Valproic acid radiosensitizes anaplastic thyroid cells through a decrease of the DNA damage repair capacity.

BACKGROUND: Anaplastic thyroid cancer (ATC) represents a rare lethal human malignancy with poor prognosis. Multimodality treatment, including radiotherapy, is recommended to improve local control and survival. Valproic acid (VA) is a clinically available histone deacetylase inhibitor with a well-documented side effect profile. In this study, we aim to investigate the combined effect of VA with photon irradiation in vitro. METHODS: Anaplastic thyroid cancer cells (8505c) were used to investigate the radiosensitizing effect of VA. RESULTS: VA sensitized cells to photon irradiation. VA increased radiation-induced apoptosis and radiation-induced DNA damage measured by γH2AX foci induction. Furthermore, VA prolonged γH2AX foci disappearance over time in irradiated cells and decreased the radiation-induced levels of mRNA of key DNA damage repair proteins of the homologous recombination (HR) and the nonhomologous end joining (NHEJ) pathways. CONCLUSIONS: VA at a clinically safe dose enhance the radiosensitivity of 8505c cells through an increase in radiation-induced apoptosis and a disruption in the molecular mechanism of HR and NHEJ DNA damage repair pathways.

Environmental Effects Determine the Structure of Potential ß-Amino Acid Based Foldamers.

This work shows that hybrid peptides formed by alternating trans-2-aminocyclopentanecarboxylic acid (trans-ACPC) and trans-2-aminocyclohexanecarboxylic acid (trans-ACHC) do not fold in the solvents typically used in the study of their homo-oligomers. Only when the peptides are assayed in SDS micelles are the predicted helical structures obtained. This indicates that the environment could play an equally important role (as the backbone stereochemistry) in determining their fold, possibly by providing a sequestered environment.

Computer-aided structure-based design of multitarget leads for Alzheimer's disease.

Alzheimer's disease is a neurodegenerative pathology with unmet clinical needs. A highly desirable approach to this syndrome would be to find a single lead that could bind to some or all of the selected biomolecules that participate in the amyloid cascade, the most accepted route for Alzheimer disease genesis. In order to circumvent the challenge posed by the sizable differences in the binding sites of the molecular targets, we propose a computer-assisted protocol based on a pharmacophore and a set of required interactions with the targets that allows for the automated screening of candidates. We used a combination of docking and molecular dynamics protocols in order to discard nonbinders, optimize the best candidates, and provide a rationale for their potential as inhibitors. To provide a proof of concept, we proceeded to screen the literature and databases, a task that allowed us to identify a set of carbazole-containing compounds that initially showed affinity only for the cholinergic targets in our experimental assays. Two cycles of design based on our protocol led to a new set of analogues that were synthesized and assayed. The assay results revealed that the designed inhibitors had improved affinities for BACE-1 by more than 3 orders of magnitude and also displayed amyloid aggregation inhibition and affinity for AChE and BuChE, a result that led us to a group of multitarget amyloid cascade inhibitors that also could have a positive effect at the cholinergic level.

Effect of pH and ligand charge state on BACE-1 fragment docking performance.

In this work we propose a protocol for estimating the effect of pH on the docking performance to BACE-1, which affords the charge state of the inhibitor as well as the protonation state of all ionisable residues in the protein at a given pH value. To the best of our knowledge, this is the first report of a protocol predicting the BACE-1 ligand docking poses not only at the neutral pH at which most crystallographic structures were obtained, but also at the optimal pH of the enzyme (in the acidic range), at which most of the BACE-1 binding affinity assays are performed. We have applied this protocol to a set of 23 fragment-like BACE-1 ligands that span four orders of magnitude in their binding affinities. The pK a values of the BACE-1 acidic residues deviate substantially from the estimates for model compounds in solution and display a ligand dependent variability, especially in the case of the catalytic Asp dyad residues. This outcome should have a strong bearing on the design of protocols for docking based BACE-1 screening campaigns. Finally, we were able to find an explanation for the poor docking success rate of some fragments based on the availability of anchoring points, a rationale that could help to improve hit rates in BACE-1 screening campaigns.

Experimental and 'in silico' analysis of the effect of pH on HIV-1 protease inhibitor affinity: implications for the charge state of the protein ionogenic groups.

The pH dependence of the HIV-1 protease inhibitor affinity was studied by determining the interaction kinetics of a series of inhibitors at three pH values by surface plasmon resonance (SPR) biosensor analysis. The results were rationalized by molecular mechanics based protocols that have as a starting point the structures of the HIV-1 protease inhibitor complexes differing in the protonation states as predicted by our calculations. The SPR experiments indicate a variety of binding affinity pH dependencies which are rather well reproduced by our simulations. Moreover, our calculations are able to pinpoint the possible changes in the charged state of the protein binding site and of the inhibitor that underlie the observed effects of the pH on binding affinity. The combination of SPR and molecular mechanics calculations has afforded novel insights into the pH dependence of inhibitor interactions with their target. This work raises the possibility of designing inhibitors with different pH binding affinity profiles to the ones described here.

Effect of the protonation state of the titratable residues on the inhibitor affinity to BACE-1.

BACE-1 is one of the aspartic proteases involved in the cleavage of beta amyloid peptide, an initial step in the formation of amyloid plaques whose toxicity induces neuron death in Alzheimer's disease patients. One of the central issues in the search of novel BACE-1 inhibitors is the optimum pH for the binding of inhibitors to the enzyme. It is known that the enzyme has optimal catalytic activity at acidic pH, while cell active inhibitors may bind optimally at higher pH. In this work we determine the effect of the pH on the affinities of a set of inhibitors, with a variety of chemical motifs, for the ectodomain region of BACE-1 by a surface plasmon resonance (SPR) biosensor based assay. In order to understand the molecular interactions that underlie the diverse optimum pH for the binding of the various inhibitors as observed experimentally, we have calculated the titration curves for a set of BACE-1 ligand complexes. The results indicate that the pK(a) values of the titratable residues of the protein depend on the nature of the ligand involved, in disagreement with previous work. The enzyme-inhibitor structures with the resulting protonation states at pH values 4.5 and 7.4 served as the starting point for the prediction of the pH-dependent binding ranking. Our calculations reproduced the entire affinity ranking observed upon pH increase and most of the binding trends among inhibitors, especially at low pH. Finally, our cell-based assays indicate a possible correlation between high inhibitor affinity at both acidic and neutral pH values, with optimal cell response, a result that may open new venues for the search of potent BACE-1 inhibitors that are active at the cellular level.

Suicide gene therapy on spontaneous canine melanoma: correlations between in vivo tumors and their derived multicell spheroids in vitro.

To validate the use of multicellular spheroids to predict the efficacy of herpes simplex thymidine kinase/ganciclovir (HSVtk/GCV) suicide gene therapy in the respective in vivo tumors, we established and characterized 15 melanoma-derived cell lines from surgically excised melanoma tumors. Three HSVtk-lipofected cell lines were not sensitive to GCV in any culture configuration, other five displayed similar sensitivity as monolayers or spheroids, and only one resulted more sensitive when grown as spheroids. Other six cell lines manifested a relative multicellular resistance (MCR) phenotype growing as spheroids, compared with the same cells growing as monolayers. The reverse correlation between the MCR and the monolayers survival to HSVtk/GCV suggests that one of the main causes of MCR would be the rapid cell repopulation after suicide gene treatment. The high correlation of MCR with the spheroids radial growth and with the mitotic index of the respective originary tumors supported this re-growth involvement. A remarkable finding was the high correlation in HSVtk/GCV sensitivity between in vivo tumor and the corresponding derived cell lines growing as spheroids (R(2) = 0.85). This strongly encourages the implementation of spheroids as highly realistic experimental model for optimizing and predicting the in vivo response of the respective tumors to therapeutic strategies.

Factors predicting mortality in elderly patients on dialysis.

UNLABELLED: Elderly patients are increasingly enrolled in dialysis programs and present a series of special characteristics due to their high morbidity and mortality. OBJECTIVE: To describe the characteristics of incident dialysis patients aged >75 years, their comorbidities and their admissions, with a view to determining the factors that influence their course and mortality. PATIENTS AND METHODS: The study included all patients aged >75 years who started dialysis in our center since January 2000. The mean duration of follow-up was 3.3 +/- 2.2 years. Data were collected on incident comorbidity, admissions and their causes. A total of 139 patients were included, with a mean age of 78.6 +/- 2.6 years (67.6% males, 33.8% diabetic and 7.9% on peritoneal dialysis). Three groups were established according to age: 75-79, 80-85 and >85 years. The most frequent comorbidities were chronic obstructive pulmonary disease (25.9%), ischemic heart disease (25.2%), heart failure (25.9%), neoplasms (23.7%), peripheral vascular disease (23.7%), cerebrovascular disease (18.7%) and arterial hypertension (81%). The Charlson index was calculated, not adjusted for age, and comorbidity tertiles were established. RESULTS: During follow-up, the patients presented 0.82 +/- 0.99 admissions/patient/year, with a duration of 12.1 +/- 20.6 days/patient/year. The main causes of admission were infection (33%), vascular access problems (27%) and peripheral vascular events (14%). A total of 61 patients died (44%), and 4 underwent kidney transplantation (2.9%). The mean duration of follow-up of the transplanted patients was 3.6 +/- 1.8 years. The main causes of death were infection (32%), cardiovascular problems (28.3%) and neoplastic disease (11.3%). The global survival rate was 90, 82 and 53% after 1, 2 and 5 years, respectively. No significant differences in survival or annual admission rate were found in relation to age group and dialysis technique. In contrast, the annual admission rate and days of admission were directly correlated to the Charlson index (p = 0.009 and p = 0.032, respectively). No significant differences in the Charlson index were found between the patients on hemodialysis and those subjected to peritoneal dialysis. In the univariate model, the factors associated to mortality were diabetes, chronic obstructive pulmonary disease, heart failure and the Charlson index. In the multivariate model, only the Charlson index remained as an independent predictive factor (p = 0.006). CONCLUSIONS: Unlike the general population, age does not influence mortality or admissions in elderly patients on dialysis. Incident comorbidity is the factor exerting the greatest influence upon mortality and admissions. Advanced age in itself should not be regarded as an excluding factor for starting dialysis.

Beauveria bassiana infection alters colony development and defensive secretions of the beetles Tribolium castaneum and Ulomoides dermestoides (Coleoptera: Tenebrionidae).

We studied the effect of the entomopathogenic fungus Beauveria bassiana strain GHA on a) colony development of the beetles Tribolium castaneum (Herbst) and Ulomoides dermestoides (Fairmaire) (Coleoptera: Tenebrionidae) under laboratory conditions; and 2) the volatile blend released by both beetles, containing defensive pheromones, by using the solid phase microextraction technique. Colony development of both species was strongly altered 3 mo after treatment with B. bassiana, showing a significant reduction in progeny of 37.5% for T. castaneum and 50.0% for U. dermestoides. We also showed that the volatiles released by T. castaneum diminished close to 20% compared with those of healthy beetles, whereas in U. dermestoides secretions dramatically dropped to 5%, 7 d after immersion in 1 x 10(9) conidia per ml. These results suggest that after infection events take place, fungus-induced diminished secretion of the defensive pheromones may be a physiologic clue for behavioral changes in infected beetles.

[Evolution of the darbepoetin alpha resistance index in patients on dialysis who change from weekly to fortnightly treatments in clinical practice]. / Evolución del índice de resistencia a darbepoetina alfa en pacientes dializados que cambian de administración semanal a quincenal en la práctica clínica.

BACKGROUND: Darbepoetin alpha (DA) administered every-other-week (Q2W) is efficacious and safe for the treatment of anaemia in patients undergoing dialysis. There are no data available regarding the evolution of erythropoietic resistance index (ERI) after conversion from weekly (QW) to Q2W administration of DA in clinical practice. MATERIAL AND METHODS: Multicenter, observational, retrospective, 16-weeks study, which included stable patients undergoing dialysis who were converted from DA QW to DA Q2W in clinical practice. Conversion was done according to product specifications (duplicating QW dose). The ERI to DA was calculated by dividing the weekly DA dose per kilogram of weight (microg/wk.kg)*200 by the Hb level (g/dL). ERI evolution with time was evaluated by multivariate repeated measures ANOVA, adjusting for significant covariates. RESULTS: A total of 202 patients were included (137 patients undergoing haemodialysis [HD], intravenous (IV) DA, and 65 patients receiving peritoneal dialysis [PD], subcutaneous DA). Mean (SD) age was 66 (17) years; 61% of patients were men. Large intercentre variability was observed for the ERI at conversion time (coefficient of variation of 88%, p < 0.001 for differences between centres). In the univariate analysis, predictor factors for high baseline ERI were low albumin level (r = -0.29; p =0.001), HD (mean ERI of 9.3 [8.4] vs 6.8 [4.6] for PD; p = 0.005), or previous cardiovascular disease (9.9 [8.7] vs 7.4 [6.3] for patients without history; p =0.025). During the follow up, the ERI was slightly increased in HD patients (9.3 [8.4] at conversion vs 11.1 [7.3] at 16 weeks; p < 0.05), and remained stable in PD patients (6.8 [4.6] vs 6.7 [4.0], respectively; NS). In the multivariate analysis, there were no significant differences in ERI during the 16 weeks post-conversion after adjusting for albumin levels and centre (adjusted baseline mean [95% CI] of 10.0 [8.7-11.4] vs 10.5 [9.3-11.8] at 16 weeks, adjusted change of +0.5 [-0.67; 1.67]; NS). After 16 weeks, only 7 patients (3.5%) had discontinued Q2W administration. CONCLUSIONS: Extension from weekly to once every other-week darbepoetin alpha allows to simplify anaemia treatment without increasing the resistance index, regardless of dialysis type. The multivariate analysis shows that, after adjusting by center and inflammation/nutritional status, there were no changes in the response to darbepoetin alpha during the first 16 weeks after conversion in clinical practice.

Generation, establishment and characterization of a pluripotent stem cell line (CVTTHi001-A) from primary fibroblasts isolated from a patient with activated PI3 kinase delta syndrome (APDS2).

APDS2 is caused by mutations in PIK3R1 gene resulting in constitutive PI3Kδ activation. PI3Kδ is predominantly expressed in leukocytes and plays critical roles in regulating immune responses. Here we first derived fibroblast primary cells from a skin biopsy of a patient carrying a heterozygous single T deletion in intron 11 of the PIK3R1 gene. We next present the derivation of an induced pluripotent stem cell (iPS) line using a non-integrative reprogramming technology. Pluripotent-related hallmarks are further shown, including: iPSCs self-renewal and expression of pluripotent and differentiation markers after in vitro differentiation towards embryonic germ layers, assessed by RT-PCR and immunofluorescence.

Prediction and analysis of binding affinities for chemically diverse HIV-1 PR inhibitors by the modified SAFE_p approach.

One of the biggest challenges in the "in silico" screening of enzyme ligands is to have a protocol that could predict the ligand binding free energies. In our group we have developed a very simple screening function (referred to as solvent accessibility free energy of binding predictor, SAFE_p) which we have applied previously to the study of peptidic HIV-1 protease (HIV-1 PR) inhibitors and later to cyclic urea type HIV-1 PR inhibitors. In this work, we have extended the SAFE_p protocol to a chemically diverse set of HIV-1 PR inhibitors with binding constants that differ by several orders of magnitude. The resulting function is able to reproduce the ranking and in many cases the value of the inhibitor binding affinities for the HIV-1 PR, with accuracy comparable with that of costlier protocols. We also demonstrate that the binding pocket SAFE_p analysis can contribute to the understanding of the physical forces that participate in ligand binding. The analysis tools afforded by our protocol have allowed us to identify an induced fit phenomena mediated by the inhibitor and have demonstrated that larger fragments do not necessarily contribute the most to the binding free energy, an outcome partially brought about by the substantial role the desolvation penalty plays in the energetics of binding. Finally, we have revisited the effect of the Asp dyad protonation state on the predicted binding affinities.

Searching the conformational space of cyclic beta-amino acid peptides.

There is an increasing interest in the secondary structure of beta-amino-acid-containing peptides, since these compounds exhibit an intrinsic propensity to form stable folds even for short peptides, a feature that is rarely observed in alpha-amino-acid-containing peptides. In this work, we use a multiple trajectory molecular dynamics approach to study a panel of cyclic beta-amino-acid-containing peptides with a variety of motifs that differ in the ring size, ring substituents, and terminal protecting groups. We find a reasonable agreement between the predicted and the experimentally observed structures, in spite of the simple solvent representation used, indicating that in most cases the folding proceeds energetically downhill and it is driven to a great extent by structural preferences coded in the internal degrees of freedom, a result supported by our energy partition analysis. Our results also show that when the N-terminal end is unprotected, it is likely to be charged in a protic polar solvent. In that case, we find that only a molecular dynamics simulation with an "all atom" solvent representation is capable of reproducing the experimentally observed secondary structure of the peptide. Finally, the time evolution analysis of the hydrogen-bond-induced turns as well as of the root-mean-square deviation from the observed structure indicates that some peptides could have a higher intrinsic flexibility than others, within a given fold, a result that correlates to some degree with our molecular mechanics energy analysis.

Chain-Branched Polyhydroxylated Octahydro-1H-Indoles as Potential Leads against Lysosomal Storage Diseases.

Here, the synthesis and glycosidase inhibition properties of the two first known 3-ethyloctahydro-1H-indole-4,5,6-triols are reported. This study shows the transformation of d-glucose into polyhydroxylated 1-(2-nitrocyclohexane) acetaldehydes, followed by a protocol involving the formation of the azacyclopentane ring. Results of inhibitory potency assays and docking calculations show that at least one of them could be a lead for optimization in the search for compounds that behave like folding chaperones in lysosomal storage diseases.

Design, synthesis, evaluation, and crystallographic-based structural studies of HIV-1 protease inhibitors with reduced response to the V82A mutation.

In our quest for HIV-1 protease inhibitors that are not affected by the V82A resistance mutation, we have synthesized and tested a second generation set of C2-symmetric HIV-1 protease inhibitors that contain a cyclohexane group at P1 and/or P1'. The binding affinity results indicate that these compounds have an improved response to the appearance of the V82A mutation than the parent compound. The X-ray structure of one of these compounds with the V82A HIV-1 PR variant provides the structural rationale for the better resistance profile of these compounds. Moreover, scrutiny of the X-ray structure suggests that the ring of the Cha side chain might be in a boat rather than in the chair conformation, a result supported by molecular dynamics simulations.

[Resistance index to epoetin alpha and to darbepoetin-alpha in chronic hemodialysis patients: a cohort study]. / Estudio de dos cohortes de pacientes para evaluar el índice de resistencia a epoetina alfa y a darbepoetin alfa en pacientes en hemodiálisis crónica.

The effectiveness of the erythropoietic response can be evaluated using the resistance index (RI) to erythropoietic agents (EA) that measures the relationship between the dose administered and the hemoglobin levels attained. In a hemodialysis population, the RI is associated with several clinical and biochemical parameters, such as albumin levels, C-reactive protein (CRP), body mass index (BMI) and Kt/V. This index therefore reflects an important group of parameters that indicate comorbidities and measures the effectiveness of the treatment received. A substantial proportion of chronic hemodialysis patients show a relative resistance to human recombinant erythropoietin (rHuEPO) and require high doses to reach hemoglobin levels above 11 g/dl. Darbepoetin alpha is a new erythropoietic agent with a longer half-life than rHuEPO and greater biological activity in vivo. Furthermore, it remains at clinically effective plasma levels for much longer than rHuEPO. This study evaluated the effect on RI of switching from epoetin alpha to darbepoetin alpha in hemodialysis patients requiring i.v. rHuEPO at either high ( >10,000 UI/w) or low ( <4,000 UI/w) doses, compared to a control group receiving epoetin alpha. Unlike the control group, both groups of patients who switched to darbepoetin alpha showed a reduction in RI and a progressive reduction in the dose required of darbepoetin alpha with respect to the equivalent dose at treatment conversion. In the group requiring high doses, darbepoetin alpha RI (DRI) at week 24 was a significant 23.9% lower than epoetin alpha RI (ERI) at conversion (week 0) (p <0.01). In the group requiring low doses, DRI at week 24 was 13.4% lower than the ERI at conversion (p = NS). In both control groups, ERI at week 24 was higher than ERI at week 0. All groups showed stable hemoglobin levels across the study, with mean levels between 11.5 and 13.3 g/dl. CRP at week 24 was significantly related to albumin levels (p <0.001). In conclusion, switching hemodialysis patients from epoetin alpha to darbepoetin alpha was associated with a significant improvement in RI in the group of patients with high doses of EA, which we consider to be an important indicator of the effectiveness and quality of the treatment administered.

Solvent accessibility as a predictive tool for the free energy of inhibitor binding to the HIV-1 protease.

We have developed a simple approach for the evaluation of the free energies of inhibitor binding to the protease of the human immunodeficiency virus (HIV-1 PR). Our algorithm is based on the observation that most groups that line the binding pockets of this enzyme are hydrophobic in nature. Based on this fact, we have likened the binding of an inhibitor to this enzyme to its transfer from water to a medium of lower polarity. The resulting expression produced values for the free energy of binding of inhibitors to the HIV-1 PR that are in good agreement with experimental values. The additive nature of this approach has enabled us to partition the free energy of binding into the contributions of single fragments. The resulting analysis clearly indicates the existence of a ranking in the participation of the enzyme's subsites in binding. Although all the enzyme's pockets contribute to binding, the ones that bind the P2-P'2 span of the inhibitor are in general the most critical for high inhibitor potency. Moreover, our method has allowed us to determine the nature of the functional groups that fit into given enzyme binding pockets. Perusal of the energy contributions of single side chains has shown that a large number of hydrophobic and aromatic groups located in the central portion of the HIV-1 PR inhibitors present optimal binding. All of these observations are in agreement with experimental evidence, providing a validation for the physical relevancy of our model.

Solvation effects are responsible for the reduced inhibitor affinity of some HIV-1 PR mutants.

The formulation of HIV-1 PR inhibitors as anti-viral drugs has been hindered by the appearance of protease strains that present drug resistance to these compounds. The mechanism by which the HIV-1 PR mutants lower their affinity for the inhibitor is not yet fully understood. We have applied a modified Poisson-Boltzmann method to the evaluation of the molecular interactions that contribute to the lowering of the inhibitor affinity to some polar mutants at position 82. These strains present drug resistance behavior and hence are ideally suited for these studies. Our results indicate that the reduction in binding affinity is due to the solvation effects that penalize the binding to the more polar mutants. The inhibitor binding ranking of the different mutants can be explained from the analysis of the different components of our free energy scoring function.

Predicting the cell differentiation activity of 1 alpha,25-dihydroxyvitamin D3 side chain analogues from docking simulations.

We present a receptor-based protocol for the prediction of the cell differentiation activities of a series of side chain analogues of 1 alpha,25-dihydroxyvitamin D(3), a compound that exhibits a very large variety of biological functions. Our protocol is able to reproduce the activity of the compounds studied here. It also sheds light on the relative importance of binding site residues in the biological activity and on the mechanism behind it.

Perioperative nursing in the college curriculum. A custom fit.

Although this course is in its infancy, it has become popular among baccalaureate students. Incoming junior students are enthusiastic about an elective course that provides them an opportunity to focus on an aspect of nursing that is no longer available to them in most nursing programs. The morale of the operating room nursing staff, particularly among the preceptors, has increased tenfold. In an era of nursing shortages, creative and innovative methods of recruiting students and retaining experienced nurses in all fields are vital. This unique course may be one of those methods. It is widely known that high morale yields a more productive work environment, lower turnover, and a cohesive work force that provides high quality nursing care in a most cost-effective manner.