• Proceedings of the PSK Conference
• /
• 2003.10b
• /
• pp.65.2-65.2
• /
• 2003

88 selective COX-2 inhibitors belonging to three chemical classes (triaryl rings, diaryl cycloalkanopyrazoles, and diphenyl hydrazides) were studied using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Partial least squares analysis produced statistically significant models with q values of 0.84 and 0.79 for CoMFA and CoMSIA, respectively. The key spatial properties were detected by careful analysis of the isocontour maps. The binding energies calculated from flexible docking correlated with inhibitory activities by the least-squares fit method. (omitted)

• Proceedings of the Korea Air Pollution Research Association Conference
• /
• 2005.11a
• /
• pp.520-522
• /
• 2005

• Proceedings of the PSK Conference
• /
• 2001.04a
• /
• pp.193.2-193.2
• /
• 2001

• Proceedings of the PSK Conference
• /
• 2001.10a
• /
• pp.243.2-243.2
• /
• 2001

• Bulletin of the Korean Chemical Society
• /
• v.31 no.5
• /
• pp.1361-1367
• /
• 2010

A series of O,O-dialkyl-1-phenoxyacetoxy-1-methylphosphonate analogues (1~22) as a new class of potent inhibitors of pyruvate dehydrogenase were synthesized and 3D-QSARs (three dimensional qantitative structure-activity relationships) models on the pre-emergency herbicidal activity against the seed of cucumber (Cucumus Sativa L.) were derived and discussed quantitatively using comparative molecular field analysis (CoMFA) and comparative molecular similarity indeces analysis (CoMSIA) methods. The statistical values of CoMSIA models were better predictability and fitness than those of CoMFA models. The inhibitory activities according to the optimized CoMSIA model I were dependent on the electrostatic field (41.4%), the H-bond acceptor field (26.0%), the hydrophobic field (20.8%) and the steric field (11.7%). And also, it was found that the optimized CoMSIA model I with the sensitivity to the perturbation ($d_q{^{2'}}/dr^2{_{yy'}}$ = 0.830) and the prediction ($q^2$ = 0.503) produced by a progressive scrambling analyses were not dependent on chance correlation. From the results of graphical analyses on the contour maps with the optimized CoMSIA model I, it is expected that the structural distinctions and descriptors that subscribe to herbicidal activities will be able to apply new an herbicide design.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2003.10a
• /
• pp.251-257
• /
• 2003

Metabolic engineering has become a new paradigm for the more efficient production of desired bioproducts. Metabolic engineering can be defined as directed modification of cellular metabolism and properties through the introduction, deletion, and modification of metabolic pathways by using recombinant DNA and other molecular biological tools. During the last decade, metabolic flux analysis(MFA) has become an essential tool fur metabolic engineering. By MFA, the intracellular metabolic fluxes can be quantified by the measurement of extracellular metabolite concentrations in combination with the stoichiometry of intracellular reactions and mass balances. The usefulness and functionality of MFA are demonstrated by applying to metabolic pathways in E. coli. First, a large-scale in silico E. coli model is constructed, and then the effects of carbon sources on intracellular flux distributions and succinic acid production were investigated on the basis of the uptake and secretion rates of the relevant metabolites. The results indicated that succinic acid yields increased in order of gluconate, glucose and sorbitol. Acetic acid and lactic acid were produced as major products rather than when gluconate and glucose were used carbon sources. The results indicated that among three carbon sources available, the most reduced substrate is sorbitol which yields efficient succinic acid production.

• Journal of Integrative Natural Science
• /
• v.8 no.4
• /
• pp.285-292
• /
• 2015

LIM kinases belong to the serine/Threonine kinase family. The members of the LIM kinase (LIMK) family include LIMK 1 and 2 which are involved in the regulation of actin polymerisation and microtubule disassembly. LIMK1 was shown to be involved in cancer metastasis, while LIMK2 activation promotes cells cycle progression. Since LIMK2 plays a vital role in many disease conditions such as pulmonary hypertension, cancer and viral diseases, and till date there are not much selective inhibitors been reported, LIMK2 becomes an interesting therapeutic target among the kinases. 3D QSAR study was carried out on a series of pyrrolopyrimidines based derivatives as LIMK2 inhibitors. A reasonable CoMFA ($q^2$=0.888; ONC=3; $r^2$=0.974) with good statistical values was developed. The developed model was validated using 1000 runs of boostrapping and was found to be predictable. The results of CoMFA contour map analysis suggested that the bulky substitution at $R_4$ and $R_5$ position are highly desirable to increase the activity. Similarly, positive substitution at $R_3$ position is also required to increase the activity. It is also noted that bulky substitution at $R_1$ position must be avoided. Our results could provide valuable information to enhance the activity of the LIMK2 inhibitors and to design potent pyrrolopyrimidines derivatives.

• YAKHAK HOEJI
• /
• v.38 no.2
• /
• pp.202-210
• /
• 1994

To investigate the feasibility of mucosal delivery of $[D-Ala^6]$ LHRH, a potent analogue of LHRH, enzymatic proteolysis of $[D-Ala^6]$ LHRH and inhibitory effect of medium chain fatty acid salts(MFA) were studied using rabbit mucosal homogenate. $[D-Ala^6]$ LHRH incubated in homogenates of rectal(RE), nasal(NA) and vaginal(VA) mucosa were assayed by HPLC. The degradation of $[D-Ala^6]$ LHRH followed the first order kinetics. The degradation products were found as $[D-Ala^6]$ $LHRH^{1-7}$(m-i), to a lesser extent, $[D-Ala^6]$ $LHRH^{1-9}$(m-ii) and $[D-Ala^6]$ $LHRH^{1-3}$(m-iii) by the method of amino acid analysis(PITC method). The formation of$[D-Ala^6]$ $LHRH^{1-7}$ was not inhibited by the addition of disodium ethylenediaminetetraacetic acid but inhibited by sodium tauro-24,25-dihydrofusidate, suggesting that endopeptidase 24.11(EP 24.11) cleaves the $Leu^7-Arg^8$ bond of $[D-Ala^6]$ LHRH and is the primary $[D-Ala^6]$ LHRH degrading enzyme. The patterns of $[D-Ala^6]$ LHRH degradation indicated that EP 24.11 exists in each mucosal homogenate with the order of RE>NA>VA. MFA significantly inhibited the proteolysis of $[D-Ala^6]$ LHRH. The addition of sodium caprate(1.0%) or sodium laurate(0.5%) to the each mucosal homogenate completely protected $[D-Ala^6]$ LHRH from the degradation.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.3
• /
• pp.613-617
• /
• 2009

3D-QSARs for the inhibition activities against protox by herbicidal 2-N-phenylisoindolin-1-one derivatives were studied quantitatively using CoMFA and CoMSIA methods. The result of the statistical quality of optimized CoMSIA model 2 ($FF:\;{r^2}_{cv.};\;0.973\;&\;{r^2}_{ncv.};\;0.612$) was higher than that of CoMFA model 1 ($AF:\;{r^2}_{cv.};\;0.414\;&\;{r^2}_{ncv.};\;0.909$). Also, the relative contribution of the optimized CoMSIA model 2 showed the steric (24.6%), electrostatic (31.0%), hydrophobic (ClogP, 23.4%) and H-bond acceptor field (21.0%), respectively. From the results of the contour maps, the protox inhibition activities are expected to increase when steric favor and H-bond acceptor favor groups are substituted on $R_2$ position and positive favor group are substituted on $C_2,\;C_3,\;and\;C_5$ atom in phenyl ring of $R_2$ position. And the inhibition activities are expected to increase when hydrophobic favor group is substituted on $C_1,\;C_3$ atom in phenyl ring of $R_2$ position and $C_1$ atom of $R_2$ position and hydrophilic favor groups are substituted on $C_4$ atom in phenyl ring of $R_1$ position and the terminal group of $R_1$ position.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.8
• /
• pp.2387-2393
• /
• 2013

Benzotriazole is an important synthetic auxiliary for potential clinical applications. A series of benzotriazoles as potential antiproliferative agents by inhibiting histone deacetylase (HDAC) were recently reported. Three-dimensional quantitative structure-activity relationship (3D-QSAR), including comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA), were performed to elucidate the 3D structural features required for the antiproliferative activity. The results of both ligand-based CoMFA model ($q^2=0.647$, $r^2=0.968$, ${r^2}_{pred}=0.687$) and CoMSIA model ($q^2=0.685$, $r^2=0.928$, ${r^2}_{pred}=0.555$) demonstrated the highly statistical significance and good predictive ability. The results generated from CoMFA and CoMSIA provided important information about the structural characteristics influence inhibitory potency. In addition, docking analysis was applied to clarify the binding modes between the ligands and the receptor HDAC. The information obtained from this study could provide some instructions for the further development of potent antiproliferative agents and HDAC inhibitors.