Mining Predicted Essential Genes of Brugia malayi for Nematode Drug Targets

We report results from the first genome-wide application of a rational drug target selection methodology to a metazoan pathogen genome, the completed draft sequence of Brugia malayi, a parasitic nematode responsible for human lymphatic filariasis. More than 1.5 billion people worldwide are at risk of contracting lymphatic filariasis and onchocerciasis, a related filarial disease. Drug treatments for filariasis have not changed significantly in over 20 years, and with the risk of resistance rising, there is an urgent need for the development of new anti-filarial drug therapies. The recent publication of the draft genomic sequence for B. malayi enables a genome-wide search for new drug targets. However, there is no functional genomics data in B. malayi to guide the selection of potential drug targets. To circumvent this problem, we have utilized the free-living model nematode Caenorhabditis elegans as a surrogate for B. malayi. Sequence comparisons between the two genomes allow us to map C. elegans orthologs to B. malayi genes. Using these orthology mappings and by incorporating the extensive genomic and functional genomic data, including genome-wide RNAi screens, that already exist for C. elegans, we identify potentially essential genes in B. malayi. Further incorporation of human host genome sequence data and a custom algorithm for prioritization enables us to collect and rank nearly 600 drug target candidates. Previously identified potential drug targets cluster near the top of our prioritized list, lending credibility to our methodology. Over-represented Gene Ontology terms, predicted InterPro domains, and RNAi phenotypes of C. elegans orthologs associated with the potential target pool are identified. By virtue of the selection procedure, the potential B. malayi drug targets highlight components of key processes in nematode biology such as central metabolism, molting and regulation of gene expression

Clinical features and outcomes of elderly hospitalised patients with chronic obstructive pulmonary disease, heart failure or both

Background and objective: Chronic obstructive pulmonary disease (COPD) and heart failure (HF) mutually increase the risk of being present in the same patient, especially if older. Whether or not this coexistence may be associated with a worse prognosis is debated. Therefore, employing data derived from the REPOSI register, we evaluated the clinical features and outcomes in a population of elderly patients admitted to internal medicine wards and having COPD, HF or COPD + HF. Methods: We measured socio-demographic and anthropometric characteristics, severity and prevalence of comorbidities, clinical and laboratory features during hospitalization, mood disorders, functional independence, drug prescriptions and discharge destination. The primary study outcome was the risk of death. Results: We considered 2,343 elderly hospitalized patients (median age 81 years), of whom 1,154 (49%) had COPD, 813 (35%) HF, and 376 (16%) COPD + HF. Patients with COPD + HF had different characteristics than those with COPD or HF, such as a higher prevalence of previous hospitalizations, comorbidities (especially chronic kidney disease), higher respiratory rate at admission and number of prescribed drugs. Patients with COPD + HF (hazard ratio HR 1.74, 95% confidence intervals CI 1.16-2.61) and patients with dementia (HR 1.75, 95% CI 1.06-2.90) had a higher risk of death at one year. The Kaplan-Meier curves showed a higher mortality risk in the group of patients with COPD + HF for all causes (p = 0.010), respiratory causes (p = 0.006), cardiovascular causes (p = 0.046) and respiratory plus cardiovascular causes (p = 0.009). Conclusion: In this real-life cohort of hospitalized elderly patients, the coexistence of COPD and HF significantly worsened prognosis at one year. This finding may help to better define the care needs of this population

Trends in open abdomen management in Italy: a subgroup analysis from the IROA project

Use of open abdomen (OA) progressively acquired increasing importance with the diffusion of the damage control management of critical patients. The purpose of the present study is to identify the state of the art about the use of OA in Italy, focusing on techniques, critical issues and clinical outcomes. A prospective analysis of adult patients enrolled in the IROA, limited to the Italian participating centres was performed. 375 patients were enrolled. Mean age was 64 +/- 16 years old, 56% of the patients were male, mean BMI was 26.9 +/- 5.2. Main indications for using OA were secondary peritonitis (32.5%), post-operative peritonitis (22.9%) and trauma (11.7%). Main OA techniques used were commercial negative pressure wound therapy (49.6%) and Bogota bag (27.7%). Definitive closure of the abdomen was reached in 82.4% of patients after 6 +/- 7 days of OA. The primary fascia closure rate was 84.7%. Overall mortality was 29.1%. The complication rate was 50.8%, with an enteroatmospheric fistula incidence: 7.5%. A univariate analysis performed on complication type found the duration of OA treatment (p = 0.024) to be statistically significant. Univariate analysis on mortality risk identified as significant age, duration of OA (in days) and pancreatitis as indication; multivariate analysis confirmed age (p < 0.001) and pancreatitis (p = 0.002) as statistically significant. A large variety of behaviours towards the patient requiring OA exists. A strong acceptance of common, recognized and evidence-based guidelines is essential, to obtain more uniformity in patient management and coherence of collected data, thus leading to improvement in outcomes and reduction of costs

Cofactor-independent phosphoglycerate mutase from nematodes has limited druggability, as revealed by two high-throughput screens.

Cofactor-independent phosphoglycerate mutase (iPGAM) is essential for the growth of C. elegans but is absent from humans, suggesting its potential as a drug target in parasitic nematodes such as Brugia malayi, a cause of lymphatic filariasis (LF). iPGAM's active site is small and hydrophilic, implying that it may not be druggable, but another binding site might permit allosteric inhibition. As a comprehensive assessment of iPGAM's druggability, high-throughput screening (HTS) was conducted at two different locations: ∼220,000 compounds were tested against the C. elegans iPGAM by Genzyme Corporation, and ∼160,000 compounds were screened against the B. malayi iPGAM at the National Center for Drug Screening in Shanghai. iPGAM's catalytic activity was coupled to downstream glycolytic enzymes, resulting in NADH consumption, as monitored by a decline in visible-light absorbance at 340 nm. This assay performed well in both screens (Z'-factor >0.50) and identified two novel inhibitors that may be useful as chemical probes. However, these compounds have very modest potency against the B. malayi iPGAM (IC50 >10 µM) and represent isolated singleton hits rather than members of a common scaffold. Thus, despite the other appealing properties of the nematode iPGAMs, their low druggability makes them challenging to pursue as drug targets. This study illustrates a "druggability paradox" of target-based drug discovery: proteins are generally unsuitable for resource-intensive HTS unless they are considered druggable, yet druggability is often difficult to predict in the absence of HTS data

Results of NCDS's HTS of 160,000 compounds against the <i>B. malayi</i> iPGAM.

<p>The distribution of compounds is shown as a function of percent inhibition of the enzyme.</p

Robustness of the HTS assays performed at Genzyme (top) and NCDS (bottom).

<p>TOP: scattergram of percent inhibition data from all plates in the Genzyme HTS. Green: 100% inhibition control; red: 50% inhibition control; black: 0% inhibition control; blue: data for test compounds screened at 10 µM. BOTTOM: scattergram of NCDS data representing uninhibited iPGAM (2% DMSO, shown in red) and inhibited iPGAM (200 µM tannic acid, shown in black). 1120 wells for each condition, spread over seventy 384-well plates, are shown. Dashed lines indicate means ±3× standard deviation (SD).</p

Dose-response curve of the confirmed hit NCDS-1. NCDS-1 and control inhibitor tannic acid were tested at concentrations from 0.78 µM to 400 µM.

<p>Note that tannic acid may inhibit iPGAM via nonspecific aggregation <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002628#pntd.0002628-Pohjala1" target="_blank">[40]</a>; this would render it unsuitable as a chemical probe, but does not prevent its use as a control inhibitor for comparison of inhibited and uninhibited samples. Nonlinear regression and IC₅₀ value were analyzed with GraphPad Prism software (GraphPad, San Diego, CA, USA). Data are expressed as means ± SEM of at least 3 independent experiments.</p

Novel inhibitors of <i>B. malayi</i> iPGAM.

<p>N.D. = Not determined.</p

A summary of the screening workflow at the two HTS sites, along with the number of compounds passing through each step.

<p>See <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002628#s2" target="_blank">Methods</a> for details.</p