Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge

A continuing challenge in modern medicine is the identification of safer and more efficacious drugs. Precision therapeutics, which have one molecular target, have been long promised to be safer and more effective than traditional therapies. This approach has proven to be challenging for multiple reasons including lack of efficacy, rapidly acquired drug resistance, and narrow patient eligibility criteria. An alternative approach is the development of drugs that address the overall disease network by targeting multiple biological targets (‘polypharmacology’). Rational development of these molecules will require improved methods for predicting single chemical structures that target multiple drug targets. To address this need, we developed the Multi-Targeting Drug DREAM Challenge, in which we challenged participants to predict single chemical entities that target pro-targets but avoid anti-targets for two unrelated diseases: RET-based tumors and a common form of inherited Tauopathy. Here, we report the results of this DREAM Challenge and the development of two neural network-based machine learning approaches that were applied to the challenge of rational polypharmacology. Together, these platforms provide a potentially useful first step towards developing lead therapeutic compounds that address disease complexity through rational polypharmacology.     

Thymoquinone Induces Telomere Shortening,DNA Damage and Apoptosis in Human Glioblastoma Cells

Background

A major concern of cancer chemotherapy is the side effects caused by the non-specific targeting of both normal and cancerous cells by therapeutic drugs. Much emphasis has been placed on discovering new compounds that target tumour cells more efficiently and selectively with minimal toxic effects on normal cells.

Methodology/Principal Findings

The cytotoxic effect of thymoquinone, a component derived from the plant Nigella sativa, was tested on human glioblastoma and normal cells. Our findings demonstrated that glioblastoma cells were more sensitive to thymoquinone-induced antiproliferative effects. Thymoquinone induced DNA damage, cell cycle arrest and apoptosis in the glioblastoma cells. It was also observed that thymoquinone facilitated telomere attrition by inhibiting the activity of telomerase. In addition to these, we investigated the role of DNA-PKcs on thymoquinone mediated changes in telomere length. Telomeres in glioblastoma cells with DNA-PKcs were more sensitive to thymoquinone mediated effects as compared to those cells deficient in DNA-PKcs.

Conclusions/Significance

Our results indicate that thymoquinone induces DNA damage, telomere attrition by inhibiting telomerase and cell death in glioblastoma cells. Telomere shortening was found to be dependent on the status of DNA-PKcs. Collectively, these data suggest that thymoquinone could be useful as a potential chemotherapeutic agent in the management for brain tumours.     

Cube - An Online Tool for Comparison and Contrasting of Protein Sequences

When comparing sequences of similar proteins, two kinds of questions can be asked, and the related two kinds of inference made. First, one may ask to what degree they are similar, and then, how they differ. In the first case one may tentatively conclude that the conserved elements common to all sequences are of central and common importance to the protein''s function. In the latter case the regions of specialization may be discriminative of the function or binding partners across subfamilies of related proteins. Experimental efforts - mutagenesis or pharmacological intervention - can then be pointed in either direction, depending on the context of the study.Cube simplifies this process for users that already have their favorite sets of sequences, and helps them collate the information by visualization of the conservation and specialization scores on the sequence and on the structure, and by spreadsheet tabulation. All information can be visualized on the spot, or downloaded for reference and later inspection.Server homepage: http://eopsf.org/cube     

Quantification of acid-base interactions based on contact angle measurement allows XDLVO predictions to attachment of Campylobacter jejuni but not Salmonella

Acid-base (AB) interactions play the most important role in bacterial attachment to surfaces and can be quantified based on electron donor/electron acceptor data from contact angle measurement (CAM) according to the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory. It follows that the XDLVO theory could fail to explain attachment numbers if differences in AB interactions between strains are not apparent by CAM. This study aimed to investigate the validity of the above assumptions by comparing empirical data on attachment of six bacterial strains (three strains of Campylobacter jejuni and three strains of Salmonella) to stainless steel and XDLVO theory predictions. A significant difference (P < 0.05) in AB interactions, apparent by CAM, between C. jejuni strains allowed prediction of attachment of this species by the XDLVO theory. However, the theory failed to explain the attachment numbers for Salmonella due to similar AB interactions, as established by CAM, between the three Salmonella strains. Qualitative analysis of AB interactions by microbial adhesion to solvents (MATS) revealed a significant difference (P < 0.05) in electron donor property between the three Salmonella strains suggesting that these strains may differ with respect to AB interactions. No significant correlation with respect to electron donor property (P = 0.502, r² = 12%) was apparent between CAM and MATS. These data suggest that CAM may not always reflect exactly AB interactions and that the difference in the outcomes from MATS and CAM should be considered when the XDLVO theory is used to predict bacterial attachment to surfaces.     

New meta-heuristics for the resource-constrained project scheduling problem

In this paper, we study the resource-constrained project scheduling problem and introduce an annealing-like search heuristic which simulates the cooling process of a gas into a highly-ordered crystal. To achieve this, we develop diversification procedures that simulate the motion of high energy molecules as well as a local refinement procedure that simulates the motion of low energy molecules. We further improve the heuristic by incorporating a genetic algorithm framework. The meta-heuristic algorithms are applied to Kolisch’s PSPLIB J30, J60 and J120 RCPSP instances. Experimental results show that they are effective and are among the best performing algorithms for the RCPSP.     

Deconvolution of overlapping isotopic clusters improves quantification of stable isotope-labeled peptides

High-resolution mass spectrometry and the use of stable isotopes have greatly improved our ability to quantify proteomes. Typically, the relative abundance of peptides is estimated by identifying the isotopic clusters and by comparing the peak intensities of peptide pairs. However, when the mass shift between the labeled peptides is small, there can be the possibility for overlap of the isotopic clusters which will hamper quantification accuracy with a typical upwards bias for the heavier peptide. Here, we investigated the impact of the overlapping peak issue with respect to dimethyl based quantification and we confirmed there can be need for correction. In addition, we present a tool that can correct overlapping issues when they arise which is based on modeling isotopic distributions. We demonstrate that our approach leads to improved accuracy and precision of protein quantification.     

Molecular mechanistic insights into the endothelial receptor mediated cytoadherence of Plasmodium falciparum-infected erythrocytes

Cytoadherence or sequestration is essential for the pathogenesis of the most virulent human malaria species, Plasmodium falciparum (P. falciparum). Similar to leukocyte-endothelium interaction in response to inflammation, cytoadherence of P. falciparum infected red blood cells (IRBCs) to endothelium occurs under physiological shear stresses in blood vessels and involves an array of molecule complexes which cooperate to form stable binding. Here, we applied single-molecule force spectroscopy technique to quantify the dynamic force spectra and characterize the intrinsic kinetic parameters for specific ligand-receptor interactions involving two endothelial receptor proteins: thrombospondin (TSP) and CD36. It was shown that CD36 mediated interaction was much more stable than that mediated by TSP at single molecule level, although TSP-IRBC interaction appeared stronger than CD36-IRBC interaction in the high pulling rate regime. This suggests that TSP-mediated interaction may initiate cell adhesion by capturing the fast flowing IRBCs whereas CD36 functions as the 'holder' for providing stable binding.     

Resident phenotypically modulated vascular smooth muscle cells in healthy human arteries

Vascular interstitial cells (VICs) are non‐contractile cells with filopodia previously described in healthy blood vessels of rodents and their function remains unknown. The objective of this study was to identify VICs in human arteries and to ascertain their role. VICs were identified in the wall of human gastro‐omental arteries using transmission electron microscopy. Isolated VICs showed ability to form new and elongate existing filopodia and actively change body shape. Most importantly sprouting VICs were also observed in cell dispersal. RT‐PCR performed on separately collected contractile vascular smooth muscle cells (VSMCs) and VICs showed that both cell types expressed the gene for smooth muscle myosin heavy chain (SM‐MHC). Immunofluorescent labelling showed that both VSMCs and VICs had similar fluorescence for SM‐MHC and αSM‐actin, VICs, however, had significantly lower fluorescence for smoothelin, myosin light chain kinase, h‐calponin and SM22α. It was also found that VICs do not have cytoskeleton as rigid as in contractile VSMCs. VICs express number of VSMC‐specific proteins and display features of phenotypically modulated VSMCs with increased migratory abilities. VICs, therefore represent resident phenotypically modulated VSMCs that are present in human arteries under normal physiological conditions.