Molecular dynamics simulation studies on structural and conformational changes in tyrosine-67 nitrated cytochrome c

Protein tyrosine nitration is well-established post-translational modification occurring in a number of diseases, viz. neurodegenerative, cardiovascular diseases, ageing, etc. Tyrosine-67 (Tyr-67) nitration of cytochrome c (cyt c) was observed under oxidative stress affecting its structure and electron transfer properties. Hence, in this study, molecular dynamics (MD) simulations were carried out at room temperature to investigate the structural and conformational changes in the nitrated cyt c's. MD results revealed that the bond between FE (Heme-105) and S (Met-80) considerably weakened, radius of gyration, backbone and Cα root-mean-square deviations decreased and hydrogen bonding increased in the nitrated cyt c's relative to wild type (WT) cyt c. Ramachandran plot analysis revealed that N- and C-terminal helices also affected by nitration at CE2 carbon atom. Furthermore, essential dynamics analysis showed that amplitude of concerted motion decreased in the nitrated cyt c's, perhaps due to the increase in the hydrogen bonding interaction. Taken together, the structural and conformational changes in the active site Tyr-67 nitrated cyt c may have implications in the loss of electron/proton transfer and gain of apoptotic properties.     

Optimization of extracellular keratinase production by poultry farm isolate Scopulariopsis brevicaulis

A Scopulariopsis brevicaulis poultry farm isolate was chosen to study factors influencing keratinase production. The parameters were optimized by factorial design. The highest enzyme production by this fungus was obtained at pH 7.5, a temperature of 30 degrees C and a growth period of 5 weeks. The production of the enzyme was enhanced when the culture medium was supplemented with glucose (1%), sodium nitrate (2%), feather (1.5%) and CaCl(2) (1 mM). According to the responses from the experimental design, the effects of each variable were calculated, and the interactions between them were determined. The experimental values were found to be in accordance with the predicted values, the correlation coefficient is 0.9978.     

Actin cytoskeleton as a putative target of the neem limonoid Azadirachtin A

Limonoids isolated from the Indian neem tree (Azadirachta indica) have been gaining global acceptance in agricultural applications and in contemporary medicine for their myriad but discrete properties. However, their mode of action is still not very well understood. We have studied the mode of action of Azadirachtin A, the major limonoid of neem seed extracts, using Drosophila melanogaster as the model system. Azadirachtin A induces moderate-to-severe phenotypes in different tissues in a dose-dependent manner. At the cellular level, Azadirachtin A induces depolymerization of Actin leading to arrest of cells and subsequently apoptosis in a caspase-independent manner. Azadirachtin A-induced phenotypes were rescued by the over-expression of Cyclin E in a tissue-dependent manner. Cyclin E, which caused global rescue of Azadirachtin A-induced phenotypes, also effected rearrangement of the actin filaments. These results suggest that probably actin is a target of Azadirachtin A activity.     

Single nucleotide polymorphism of CYP3A5*3 contributes to clopidogrel resistance in coronary artery disease patients among Tamilian population

Clopidogrel is an antiplatelet drug. It is used for the treatment as well as for the prophylaxis of coronary artery disease. Clopidogrel resistance is an emerging problem in clinical settings. The aim of the present study was to evaluate the effect of CYP3A5*3 genetic polymorphism on clopidogrel resistance. One hundred and forty-seven patients from outpatient Department of Cardiology on 75 mg/day of clopidogrel as maintenance dose were recruited from April 2010 to July 2011. All subjects gave written informed consent to participate in the study. DNA extraction was performed using phenol chloroform extraction procedure and genotyping by standard Taqman based RT-PCR method. Platelet aggregation was done at the end of 7th and 14th day by using chronolog lumi Aggregometer which is expressed as impedance in ohms. Impedance values of >5 ohms at the end of 6 min were considered as clopidogrel resistance. Subjects (N = 147) were analysed for CYP3A5*3 polymorphism, of which 49 (33 %) were found to be clopidogrel resistant. Homomutants of CYP3A5*3 gene had 2.78 (0.97–7.98; p < 0.05) fold risk and heteromutants had 2.4 (0.93–6.46; p < 0.05) fold risk of developing clopidogrel resistance. Carriers of defective allele G of CYP3A5*3 had higher propensity to cause clopidogrel resistance with an odds ratio of 1.63. Variant alleles and genotypes of CYP3A5*3 polymorphism contributed significantly to clopidogrel resistance with a higher odds ratio. Thus, pharmacogenomics paves way for the emergence of stratified medicine in clopidogrel therapy and personalised pharmacotherapy in ischaemic heart disease.     

Biodegradation of nicotine by a novel nicotine-degrading bacterium, Pseudomonas plecoglossicida TND35 and its new biotransformation intermediates

Tobacco wastes that contain nicotine alkaloids are harmful to human health and the environment. In the investigation, a novel nicotine-biodegrading bacterium TND35 was isolated and identified as Pseudomonas plecoglossicida on the basis of phenotypic, biochemical characteristics and 16S rRNA sequence homology. We have studied the nicotine biodegradation potential of strain TND35 by detecting the intermediate metabolites using an array of approaches such as HPLC, GC–MS, NMR and FT-IR. Biotransformation metabolites, N-methylmyosmine, 4-hydroxy-1-(3-pyridyl)-1-butanone (HPB) and other three new intermediate metabolites namely, 3,5-bis (1-methylpyrrolidin-2-yl) pyridine, 2,3-dihydro-1-methyl-5-(pyridin-3-yl)-1H-pyrrol-2-ol and 5-(pyridin-3-yl)-1H-pyrrol-2(3H)-one have been identified. Interestingly, these intermediate metabolites suggest that the strain TND35 employs a novel nicotine biodegradation pathway, which is different from the reported pathways of Aspergillus oryzae 112822, Arthrobacter nicotinovorans pAO1, Agrobacterium tumefaciens S33 and other species of Pseudomonas. The metabolite, HPB reported in this study can also be used as biochemical marker for tobacco related cancer studies.     

Antihyperglycemic and antioxidant effects of a flavanone, naringenin, in streptozotocin–nicotinamide-induced experimental diabetic rats

In the present study, the putative antihyperglycemic and antioxidant effects of a flavanone, naringenin, were evaluated in comparison with those of glyclazide, a standard drug for therapy of diabetes mellitus. Diabetes was induced experimentally in 12-h-fasted rats by intraperitoneal injections of first streptozotocin (50 mg/kg b.w.) and then of nicotinamide (110 mg/kg b.w.) after a 15-min interval. Untreated diabetic rats revealed the following in comparison with normal rats: significantly higher mean levels of blood glucose and glycosylated hemoglobin, significantly lower mean levels of serum insulin, significantly lower mean activities of pancreatic antioxidant enzymes (superoxide dismutase, catalase, glutathione peroxidase, glutathione-S-transferase), significantly lower mean levels of plasma non-enzymatic antioxidants (reduced glutathione, vitamin C , vitamin E), significantly elevated mean levels of pancreatic malondialdehyde (MDA) and significantly elevated mean activities of serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and lactate dehydrogenase (LDH). Following oral administration of naringenin (50 mg/kg b.w./day) to diabetic rats for 21 days, the following observations were made in comparison with untreated diabetic rats: significantly lower mean levels of fasting blood glucose and glycosylated hemoglobin, significantly elevated serum insulin levels, significantly higher mean activities of pancreatic enzymatic antioxidants, significantly higher mean levels of plasma non-enzymatic antioxidants, lower mean pancreatic tissue levels of MDA and lower mean activities of ALT, AST, ALP and LDH in serum. The values obtained in the naringenin-treated animals approximated those observed in glyclazide-treated animals. Histopathological studies appeared to suggest a protective effect of naringenin on the pancreatic tissue in diabetic rats. These results suggest that naringenin exhibits antihyperglycemic and antioxidant effects in experimental diabetic rats.     

Olmesartan medoxomil treatment potently improves cardiac myosin-induced dilated cardiomyopathy via the modulation of ACE-2 and ANG 1-7 mas receptor

Angiotensin converting enzyme-2 (ACE-2) is a monocarboxypeptidase that metabolises angiotensin (ANG)-II into angiotensin 1-7 (ANG 1-7), thereby functioning as a negative regulator of the renin-angiotensin system. We investigated whether treatment with ANG-II type 1 receptor blocker, olmesartan medoxomil is associated with the attenuation of cardiac myosin-induced dilated cardiomyopathy (DCM) through recently established new axis of ACE-2/ANG 1-7 mas receptor. DCM was elicited in Lewis rats by immunisation with cardiac myosin, and 28 days after immunisation, the surviving Lewis rats were divided into two groups and treated with either olmesartan medoxomil (10 mg/kg/day) or vehicle. Myocardial protein and mRNA levels of ACE-2, ANG 1-7 mas receptor were upregulated in the olmesartan-treated group compared with those of vehicle-treated DCM rats. In contrast, Olmesartan treatment effectively suppressed the myocardial protein and mRNA expressions of inflammatory markers in comparison to the vehicle-treated DCM rats. Olmesartan treatment significantly reduced fibrosis, hypertrophy and their marker molecules (OPN, CTGF, ANP and GATA-4, respectively), as well as matrix metalloproteinases compared with those of vehicle-treated DCM rats. Enhanced myocardial protein levels of phospho-p38 MAPK, phospho-JNK and phospho MAPKAPK-2 in the vehicle-treated DCM rats were prevented by olmesartan treatment. In addition, olmesartan treatment significantly lowered the protein expressions (Nitrotyrosine, p47phox and p67phox) and superoxide radical production compared with those of vehicle-treated DCM rats. Our present study might serve as a new therapeutic target of DCM in cardiovascular diseases and cardiac myosin-induced DCM via the modulation of ACE-2/ANG 1-7 mas receptor axis in rats with DCM after myosin-immunisation.     

An evaluation study of trace element content in colorectal liver metastases and surrounding normal livers by X-ray fluorescence

Background Trace elements are involved in many key pathways involving cell cycle control. The levels of trace metals such as iron, copper, and zinc in colorectal liver metastases have not previously been assessed. Methods The trace element content in snap-frozen cancerous liver tissue from patients who underwent liver resection for colorectal liver metastases was compared with the normal surrounding liver (distant from the cancer) using X-ray fluorescence (XRF). Results X-ray fluorescence was performed on a total of 60 samples from 30 patients. Of these 29 matched pairs (of cancer and normal liver distant from cancer from the same patient) were eligible for univariate analysis. Iron (0.00598 vs. 0.02306), copper (0.00541 vs. 0.00786) and zinc (0.01790 vs. 0.04873) were statistically significantly lower in the cancer tissue than the normal liver. Iron, copper, and zinc were lower in the cancer tissue than in the normal liver in 24/29 (82.8%), 23/29 (79.3%), and 28/29 (96.6%) of cases respectively. Multivariate analysis of the 60 samples revealed that zinc was the only trace element decreased in the cancer tissue after adjusting for the other elements. Zinc levels were not affected by any of the histopathological variables. Conclusion Iron, copper, and zinc are lower in colorectal liver metastases than normal liver. An investigation into the pathways underlying these differences may provide a new understanding of cancer development and possible novel therapeutic targets.