Rational design of serine protease inhibitors

Proteases regulate a spectrum of diverse physiological processes, and dysregulation of proteolytic activity drives a plethora of pathological conditions. Understanding protease function is essential to appreciating many aspects of normal physiology and progression of disease. Consequently, development of potent and specific inhibitors of proteolytic enzymes is vital to provide tools for the dissection of protease function in biological systems and for the treatment of diseases linked to aberrant proteolytic activity. The studies in this thesis describe the rational design of potent inhibitors of three proteases that are implicated in disease development. Additionally, key features of the interaction of proteases and their cognate inhibitors or substrates are analysed and a series of rational inhibitor design principles are expounded and tested. Rational design of protease inhibitors relies on a comprehensive understanding of protease structure and biochemistry. Analysis of known protease cleavage sites in proteins and peptides is a commonly used source of such information. However, model peptide substrate and protein sequences have widely differing levels of backbone constraint and hence can adopt highly divergent structures when binding to a protease’s active site. This may result in identical sequences in peptides and proteins having different conformations and diverse spatial distribution of amino acid functionalities. Regardless of this, protein and peptide cleavage sites are often regarded as being equivalent. One of the key findings in the following studies is a definitive demonstration of the lack of equivalence between these two classes of substrate and invalidation of the common practice of using the sequences of model peptide substrates to predict cleavage of proteins in vivo. Another important feature for protease substrate recognition is subsite cooperativity. This type of cooperativity is commonly referred to as protease or substrate binding subsite cooperativity and is distinct from allosteric cooperativity, where binding of a molecule distant from the protease active site affects the binding affinity of a substrate. Subsite cooperativity may be intramolecular where neighbouring residues in substrates are interacting, affecting the scissile bond’s susceptibility to protease cleavage. Subsite cooperativity can also be intermolecular where a particular residue’s contribution to binding affinity changes depending on the identity of neighbouring amino acids. Although numerous studies have identified subsite cooperativity effects, these findings are frequently ignored in investigations probing subsite selectivity by screening against diverse combinatorial libraries of peptides (positional scanning synthetic combinatorial library; PS-SCL). This strategy for determining cleavage specificity relies on the averaged rates of hydrolysis for an uncharacterised ensemble of peptide sequences, as opposed to the defined rate of hydrolysis of a known specific substrate. Further, since PS-SCL screens probe the preference of the various protease subsites independently, this method is inherently unable to detect subsite cooperativity. However, mean hydrolysis rates from PS-SCL screens are often interpreted as being comparable to those produced by single peptide cleavages. Before this study no large systematic evaluation had been made to determine the level of correlation between protease selectivity as predicted by screening against a library of combinatorial peptides and cleavage of individual peptides. This subject is specifically explored in the studies described here. In order to establish whether PS-SCL screens could accurately determine the substrate preferences of proteases, a systematic comparison of data from PS-SCLs with libraries containing individually synthesised peptides (sparse matrix library; SML) was carried out. These SML libraries were designed to include all possible sequence combinations of the residues that were suggested to be preferred by a protease using the PS-SCL method. SML screening against the three serine proteases kallikrein 4 (KLK4), kallikrein 14 (KLK14) and plasmin revealed highly preferred peptide substrates that could not have been deduced by PS-SCL screening alone. Comparing protease subsite preference profiles from screens of the two types of peptide libraries showed that the most preferred substrates were not detected by PS SCL screening as a consequence of intermolecular cooperativity being negated by the very nature of PS SCL screening. Sequences that are highly favoured as result of intermolecular cooperativity achieve optimal protease subsite occupancy, and thereby interact with very specific determinants of the protease. Identifying these substrate sequences is important since they may be used to produce potent and selective inhibitors of protolytic enzymes. This study found that highly favoured substrate sequences that relied on intermolecular cooperativity allowed for the production of potent inhibitors of KLK4, KLK14 and plasmin. Peptide aldehydes based on preferred plasmin sequences produced high affinity transition state analogue inhibitors for this protease. The most potent of these maintained specificity over plasma kallikrein (known to have a very similar substrate preference to plasmin). Furthermore, the efficiency of this inhibitor in blocking fibrinolysis in vitro was comparable to aprotinin, which previously saw clinical use to reduce perioperative bleeding. One substrate sequence particularly favoured by KLK4 was substituted into the 14 amino acid, circular sunflower trypsin inhibitor (SFTI). This resulted in a highly potent and selective inhibitor (SFTI-FCQR) which attenuated protease activated receptor signalling by KLK4 in vitro. Moreover, SFTI-FCQR and paclitaxel synergistically reduced growth of ovarian cancer cells in vitro, making this inhibitor a lead compound for further therapeutic development. Similar incorporation of a preferred KLK14 amino acid sequence into the SFTI scaffold produced a potent inhibitor for this protease. However, the conformationally constrained SFTI backbone enforced a different intramolecular cooperativity, which masked a KLK14 specific determinant. As a consequence, the level of selectivity achievable was lower than that found for the KLK4 inhibitor. Standard mechanism inhibitors such as SFTI rely on a stable acyl-enzyme intermediate for high affinity binding. This is achieved by a conformationally constrained canonical binding loop that allows for reformation of the scissile peptide bond after cleavage. Amino acid substitutions within the inhibitor to target a particular protease may compromise structural determinants that support the rigidity of the binding loop and thereby prevent the engineered inhibitor reaching its full potential. An in silico analysis was carried out to examine the potential for further improvements to the potency and selectivity of the SFTI-based KLK4 and KLK14 inhibitors. Molecular dynamics simulations suggested that the substitutions within SFTI required to target KLK4 and KLK14 had compromised the intramolecular hydrogen bond network of the inhibitor and caused a concomitant loss of binding loop stability. Furthermore in silico amino acid substitution revealed a consistent correlation between a higher frequency of formation and the number of internal hydrogen bonds of SFTI-variants and lower inhibition constants. These predictions allowed for the production of second generation inhibitors with enhanced binding affinity toward both targets and highlight the importance of considering intramolecular cooperativity effects when engineering proteins or circular peptides to target proteases. The findings from this study show that although PS-SCLs are a useful tool for high throughput screening of approximate protease preference, later refinement by SML screening is needed to reveal optimal subsite occupancy due to cooperativity in substrate recognition. This investigation has also demonstrated the importance of maintaining structural determinants of backbone constraint and conformation when engineering standard mechanism inhibitors for new targets. Combined these results show that backbone conformation and amino acid cooperativity have more prominent roles than previously appreciated in determining substrate/inhibitor specificity and binding affinity. The three key inhibitors designed during this investigation are now being developed as lead compounds for cancer chemotherapy, control of fibrinolysis and cosmeceutical applications. These compounds form the basis of a portfolio of intellectual property which will be further developed in the coming years.

Natural, engineered and synthetic inhibitors of kallikrein-related peptidases

There is a rapidly growing appreciation of the important physiological roles played by kallikreins and kallikrein-related peptidases (KLKs). Recent studies have revealed that these enzymes control key events in processes as diverse as inflammation and skin desquamation. Accordingly, there is considerable interest in developing tools to further dissect kallikrein activity, and a burgeoning effort aimed at producing lead inhibitors for therapeutic development. Indeed, several candidate inhibitors are already in clinical trials. This chapter surveys the naturally occurring kallikrein inhibitors, together with strategies for employing these molecules as bioscaffolds, as well as current progress in the development of small-molecule kallikrein inhibitors.

Engineered protease inhibitors based on sunflower trypsin inhibitor-1 (SFTI-1) provide insights into the role of sequence and conformation in Laskowski mechanism inhibition

Laskowski inhibitors regulate serine proteases by an intriguing mode of action that involves deceiving the protease into synthesizing a peptide bond. Studies exploring naturally occurring Laskowski inhibitors have uncovered several structural features that convey the inhibitor's resistance to hydrolysis and exceptional binding affinity. However, in the context of Laskowski inhibitor engineering, the way that various modifications intended to fine-tune an inhibitor's potency and selectivity impact on its association and dissociation rates remains unclear. This information is important as Laskowski inhibitors are becoming increasingly used as design templates to develop new protease inhibitors for pharmaceutical applications. In this study, we used the cyclic peptide, sunflower trypsin inhibitor-1 (SFTI-1), as a model system to explore how the inhibitor's sequence and structure relate to its binding kinetics and function. Using enzyme assays, MD simulations and NMR spectroscopy to study SFTI variants with diverse sequence and backbone modifications, we show that the geometry of the binding loop mainly influences the inhibitor's potency by modulating the association rate, such that variants lacking a favourable conformation show dramatic losses in activity. Additionally, we show that the inhibitor's sequence (including both the binding loop and its scaffolding) influences its potency and selectivity by modulating both the association and the dissociation rates. These findings provide new insights into protease inhibitor function and design that we apply by engineering novel inhibitors for classical serine proteases, trypsin and chymotrypsin and two kallikrein-related peptidases (KLK5 and KLK14) that are implicated in various cancers and skin diseases.

From literacy to multiliteracies : diverse learners and pedagogical practice

In this paper, we provide specific examples of the educational promises and problems that arise as multiliteracies pedagogical initiatives encounter conventional institutional beliefs and practices in mainstream schooling. This paper documents and characterizes the ways in which two specific digital learning initiatives were played out in two distinctive traditional schooling contexts, as experienced by two different student groups: one comprising an elite mainstream and the other an excluded minority. By learning from the instructive complications that arose out of attempts by innovative and well-meaning educators to provide students with more relevant learning experiences than currently exist in mainstream schooling, this paper contributes fresh perspectives and more nuanced understandings of how diverse learners and their teachers negotiate the opportunities and challenges of the New London Group's vision of a multiliteracies approach to literacy and learning. We conclude by arguing that, where multiliteracies are understood as “garnish” to the “pedagogical roast” of traditional code-based and print-based academic literacies, they will continue to work on the sidelines of mainstream schooling and be seen only as either useful extensions or helpful interventions for high-performing and at-risk students respectively.

User-Generated Content als Qualitätsmedium? Alternative Anreize für Qualitätscontent

Angetrieben und unterstützt durch Web-2.0-Technologien, gibt es heute einen Trend zur Verbindung der Nutzung und Produktion von Inhalten als Produtzung (engl. produsage ). Um dabei die Qualität der erstellten Inhalte und eine nachhaltige Teilnahme der Nutzer sicherzustellen, müsen vier grundlegende Prinzipien eingehalten werden: * Größtmögliche Offenheit. * Ankurbeln der Gemeinschaft durch Inhalte und Hilfsmittel. * Unterstützung der Gruppendynamik und Abtretung von Verantwortung. * Keine Ausbeutung der Gemeinschaft und ihrer Arbeit.

The PG500 series : novel heparan sulfate mimetics as potent angiogenesis and heparanase inhibitors for cancer therapy

Heparan sulfate mimetics, which we have called the PG500 series, have been developed to target the inhibition of both angiogenesis and heparanase activity. This series extends the technology underpinning PI-88, a mixture of highly sulfated oligosaccharides which reached Phase III clinical development for hepatocellular carcinoma. Advances in the chemistry of the PG500 series provide numerous advantages over PI-88. These new compounds are fully sulfated, single entity oligosaccharides attached to a lipophilic moiety, which have been optimized for drug development. The rational design of these compounds has led to vast improvements in potency compared to PI-88, based on in vitro angiogenesis assays and in vivo tumor models. Based on these and other data, PG545 has been selected as the lead clinical candidate for oncology and is currently undergoing formal preclinical development as a novel treatment for advanced cancer.

Accommodating the diverse cultural needs of cancer patients and their families in palliative care

Cultural issues have become an increasingly important consideration in healthcare. Such cultural issues, however, are underresearched in Australia, especially in palliative care. This study has sought to address this gap, exploring the social construction of cultural issues in palliative care by oncology nurses. A grounded theory approach was used. Semistructured interviews with 7 Australian oncology nurses provided the data for the study. The core category emerging from the study was that of accommodating cultural needs whereby to meet patients' specific cultural requirements, nurses actively found ways to accommodate the needs of patients and their families. This process often included compromise and negotiation whereby limits were set. In addition, the use of cross-cultural communication strategies emerged from the data as an important feature of cultural care. A series of subcategories were also identified as factors that could influence the process by which nurses would accommodate cultural needs.

Collaborative staff development across a diverse organisation

This paper examines the role of staff training and support in the experience of staff with online teaching at Australian Catholic University. Australian Catholic University’s online education is differentiated from other Australian universities for two reasons: 1) It has 6 nationally based campuses spread across a geographical reach of 2,500 kilometres, 2) It has no internal Flexible Learning or Distance Education unit as such, and out sources the provision of web based teaching and learning services to NextEd Pty Ltd, a commercial online education company. Both factors provide challenges and benefits to the effective training, support and coordination of online education in the university.

Comprehension and content : planning literacy curriculum in low socioeconomic and culturally diverse schools

This article reframes comprehension as a social and intellectual practice. It reviews literature on current approaches to reading instruction for linguistically and culturally diverse and low socioeconomic students, noting the current policy emphasis on the teaching of comprehension as autonomous skills and ‘strategies’. The Four Resources model (Freebody & Luke, 1990) is used to situate comprehension instruction with an emphasis on student cultural and community knowledge, and substantive intellectual and sociocultural content in elementary and middle school curricula. Illustrations are drawn from research underway on the teaching of literacy in low socioeconomic schools.

Transition to school of diverse learners

This thesis examines the approaches taken by early years teachers in supporting the inclusive school transition of diverse learners. A Thesis by Publication format has been employed, where instead of traditional thesis chapters, scholarly journal articles are presented in an ordered sequence in two sections. The first set of journal articles establishes a synthesis of approaches to diversity and inclusion and to transition to school, in order to set a clear theoretical position arising from the literature. The second set of journal articles reports empirical evidence from three school sites on diversity, inclusion and transition to school, discussed in relation to both the first set of papers and to additional literature. The relationship between these articles, and the methodology used for the theoretical papers, is outlined in linking summaries of the challenges the papers seek to address.