For establishing the efficacy against breast cancer occurrence, women's mammographic breast density and hot flush remission related to pre and post-menopausal symptoms were selected as biomarkers. Meta analysis applied the final selection of 40 papers from Medline to assess the efficacy of isoflavone-rich soy or supplements versus placebo under randomized controlled trials. Interestingly, the exposure to the purified isoflavones was more effective than the exposure to the crude extract of soy isoflavones for hot flush suppression. The length and the amount of dosage dependency is the most appropriately suggested to be one year long with 50~100 mg/day of isoflavone-rich soy or supplements. Funnel plots was used to interpret the results, overall effect of isoflavones on breast density in post-menopausal women was revealed to be less effect [effect size: 0.062, 95% confidence interval (CI): 0.005 to 0.12], than that of pre-menopausal women (effect size: 0.101, CI: -0.003 to 0.205). The reason why breast density was found higher among the pre-menopausal than the post-menopausal women is that the phytoestrogens of dietary isoflavones were antagonized against estrogen by the basis of estrogen receptor binding affinity. Overall, the Meta analysis reported that isoflavone had limited influence on breast density by suppressing the expansion by only 2%, while it was more effective to suppressing the hot flush, showing a dramatic decrease of 23%.
The behavior of peptide or protein solutes in saline aqueous solution is a fundamental topic in physical chemistry. Addition of ions can strongly alter the thermodynamic and physical properties of peptide molecules in solution. In order to study the effects of added ionic salts on protein conformation and dynamics, we have used the molecular dynamics (MD) simulations to investigate the behavior of Staphylococcus aureus Hfq protein under two different ionic concentrations: 0.1 M NaCl and 1.0 M NaCl in presence and absence of RNA (a hepta-oligoribonucleotide AU5G). Hfq, a global regulator of gene expression is highly conserved and abundant RNA-binding protein. It is already reported that in vivo the increase of ionic strength results in a drastic reduction of Hfq affinity for $Q{\beta}$ RNA and reduces the tendency of aggregation of Escherichia coli host factor hexamers. Our results revealed the crucial role of 0.1 M NaCl Hfq system on the bases with strong hydrogen bonding interactions and by stabilizing the aromatic stacking of Tyr42 residue of the adjacent subunits/monomers with the adenine and uridine nucleobases. An increase in RNA pore diameter and weakened compactness of the Hfq-RNA complex was clearly observed in 1.0 M NaCl Hfq system with bound RNA. Aggregation of monomers in Hfq and the interaction of Hfq with RNA are greatly affected due to the presence of high ionic strength. Higher the ionic concentration, weaker is the aggregation and interaction. Our results were compatible with the experimental data and this is the first theoretical report for the experimental study done in 1980 by Uhlenbeck group for the present system.
Background: Multidrug resistance (MDR) to chemotherapy drugs remains a major challenge in clinical cancer treatment. Here we investigated whether and how ginsenoside Rg5 overcomes the MDR mediated by ABCB1 transporter in vitro and in vivo. Methods: Cytotoxicity and colon formation as well as the intracellular accumulation of ABCB1 substrates were carried out in MDR cancer cells A2780/T and A549/T for evaluating the reversal effects of Rg5. The expressions of ABCB1 and Nrf2/AKT pathway were determined by Western blotting. An A549/T cell xenograft model was established to investigate the MDR reversal activity of Rg5 in vivo. Results: Rg5 significantly reversed ABCB1-mediated MDR by increasing the intracellular accumulation of ABCB1 substrates without altering protein expression of ABCB1. Moreover, Rg5 activated ABCB1 ATPase and reduced verapamil-stimulated ATPase activity, suggesting a high affinity of Rg5 to ABCB1 binding site which was further demonstrated by molecular docking analysis. In addition, co-treatment of Rg5 and docetaxel (TXT) suppressed the expression of Nrf2 and phosphorylation of AKT, indicating that sensitizing effect of Rg5 associated with AKT/Nrf2 pathway. In nude mice bearing A549/T tumor, Rg5 and TXT treatment significantly suppressed the growth of drug-resistant tumors without increase in toxicity when compared to TXT given alone at same dose. Conclusion: Therefore, combination therapy of Rg5 and chemotherapy drugs is a strategy for the adjuvant chemotherapy, which encourages further pharmacokinetic and clinical studies.
Gopal, Velmani;AL Rashid, Mohammad Harun;Majumder, Sayani;Maiti, Partha Pratim;Mandal, Subhash C
Journal of Pharmacopuncture
/
v.18
no.2
/
pp.7-18
/
2015
Objectives: Lawsone (1,4 naphthoquinone) is a non redox cycling compound that can be catalyzed by DT diaphorase (DTD) into 1,2,4-trihydroxynaphthalene (THN), which can generate reactive oxygen species by auto oxidation. The purpose of this study was to evaluate the toxicity of the phytomarker 1,4 naphthoquinone and its metabolite THN by using the molecular docking program AutoDock 4. Methods: The 3D structure of ligands such as hydrogen peroxide ($H_2O_2$), nitric oxide synthase (NOS), catalase (CAT), glutathione (GSH), glutathione reductase (GR), glucose 6-phosphate dehydrogenase (G6PDH) and nicotinamide adenine dinucleotide phosphate hydrogen (NADPH) were drawn using hyperchem drawing tools and minimizing the energy of all pdb files with the help of hyperchem by $MM^+$ followed by a semi-empirical (PM3) method. The docking process was studied with ligand molecules to identify suitable dockings at protein binding sites through annealing and genetic simulation algorithms. The program auto dock tools (ADT) was released as an extension suite to the python molecular viewer used to prepare proteins and ligands. Grids centered on active sites were obtained with spacings of $54{\times}55{\times}56$, and a grid spacing of 0.503 was calculated. Comparisons of Global and Local Search Methods in Drug Docking were adopted to determine parameters; a maximum number of 250,000 energy evaluations, a maximum number of generations of 27,000, and mutation and crossover rates of 0.02 and 0.8 were used. The number of docking runs was set to 10. Results: Lawsone and THN can be considered to efficiently bind with NOS, CAT, GSH, GR, G6PDH and NADPH, which has been confirmed through hydrogen bond affinity with the respective amino acids. Conclusion: Naphthoquinone derivatives of lawsone, which can be metabolized into THN by a catalyst DTD, were examined. Lawsone and THN were found to be identically potent molecules for their affinities for selected proteins.
Lewis, Kevin M.;Sattler, Steven A.;Kang, ChulHee;Wu, Hong Min;Kim, Sang Geon;Kim, Han Bok
Korean Journal of Microbiology
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v.54
no.3
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pp.208-213
/
2018
Activation of nuclear factor kappa B ($NF{\kappa}B$) leads to the inflammatory process. During this $NF{\kappa}B$-dependent inflammation process, inducible nitric oxide synthase (iNOS) are expressed in the inflammatory cells. Our previous data indicated that a specific septapeptide (GVAWWMY) from the soybean extract fermented by Bacillus licheniformis B1 inhibited iNOS mRNA expression and NO production in cultured macrophage cells. Our further experiments revealed that treatment of same septapeptide resulted in inhibition of LPS-induced $NF{\kappa}B$ activation by reversing degradation of $I{\kappa}B{\alpha}$, an inhibitory protein for $NF{\kappa}B$. The molecular docking indicated that the septapeptide binds to $I{\kappa}B$ kinase ${\beta}$ ($IKK{\beta}$), and thus it can inhibit phosphorylation of $I{\kappa}B{\alpha}$. Supporting this, the binding site for the septapeptide has the highest affinity (-8.7 kcal/mol) and the site was located at the kinase domain (KD) of $IKK{\beta}$, which can significantly affect the kinase activity of $IKK{\beta}$.
Seo, Jin-Wook;Lee, Hak-Sung;Lee, Min-Jun;Kim, Mi-Ra;Shin, Cha-Gyun
Archives of Pharmacal Research
/
v.27
no.1
/
pp.77-82
/
2004
DA-125, a novel derivative of adriamycin, is known for its anti-cancer activity. In this study, the inhibitory mechanism of DA-125 on topoisomerase was investigated in the simian virus 40 (SV40) replicating CV-1 cell by studying the SV40 DNA replication intermediates and DNA-topoisomerase complexes. DNA-protein complexes that were formed in the drug-treated cells were quantitated by using a glass filter assay. SV40 DNA replication intermediates that were accumulated in the drug-treated CV-1 cell were analyzed in a high resolution gel. DA-125 did not accumulate B-dimers of SV40 DNA replication intermediates which were found in the adriamycin-treated CV-1 cells. DA-125 induced a dose-dependent formation of the DNA-protein complexes, while adriamycin did not. When adriamycin and etoposide (VP16) were added to the SV40-infected cells at the same time, adriamycin blocked the formation of the DNA-protein complexes induced by VP16 in a dose-dependent manner. However, DA-125 blocked the formation of the DNA-protein complexes induced by VP16 up to the maximum level of the DNA-protein complexes that were induced by DA-125 alone. Adriamycin and DA-125 did not inhibit the formation of the DNA-protein complexes that were caused by camptothecin, a known topoisomerase I poison. DA-125 is bifunctional in inhibiting topoisomerase II because it simultaneously has the properties of the topoisomerase II poison and the DNA intercalator. As a topoisomerase II poison, DA-125 alone induced dose-dependent formation of the DNA-protein complexes. However, as a DNA intercalator, it quantitatively inhibited the formation of the DNA-protein complexes induced by a strong topoisomerase II poison VP16. Furthermore considering that the levels of the DNA-protein complex induced by VP16 were decreased by DA-125 in terms of the topoisomerase II poison, we suggest that DA-125 has a higher affinity to the drug-binding sites of DNA than VP16 has.
The orthogonal pair of Saccharomyces cerevisiae tyrosyl-tRNA synthetase (Sc YRS) and a variant of E. coli initiator tRNA, fMam $tRNA_{CUA}$ which recognizes the amber stop codon is an effective tool for site-specific incorporation of unnatural amino acids into the protein in E. coli. To evolve the amber suppression activity of the orthogonal pair, we generated a mutant library of Sc YRS by randomizing two amino acids at 320 and 321 which involve recognition of the first base of anticodon in fMam $tRNA_{CUA}$. Two positive clones are selected from the library screening with chloramphenicol resistance mediated by amber suppression. They showed growth resistance against high concentration of chloramphenicol and their $IC_{50}$ values were approximately 1.7~2.3 fold higher than the wild type YRS. In vivo amber suppression assay reveals that mutant YRS-3 (mYRS-3) clone containing amino acid substitutions of P320A and D321A showed 6.5-fold higher activity of amber suppression compared with the wild type. In addition, in vitro aminoacylation kinetics of mYRS-3 also showed approximately 7-fold higher activity than the wild type, and the enhancement was mainly due to the increase of tRNA binding affinity. These results demonstrate that optimization of anticodon recognition by engineered aminoacyl tRNA synthetase improves the efficiency of unnatural amino acid incorporation in response to nonsense codon.
Most problematic antibiotic resistance mechanism for MLS (macrolide-lincosamide-streptogramn B) antibiotics encountered in clinical practice is mono- or dimethylation of specific adenine residue at 2058 (E. coli coordinate) of 23S rRNA which is performed by Erm (erythromycin ribosome resistance) protein through which bacterial ribosomes reduce the affinity to the antibiotics and become resistant to them. ErmSF is one of the four gene products produced by Streptomyces fradiae to be resistant to its own antibiotic, tylosin. Unlike other Erm proteins, ErmSF harbors idiosyncratic long N-terminal end region (NTER) 25% of which is comprised of arginine well known to interact with RNA. Furthermore, NTER was found to be important because when it was truncated, most of the enzyme activity was lost. Based on these facts, capability of NTER peptide to inhibit the enzymatic activity of ErmSF was sought. For this, expression system for two different proteins to be expressed in one cell was developed. In this system, two plasmids, pET23b and pACYC184 have unique replication origins to be compatible with each other in a cell. And expression system harboring promoter, ribosome binding site and transcription termination signal is identical but disparate amount of protein could be expressed according to the copy number of each vector, 15 for pACYC and 40 for pET23b. Expression of NTER peptide in pET23b together with ErmSF in pACYC 184 in E. coli successfully gave more amounts of NTER than ErmSF but no inhibitory effects were observed suggesting that there should be dynamicity in interaction between ErmSF and rRNA rather than simple and fixed binding to each other in methylation of 23S rRNA by ErmSF.
Thymosin β-4 (TB4) is a small peptide composed of 43 amino acids. To obtain sufficient biologically active mouse TB4 economically, we cloned and overexpressed this gene in an Escherichia coli system. With the isopropyl β-D-1-thiogalactopyranoside induction of the E. coli transformant, TB4 fusion protein with intein- and chitin-binding domain was successfully expressed in the soluble fraction within the E. coli cell. The TB4-intein - chitin-binding domain fusion protein was purified from the soluble fraction of E. coli cell lysate. The affinity chromatography with chitin beads and dithiothreitol-mediated intein self-cleavage reaction releases the TB4 peptide into the stripping solution. Sodium dodecyl sulphate - polyacrylamide gel electrophoresis and Western blot analyses were used to confirm that the recombinant TB4 peptide was produced with the expected size of 5 kDa. We found that the recombinant TB4 stimulated cell migration in the transwell plate chamber assay. After 18 hr of the treatment of the recombinant TB4 with 1 ng/ml concentration, the migration of the HT1080 cell was increased by 20% compared with that of the chemically synthesized TB4. The recombinant TB4 was also observed to promote the healing of a wound area in C57BL/6 mice by as high as 35% compared with that of the chemically synthesized TB4. These results suggest that the recombinant TB4 has better biological activity for cell migration and wound healing than that of the chemically synthesized TB4 peptide.
Animal mucins have structural characteristics similar to human salivary mucins. Animal mucins have been regarded as suitable substances for saliva substitutes. Since animal mucin molecules in saliva substitutes and host-derived antimicrobial salivary molecules exist simultaneously in whole saliva and the pellicles of patients with dry mouth, interactions may occur between these molecules. The purpose of this study was to investigate the influence of animal mucins on peroxidase activity in solution and on the surface of hydroxyapatite(HA) surfaces. The effects of animal mucins on peroxidase activity were examined by incubating porcine gastric mucin(PGM) or bovine submaxillary mucin (BSM) with either bovine lactoperoxidase(bLPO) or saliva samples. For solid-phase assays, immobilized animal mucins or peroxidase on three different HA surfaces(HA beads, HA disc, and bovine tooth) were used. Peroxidase activity was determined with an NbsSCN assay. The obtained results were as follows: 1. PGM enhanced the enzymatic activity of bLPO in solution phase. PGM did not affect the enzymatic activity of peroxidase in saliva sample(POS). 2. BSM did not affect the enzymatic activities of both bLPO and POS in solution phase. 3. HA-adsorbed PGM increased subsequent bLPO adsorption in all three HA phases. The activity of POS was increased on both the HA beads and bovine tooth. 4. The peroxidase activities on the HA beads and disc were increased when the HA surfaces were exposed to a mixture of bLPO and PGM. 5. The binding affinity of bLPO to PGM was greater than that of bLPO to BSM. Collectively, our results suggest that animal mucins affects the enzymatic activity of peroxidase on the HA surfaces as well as in solution. Saliva substitutes containing animal mucins may affect the function of antimicrobial components in natural saliva and saliva substitutes.
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