Molecular docking and simulation studies against nucleoside diphosphate kinase (NDK) of Pseudomonas aeruginosa with secondary metabolite identified by genome mining from paenibacillusehimensis

Pseudomonas aeruginosa is one of the leading opportunistic pathogens that causes nosocomial pneumonia and mostly in people with cystic fibrosis. In the present study, an in-silicoapproach was adopted to identify the novel drug target against Pseudomonas aeruginosa by employing subtractive genomics and molecular docking studies. Each step in the subtractive genomics scrutinized the bacterial proteome and determined a potential drug target against Pseudomonas aeruginosa. 71 essential proteins were obtained from the subcellular localization method that resides in the extracellular region. Metabolic pathways were studied to elucidate the unique pathways where the involvement of proteins present in the pathogen was predicted and a total of 6 unique pathways were determined. By, Genome mining of the source organism Paenibacillusehimensis, 9 ligands were obtained. The molecular docking analysis between the binding site of target protein NDK and ligands was carried out by employing the AutoDock Vina tool. Based on the highest binding affinity, Paenibactin, AnabaenopeptinNZ857 and Nostamide A complex with NDK protein with a lower binding energy of -7.5 kcal/mol, -7.4and -7.2 kcal/molrespectively were considered for the simulation studies. Molecular dynamics simulation studies showed the ligand in complex with protein was highly stable and rigid for a duration of 150 ns. For Paenibactin, AnabaenopeptinNZ857 and Nostamide Acomplex with protein, RMSD plot showed a deviation of ∼0.2-0.3 nm till ∼30ns/50 ns-110ns and further stabilized. The radius of the gyration plot clearly showed that the values stayed at ∼1.45 nm- 1.55 nm showing compactness and stability. The SASA stayed at the range ∼80nm2 and at least one total number of hydrogen bonds was shown throughout the 150 ns simulation for all three possible ligand-protein complexes. In the RMSF plot, the maximum fluctuation was ranged from ∼0.4-0.42 nm at the range between ∼57ns-60ns.The Paenibactin, AnabaenopeptinNZ857 and Nostamide A complex with NDK protein showed a stable, rigid and compact interaction throughout the simulation of duration 150 ns.Communicated by Ramaswamy H. Sarma.

In-vitro cytotoxic effects of Solanum macranthum fruit. Dunal extract with antioxidant potential

Background

The current study undertaken to evaluate antioxidant property of Solanum macranthum fruit methanol extract and its in-vitro cytotoxic effects on breast cancer MDA-MB-231 and mice embryo fibroblast (MEF-L929) cell line.

Methods

The total alkaloids, phenols and flavonoids content in the methanol extract of S.macranthum fruit were estimated. The antioxidant activity was evaluated by FRAP assay, H2O2 scavenging assay and DPPH assay. Anti-inflammatory protein denaturation inhibition assay was carried out using bovine serum albumin. Anticancer property of the extract was evaluated against breast cancer MDA-MB-231 by MTT assay and comparative study was carried out on normal cells using MEF-L929 cell line.

Results

Phytochemical estimation revealed that total alkaloid content was measurable high (13.6 g/100 g of extract), where as the total phenolics and flavonoids content was 115.5 mg/GAE and 142.6 mg/QE. Further, the antioxidant effect of methanol extract by H2O2 assay showed considerably higher scavenging activity with 99.6% at 400 μg/ml, where as by FRAP assay the relative reducing power was estimated to be 39.1% at 400 μg/ml and in case of DPPH assay it was found to be 47.9% at 400 μg/ml. EC50 value of anti-inflammatory assay was found to be 112.96 μg/ml. Anticancer studies showed that the IC50 value was found to be 373.77 μg /ml against MDA-MB-231 breast cancer cell line, where as the methanol extract showed negligible cytotoxic effect against normal cells (MEF -L929 cell line), indicating its cancer specific effect.

Conclusion

Based on the results obtained, methanol extract of Solanum macranthum fruit was found to possess significant antioxidant properties and also showed potential anticancer property against MDA-MB-231 breast cancer cell line with negligible cytotoxic effect on normal cells revealing its potential application as an anticancer agent.

Genomic DNA of MCF-7 breast cancer cells not an ideal choice as positive control for PCR amplification based detection of Mouse Mammary Tumor Virus-Like Sequences

The identification of the etiology of breast cancer is a crucial research issue for the development of an effective preventive and treatment strategies. Researchers are exploring the possible involvement of Mouse Mammary Tumor Virus (MMTV) in causing human breast cancer. Hence, it becomes very important to use a consistent positive control agent in PCR amplification based detection of MMTV-Like Sequence (MMTV-LS) in human breast cancer for accurate and reproducible results. This study was done to investigate the feasibility of using genomic DNA of MCF-7 breast cancer cells to detect MMTV-LS using PCR amplification based detection. MMTV env and SAG gene located at the 3' long terminal repeat (LTR) sequences were targeted for the PCR based detection. No amplification was observed in case of the genomic DNA of MCF-7 breast cancer cells. However, the 2.7 kb DNA fragment comprising MMTV env and SAG LTR sequences yielded the products of desired size. From these results it can be concluded that Genomic DNA of MCF-7 cell is not a suitable choice as positive control for PCR or RT-PCR based detection of MMTV-LS. It is also suggested that plasmids containing the cloned genes or sequences of MMTV be used as positive control for detection of MMTV-LS.

Mutation Analysis of the LDL Receptor Gene in Indian Families with Familial Hypercholesterolemia

Objective: Familial Hypercholesterolemia (FH) is a metabolic disorder inherited as an autosomal dominant trait characterized by an increased plasma low-density lipoprotein (LDL) level. The disease is caused by several different mutations in the LDL receptor (LDLR) gene. Several mutations have been reported in this gene in patients from several ethnic groups. Early identification of individuals carrying the defective gene could be useful in reducing the risk of atherosclerosis and myocardial infraction by the available therapeutic methods. The techniques available for determining the number of the functional LDLR molecules are difficult to carry out and expensive. Our study presents mutation analysis of the LDLR gene in 24 Indian families with FH. Material & Methods: Peripheral blood samples were obtained form individuals after taking informed consent on the condition that each of these individuals had at least one first-degree relative affected with FH. Genomic DNA was isolated, exon-specific intronic primers were designed and used to amplify DNA samples from individuals.PCR products were directly subjected to automated DNA sequencing to detect the mutations. Along with the affected individuals, ten ethnically matched controls were also analyzed to determine the presence of the same mutations. Patients with Nephrotic Syndrome admitted to hospital were excluded from the study. Results: All the 24 patients had total cholesterol level above 300 mg/dl and LDL cholesterol level above 200mg/dl. Sequence analysis of the LDL receptor (LDLR) gene showed 3 novel mutations which have never been reported elsewhere. In exon 10 we reported g.29372_29373insC, which was found in all the 24 patients and was missence mutation coding for C (cysteine) instead of V (valine). Conclusion: Our study reported 3 novel mutations in 24 Indian families. These novel mutations are predicted to produce change in the amino acid and thus leading to the conformational changes in the structure of LDLR protein. Change in the LDLR protein makes the LDL receptor unable to transport the cholesterol in to the cell and hence cholesterol starts accumulating in the blood stream and leads to FH. Key Words: Familial Hypercholesterolemia; Mutation analysis; LDL Receptor geneDOI: http://dx.doi.org/10.3126/ajms.v2i2.4573Asian Journal of Medical Sciences 2 (2011) 82-86

Prevalence and risk of leukemia in the multi-ethnic population of North Karnataka

BACKGROUND

The aim of this study was to analyze the trends in the incidence rates of four major types of leukemia in the population of North Karnataka, which accounts for the 2.5% of the whole population of India. Due to the lack of any nationwide leukemia screening program, the majority of the people are not aware of the disease. Epidemiological study can play a vital role in understanding the occurrence and outcome of the disease.

PATIENTS AND METHODS

Focusing on variables like age, sex, race, blood group and lifestyle habits, detailed reports of 417 males and 230 females (M:F ratio 1.8:1) were collected from different hospitals of North Karnataka and analyzed for their risk of leukemia.

RESULTS

Compared to female patients, Hindu males were found to have greater risk of occurrence of leukemia (p=0.0333). The males of scheduled caste (SC) and Lingayat communities showed a high risk than other communities (p=0.000). The occurrence of AML showed a significant relationship with ABO blood groups (p=0.0090). The frequency of leukemia is quite high in Belgaum district when compared to others districts of North Karnataka and totally absent in Bidar district. The reasons need precise molecular and genetical studies of the population.

CONCLUSIONS

The localized communities of Lingayat and SCs needs to be further studied to get a better understanding of the higher risk of occurrence of leukemia in males. Moreover, since the spectrum of cancer epidemiology seen in India is different from that in developed countries more emphasis should be placed on better development of regional and national registries.

Prevalence and distribution of high risk human papillomavirus (HPV) Types 16 and 18 in Carcinoma of cervix, saliva of patients with oral squamous cell carcinoma and in the general population in Karnataka, India

BACKGROUND

In view of conducting HPV vaccination in India it is most important to understand the prevalence of HPV genotypes in this population, not only in squamous cell carcinoma of cervix and oral cavity but also in the general population. In this study we explored the prevalence and distribution of high-risk HPV types 16 and 18 in carcinoma of cervix, saliva of patients with oral squamous cell carcinoma and in general population in Karnataka.

METHODS

Cervical cancer specimens after punch biopsy (n=60) were obtained from women attending Karnataka Institute of Medical Sciences and Karnataka Cancer Therapy and Research Institute, Hubli (KCTRI). Saliva rinse of (n=34) OSCC patients from KCTRI and (n=396) normal individuals from different regions of North Karnataka, were collected and PCR based high-risk HPV genotyping was carried out.

RESULTS

Using consensus PCR primers it was observed that 96.7% patients were infected with HPV irrespective of specific type in cervical cancer. Among them, HPV 16 was observed in 89.7%, HPV 18 in 86.2% and both HPV 16 and 18 in 79.3% patients. In OSCC, 70.6% were positive for HPV, among which HPV 16 prevalence was observed in 45.8%, HPV 18 in 54.2%, and HPV 16 and 18 multiple infection in 4.18%. In general population, HPV prevalence was observed in 84.4%. Among them, HPV 16 was observed in 2.75% and HPV 18 in 22.0% patients. In general population, multiple infection with HPV 16 and 18 was not observed but 75.3% were found to be infected by HPV genotypes other than HPV 16 and 18.

CONCLUSIONS

Our study reveals that multiple infection of HPV 16 and 18 is quite high in cervical cancer and in case of OSCC, it was in conformity with the other studies. In general population HPV 18 prevalence was observed to be high. With this, we can conclude that both HPV 16 and 18 vaccinations will reduce the burden of cervical cancer and OSCC in Karnataka.

The anti-inflammatory activity of some sulphonamides in albino rats

Clinically equivalent doses of dapsone, sulphasalasine and sulphamethizole in albino rats showed significant (P < 0.05) anti-inflammatory activity in carrageenan and cotton pellet induced inflammation. Their activity was comparable to that of aspirin (200 mg/kg) and was confirmed by granuloma histology. Further, these compounds also showed significant (P < 0.01) analgesic activity which was comparable to that of aspirin. The ulcer index for sulphamethizole was comparable to that of control animals, whereas dapsone and sulphasalazine showed significant ulcerogenicity (P < 0.01). Other sulphonamides like sulphadiazine, sulphanilamide, sulphamoxole and cotrimoxazole did not show significant anti-inflammatory and analgesic activities.

Bile acids. LXXIII. Synthesis of analogs of 7 alpha-hydroxy-4-cholesten-3-one as substrates for hepatic steroid 12 alpha-hydroxylase

Analogs of 7 alpha-hydroxy-4-cholesten-3-one were prepared to ascertain structural features necessary for maximal activity of hepatic microsomal 12 alpha-steroid hydroxylase. Methyl 3 alpha,7 alpha-dihydroxy-5 beta-cholane-24-carboxylate derived from chenodeoxycholic acid was oxidized at C-3 with silver carbonate/Celite. The product was hydrolyzed and dehydrogenated with SeO2 to provide 3-oxo-7 alpha-hydroxy-4-cholene-24-carboxylic acid. 5 beta-Cholestane-3 alpha,7 alpha,25-triol and 5 beta-cholestane-3 alpha,7 alpha,12 alpha,25-tetrol were similarly oxidized at C-3 and dehydrogenated to provide 7 alpha,25-dihydroxy-4-cholesten-3-one and 7 alpha,12 alpha,25-trihydroxy-4-cholesten-3-one, respectively. The products were characterized by thin-layer and gas chromatography, ultraviolet, infrared, proton resonance and mass spectrometry.

Bile acids. LXIV. Synthesis of 5 alpha-cholestane-3 alpha, 7 alpha, 25-triol and esters of new 5 alpha-bile acids

Interest in the structural requirements of a sterol or bile acid for maximal activity by an hepatic microsomal steroid 12 alpha-hydroxylase prompted the preparation of 5 alpha-cholestane-3 alpha, 7 alpha, 25-triol and 5 alpha-analogs of 3 alpha, 7 alpha-dihydroxy-5 beta-cholane-24-carboxylic acid. Methyl 3 alpha, 7 alpha-dihydroxy-5 beta-cholane-24-carboxylate derived from methyl chenodeoxycholate via the Arndt-Eistert reaction was allomerized with Raney nickel in boiling p-cymene to provide a number of product of which methyl 3, 7-dioxo-5 beta- and 5 alpha-cholane-24-carboxylates, methyl 3-oxo-7 alpha-hydroxy-5 beta-and 5 alpha-cholane-24-carboxylates, were identified. Reduction with K-Selectride of methyl 3-oxo-7 alpha-hydroxy-5 beta-cholane-24-carboxylate, provided a high yield of methyl 3 alpha, 7 alpha-dihydroxy-5 alpha-cholane-24-carboxylate. Treatment of this ester with an excess of methyl magnesium iodide afforded 5 alpha-cholestane-3 alpha, 7 alpha, 25-triol. The products were characterized by thin-layer and gas liquid chromatography, proton resonance, infrared and mass spectrometry.