A critical review of four novels

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonIn this critical review I will explore the aims and influences; themes, characterisation, genre and plot summaries; research impact, publication histories and critical reception of my four novels: Hitman, The Fixer, Baptism and Sacrifice. In addition, I will provide a commentary on the processes and methodology I employed in the writing of the four novels as well as a critical reflection on them. Published between 2000 and 2013, my books represent a body of work that is rooted within the British crime thriller genre. However, in the nature of the novels’ construction and target readerships, they also represent two distinct literary styles. The first two novels, Hitman and The Fixer, published in 2000 and 2001 respectively are satirical thrillers in which I experiment with genre with the intention of unsettling and confounding readers’ expectations while at the same time, testing the boundaries of what the crime fiction genre can sustain. In these two novels, I draw on a range of influences and traditions in literature, film and popular culture. The second two novels, Baptism and Sacrifice, published in 2012 and 2013 are more closely aligned to the accepted conventions of the thriller genre but are no less ambitious in their intention to explore new forms of plotting and characterisation. In their writing, I was influenced more by contemporary geo-politics, particularly surveillance, intelligence, cyber warfare and the terrorist attacks of 9/11 and 7/7 than I was by literature and film. The latter two books continue a theme of experimentation I began in the first two, combining disparate influences to create original fiction. Further reflection will be made on the part that these novels have played, and continue to play, within my ongoing body of work as a novelist, screenwriter and Creative Writing academic

Wireless Operator

Wireless Operator recreates the physical experience and emotional turmoil of one night in a Lancaster Bomber on a bombing raid over Germany in 1945.Wireless Operator tells the gripping story of a terrifying night-time Lancaster Bomber raid in WW2. This compelling play is told through the eyes and ears of the wireless operator. Confined in the claustrophobic aircraft the young crew struggle to survive. They avoid searchlights and flak; witness fellow airmen blown out of the sky and plunge into zero gravity corkscrew manoeuvres to evade enemy aircraft. As they unleash their deadly cargo onto the city below, the wireless operator agonises about the real cost of their mission. The play reveals the triggers to the lifelong legacy that traumatised those airmen who survived

Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis

The rise of multi-drug resistant (MDR) and extensively drug resistant (XDR) tuberculosis around the world, including in industrialized nations, poses a great threat to human health and defines a need to develop new, effective and inexpensive anti-tubercular agents. Previously we developed a chemical systems biology approach to identify off-targets of major pharmaceuticals on a proteome-wide scale. In this paper we further demonstrate the value of this approach through the discovery that existing commercially available drugs, prescribed for the treatment of Parkinson's disease, have the potential to treat MDR and XDR tuberculosis. These drugs, entacapone and tolcapone, are predicted to bind to the enzyme InhA and directly inhibit substrate binding. The prediction is validated by in vitro and InhA kinetic assays using tablets of Comtan, whose active component is entacapone. The minimal inhibition concentration (MIC99) of entacapone for Mycobacterium tuberculosis (M.tuberculosis) is approximately 260.0 µM, well below the toxicity concentration determined by an in vitro cytotoxicity model using a human neuroblastoma cell line. Moreover, kinetic assays indicate that Comtan inhibits InhA activity by 47.0% at an entacapone concentration of approximately 80 µM. Thus the active component in Comtan represents a promising lead compound for developing a new class of anti-tubercular therapeutics with excellent safety profiles. More generally, the protocol described in this paper can be included in a drug discovery pipeline in an effort to discover novel drug leads with desired safety profiles, and therefore accelerate the development of new drugs

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

How easy is it to reproduce the results found in a typical computational biology paper? Either through experience or intuition the reader will already know that the answer is with difficulty or not at all. In this paper we attempt to quantify this difficulty by reproducing a previously published paper for different classes of users (ranging from users with little expertise to domain experts) and suggest ways in which the situation might be improved. Quantification is achieved by estimating the time required to reproduce each of the steps in the method described in the original paper and make them part of an explicit workflow that reproduces the original results. Reproducing the method took several months of effort, and required using new versions and new software that posed challenges to reconstructing and validating the results. The quantification leads to “reproducibility maps” that reveal that novice researchers would only be able to reproduce a few of the steps in the method, and that only expert researchers with advance knowledge of the domain would be able to reproduce the method in its entirety. The workflow itself is published as an online resource together with supporting software and data. The paper concludes with a brief discussion of the complexities of requiring reproducibility in terms of cost versus benefit, and a desiderata with our observations and guidelines for improving reproducibility. This has implications not only in reproducing the work of others from published papers, but reproducing work from one’s own laboratory

Screening for trisomies by cell-free DNA testing of maternal blood: consequences of a failed result

Objectives: First, to report the distribution of fetal fraction and the rate of failed result in trisomies 21, 18 and 13 , by comparison with pregnancies unaffected by these trisomies, secondly, examine the possible effects of maternal and fetal characteristics on the fetal fraction and thirdly, consider the options for the further management of pregnancies with failed cfDNA result. Methods: This was a cohort study of 10,698 singleton pregnancies undergoing screening for fetal trisomies 21, 18 and 13 by cfDNA testing at 10 14 weeks’ gestation There were 160 cases of trisomy 21, 50 of trisomy 18, 16 of trisomy 13 and 10,472 unaffected by these trisomies. Multivariate regression analysis was used to determine significant predictors of fetal fraction and failed result amongst maternal and fetal characteristics. Results: Fetal fraction decreased with increasing body m ass index and maternal age, was lower in women of South Asian racial origin than in Caucasians and in assisted than natural conceptions, and increased with fetal crown rump length, serum PAPP A and free hCG. The median fetal fraction was 11.0% (IQR 8.3-14.4%) in the unaffected group, 10.7% (IQR 7.8-14.3%) in trisomy 21, 8.6% (IQR 5.0-10.2%) in trisomy 18 and 7.0% (IQR 6.0-9.4%) in trisomy 13. There was a failed result from cfDNA testing after first sampling in 2.9% of the unaffected group, 1.9% of trisomy 21, 8.0% of trisomy 18 and 6.3% of trisomy 13. In the cases of failed result, 7% of women had invasive testing, mainly because of high risk from the combined test and/or presence of sonographic features suggestive of trisomies 18 and 13. All cases of trisomies were detected prenatally. Conclusions: In cases of failed cfDNA test the rate of trisomies 18 and 13, but not trisomy 21, are higher than in those with a successful test. In the management of such cases, the decision in favor of invasive testing sh ould depend on the risk of prior screening and the results of detailed ultrasound examination

SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison

The proteome-wide characterization and analysis of protein ligand-binding sites and their interactions with ligands can provide pivotal information in understanding the structure, function and evolution of proteins and for designing safe and efficient therapeutics. The SMAP web service (SMAP-WS) meets this need through parallel computations designed for 3D ligand-binding site comparison and similarity searching on a structural proteome scale. SMAP-WS implements a shape descriptor (the Geometric Potential) that characterizes both local and global topological properties of the protein structure and which can be used to predict the likely ligand-binding pocket [Xie,L. and Bourne,P.E. (2007) A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand-binding sites. BMC bioinformatics, 8 (Suppl. 4.), S9.]. Subsequently a sequence order independent profile–profile alignment (SOIPPA) algorithm is used to detect and align similar pockets thereby finding protein functional and evolutionary relationships across fold space [Xie, L. and Bourne, P.E. (2008) Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments. Proc. Natl Acad. Sci. USA, 105, 5441–5446]. An extreme value distribution model estimates the statistical significance of the match [Xie, L., Xie, L. and Bourne, P.E. (2009) A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery. Bioinformatics, 25, i305–i312.]. These algorithms have been extensively benchmarked and shown to outperform most existing algorithms. Moreover, several predictions resulting from SMAP-WS have been validated experimentally. Thus far SMAP-WS has been applied to predict drug side effects, and to repurpose existing drugs for new indications. SMAP-WS provides both a user-friendly web interface and programming API for scientists to address a wide range of compute intense questions in biology and drug discovery

PROMISCUOUS: a database for network-based drug-repositioning

The procedure of drug approval is time-consuming, costly and risky. Accidental findings regarding multi-specificity of approved drugs led to block-busters in new indication areas. Therefore, the interest in systematically elucidating new areas of application for known drugs is rising. Furthermore, the knowledge, understanding and prediction of so-called off-target effects allow a rational approach to the understanding of side-effects. With PROMISCUOUS we provide an exhaustive set of drugs (25 000), including withdrawn or experimental drugs, annotated with drug–protein and protein–protein relationships (21 500/104 000) compiled from public resources via text and data mining including manual curation. Measures of structural similarity for drugs as well as known side-effects can be easily connected to protein–protein interactions to establish and analyse networks responsible for multi-pharmacology. This network-based approach can provide a starting point for drug-repositioning. PROMISCUOUS is publicly available at http://bioinformatics.charite.de/promiscuous

The progress made in determining the Mycobacterium tuberculosis structural proteome

Mycobacterium tuberculosis is a highly infectious pathogen that is still responsible for millions of deaths annually. Effectively treating this disease typically requires a course of antibiotics, most of which were developed decades ago. These drugs are, however, not effective against persistent tubercle bacilli and the emergence of drug-resistant stains threatens to make many of them obsolete. The identification of new drug targets, allowing the development of new potential drugs, is therefore imperative. Both proteomics and structural biology have important roles to play in this process, the former as a means of identifying promising drug targets and the latter allowing understanding of protein function and protein–drug interactions at atomic resolution. The determination of M. tuberculosis protein structures has been a goal of the scientific community for the last decade, who have aimed to supply a large amount of structural data that can be used in structure-based approaches for drug discovery and design. Only since the genome sequence of M. tuberculosis has been available has the determination of large numbers of tuberculosis protein structures been possible. Currently, the molecular structures of 8.5% of all the pathogen's protein-encoding ORFs have been determined. In this review, we look at the progress made in determining the M. tuberculosis structural proteome and the impact this has had on the development of potential new drugs, as well as the discovery of the function of crucial mycobaterial proteins

Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome

The protein kinases are a large family of enzymes that play fundamental roles in propagating signals within the cell. Because of the high degree of binding site similarity shared among protein kinases, designing drug compounds with high specificity among the kinases has proven difficult. However, computational approaches to comparing the 3-dimensional geometry and physicochemical properties of key binding site residue positions have been shown to be informative of inhibitor selectivity. The Combinatorial Clustering Of Residue Position Subsets (CCORPS) method, introduced here, provides a semi-supervised learning approach for identifying structural features that are correlated with a given set of annotation labels. Here, CCORPS is applied to the problem of identifying structural features of the kinase ATP binding site that are informative of inhibitor binding. CCORPS is demonstrated to make perfect or near-perfect predictions for the binding affinity profile of 8 of the 38 kinase inhibitors studied, while only having overall poor predictive ability for 1 of the 38 compounds. Additionally, CCORPS is shown to identify shared structural features across phylogenetically diverse groups of kinases that are correlated with binding affinity for particular inhibitors; such instances of structural similarity among phylogenetically diverse kinases are also shown to not be rare among kinases. Finally, these function-specific structural features may serve as potential starting points for the development of highly specific kinase inhibitors

Drug Repurposing: Far Beyond New Targets for Old Drugs

Repurposing drugs requires finding novel therapeutic indications compared to the ones for which they were already approved. This is an increasingly utilized strategy for finding novel medicines, one that capitalizes on previous investments while derisking clinical activities. This approach is of interest primarily because we continue to face significant gaps in the drug–target interactions matrix and to accumulate safety and efficacy data during clinical studies. Collecting and making publicly available as much data as possible on the target profile of drugs offer opportunities for drug repurposing, but may limit the commercial applications by patent applications. Certain clinical applications may be more feasible for repurposing than others because of marked differences in side effect tolerance. Other factors that ought to be considered when assessing drug repurposing opportunities include relevance to the disease in question and the intellectual property landscape. These activities go far beyond the identification of new targets for old drugs