• Bulletin of the Korean Chemical Society
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• v.29 no.1
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• pp.61-68
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• 2008

High initial (2 minutes after iv injection) brain-uptake of PET agents is required to deliver the agent to binding sites in brain tissue but, for quantification of the specific binding, relatively rapid washout of free and non-specifically bound PET agents from the brain (30 minutes after injection) also is required. In order to compare the physicochemical properties of the PET agents which are responsible for early brain-uptake and rapid washout, respectively, chemometric analysis on brain-uptake of PET agents was performed via a classical VolSurf approach. According to the PCA and PLS results, high 2-30 min brain-uptake ratio seems to be related to the large hydrophobic regions in the PET agents which are not confined to a particular surface.

• Bulletin of the Korean Chemical Society
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• v.28 no.7
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• pp.1141-1150
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• 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.

• Bulletin of the Korean Chemical Society
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• v.30 no.3
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• pp.599-607
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• 2009

A series of conjugated cyclic and linear enkephalin analogs, Tyr-c[D-A2bu-Gly-Phe-Asp(NH-X)], where X = methyl, stearyl or$ PEG_350$, and Tyr-D-Ala-Gly-Phe-Cys(S-X), where X = methyl, octyl, or farnesyl, were synthesized in solution to investigate the receptor selectivity of opioids based on Schwyzer's membrane compartment $concepts.^{5,6}$ Cyclizations of the target compounds were achieved in high yields (> 60%) employing BOP, $NaHCO_3$ in DMF despite the steric hindrance of the bulky pendant groups. In the binding assay, the hydrophobic fatty acyl conjugates retained $\mu$-receptor selectivity. The unsaturated farnesyl conjugate exhibited the increased binding affinity than the saturated stearyl conjugate for both $\mu$-and $\delta$-opioid receptors. The PEG conjugates displayed the $\delta$-receptor selectivity. The low molecular weight $PEG_350$ conjugate exhibited the increase selectivity than the high molecular weight $PEG_5000$ conjugate to the $\delta$-receptor. The results of this study support the membrane compartment concepts.

• Bulletin of the Korean Chemical Society
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• v.24 no.5
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• pp.547-551
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• 2003

In the present work, the interaction of three water soluble porphyrins, tetra(p-trimethyle) ammonium phenyl porphyrin iodide (TAPP) as a cationic porphyrin, tetra sodium meso-tetrakis (p-sulphonato phenyle) porphyrin (TSPP) as an anionic porphyrin and manganese tetrakis (p-sulphonato phenyl) porphinato acetate (MnTSPP) as a metal porphyrin, with histone H₂B have been studied by isothermal titration microcalorimetry at 8 mM phosphate buffer, pH 6.8 and 27 °C. The values of binding constant, entropy, enthalpy and Gibbs free energy changes for binding of the first MnTSPP, and first and second TSPP and TAPP molecules were estimated from microcalorimetric data analysis. The results represent that the process is both entropy and enthalpy driven and histone induces self-aggregation of the porphyrins. The results indicate that both columbic and hydrophobic interactions act as self-aggregation driving forces for the formation of aggregates around histone.

• Journal of Soil and Groundwater Environment
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• v.9 no.3
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• pp.12-19
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• 2004

Binding mechanisms of polycyclic aromatic hydrocarbons (PAHs) with a purified Aldrich humic acid (PAHA) and its ultrafiltration (UF) size fractions were investigated. Organic carbon normalized binding coefficient ($K_oc$) values were estimated by both a conventional Stern-Volmer fluorescence quenching technique and a modified fluorescence quenching method. Pyrene $K_oc$ values depended on PAHA concentration as well as freely dissolved pyrene concentration. Such nonlinear sorption-type behaviors suggested the existence of specific interactions. Smaller molecular size PAH (naphthalene) exhibited higher $K_oc$ value with medium-size PAHA UF fractions whereas larger size PAH (pyrene) had higher extent of binding with larger PAHA UF fractions. The inconsistent observation for naphthalene versus pyrene was well explained by size exclusion effect, one of the previously suggested specific mechanisms for PAH binding. In general, the extent of pyrene binding increased with lower pH likely due to the neutralization of acidic functional groups in HS and the subsequent increase in hydrophobic HS region. However, pyrene $K_oc$ results with a large UF fraction (>100K Da) corroborated the existence of the size exclusion effect as demonstrated by an increase in $K_oc$ values at a certain higher pH range. The size exclusion effect appears to be effective only for the specific conditions (HS size or pH) that render HS hole st겨ctures to fit a target PAH.

• BMB Reports
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• v.29 no.3
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• pp.230-235
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• 1996

The interaction of ${\alpha}-ketoglutarate$ dehydrogenase complex (${\alpha}-KGDC$) with a hydrophobic fluorescent probe [1,1'-bi(4-aniline)naphthalene-5,5'-disulfonic acid] (bis-ANS) was studied. The punfied ${\alpha}-KGDC$ was potently inhibited by bis-ANS with an apparent half maximal inhibitory concentration ($IC_{50}$) of 9.8 ${\mu}m$ at pH 8.0. The catalytic activities of both the E1o and E2o subunits were predominantly inhibited while that of the E3 component was hardly affected. The binding of bis-ANS to the enzyme caused a marked enhancement and blue shift from 523 nm to 482 nm in the fluorescence emission spectrum. The dissociation constant ($K_d$) and the number of binding sites (n) were calculated to be 0.87 mM and 158, respectively. Allosteric regulators such as purine nucleotides and divalent cations further increased the fluorescence intensity of the $bis-ANS-{\alpha}-KGDC$ binary complex. These data suggest that the binding of these allosteric regulators to ${\alpha}-KGDC$ may cause the conformational changes in the enzyme and that bis-ANS could be used as a valuable probe to study the interaction of the multi-enzyme complex and its allosteric regulators.

• Molecules and Cells
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• v.42 no.12
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• pp.850-857
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• 2019

The Gram-negative opportunistic pathogen, Pseudomonas aeruginosa, has multiple multidrug efflux pumps. MexT, a LysR-type transcriptional regulator, functions as a transcriptional activator of the MexEF-OprN efflux system. MexT consists of an N-terminal DNA-binding domain and a C-terminal regulatory domain (RD). Little is known regarding MexT ligands and its mechanism of activation. We elucidated the crystal structure of the MexT RD at 2.0 Å resolution. The structure comprised two protomer chains in a dimeric arrangement. MexT possessed an arginine-rich region and a hydrophobic patch lined by a variable loop, both of which are putative ligand-binding sites. The three-dimensional structure of MexT provided clues to the interacting ligand structure. A DNase I footprinting assay of full-length MexT identified two MexT-binding sequence in the mexEF-oprN promoter. Our findings enhance the understanding of the regulation of MexT-dependent activation of efflux pumps.

• YAKHAK HOEJI
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• v.53 no.4
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• pp.222-227
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• 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.

• Journal of Soil and Groundwater Environment
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• v.10 no.5
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• pp.61-69
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• 2005

Changes in pyrene binding by dissolved and kaolinite-associated humic substances (HS) due to HS adsorptive fractionation processes were examined using purified Aldrich humic acid (PAHA) at different pH (4, 7 and 9). Irrespective of solution pH, molecular weight (MW) fractionation occurred upon adsorption of PAHA onto kaolinite, resulting in the deviation of residual PAHA MW from the original MW prior to sorption. Variation in $K_{OC}$ by bulk PAHA was observed at different pH due to relative contributions of partitioning and size exclusion effects (i.e., specific interactions). For all pH conditions investigated, carbon-normalized pyrene binding coefficients for nonadsorbed, residual fractions $(K_{OC}(res))$ were different from the original dissolved PAHA $K_{OC}$ value $(K_{OC}(orig))$ prior to contact with the kaolinite suspensions. Positive correlations between pyrene $(K_{OC}(res))$ and weight-average molecular weight $(MW_W)$ for residual PAHA fractions were observed for pH 7 and 9. However, such a positive correlation was not found at pH 4 due to the absence of the dramatic fractionation observed for high pH conditions (i.e., exclusive fractionation with respect to higher MW), suggesting that actual MW distribution pattern is more important for sorption-fractionated HS than the composite MW value. For adsorbed PAHA, conformational changes of PAHA upon adsorption seem to be important for the extent of pyrene binding. At relatively high pH (7 and 9), lower extent of pyrene binding was observed for adsorbed PAHA versus nonadsorbed PAHA. The conformation effects were more pronounced at higher pH.

• Archives of Pharmacal Research
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• v.19 no.4
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• pp.307-311
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• 1996

The activity of fucosidase shows different value depending on disease, eg) fucosidosis and I cell disease are characterized by the absence or deficiences of .alpha.-fucosidase, and sera of ovarian cancer patients exhibited a statistically significant deficiency of .alpha.-L-fucosidase activity (Zielke et al., 1972; Kress et al., 1980; Barlow et al., 1981). For the purpose of diagnosis of these disease easily, the manual of test can be developed by preparing kits of hydrophobic-binding substrate of fucosidase that bind C18-column.