• 제목, 요약, 키워드: inhibitor binding

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The Binding Energy of HIV-1 Protease Inhibitor

  • 가재진;박상현;김호징
    • Bulletin of the Korean Chemical Society
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    • v.17 no.1
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    • pp.19-24
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    • 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.

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In vitro Ccovalent Binding of SC-42867, PGE2 Antagonist, to Rat Liver Microsomal Proteins

  • Lee, Kyung-Tae
    • Archives of Pharmacal Research
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    • v.18 no.6
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    • pp.381-384
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    • 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.

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Dihydrofolate Reductase-저해제 복합체에 대한 X-선 결정체 구조와 docking model의 구조 비교 (Comparison of X-ray Crystallographic Structures and Docking Models of Dihydrofolate Reductase-Inhibitor Complexes)

  • 안미현;최인희;김춘미
    • 약학회지
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    • v.46 no.6
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    • pp.416-425
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    • 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.

푸로세미드와 안지오텐신 차단제와 상호작용 (Interaction of Furosemide and Angiotensin Inhibitor)

  • 최준식;이진환;범진필
    • 약학회지
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    • v.33 no.6
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    • pp.345-349
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    • 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.

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Molecular Cloning and Characterization of Chymotrypsin Inhibitor and Chitin-Binding Protein Homologs from the Bumblebee Bombus terrestris

  • Qiu, Yuling;Yoon, Hyung-Joo;Jin, Byung-Rae
    • International Journal of Industrial Entomology
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    • v.25 no.1
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    • pp.115-121
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    • 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.

The Slow and Tight Binding of MR-387A to Aminopeptidase N

  • CHUNG, MYUNG-CHUL;HYO-KON CHUN;HO-JAE LEE;CHOONG-HWAN LEE;SU-IL KIM;YUNG-HEE KHO
    • Journal of Microbiology and Biotechnology
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    • v.6 no.4
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    • pp.250-254
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    • 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.

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Understanding Drug-Protein Interactions in Escherichia coli FabI and Various FabI Inhibitor Complexes

  • Lee, Han-Myoung;Singh, N. Jiten
    • Bulletin of the Korean Chemical Society
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    • v.32 no.1
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    • pp.162-168
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    • 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.

PKR인산화효소 억제인자인 이중선RNA결합단백질 (RBF)의 RNA결합특이성 (RNA Binding Specificities of Double-Stranded RNA Binding Protein (RBF) as an Inhibitor of PRK Kinase)

  • 박희성;최장원
    • 생명과학회지
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    • v.6 no.4
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    • pp.234-240
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    • 1996
  • PKR인산화효소의 억제인자로서 밝혀진 이중선RNA결합단백질 (RBF)의 RNA결합특이성을 정기영도에 의한 RNA 이동변화실험과 여과막결합도실험에 의해 측정하였다. RBF는 바이러스RNA나 stem/loop구조를 지니는 합성 RNA들에 대한 다양한 친화력을 지니는 것으로 나타났으며 충분한 GC가 포함된 11염기쌍으로 이루어진 RNA stem helix RBF가 결합하기 위한 최소한의 RNA구조로 제시되고 있다. 자연적 RNA구조에 대한 RBF의 결합은 poly(I) : poly(C)의 첨가에 의해 반전되었으며 E. coli 5S RNA경우는 효과를 거의 나타내지 않았다.

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In silico Study on the Interaction between P-glycoprotein and Its Inhibitors at the Drug Binding Pocket

  • Kim, Namseok;Shin, Jae-Min;No, Kyoung Tai
    • Bulletin of the Korean Chemical Society
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    • v.35 no.8
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    • pp.2317-2325
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    • 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.

Binding Subsites In the Active Site of $Zn^{2+}$-Glycerophosphocholine Cholinephosphodiesterase

  • Sok, Dai-Eun;Kim, Mee-Ree
    • BMB Reports
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    • v.28 no.2
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    • pp.94-99
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    • 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.

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