Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations

Background: Protein/receptor explicit flexibility has recently become an important feature of molecular docking simulations. Taking the flexibility into account brings the docking simulation closer to the receptors’ real behaviour in its natural environment. Several approaches have been developed to address this problem. Among them, modelling the full flexibility as an ensemble of snapshots derived from a molecular dynamics simulation (MD) of the receptor has proved very promising. Despite its potential, however, only a few studies have employed this method to probe its effect in molecular docking simulations. We hereby use ensembles of snapshots obtained from three different MD simulations of the InhA enzyme from M. tuberculosis (Mtb), the wild-type (InhA_wt), InhA_I16T, and InhA_I21V mutants to model their explicit flexibility, and to systematically explore their effect in docking simulations with three different InhA inhibitors, namely, ethionamide (ETH), triclosan (TCL), and pentacyano (isoniazid)ferrate(II) (PIF). Results: The use of fully-flexible receptor (FFR) models of InhA_wt, InhA_I16T, and InhA_I21V mutants in docking simulation with the inhibitors ETH, TCL, and PIF revealed significant differences in the way they interact as compared to the rigid, InhA crystal structure (PDB ID: 1ENY). In the latter, only up to five receptor residues interact with the three different ligands. Conversely, in the FFR models this number grows up to an astonishing 80 different residues. The comparison between the rigid crystal structure and the FFR models showed that the inclusion of explicit flexibility, despite the limitations of the FFR models employed in this study, accounts in a substantial manner to the induced fit expected when a protein/receptor and ligand approach each other to interact in the most favourable manner. Conclusions: Protein/receptor explicit flexibility, or FFR models, represented as an ensemble of MD simulation snapshots, can lead to a more realistic representation of the induced fit effect expected in the encounter and proper docking of receptors to ligands. The FFR models of InhA explicitly characterizes the overall movements of the amino acid residues in helices, strands, loops, and turns, allowing the ligand to properly accommodate itself in the receptor’s binding site. Utilization of the intrinsic flexibility of Mtb’s InhA enzyme and its mutants in virtual screening via molecular docking simulation may provide a novel platform to guide the rational or dynamicalstructure-based drug design of novel inhibitors for Mtb’s InhA. We have produced a short video sequence of each ligand (ETH, TCL and PIF) docked to the FFR models of InhA_wt. These videos are available at http://www.inf.pucrs. br/~osmarns/LABIO/Videos_Cohen_et_al_19_07_2011.htm

No relationship between bone mineral density and syndesmophyte formation at the same level in the lumbar spine of patients with radiographic axial Spondyloarthritis

Objective: To investigate if in radiographic axial Spondyloarthritis (r-axSpA) low vertebral bone mineral density (BMD) is associated with development of new syndesmophytes at the same vertebral level. / Methods: In a post-hoc analysis from the ASSERT trial (infliximab vs placebo), dual-energy X-ray absorptiometry was used to measure baseline BMD (g/cm2) of the lumbar spine L1 to L4. Syndesmophyte formation was assessed in the same vertebrae on conventional radiographs defined as an increase in modified Stoke Ankylosing Spondylitis Spine Score from 0 or 1 to 2 or 3 after 2 years. Radiographs were scored by two readers. Generalised estimating equations (GEE) adjusted for within-patient correlation across multiple vertebrae, taking potential confounders into account. / Results: We analysed 599 vertebrae in 165 r-axSpA patients (78% male, mean (SD) age 38 (10) years, 67% with at least one syndesmophyte anywhere in the spine). In total, 24 to 74 new syndesmophytes developed in 9 (5%) to 30 (18%) patients and 13 (2%) to 39 (7%) vertebrae, if either a syndesmophyte was seen by both or only one of the readers (ie, specific and sensitive definitions) respectively. In multivariable analyses, no association was found between baseline local vertebral BMD and new syndesmophyte formation after 2 years: adjOR (95% CI): 0.56 (0.01, 44.45) (specific definition) and 0.26 (0.03, 2.63) (sensitive definition). / Conclusion: In patients with active and established r-axSpA, with an observed low incidence of lumbar spine syndesmophyte formation over 2 years, no relationship was found between baseline BMD and new radiographic syndesmophyte formation at the same vertebra

FReDoWS: a method to automate molecular docking simulations with explicit receptor flexibility and snapshots selection

<p>Abstract</p> <p>Background</p> <p><it>In silico</it> molecular docking is an essential step in modern drug discovery when driven by a well defined macromolecular target. Hence, the process is called structure-based or rational drug design (RDD). In the docking step of RDD the macromolecule or receptor is usually considered a rigid body. However, we know from biology that macromolecules such as enzymes and membrane receptors are inherently flexible. Accounting for this flexibility in molecular docking experiments is not trivial. One possibility, which we call a fully-flexible receptor model, is to use a molecular dynamics simulation trajectory of the receptor to simulate its explicit flexibility. To benefit from this concept, which has been known since 2000, it is essential to develop and improve new tools that enable molecular docking simulations of fully-flexible receptor models.</p> <p>Results</p> <p>We have developed a Flexible-Receptor Docking Workflow System (FReDoWS) to automate molecular docking simulations using a fully-flexible receptor model. In addition, it includes a snapshot selection feature to facilitate acceleration the virtual screening of ligands for well defined disease targets. FReDoWS usefulness is demonstrated by investigating the docking of four different ligands to flexible models of <it>Mycobacterium tuberculosis’</it> wild type InhA enzyme and mutants I21V and I16T. We find that all four ligands bind effectively to this receptor as expected from the literature on similar, but wet experiments.</p> <p>Conclusions</p> <p>A work that would usually need the manual execution of many computer programs, and the manipulation of thousands of files, was efficiently and automatically performed by FReDoWS. Its friendly interface allows the user to change the docking and execution parameters. Besides, the snapshot selection feature allowed the acceleration of docking simulations. We expect FReDoWS to help us explore more of the role flexibility plays in receptor-ligand interactions. FReDoWS can be made available upon request to the authors.</p

Morphological characterization of a human glioma cell l ine

A human malignant continuous cell line, named NG97, was recently established in our laboratory. This cell line has been serially subcultured over 100 times in standard culture media presenting no sign of cell senescence. The NG97 cell line has a doubling time of about 24 h. Immunocytochemical analysis of glial markers demonstrated that cells are positive for glial fibrillary acidic protein (GFAP) and S-100 protein, and negative for vimentin. Under phase-contrast microscope, cultures of NG97 showed cells with variable morphological features, such as small rounded cells, fusiform cells (fibroblastic-like cells), and dendritic-like cells. However, at confluence just small rounded and fusiform cells can be observed. At scanning electron microscopy (SEM) small rounded cells showed heterogeneous microextentions, including blebs and filopodia. Dendritic-like cells were flat and presented extensive prolongations, making several contacts with small rounded cells, while fusiform cells presented their surfaces dominated by microvilli. We believe that the knowledge about NG97 cell line may be useful for a deeper understanding of biological and immunological characteristics of gliomas

Iodine Availability through Iodized Salt in Portugal: 2010-2021 Sales Evolution and Distribution

Salt iodization programs are considered the most cost-effective measures to ensure adequate iodine intake in iodine-deficient populations. Portuguese women of childbearing age and pregnant women were reported to be iodine-deficient, which led the health authorities, in 2013, to issue a recommendation for iodine supplementation during preconception, pregnancy and lactation. In the same year, iodized salt became mandatory in school canteens. Of note, no regulation or specific programs targeting the general population, or the impact of iodized salt availability in retailers, are known. The present study analyzed iodized salt supermarket sales from 2010 to 2021 from a major retailer, identifying the proportion of iodized salt in total salt sales and its distribution in mainland Portugal. Data on iodine content were collected through the nutritional label information. Of a total of 33 salt products identified, 3 were iodized (9%). From 2010 to 2021, the weighted sales of iodized salt presented a growing tendency, reaching the maximum of 10.9% of total sales (coarse plus fine salt) in 2021. Iodized salt reached a maximum of 11.6% of total coarse salt in 2021, a maximum of 2.4% of the total fine salt in 2018. The overall sales of iodized salt and their contribution to iodine intake are extremely low, prompting additional studies to understand the consumer's choice and awareness of the benefits of iodized salt

Barriers to participation in a placebo-surgical trial for lumbar spinal stenosis

© 2019 Background: Placebo-controlled trials are an important tool when assessing the efficacy of spinal surgical procedures. The most common spinal surgical procedure in older adults is decompression for lumbar spinal stenosis. Before conducting a placebo-surgical trial on decompression surgery, an investigation of patients’ willingness to participate in a placebo-controlled trial of decompression surgery and barriers to participation were explored. Materials: An online survey. Methods: Descriptive analyses of demographic and clinical data, and participants' willingness to participate in a placebo-surgical trial. Logistic regression was used to examine potential predictors of willingness to participate. Two independent researchers performed a coded framework analysis of patients’ barriers to participation. Results: 68 patients were invited and 63 participants completed the survey (91.3% response, mean (SD) age 69.5 (10.9) years, 52% females), 71% suffered from moderate to very severe pain. Ten participants (15.9%) were willing to participate in a placebo-controlled trial. Being married was associated with decreased odds of participating (OR: 0.2; 95% CI, 0.05 to 0.8; P = 0.03), while the main barriers were a lack of information about the procedure, reassurance of a positive outcome with participation, and concerns about the risks and benefits of placebo surgery. Conclusions: A minority of patients with lumbar spinal stenosis were willing to participate in a placebo-controlled trial of surgery. The identified barriers indicate that educating eligible patients about: the need for placebo-surgical trials, the personal risks and benefits of participation, and the importance and potential benefits of placebo trials to others, may be crucial to ensure adequate recruitment into the placebo-controlled surgical trial. Conclusions should be read cautiously however, given the small sample size present in this study

Trends in method-specific suicide in Brazil from 2000 to 2017

Purpose: Understanding long-term patterns of suicide methods can inform public health policy and prevention strategies. In Brazil, firearm-related policies may be one salient target for suicide prevention. This study describes trends in method-specific suicide at the national and state-levels in Brazil, with a particular focus on firearm-related suicides. / Methods: Brazilian mortality data for suicide and undetermined intent among people aged 10 years and older between 2000 and 2017 were obtained from the National Mortality Information System. We examined national and state-level trends in age-standardised suicide rates for hanging, self-poisoning, firearms, jumping from a high place, other, and unspecified methods. We also compared total rates of mortality from suicide and undetermined intent over the period. Applying Joinpoint regression, we tested changes in trends of firearm-specific suicide rates. / Results: The total suicide rate increased between 2000 and 2017. Rates of hanging, self-poisoning by drugs or alcohol and jumping from a high place showed the largest increases, while firearm-specific suicide rates decreased over the study period. Trends in methods of suicide varied by sex and state. / Conclusion: It is of public health concern that suicide rates in Brazil have risen this millennium. Restricting access to firearms might be an effective approach for reducing firearm-specific suicides, especially in states where firearm availability remains particularly high. Treatment and management of substance misuse may also be an important target for suicide prevention policies. More work is needed to understand the causes of rising suicide rates in Brazil and to improve the mental health of the population

Association between homicide rates and suicide rates: a countrywide longitudinal analysis of 5507 Brazilian municipalities

Objective: To estimate the association between homicide and suicide rates in Brazilian municipalities over a period of 7 years. / Design: We conducted a longitudinal ecological study using annual mortality data from 5507 Brazilian municipalities between 2008 and 2014. Multivariable negative binomial regression models were used to examine the relationship between homicide and suicide rates. Robustness of results was explored using sensitivity analyses to examine the influence of data quality, population size, age and sex on the relationship between homicide and suicide rates. / Setting: A nationwide study of municipality-level data. / Participants: Mortality data and corresponding population estimates for municipal populations aged 10 years and older. / Primary and secondary outcome measures: Age-standardised suicide rates per 100 000. / Results: Municipal suicide rates were positively associated with municipal homicide rates; after adjusting for socioeconomic and demographic factors, a doubling of the homicide rate was associated with 22% increase in suicide rate (rate ratio=1.22, 95% CI: 1.13 to 1.33). A dose–response effect was observed with 4% increase in suicide rates at the third quintile, 9% at the fourth quintile and 12% at the highest quintile of homicide rates compared with the lowest quintile. The observed effect estimates were robust to sensitivity analyses. / Conclusions: Municipalities with higher homicide rates have higher suicide rates and the relationship between homicide and suicide rates in Brazil exists independently of many sociodemographic and socioeconomic factors. Our results are in line with the hypothesis that changes in homicide rates lead to changes in suicide rates, although a causal association cannot be established from this study. Suicide and homicide rates have increased in Brazil despite increased community mental health support and incarceration, respectively; therefore, new avenues for intervention are needed. The identification of a positive relationship between homicide and suicide rates suggests that population-based interventions to reduce homicide rates may also reduce suicide rates in Brazil