Dynamics of fluoroquinolones induced resistance in DNA gyrase of Mycobacterium tuberculosis

DNA gyrase is a validated target of fluoroquinolones which are key components of multidrug resistance tuberculosis (TB) treatment. Most frequent occurring mutations associated with high level of resistance to fluoroquinolone in clinical isolates of TB patients are A90V, D94G, and A90V–D94G (double mutant [DM]), present in the larger subunit of DNA Gyrase. In order to explicate the molecular mechanism of drug resistance corresponding to these mutations, molecular dynamics (MD) and mechanics approach was applied. Structure-based molecular docking of complex comprised of DNA bound with Gyrase A (large subunit) and Gyrase C (small subunit) with moxifloxacin (MFX) revealed high binding affinity to wild type with considerably high Glide XP docking score of ?7.88 kcal/mol. MFX affinity decreases toward single mutants and was minimum toward the DM with a docking score of ?3.82 kcal/mol. Docking studies were also performed against 8-Methyl-moxifloxacin which exhibited higher binding affinity against wild and mutants DNA gyrase when compared to MFX. Molecular Mechanics/Generalized Born Surface Area method predicted the binding free energy of the wild, A90V, D94G, and DM complexes to be ?55.81, ?25.87, ?20.45, and ?12.29 kcal/mol, respectively. These complexes were further subjected to 30 ns long MD simulations to examine significant interactions and conformational flexibilities in terms of root mean square deviation, root mean square fluctuation, and strength of hydrogen bond formed. This comparative drug interaction analysis provides systematic insights into the mechanism behind drug resistance and also paves way toward identifying potent lead compounds that could combat drug resistance of DNA gyrase due to mutations.     

Bacteriocins: perspective for the development of novel anticancer drugs

Antimicrobial peptides (AMPs) from prokaryotic source also known as bacteriocins are ribosomally synthesized by bacteria belonging to different eubacterial taxonomic branches. Most of these AMPs are low molecular weight cationic membrane active peptides that disrupt membrane by forming pores in target cell membranes resulting in cell death. While these peptides known to exhibit broad-spectrum antimicrobial activity, including antibacterial and antifungal, they displayed minimal cytotoxicity to the host cells. Their antimicrobial efficacy has been demonstrated in vivo using diverse animal infection models. Therefore, we have discussed some of the promising peptides for their ability towards potential therapeutic applications. Further, some of these bacteriocins have also been reported to exhibit significant biological activity against various types of cancer cells in different experimental studies. In fact, differential cytotoxicity towards cancer cells as compared to normal cells by certain bacteriocins directs for a much focused research to utilize these compounds as novel therapeutic agents. In this review, bacteriocins that demonstrated antitumor activity against diverse cancer cell lines have been discussed emphasizing their biochemical features, selectivity against extra targets and molecular mechanisms of action.

     

Properties of the sarcoplasmic reticulum Ca2+-pump in coronary artery skinned smooth muscle

Pig coronary artery cultured smooth muscle cells were skinned using saponin. In the presence of an ATP-regenerating system and oxalate, the skinned cells showed an ATP-dependent azide insensitive Ca²⁺-uptake which increased linearly with time for >1 h. The Ca²⁺-uptake occurred with K_m values of 0.20±0.03 M for Ca²⁺ and 400±34 M for MgATP^2–. Thapsigargin and cyclopiazonic acid inhibited this uptake with IC₅₀ values of 0.13±0.02 and 0.56±0.04 M, respectively. These properties of SR Ca²⁺-pump are similar to those reported for membrane fractions isolated from fresh smooth muscle of coronary artery and other arteries. However, optimum pH of the uptake in the skinned cells (6.2) was lower than that reported previously using isolated membranes (6.4–6.8).Abbreviations SR sarcoplasmic reticulum - ER endoplasmic reticulum - PM plasma membrane - CPA cyclopiazonic acid - DTT dithiothreitol     

Kinetic interactions of glycine with substrates and effectors of phosphenolpyruvate carboxylase from maize leaves

Glycine enhanced the sensitivity of maize phosphenolpyruvate carboxylase to the activator glucose 6-phosphate and reduced the sensitivity of the enzyme to the inhibitors malate and aspartate. The effects of glycine on the kinetic constants for these other effectors were greater than its effect on the K_m for substrate, raising the K_i(malate) 11-fold and reducing K_{a(glucose6-P)} 7-fold, while reducing the K_m(PEP) by 3-fold. Kinetically saturating levels of glycine and glucose 6-phosphate acted synergistically to raise K_i(malate) higher than that observed with either activator alone. Glycine and glucose 6-phosphate also synergistically reduced aspartate inhibition. Dual inhibitor analysis indicated that aspartate and malate bind in a mutually exclusive manner, and thus probably compete for the same inhibitor site. In contrast, the synergism between glycine and glucose 6-phosphate indicate that these activators bind at separate sites. Glycine also reduced the K_m(Mg) by 3-fold but had no significant effect on the K_m of bicarbonate.Abbreviation PEP phosphoenolpyruvate     

Genetic analysis of shoot fresh weight in a cross of wild (<Emphasis Type="Italic">G. soja</Emphasis>) and cultivated (<Emphasis Type="Italic">G. max</Emphasis>) soybean

Shoot fresh weight (SFW) is one of the parameters, used to estimate the total plant biomass yield in soybean. In the present study, a total of 188 F_5:8 recombinant inbred lines (RIL) derived from an interspecific cross of PI 483463 (Glycine soja) and Hutcheson (Glycine max) were investigated for SFW variation in the field for three consecutive years. The parental lines and RILs were phenotyped in the field at the R6 stage by measuring total biomass in kg/plot to identify the QTLs for SFW. Three QTLs qSFW6_1, qSFW15_1, and qSFW19_1 influencing SFW were identified on chromosome 6, 15, and 19, respectively. The QTL qSFW19_1 flanked between the markers BARC-044913-08839 and BARC-029975-06765 was the stable QTL expressed in all the three environments. The phenotypic variation explained by the QTLs across all environments ranged from 6.56 to 21.32 %. The additive effects indicated contribution of alleles from both the parents and additive × environment interaction effects affected the expression of SFW QTL. Screening of the RIL population with additional SSRs from the qSFW19_1 region delimited the QTL between the markers SSR19-1329 and BARC-29975-06765. QTL mapping using bin map detected two QTLs, qSFW19_1A and qSFW19_1B. The QTL qSFW19_1A mapped close to the Dt1 gene locus, which affects stem termination, plant height, and floral initiation in soybean. Potential candidate genes for SFW were pinpointed, and sequence variations within their sequences were detected using high-quality whole-genome resequencing data. The findings in this study could be useful for understanding genetic basis of SFW in soybean.     

Antibody-Guided In Vivo Imaging for Early Detection of Mammary Gland Tumors

BACKGROUND: Earlier detection of transformed cells using target-specific imaging techniques holds great promise. We have developed TAB 004, a monoclonal antibody highly specific to a protein sequence accessible in the tumor form of MUC1 (tMUC1). We present data assessing both the specificity and sensitivity of TAB 004 in vitro and in genetically engineered mice in vivo. METHODS: Polyoma Middle T Antigen mice were crossed to the human MUC1.Tg mice to generate MMT mice. In MMT mice, mammary gland hyperplasia is observed between 6 and 10 weeks of age that progresses to ductal carcinoma in situ by 12 to 14 weeks and adenocarcinoma by 18 to 24 weeks. Approximately 40% of these mice develop metastasis to the lung and other organs with a tumor evolution that closely mimics human breast cancer progression. Tumor progression was monitored in MMT mice (from ages 8 to 22 weeks) by in vivo imaging following retro-orbital injections of the TAB 004 conjugated to indocyanine green (TAB-ICG). At euthanasia, mammary gland tumors and normal epithelial tissues were collected for further analyses. RESULTS: In vivo imaging following TAB-ICG injection permitted significantly earlier detection of tumors compared with physical examination. Furthermore, TAB-ICG administration in MMT mice enabled the detection of lung metastases while sparing recognition of normal epithelia. CONCLUSIONS: The data highlight the specificity and the sensitivity of the TAB 004 antibody in differentiating normal versus tumor form of MUC1 and its utility as a targeted imaging agent for early detection, tumor monitoring response, as well as potential clinical use for targeted drug delivery.     

Hydrophobic Interactions Are a Key to MDM2 Inhibition by Polyphenols as Revealed by Molecular Dynamics Simulations and MM/PBSA Free Energy Calculations

p53, a tumor suppressor protein, has been proven to regulate the cell cycle, apoptosis, and DNA repair to prevent malignant transformation. MDM2 regulates activity of p53 and inhibits its binding to DNA. In the present study, we elucidated the MDM2 inhibition potential of polyphenols (Apigenin, Fisetin, Galangin and Luteolin) by MD simulation and MM/PBSA free energy calculations. All polyphenols bind to hydrophobic groove of MDM2 and the binding was found to be stable throughout MD simulation. Luteolin showed the highest negative binding free energy value of -173.80 kJ/mol followed by Fisetin with value of -172.25 kJ/mol. It was found by free energy calculations, that hydrophobic interactions (vdW energy) have major contribution in binding free energy.