The face of hepatitis C virus (HCV) therapy is changing dramatically. Direct-acting antiviral agents (DAAs) specifically targeting HCV proteins have been developed and entered clinical practice in ...2011. However, despite high sustained viral response (SVR) rates of more than 90%, a fraction of patients do not eliminate the virus and in these cases treatment failure has been associated with the selection of drug resistance mutations (RAMs). RAMs may be prevalent prior to the start of treatment, or can be selected under therapy, and furthermore they can persist after cessation of treatment. Additionally, certain DAAs have been approved only for distinct HCV genotypes and may even have subtype specificity. Thus, sequence analysis before start of therapy is instrumental for managing DAA-based treatment strategies. We have created the interpretation system geno2phenoHCV (g2pHCV) to analyse HCV sequence data with respect to viral subtype and to predict drug resistance. Extensive reviewing and weighting of literature related to HCV drug resistance was performed to create a comprehensive list of drug resistance rules for inhibitors of the HCV protease in non-structural protein 3 (NS3-protease: Boceprevir, Paritaprevir, Simeprevir, Asunaprevir, Grazoprevir and Telaprevir), the NS5A replicase factor (Daclatasvir, Ledipasvir, Elbasvir and Ombitasvir), and the NS5B RNA-dependent RNA polymerase (Dasabuvir and Sofosbuvir). Upon submission of up to eight sequences, g2pHCV aligns the input sequences, identifies the genomic region(s), predicts the HCV geno- and subtypes, and generates for each DAA a drug resistance prediction report. g2pHCV offers easy-to-use and fast subtype and resistance analysis of HCV sequences, is continuously updated and freely accessible under http://hcv.geno2pheno.org/index.php. The system was partially validated with respect to the NS3-protease inhibitors Boceprevir, Telaprevir and Simeprevir by using data generated with recombinant, phenotypic cell culture assays obtained from patients' virus variants.
Inhibition of HIV replication initially targeted viral enzymes, which are exclusively expressed by the virus and not present in the human cell. The development of reverse transcriptase (RT) ...inhibitors started with the discovery of antiretroviral activity of the nucleoside analog zidovudine in March 1987. Currently, six major classes of antiretroviral drugs are used for the treatment of HIV-infected patients: the RT inhibitors, nucleoside inhibitors and nonnucleoside inhibitors, the protease inhibitors, the integrase inhibitor raltegravir, the fusion inhibitor enfuvirtide (T-20), and the chemokine receptor 5 antagonist maraviroc. A seventh class, the maturation inhibitors, has not yet been approved as their effectiveness is impaired by HIV-1 polymorphisms naturally occurring in 30-40% of HIV-1 therapy-naive isolates. The use of antiretroviral combination therapy has proven to be effective in delaying progression to AIDS and to reconstitute the immune system of HIV-infected individuals. During the last 5 years, the introduction of the newest antiretrovirals has increased treatment efficacy tremendously. However, the development and accumulation of resistance to all antiretroviral drug classes are still a major problem. Additional targets will have to be defined to achieve the ultimate goal: the eradication of the virus from the infected human body.
There is growing evidence to support the hypothesis that statins may act as neuroprotectants in several neuropathological conditions, including Alzheimer's disease. The mechanisms for neuroprotection ...are only partially understood, however, and pleiotropic phenomena could be involved. We have made a comparative study of 9 statins (lovastatin, mevastatin, pravastatin, simvastatin, cerivastatin, atorvastatin, fluvastatin, pitavastatin, and rosuvastatin), analyzing several parameters that could be related to neuroprotection, such as chemical structure, lipophilicity, potential blood-brain-barrier penetration (BBB), 3-hydroxy-3-methylglutaryl co-enzyme A reductase inhibition, cholesterol modulation in neurons, glia, and human hepatocyte cell lines, and protection against neurodegeneration caused by tau hyperphosphorylation induced by okadaic acid. Our results indicate that monacolin J derivatives (natural and semi-synthetic statins) are the best candidates for the prevention of neurodegenerative conditions due to their higher potential BBB penetration capacity, cholesterol lowering effect on neurons with a satisfactory safety profile, and in vitro protection against cell death caused by okadaic acid in culture. Among the nine statins studied, simvastatin presented the best characteristics for preventing neurodegenerative conditions.
Flavonoids possess several biological/pharmacological activities including anticancer, antimicrobial, antiviral, anti-inflammatory, immunomodulatory and antioxidant. The aim of this study was to ...evaluate the effect of flavonoids on macrophage physiology. For this purpose we selected some flavonoids belonging to the most common and abundant groups (flavonols—quercetin and kaempferol; flavones—diosmetin, apigenin, chrysin and luteolin; isoflavones—genistein and daidzein and flavanones—hesperetin). We decided to use primary bone marrow-derived macrophages (BMDM) as cellular model, since they represent a homogenous, non-transformed population of macrophages that can be stimulated
in vitro to proliferate by macrophage colony-stimulating factor (M-CSF) or activated by LPS. In this regard, we demonstrated that most of the flavonoids assayed reduce macrophage M-CSF-induced proliferation without affecting cellular viability. Moreover, some flavonoids also inhibit TNFα production as well as iNOS expression and NO production in LPS-activated macrophages, an effect that has been associated with the inhibition of the NF-κB pathway. We also found that luteolin and quercetin are able to stimulate the expression of the anti-inflammatory cytokine IL-10 at low concentrations (<50
μM). Analysis of the structure–activity relationship showed that four hydroxylations at positions 5, 7, 3′ and 4′, together with the double bond at C
2–C
3 and the position of the B ring at 2, seem to be necessary for the highest anti-inflammatory effect.
Abstract Objective We studied the coadjuvant capability of oral consumption of the breast-milk–isolated strain Lactobacillus fermentum (CECT5716) for an anti-influenza vaccine. Methods A randomized, ...double-blinded, placebo-controlled human clinical trial including 50 volunteers (31 male and 19 female) was performed to address the immunologic effects of an intramuscular anti-influenza vaccine in adults (33.0 ± 7.7 y old). Fifty percent of volunteers received an oral daily dose of methylcellulose (placebo) or probiotic bacteria (1 × 1010 colony-forming units/d) 2 wk before vaccination and 2 wk after vaccination. Results Two weeks after vaccination there was an increase in the proportion of natural killer cells in the probiotic group but not in the placebo group. The vaccination induced an increase in T-helper type 1 cytokine concentrations and in T-helper and T-cytotoxic proportions in both groups; however, the probiotic group showed a significant higher induction in some of these parameters. Regarding the humoral effects, induction of antibody response in the placebo group could not be detected. In the case of the probiotic group, a significant increase in antigen specific immunoglobulin A was detected. Although an increase in total immunoglobulin M was observed, changes in anti-influenza antigen specific immunoglobulin M were not observed. The incidence of an influenza-like illness during 5 mo after vaccination (October to February) was lower in the group consuming the probiotic bacteria. Conclusion Oral administration of the strain L. fermentum CECT5716 potentates the immunologic response of an anti-influenza vaccine and may provide enhanced systemic protection from infection by increasing the T-helper type 1 response and virus-neutralizing antibodies.
Abstract Objective Intestinal microbiota plays an important role in the prevention of certain diseases during the pediatric years. Thus, there is an increasing interest in the addition of probiotics ...to infant formulas. The aim of this study was to evaluate the safety of a follow-on formula with Lactobacillus salivarius CECT5713 in 6-mo-old children. Methods The antibiotic susceptibility of L. salivarius CECT5713 was analyzed by a dilution method. A double-blinded, randomized, placebo controlled study was performed. Children ( n = 80) were distributed in two groups and consumed the formula supplemented or not with probiotics (2 × 106 colony-forming units cfu/g) during 6 mo. Fecal samples were collected at enrollment, at 3 mo, and at the end of trial. Clinical and anthropometric evaluations were performed. Depending on the variable, one-way or two-way repeated measures analysis of variance were used for the statistical analysis. Results The antibiotic susceptibility profile of the strain resulted as safe. No adverse effects associated with the consumption of the probiotic formula were reported. In addition, clinical parameters did not differ between groups. Consumption of the probiotic supplemented formula led to an increase in the fecal lactobacilli content (7.6 ± 0.2 versus 7.9 ± 0.1 log cfu/g, P < 0.05). Lactobacillus salivarius CECT5713 was detected in the feces of volunteers from the probiotic group. Probiotic consumption induced a significant increase in the fecal concentration of butyric acid at 6 mo. Conclusion Thus, a follow-on formula with L. salivarius CECT5713 is safe and well tolerated in 6-mo-old infants.
There is an increasing interest in the intestinal and immunological effects of probiotics. The aim of the present study is to evaluate the tolerance and beneficial effects in healthy adults of the ...strain,
Lactobacillus salivarius CECT5713 isolated from breast milk. A phase II, randomized, double-blinded, placebo-controlled human clinical trial was carried out in 40 healthy adults. The Probiotic group received a daily dose of 2
×
10
8 CFU of
L. salivarius CECT5713 in capsules during 4 weeks while volunteers of the control received only a placebo. Gastrointestinal and immunological parameters were analyzed. Results showed that
L. salivarius CECT5713 was well tolerated and no adverse effects were detected. Consumption of the probiotic strain increased fecal lactobacilli counts (7.9
±
0.1 vs. 7.05
±
0.2 CFU/g feces,
P
=
0.001). Also, an improvement in the frequency of defecation (
P
=
0.04) was observed. Probiotic treatment induced significantly the percentage of NK cells and monocytes, as well as the plasmatic levels of immunoglobulins M, A and G, and the regulatory cytokine IL-10 (72.3
±
11.7 in probiotic group vs. 27.3
±
6.4
pg/mL in control group,
P
<
0.01). Thus, it can be concluded that daily administration of
L. salivarius CECT5713 to healthy adults is safe and improve gut microbiota and different parameters related to immune response.
The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage. As an alternative to costly ...phenotypic assays, computational methods aim at predicting virus tropism based on the sequence and structure of the V3 loop of the virus gp120 protein. Here we present a numerical descriptor of the V3 loop encoding its physicochemical and structural properties. The descriptor allows for structure-based prediction of HIV tropism and identification of properties of the V3 loop that are crucial for coreceptor usage. Use of the proposed descriptor for prediction results in a statistically significant improvement over the prediction based solely on V3 sequence with 3 percentage points improvement in AUC and 7 percentage points in sensitivity at the specificity of the 11/25 rule (95%). We additionally assessed the predictive power of the new method on clinically derived 'bulk' sequence data and obtained a statistically significant improvement in AUC of 3 percentage points over sequence-based prediction. Furthermore, we demonstrated the capacity of our method to predict therapy outcome by applying it to 53 samples from patients undergoing Maraviroc therapy. The analysis of structural features of the loop informative of tropism indicates the importance of two loop regions and their physicochemical properties. The regions are located on opposite strands of the loop stem and the respective features are predominantly charge-, hydrophobicity- and structure-related. These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under http://structure.bioinf.mpi-inf.mpg.de/.
Russia has one of the largest and fastest growing HIV epidemics. However, epidemiological data are scarce. Sub-subtype A6 is most prevalent in Russia but its identification is challenging. We ...analysed protease/reverse transcriptase-, integrase-sequences, and epidemiological data from 303 patients to develop a methodology for the systematisation of A6 identification and to describe the HIV epidemiology in the Russian Southern Federal District. Drug consumption (32.0%) and heterosexual contact (27.1%) were the major reported transmission risks. This study successfully established the settings for systematic identification of A6 samples. Low frequency of subtype B (3.3%) and large prevalence of sub-subtype A6 (69.6%) and subtype G (23.4%) were detected. Transmitted PI- (8.8%) and NRTI-resistance (6.4%) were detected in therapy-naive patients. In therapy-experienced patients, 17.3% of the isolates showed resistance to PIs, 50.0% to NRTI, 39.2% to NNRTIs, and 9.5% to INSTIs. Multiresistance was identified in 52 isolates, 40 corresponding to two-class resistance and seven to three-class resistance. Two resistance-associated-mutations significantly associated to sub-subtype A6 samples: A62V
and G190S
. This study establishes the conditions for a systematic annotation of sub-subtype A6 to normalise epidemiological studies. Accurate knowledge on South Russian epidemiology will allow for the development of efficient regional frameworks for HIV-1 infection management.
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