Antitumor studies. Part 4: Design, synthesis, antitumor activity, and molecular docking study of novel 2-substituted 2-deoxoflavin-5-oxides, 2-deoxoalloxazine-5-oxides, and their 5-deaza analogs

Various novel 10-alkyl-2-deoxo-2-methylthioflavin-5-oxides and their 2-alkylamino derivatives were prepared by facile nitrosative cyclization of 6-(N-alkylanilino)-2-methylthiopyrimidin-4(3H)-ones followed by nucleophilic replacement of the 2-methylthio moiety by different amines, and acidic hydrolysis of the 2-methylthio moiety afforded the corresponding flavin derivatives. 2-Deoxo-2-methylthio-5-deazaalloxazines and 2-deoxo-2-methylthioalloxazine-5-oxides were also prepared by Vilsmeier reaction and by nitrosation of 6-anilino-2-methylthiopyrimidin-4(3H)-ones, respectively. Then, they were subjected to nucleophilic replacement with appropriate amines to produce the corresponding 2-alkylamino derivatives. Regiospecific N(3)-alkylation of 2-deoxo-2-methylthioalloxazine-5-oxides was carried out with various alkylating agents in the usual way. The antitumor activities against CCRF-HSB-2 and KB tumor cells have been investigated in vitro, and many compounds showed promising antitumor activities. Furthermore, AutoDock molecular docking into PTK (PDB: 1t46) has been done for lead optimization of the aforementioned compounds as potential PTK inhibitors.     

MAD-DPD: designing highly degenerate primers with maximum amplification specificity

This work introduces minimum accumulative degeneracy, a variant of the degenerate primer design problem, which is particularly useful when a large number of sequences are to be covered by a set of restricted number of primers. A primer set, which is designed on a minimum accumulative degeneracy basis, especially helps to reduce nonspecific PCR amplification of undesired DNA fragments, as fewer primer species are present in PCR. A Boltzmann machine is designed to solve the minimum accumulative degeneracy degenerate primer design problem, called the MAD-DPD Boltzmann machine. This algorithm shows great flexibility, as it can be determined either to solve the problem with strict fidelity to covering all input sequences or to exclude some input sequences if it results in less degenerate primers. This Boltzmann machine is successfully implemented in designing a new set of primers for amplification of antibody variable fragments from mouse spleen cells, which theoretically covers more diverse antibody sequences than currently available primers. The MAD-DPD Boltzmann machine is available online at bioinf.cs.ipm.ir/download/MAD_DPD08172007.zip.     

Synthesis and biological evaluation of 2-amino-7,7-dimethyl 4-substituted-5-oxo-1-(3,4,5-trimethoxy)-1,4,5,6,7,8-hexahydro-quinoline-3-carbonitrile derivatives as potential cytotoxic agents

A large number of antimitotic drugs, derived from natural sources or chemically synthesized, have been identified and shown to interfere with the tubulin system. Inhibition of tubulin polymerization is among the important targets useful in the cancer therapy.The present work reports the synthesis of some novel quinoline derivatives bearing a trimethoxyphenyl moiety. The trimethoxybenzene moiety has been reported to be crucial to obtain relevant cytotoxic and antitubulin responses. All the newly synthesized compounds were evaluated for their in vitro anticancer activity. Several compounds showed interesting cytotoxic activities compared to the used reference drug.     

Biocontrol of aflatoxin in corn by inoculation with non-aflatoxigenic Aspergillus flavus isolates

The ability of two non-aflatoxigenic Aspergillus flavus Link isolates (CT3 and K49) to reduce aflatoxin contamination of corn was assessed in a 4-year field study (2001–2004). Soil was treated with six wheat inoculant treatments: aflatoxigenic isolate F3W4; two non-aflatoxigenic isolates (CT3 and K49); two mixtures of CT3 or K49 with F3W4; and an autoclaved wheat control, applied at 20 kg ha^?1. In 2001, inoculation with the aflatoxigenic isolate increased corn grain aflatoxin levels by 188% compared to the non-inoculated control, while CT3 and K49 inoculation reduced aflatoxin levels in corn grain by 86 and 60%, respectively. In 2002, the non-toxigenic CT3 and K49 reduced aflatoxin levels by 61 and 76% compared to non-inoculated controls, respectively. In 2001, mixtures of aflatoxigenic and non-aflatoxigenic isolates had little effect on aflatoxin levels, but in 2002, inoculation with mixtures of K49 and CT3 reduced aflatoxin levels 68 and 37% compared to non-inoculated controls, respectively. In 2003 and 2004, a low level of natural aflatoxin contamination was observed (8 ng g^?1). However, inoculation with mixtures of K49?+?F3W4 and CT3?+?F3W4, reduced levels of aflatoxin 65–94% compared to the aflatoxigenic strain alone. Compared to the non-sclerotia producing CT3, strain K49 produces large sclerotia, has more rapid in vitro radial growth, and a greater ability to colonize corn when artificially inoculated, perhaps indicating greater ecological competence. Results indicate that non-aflatoxigenic, indigenous A. flavus isolates, such as strain K49, have potential use for biocontrol of aflatoxin contamination in southern US corn.     

Efficiency of diagnostic biomarkers among colonic schistosomiasis Egyptian patients

The schistosomal parasite plays a critical role in the development of malignant lesions in different organs. The pathogenesis of cancer is currently under intense investigation to identify reliable prognostic indices for disease detection. The objective of this paper is to evaluate certain biochemical parameters as diagnostic tools to efficiently differentiate between colonic carcinoma and colonic carcinoma associated with schistosomal infection among Egyptian patients. The parameters under investigation are interleukin 2 (IL-2), tumour necrosis factor alpha (TNF-α), carcinoembryonic antigen (CEA) levels, tissue telomerase, pyruvate kinase (PK), glucose-6-phosphate dehydrogenase (G-6-PD) and lactate dehydrogenase (LDH) enzyme activities. The results revealed a significant elevation in the level of the tumour markers IL-2, TNF-α and CEA as well as the activities of LDH, telomerase and G-6-PD among non-bilharzial and bilharzial colonic cancer groups, with a more potent effect in bilharzial infection-associated colonic cancer. A significant inhibition in PK activity was recorded in the same manner as compared to normal tissues. The efficacy of this biomarker was also evaluated through detecting sensitivity, specificity, negative and positive predictive values. In conclusion, schistosomal colonic carcinoma patients displayed more drastic changes in all parameters under investigation. The combination of the selected parameters succeeded in serving as biomarkers to differentiate between the two malignant types.     

Hepatitis C patient-derived glycoproteins exhibit marked differences in susceptibility to serum neutralizing antibodies: genetic subtype defines antigenic but not neutralization serotype

Neutralizing antibodies have a role in controlling hepatitis C virus (HCV) infection. A successful vaccine will need to elicit potently neutralizing antibodies that are capable of preventing the infection of genetically diverse viral isolates. However, the specificity of the neutralizing antibody response in natural HCV infection still is poorly understood. To address this, we examined the reactivity of polyclonal antibodies isolated from chronic HCV infection to the diverse patient-isolated HCV envelope glycoproteins E1 and E2 (E1E2), and we also examined the potential to neutralize the entry of pseudoparticles bearing these diverse E1E2 proteins. The genetic type of the infection was found to determine the pattern of the antibody recognition of these E1E2 proteins, with the greatest reactivity to homologous E1E2 proteins. This relationship was strongest when the component of the antibody response directed only to linear epitopes was analyzed. In contrast, the neutralization serotype did not correlate with genotype. Instead, serum-derived antibodies displayed a range of neutralization breadth and potency, while different E1E2 glycoproteins displayed different sensitivities to neutralization, such that these could be divided broadly into neutralization-sensitive and -resistant phenotypes. An important additional observation was that entry mediated by some E1E2 proteins was enhanced in the presence of some of the polyclonal antibody fractions isolated during chronic infection. These data highlight the need to use diverse E1E2 isolates, which represent extremes of neutralization sensitivity, when screening antibodies for therapeutic potential and for testing antibodies generated following immunization as part of vaccine development.     

Limnology and cyanobacterial diversity of high altitude lakes of Lahaul-Spiti in Himachal Pradesh,India

Limnological data of four high altitude lakes from the cold desert region of Himachal Pradesh, India, has been correlated with cyanobacterial diversity. Physico-chemical characteristics and nutrient contents of the studied lakes revealed that Sissu Lake is mesotrophic while Chandra Tal, Suraj Tal and Deepak Tal are ultra-oligotrophic. Based on morphology and 16S rRNA gene sequence, a total of 20 cyanobacterial species belonging to 11 genera were identified. Canonical correspondence analysis distinguished three groups of species with respect to their occurrence and nutrient/physical environment demand. The first group, which included Nostoc linckia, N. punctiforme, Nodularia sphaerocarpa, Geitlerinema acutissimum, Limnothrix redekii, Planktothrix agardhii and Plank. clathrata, was characteristic of water with high nutrient content and high temperature. The second group, including Gloeocapsopsis pleurocapsoides, Leptolyngbya antarctica, L. frigida, Pseudanabaena frigida and N. spongiaeforme, occurred in oligotrophic water with high pH and low temperature. The distribution of third group of Cyanobium parvum, Synechocystis pevalekii, L. benthonica, L. foveolarum, L. lurida, L. valderiana, Phormidium autumnale and P. chalybeum could not be associated with a particular environmental condition because of their presence in all sampling sites.     

Viscoelastic shear properties of the corneal stroma

The cornea is a highly specialized transparent tissue which covers the front of the eye. It is a tough tissue responsible for refracting the light and protecting the sensitive internal contents of the eye. The biomechanical properties of the cornea are primarily derived from its extracellular matrix, the stroma. The majority of previous studies have used strip tensile and pressure inflation testing methods to determine material parameters of the corneal stroma. Since these techniques do not allow measurements of the shear properties, there is little information available on transverse shear modulus of the cornea. The primary objectives of the present study were to determine the viscoelastic behavior of the corneal stroma in shear and to investigate the effects of the compressive strain. A thorough knowledge of the shear properties is required for developing better material models for corneal biomechanics. In the present study, torsional shear experiments were conducted at different levels of compressive strain (0–30%) on porcine corneal buttons. First, the range of linear viscoelasticity was determined from strain sweep experiments. Then, frequency sweep experiments with a shear strain amplitude of 0.2% (which was within the region of linear viscoelasticity) were performed. The corneal stroma exhibited viscoelastic properties in shear. The shear storage modulus, G′, and shear loss modulus, G″, were reported as a function of tissue compression. It was found that although both of these parameters were dependent on frequency, shear strain amplitude, and compressive strain, the average shear storage and loss moduli varied from 2 to 8 kPa, and 0.3 to 1.2 kPa, respectively. Therefore, it can be concluded that the transverse shear modulus is of the same order of magnitude as the out-of-plane Young's modulus and is about three orders of magnitude lower than the in-plane Young's modulus.     

Impact of Random Variables Probability Distribution on Public Health Risk Assessment from Contaminated Soil

Probabilistic methods are now being applied increasingly to public health risk assessment instead of the deterministic, conservative, point estimates. An essential part of the probabilistic methods is the selection of probability distribution functions to represent the uncertainty of the random variables considered. We study the effect of selection of different probability distribution functions on the probabilistic outcome using the first-order reliability method (FORM). An example of cancer risk resulting from dermal contact with benzo(a)pyrene (BaP)-contaminated soil is given. Cancer potency factor, soil concentration, and fraction of skin area exposed were assigned normal, lognormal, and uniform probability distribution functions, and the effect of probability of exceeding a target risk level (termed the probability of failure) and sensitivity measures were studied. We investigated the question: what happens when one assumes different distribution shapes with the same mean and standard deviation? The results indicate that the selection of a probability distribution function for the random variables had a moderate impact on the probability of failure when the target risk is at the 50th percentile level, while the impact was much larger for a 95th target risk percentile. We conclude that the probability distribution will have a large impact because in most cases the regulatory threshold risk is at the tail end of the risk distribution. The impact of the distributions on probabilistic sensitivity, however, showed a reversed trend, where the impact was slightly more appreciable for the 50th percentile than for the 95th percentile. The selection of distribution shape did not, however, alter the order of probabilistic sensitivity of the basic random variables.