• Bulletin of the Korean Chemical Society
• /
• v.17 no.1
• /
• pp.19-24
• /
• 1996

The potential energies of HIV-1 protease, inhibitor, and their complex have been calculated by molecular mechanics and the "binding energy", defined as the difference between the potential energy of complex and the sum of potential energies of HIV-1 protease and its inhibitor, has been compared to the free energy in inhibition reaction. The trend in these binding energies seems to agree with that in free energies.

• Archives of Pharmacal Research
• /
• v.18 no.6
• /
• pp.381-384
• /
• 1995

Covalent binding of the reactive metabolites of SC_42867 to microsomal proteins has been examined. In the absence of inhibitor of cytochrome oxydase (.alpha.-naphtyl-isothiocyanate) or a radical scavenger (3-terthiobuty-4-hydroxyanisol), up to 4.0% of total redioactivity used in the assay could irreversibly bind to proteins. In the presence of an inhibitor, the highest percentage of covalent binding observed is 0.7% a significant decrease of the metabolism of SC42876 was observed. These results suggest in a cytochrome P-450 dependent generation of SC_42867 metabolites significantly take part in the covalent binding process.

• YAKHAK HOEJI
• /
• v.46 no.6
• /
• pp.416-425
• /
• 2002

A comparative study to validate the reliability of a fully automated docking program, FlexiDock, was carried out to predict the binding modes of DHFR-inhibitor complex. The inhibitors were extracted from the crystallographically determined DHFR-NADP$^{+}$(H)-inhibitor ternary complexes of human, Escherichia coli and Candida albicans and then docked back into the remaining DHFR-NADP$^{+}$(H) binary complexes using FlexiDock. The resulting conformations and orientations were compared to the original crystal complex structures for reproducibility. Then, folate, the substrate, and known inhibitors such as methotrexate, piritrexim and trimethoprim were docked into the wild-type human DHFR and their binding modes were compared with X-ray crystallographic or other modeling data. The root mean square deviations (RMSDs) for ligands ranged from 1.14 to 1.57$\AA$, and the protein backbone RMSDs from 0.94 to 1.26$\AA$. FlexiDock reproduced the orientations and binding modes of all seven ligands in good agreement with the crystal structures. It proved to be a reliable and efficient program in studying binding modes of DHFR-inhibitor complexes of different species, and the information obtained from this work may provide additional insight into the design of new agents with improved activity.ity.

• YAKHAK HOEJI
• /
• v.33 no.6
• /
• pp.345-349
• /
• 1989

This paper was attempted to investigate effect of angiotensin inhibitor (loading dose 25, 50, $100{\mu}g/kg$ and maintenance dose 12.5, 25, $50{\mu}g/kg/hr$) on the pharmacokinetics of furosemide (5 mg/kg i.v) in rabbit. The plasma concentrations of furosemide increased by angiotensin inhibitor and the relative bioavailability of furosemide increased from 118.1% to 193.2% by the inhibitor. The protein binding of furosemide decreased by angiotensin inhibitor in bovine serum albumin ($2.17\;{\times}\;10^{-4}M$) by equilibrium dialysis method. Consequently, dosage regimen of furosemide might be adjusted carefully when furosemide is administered with angiotensin inhibitor.

• International Journal of Industrial Entomology and Biomaterials
• /
• v.25 no.1
• /
• pp.115-121
• /
• 2012

The bumblebee Bombus terrestris is widely used in greenhouses to pollinate crops. Here, we report the molecular cloning and characterization of chymotrypsin inhibitor and chitin-binding protein homologs from B. terrestris. Two cDNAs encoding chymotrypsin inhibitor (Bt-CI) and chitin-binding protein (Bt-CBP) homologs were cloned from B. terrestris. Gene sequence analysis showed that Bt-CI gene consists of three exons encoding 75 amino acids, including a predicted 20-amino acid signal peptide, while Bt-CBP consists of two exons encoding 78 amino acids, including a predicted 26-amino acid signal peptide. The mature Bt-CI and Bt-CBP peptides contain ten and six conserved cysteine residues, respectively. Database searches using the deduced sequences of Bt-CI and Bt-CBP showed similarity to those from B. impatiens (96% peptide sequence identities). Bt-CI and Bt-CBP were expressed in both the venom gland and fat body of B. terrestris worker bees. The recombinant Bt-CI and Bt-CBP peptides were expressed in baculovirus-infected insect cells. Taken together, our findings describe the molecular characterization of Bt-CI and Bt-CBP from B. terrestris.

• Journal of Microbiology and Biotechnology
• /
• v.6 no.4
• /
• pp.250-254
• /
• 1996

MR-387A [(2S, 3R)-2-hydroxy-3-amino-4-phenylbutanoyl-L-valyl-L-prolyl-(2, 4-trans)- L-4-hydroxy-proline] reversibly inhibits aminopeptidase N (BC 3.4.11.2) in a process that is remarkable for its unusual degree of time dependence. The time required to inactivate the enzyme by 50$%$ ($t_{1/2}$) for establishing steady-state levels of $EI^*$complex was approximately 5 minutes. This indicates that the inhibition is a slow-binding process. In dissociation experiments of $EI^*$ complex, enzymic activity was regained slowly in a quadratic equation, indicating that the inhibition of aminopeptidase N by MR-387A is tight-binding and reversible. Thus, the binding of MR-387A by aminopeptidase N is slow and tight, with $K_{i}$ (for initial collision complex, EI) and $K_i{^*}$ (for final tightened complex, $EI^*$) of $2.2\times10^{-8}$ M (from Lineweaver-Burk plot) and $4.4\times10^{-10}$ M (from rate constants), respectively. These data indicate that MR-387A and aminopeptidase N are bound approximately 200-fold more tightly in the final $EI^*$complex than in the initial collision EI complex.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.1
• /
• pp.162-168
• /
• 2011

Many ligands have been experimentally designed and tested for their activities as inhibitors against bacterial enoyl-ACP reductase (FabI), ENR. Here the binding energies of the reported ligands with the E. coli ENR-$NAD^+$ were calculated, analyzed and compared, and their molecular dynamics (MD) simulation study was performed. IDN, ZAM and AYM ligands were calculated to have larger binding energies than TCL and IDN has the largest binding energy among the considered ligands (TCL, S54, E26, ZAM, AYM and IDN). The contribution of residues to the ligand binding energy is larger in E. coli ENR-NAD+-IDN than in E. coli ENR-$NAD^+$-TCL, while the contribution of $NAD^+$ is smaller for IDN than for TCL. The large-size ligands having considerable interactions with residues and $NAD^+$ have many effective functional groups such as aromatic $\pi$ rings, acidic hydroxyl groups, and polarizable amide carbonyl groups in common. The cation-$\pi$ interactions have large binding energies, positively charged residues strongly interact with polarisable amide carbonyl group, and the acidic phenoxyl group has strong H-bond interactions. The residues which have strong interactions with the ligands in common are Y146, Y156, M159 and K163. This study of the reported inhibitor candidates is expected to assist the design of feasible ENR inhibitors.

• Journal of Life Science
• /
• v.6 no.4
• /
• pp.234-240
• /
• 1996

A double-stranded RNA binding factor (RBF), characterized as an inhibitor of PKR kinase in our previous study, was evaluated for its RNA binding specificities by RNA gel electrophoretic mobility shift analysis and membrane filter binding assay, RBF displayed affinities for a broad range of RNAs including viral RNAs and synthetic RNAs consiting of stem and loop structures. GC-rich RNA stem helices as short as 11 bp are suggested to represent the minimal binding motif for RBF. RBF binding to all the natural RNAs tested was reversible by poly(I): poly(C) addition, but E. coli 5S RNA was inefficient.

• Bulletin of the Korean Chemical Society
• /
• v.35 no.8
• /
• pp.2317-2325
• /
• 2014

P-glycoprotein (P-gp) is a member of the ATP-Binding Cassette transporter superfamily and mediates transmembrane efflux of many drugs. Since it is involved in multi-drug resistance activity in various cancer cells, the development of P-gp inhibitor is one of the major concerns in anticancer therapy. Human P-gp protein has at least two "functional" drug binding sites that are called "H" site and "R" site, hence it has multi-binding-specificities. Though the amino acid residues that constitute in drug binding pockets have been proposed by previous experimental evidences, the shapes and the binding poses are not revealed clearly yet. In this study, human P-gp structure was built by homology modeling with available crystal structure of mouse P-gp as a template and docking simulations were performed with inhibitors such as verapamil, hoechst33342, and rhodamine123 to construct the interaction between human P-gp and its inhibitors. The docking simulations were performed 500 times for each inhibitor, and then the interaction frequency of the amino acids at the binding poses was analyzed. With the analysis results, we proposed highly contributing residues that constitute binding pockets of the human P-gp for the inhibitors. Using the highly contributing residues, we proposed the locations and the shapes of verapamil binding site and "R" site, and suggested the possible position of "H" site.

• BMB Reports
• /
• v.28 no.2
• /
• pp.94-99
• /
• 1995

The properties of binding sites in the active site of $Zn^{2+}$-glycerophosphocholine cholinephosphodiesterase were examined using substrates and inhibitors of the enzyme. Phosphodiesterase hydrolyzed p-nitrophenylphosphocholine, p-aminophenylphosphocholine, and glycerophosphocholine, but did not hydrolyze either acylated glycerophosphocholine or bis (p-nitrophenyl)phosphate, suggesting a size limitation for interaction with a glyceryl moiety-binding subsite. The hydrolysis of p-nitrophenylphosphocholine was competitively inhibited by glycerophosphocholine and p-aminophenylphosphocholine, while glycerophosphoethanolamine was a weak inhibitor. The enzyme was also inhibited by choline, but not by ethanolamine. Thiocholine, a much more potent inhibitor than choline, was more inhibitory than cysteamine, suggesting a strict specificity of an anionic subsite adjacent to a $Zn^{2+}$ subsite. Of all oxyanions tested, the tellurite ion was found to strongly inhibit the enzyme by binding to a $Zn^{2+}$ subsite. The inhibitory role of tellurite was synergistically enhanced by tetraalkylammonium salts, but not by glycerol. Deactivation of the enzyme by diethylpyrocarbonate was partially protected by choline, but not by glycerophosphate. It is suggested that the active site of phosphodiesterase contains three binding subsites.