• Bulletin of the Korean Chemical Society
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• v.29 no.9
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• pp.1831-1834
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• 2008

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5605-5611
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• 2012

Background: In the last two decades, pioneering research on anti-tumour activity of saffron has shed light on the role of crocetin, picrocrocin and safranal, as broad spectrum anti-neoplastic agents. However, the exact mechanisms have yet to be elucidated. Identification and characterization of the targets of bioactive constituents will play an imperative role in demystifying the complex anti-neoplastic machinery. Methods: In the quest of potential target identification, a dual virtual screening approach utilizing two inverse screening systems, one predicated on idTarget and the other on PharmMapper was here employed. A set of target proteins associated with multiple forms of cancer and ranked by Fit Score and Binding energy were obtained from the two independent inverse screening platforms. The validity of the results was checked by meticulously analyzing the post-docking binding pose of the picrocrocin with Hsp90 alpha in AutoDock. Results: The docking pose reveals that electrostatic and hydrogen bonds play the key role in inter-molecular interactions in ligand binding. Picrocrocin binds to the Hsp90 alpha with a definite orientation appropriate for nucleophilic attacks by several electrical residues inside the Hsp90-alpha ATPase catalytic site. Conclusion: This study reveals functional information about the anti-tumor mechanism of saffron bioactive constituents. Also, a tractable set of anti-neoplastic targets for saffron has been generated in this study which can be further authenticated by in vivo and in vitro experiments.

• KSBB Journal
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• v.11 no.2
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• pp.225-237
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• 1996

Intrinsic binding kinetics of of 125I-bovine serum albumin (125I-BSA) and immobilized monoclonal anti-BSA (MAb 9.1) were studied. Small non-porous polystyrene beads (0.5${\mu}$m diameter) were used as a solid support to minimize the mass transfer interference on rate measurements. We demonstrated both theoretically and experimentally that the binding reaction is kinetically controlled. Rate measurements show that the association reaction is of second order and the dissociation reaction is of first order. Between 4 and $37^{\circ}C$ the measured equilibrium constant agrees well with the equilibrium constant calculated from the rate measurements. The temperature effects on association are much greater than on dissociation; the activation energy for association is about 9Kca1/mole, as compared to 2Kca1/mole for dissociation. The use of small non-porous beads as a solid support in binding studies essentially avoids mass transfer limitations; such a system makes it possible to determine the intrinsic binding characteristics of any immobilized antibody on a solid surface.

• Clinical and Experimental Reproductive Medicine
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• v.16 no.2
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• pp.131-138
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• 1989

The present study was designed to develop a new method for the determination of estrogen receptor in porcine uterus using frozen sections. Cryostat sections were incubated with $^3H$-estradiol($^3H$-$E_2$) in the presence or absence of diethylstilbestrol(DES) and the radioactivity of 3H-E2 bound to estrogen receptor(ER) was detected. The level of specific estrogen receptor was determined by Scatchard analysis. The highest ratio of specific binding against total binding was achieved in 3 sec. tions(5mm x 5mm) which was corresponded to lOO${\mu}$/ml protein concentration. Optimal binding was obtained during incubation with $^3H$-$E_2$ for 30 minutes at 23$^{\circ}C$ after treatment of sections with acetone for 20 seconds. Three time-washing of sections was proved to be appropriate for the removal of unbound 3H-E2. 200-fold molar excess of DES was substituted for the binding of $^3H$-$E_2$ to ER sufficiently(binding efficiency of 54.8%). ER was saturated with 4nM of $^3H$-$E_2$ and its dissociation constant was 0.1nM. ER assay using frozen sections(Histological radioreceptor assay, HRRA) was significantly correlated with radioreceptor assay for estradiol(RRA, 0.976 , p

• Bulletin of the Korean Chemical Society
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• v.25 no.9
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• pp.1314-1320
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• 2004

The adsorption and configuration of CO molecules adsorbed on W (110) and W (100) surfaces have been calculated by the atomic superposition and electron delocalization molecular orbital (ASED-MO) method. Referred to as the ASED-MO method, it has been used in the present study to calculate the geometries, binding energies, vibrational frequencies, orbital energies, reduced overlap population (ROP), and charges. From these results adsorption properties of ${\alpha}$-state and ${\beta}$-state were deduced. The calculated binding energies are in good agreement with the experimental result. On the W (110), the calculated average binding energies are 2.56 eV for the end-on configuration and 3.20 eV for the lying-down configuration. Calculated vibrational frequency is 1927 $cm^{-1}$ at a 1-fold site and 1161 $cm^{-1}$ at a long-bridge (2) site. These results are in reasonable agreement with experimental values. On the W(100) surface, calculated average binding energies of the end-on and the lying-down are 2.54 eV and 4.02 eV respectively. The differences for binding energy and configuration on the surfaces are explained on the basis of surface-atom coordination and atom-atom spacing. In the favored lyingdown CO configuration on the W(110) and W(100) surfaces, 4 ${\sigma}$ and 1 ${\pi}$ donation interactions, coupled with the familiar 5 ${\sigma}$ donation to the surfaces and back-donations to the CO 2 ${\pi}^{\ast}$ orbital, are responsible for adsorption to the surface.

• Natural Product Sciences
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• v.25 no.1
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• pp.28-33
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• 2019

A popular approach for the study of estrogen receptor ${\alpha}$ inhibition is to investigate the protein-protein interaction between the estrogen receptor (ER) and the coactivator surface. In our study, we investigated phytochemicals from Rubus coreanus that were able to disrupt $ER{\alpha}$ and coactivator interaction with an $ER{\alpha}$ antagonist. The E-screen assay and molecular docking analysis were performed to evaluate the effects of the estrogenic activity of R. coreanus extract and its constituents on the MCF-7 human breast cancer cell line. At $100{\mu}g/mL$, R. coreanus extract significantly stimulated cell proliferation ($574.57{\pm}8.56%$). Sanguiin H6, which was isolated from R. coreanus, demonstrated the strongest affinity for the $ER{\alpha}$ coactivator-binding site in molecular docking analysis, with a binding energy of -250.149. The initial results of the study indicated that sanguiin H6 contributed to the estrogenic activity of R. coreanus through the activation of the $ER{\alpha}$ coactivator-binding site.

• Applied Chemistry for Engineering
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• v.34 no.3
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• pp.279-284
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• 2023

Isothermal titration calorimetry (ITC) is a useful technique to obtain thermodynamic binding properties such as enthalpy, Gibbs free energy, entropy, and stoichiometry of the chelation reaction. A single independent binding site model was used to evaluate the thermodynamic binding properties in BaCl₂ and ethylenediaminetetraacetic acid (EDTA) in Trince and HEPES buffers. ITC enables us to elucidate the binding mechanism and find an optimal chelation condition for BaCl₂ and EDTA in the pH range of 7~11. Chelation of BaCl₂ and EDTA is a spontaneous endothermic reaction. As pH increased, entropic contributions dominated. The optimal pH range is narrow around pH 9.0, where 1:1 binding between BaCl₂ and EDTA occurs.

• Journal of Ginseng Research
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• v.48 no.1
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• pp.89-97
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• 2024

Background: Ginsenoside F2 (GF2), the protopanaxadiol-type constituent in Panax ginseng, has been reported to attenuate metabolic dysfunction-associated steatotic liver disease (MASLD). However, the mechanism of action is not fully understood. Here, this study investigates the molecular mechanism by which GF2 regulates MASLD progression through liver X receptor (LXR). Methods: To demonstrate the effect of GF2 on LXR activity, computational modeling of protein-ligand binding, Time-resolved fluorescence resonance energy transfer (TR-FRET) assay for LXR cofactor recruitment, and luciferase reporter assay were performed. LXR agonist T0901317 was used for LXR activation in hepatocytes and macrophages. MASLD was induced by high-fat diet (HFD) feeding with or without GF2 administration in WT and LXRα^-/- mice. Results: Computational modeling showed that GF2 had a high affinity with LXRα. LXRE-luciferase reporter assay with amino acid substitution at the predicted ligand binding site revealed that the S264 residue of LXRα was the crucial interaction site of GF2. TR-FRET assay demonstrated that GF2 suppressed LXRα activity by favoring the binding of corepressors to LXRα while inhibiting the accessibility of coactivators. In vitro, GF2 treatments reduced T0901317-induced fat accumulation and pro-inflammatory cytokine expression in hepatocytes and macrophages, respectively. Consistently, GF2 administration ameliorated hepatic steatohepatitis and improved glucose or insulin tolerance in WT but not in LXRα^-/- mice. Conclusion: GF2 alters the binding affinities of LXRα coregulators, thereby interrupting hepatic steatosis and inflammation in macrophages. Therefore, we propose that GF2 might be a potential therapeutic agent for the intervention in patients with MASLD.

• Journal of the Korean Chemical Society
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• v.44 no.1
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• pp.45-51
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• 2000

The binding mode of anthryl derivatives to synthetic polynucleotides were investigated by various spectroscopic methods. The spectroscopic properties of anthracence with metbylamine and methylethylenediamine side chains, complexed with $poly[d(A-T)_2]$ and $poly[d(G-C)_2]$, can be summarized as a red-shift, with a strong hypochromism in the absortion spectrum, similar induced CD spectra, and a strong negative LD spectrum with an $LD^r$ magnitude comparable to the DNA absorption region. These observations indicate that anthracene moiety is intercalated between the nucleo-bases of $poly[d(A-T)_2]$ and $poly[d(G-C)_2]$. The side chains did not alter the spectroscopic properties, demonstrating that the binding mode was not affected by them. A strong energy transfer was observed from poly[d(A-T),] and $poly[d(I-C)_2]$ but not from $poly[d(G-C)_2]$, as reported by Kumar et al. (J. Am. Chem. Soc.(1993) 115, 8547). Since the binding mode is the same for all the polynucleotides, the amine group of the guanine base, which protrudes into the minor groove of $poly[d(G-C)_2]$, is concluded to disrupt the energy transfer.

• Journal of the Korean Chemical Society
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• v.59 no.5
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• pp.387-396
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• 2015

The DFT and ab initio calculations have been performed to elucidate hydrogen interaction of HOOO-(H₂O)_n (n=1~5) clusters. The optimized geometries, harmonic vibrational frequencies, and binding energies are predicted at various levels of theory. The trans conformer of HOOO monomer is predicted to be thermodynamically more stable than cis form at the CCSD(T) level of theory. For HOOO-(H₂O)_n clusters, the geometries are optimized at B3LYP/aug-cc-pVTZ and CAM-B3LYP/aug-cc-pVTZ levels of theory. The binding energy of HOOO-H₂O cluster is predicted to be 6.05 kcal/mol at the MP2//CAM-B3LYP/ aug-cc-pVTZ level of theory after zero-point vibrational energy (ZPVE) and basis set superposition error (BSSE) correction. The average binding energy per H₂O is increased according to adding a H₂O moiety in HOOO-(H₂O)_n clusters up to 7.2 kcal/mol for n=5.