in the 5-phenyl substituted case, the para position of substituting ring is important. The binding occurs first at the positive site of its receptor. The charge density exhibited by the frontier orbitals suggests that charge moves from receptor site to carboxyl group. The electrostatic orientation effect makes an important contribution to the binding of the active molecules to their receptors. Also the electrostatic potential model may be able to rationalize the source of activity or inactivity of the drugs under investigation.

• Archives of Pharmacal Research
• /
• 제25권6호
• /
• pp.807-816
• /
• 2002

Dihydrofolate reductases (DHFR) of human, Candida albicans and E. coli were docked with their original ligands of X-ray crystal complex using QXP (Quick eXPlore), a docking program. Conditions to reproduce the crystal structures within the root mean square deviation (rmsd) of 2.00 $\AA$ were established. Applying these conditions, binding modes and species-specificities of a novel antibacterial compound, $N^4-(2-acetoxyethoxymethyl)-2-acetylpyridine$ thiosemicarbazone (MTSC), were studied. As the results, the docking program reproduced the crystal structures with average rmsd of six ligands as 0.91 $\AA$ ranging from 0.49 to 1.45 $\AA$. The interactions including the numbers of hydrogen bonds and hydrophobic interactions were the same as the crystal structures and superposition of the crystal and docked structures almost coincided with each other. For AATSC, the results demonstrated that it could bind to either the substrate or coenzyme sites of DHFR in all three species with different degrees of affinity. It confirms the experimentally determined kinetic behavior of uncompetitive inhibition against either the inhibitor or the coenzyme. The docked MTSC overlapped well with the original ligands and major interactions were consistent with the ones in the crystal complexes. The information generated from this work should be useful for future development of antibacterial and antifungal agents.

• Bulletin of the Korean Chemical Society
• /
• 제28권7호
• /
• pp.1141-1150
• /
• 2007

Molecular modeling study has been performed to assist in the design of PTP1B inhibitors using FlexX. FlexX dockings with 19 test ligands, whose structures have been determined by X-ray crystallography, were successful in reproducing the experimental conformations within the protein. An increase in biological activity is observed as hydrophobic character of formylchromone derivatives increases. Most ligands bind to the activesite regions of the protein successfully in two different score runs. The Drug score run gave better results than the FlexX score run based on the score, rank, binding modes and bond distance of docked structures. Consensus values from the CScore scoring function are between 3 and 5, suggesting that the scoring scheme is reliable. All formylchromone inhibitors considered in this work show unidirectional binding modes in the active site pocket, which is contrary to the bidirectional X-ray results by Malamas et al. and amino acid residues responsible for such orientation are identified to help further development of the inhibitors.

• 약학회지
• /
• 제53권4호
• /
• pp.222-227
• /
• 2009

Human topoisomerase I (Topo I) plays a pivotal role in cell replication, transcription and repair and, therefore, is an important anti-cancer target. 20S-camptothecin (CPT) is a representative Topo I inhibitor. Compounds belonging to CPT family inhibit the religation step of Topo I-DNA by binding to the DNA cleavage site. Computational docking studies with Surflex-Dock were carried out to investigate the binding modes between Topo I-DNA binary complex structure and the ligand such as 20S-CPT and 9,10-substituted 20S-CPT analogues. The docking results demonstrated that most of the compounds with $IC_{50}$ value under $0.5{\mu}M$ intercalated exactly between the -1 and +1 DNA bases, deeply toward the cleavage site. The complex was stabilized by hydrogen-bonding and hydrophobic interactions with both the enzyme and the DNA. The compounds with $IC_{50}$ value above $0.5{\mu}M$ were poorly docked and did not intercalate. In addition, the docking results confirmed the overall correlation between the $IC_{50}$ values and docking scores, indicating the possible use of the modeling for the prediction of biological activity and design of potential inhibitors.