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.

E-learning in traditional industries: balancing the preferences of an ageing workforce with the expectations of a technoloigy-savvy generation

There is widespread argument that traditional organisations and industries with a predominantly older workforce who are not using computers as an integral part of their work, are unlikely to embrace the opportunities afforded by e-learning. However, the challenge remains to engage a younger generation of learners who seem comfortable learning with technology, whilst not alienating those older learners who may prefer to learn in more traditional ways. This paper analyses data from five case organisations within the Australian rail industry to identify how the potential of e-learning can be realised whilst acknowledging the technological divide between younger and older workers.

Rational avoidance of accountability

Anthony Downs public choice theory proposes that every rational person would try to meet their own desires in preference to those of others, and that such rational persons would attempt to obtain these desires in the most efficient manner possible. This paper will demonstrate that the application of this theory would mean that public servants and politicians would perform acts of corruption and maladministration in order to efficiently meet their desires. As such action is unavoidable, political parties must appear to meet the public demand for accountability systems, but must not make these systems viable lest they expose the corruption and maladministration that would threaten the government’s chance or re-election. It is therefore logical for governments to display a commitment for accountability whilst simultaneously ensuring the systems would not be able to interfere with government control or expose its flaws.

Roll the dice, rational agent : should extra-curial punishment mitigate an offender's sentence?

It was rugby league State of Origin night 2008 and a group of adults had descended upon a house in Eagleby, Brisbane to have some drinks and to celebrate the game. At 11pm that evening, Shane Thomas Davidson entered the bedroom of the homeowner’s 10-year-old son, TC. Davidson approached the bed and began to massage the boy’s penis under his clothing, which caused TC to wake. Davidson stated, ‘Show me how big your willy is and I’ll show you how big mine is’. TC refused the request and after a small period of time, left the bedroom and told his father what had happened...

Patients undergoing subacute rehabilitation have accurate expectations of their health-related quality of life at discharge

Background Expectations held by patients and health professionals may affect treatment choices and participation (by both patients and health professionals) in therapeutic interventions in contemporary patient-centered healthcare environments. If patients in rehabilitation settings overestimate their discharge health-related quality of life, they may become despondent as their progress falls short of their expectations. On the other hand, underestimating their discharge health-related quality of life may lead to a lack of motivation to participate in therapies if they do not perceive likely benefit. There is a scarcity of empirical evidence evaluating whether patients' expectations of future health states are accurate. The purpose of this study is to evaluate the accuracy with which older patients admitted for subacute in-hospital rehabilitation can anticipate their discharge health-related quality of life. Methods A prospective longitudinal cohort investigation of agreement between patients' anticipated discharge health-related quality of life (as reported on the EQ-5D instrument at admission to a rehabilitation unit) and their actual self-reported health-related quality of life at the time of discharge from this unit was undertaken. The mini-mental state examination was used as an indicator of patients' cognitive ability. Results Overall, 232(85%) patients had all assessment data completed and were included in analysis. Kappa scores ranged from 0.42-0.68 across the five EQ-5D domains and two patient cognition groups. The percentage of exact correct matches within each domain ranged from 69% to 85% across domains and cognition groups. Overall 40% of participants in each cognition group correctly anticipated all of their self-reported discharge EQ-5D domain responses. Conclusions Patients admitted for subacute in-hospital rehabilitation were able to anticipate the discharge health-related quality of life on the EQ-5D instrument with a moderate level of accuracy. This finding adds to the foundational empirical work supporting joint treatment decision making and patient-centered models of care during rehabilitation following acute illness or injury. Accurate patient expectations of the impact of treatment (or disease progression) on future health-related related quality of life is likely to allow patients and health professionals to successfully target interventions to priority areas where meaningful gains can be achieved.

Gaps in organizational leadership : linking strategic and operational activities through design-led propositions

The relationship between design process and business systems has been of interest to both practitioners and researchers exploring the numerous opportunities and challenges of this unlikely relationship. Often the relationship is presented as building design thinking capability within an organization, which can be broadly described as the union of design and strategy. Brown (2008) notes that design thinking is ‘‘a discipline that uses the designer’s sensibility and methods to match people’s needs with what is technically feasible and what business strategy can convert into customer value and market opportunities’’ (p. 1). The value that design thinking brings to an organization is a different way of framing situations and possibilities, doing things, and tackling problems: essentially a cultural transformation of the way it undertakes its business. The work of Martin (2009) has clearly shown the generalized differences between design thinking and business thinking, highlighting many instances in which these differences have been overcome, but also noting the many obstacles of trying to unify both approaches within an organization. Liedtka (2010) encourages firms to try and persist in overcoming these barriers, as she has noted that ‘‘business strategy desperately needs design ... because design is all about action and business strategy too often turns out to be only about talk ... fewer than 10 percent of new strategies are ever fully executed’’ (p. 9).

Stakeholder service delivery expectations of military facilities management

Purpose – The purpose of this paper is to examine the quality of service of a South East Asian country's military facilities management organisation. Design/methodology/approach – An interview survey and questionnaire survey were used to obtain a description and summary of stakeholders’ expectations and the extent to which they were being satisfied by the services provided. Findings – The method provides a useful means of identifying and prioritising varying expectations between stakeholder groups and of indicating any mismatch in expectations in the management of military facilities. Social implications – The development and use of a method to test and improve the effectiveness and efficiency of the management of military facilities helps in providing better value for money. Originality/value – In addition to re-affirming Parasuraman's overall dimensions of service expectation, the empirical summary of the stakeholders’ expectations obtained in this way is of practical value for the service provider in developing a strategy for expectation management. For the case studied, it is also apparent that although the current processes in service delivery are well understood by all involved stakeholders, there is a need for further improvement with regards to their expectation levels. It is also one of the very few reported studies on the management of military facilities.

Patient expectations, outcomes and satisfaction : related, relevant or redundant?

Abstract Study design: A prospective investigation of patients undergoing lumbar spine surgery. Objective: Is there a correlation between patient’s expectations before lumbar surgery, postoperative outcomes and satisfaction levels? Methods: A prospective study of 145 patients undergoing primary, single-level surgery for degenerative lumbar conditions was conducted. Oswestry Disability Index (ODI), back visual analogue scale (VAS) and leg VAS were assessed pre-operatively and at 6 weeks and 6 months post-surgery. Patients’ expectations were measured pre-operatively by asking them to score the level of pain and disability that would be least acceptable for them to undergo surgery and be satisfied. Satisfaction was assessed six weeks post-operatively with a Likert scale. Differences in patient expectations between actual and expected improvements were quantified. Results: Most patients had a clinically relevant improvement, but only about half achieved their expectation. Satisfaction did not correlate with pre-operative pain or disability, or with patient expectation of improvement. Instead, satisfaction correlated with positive outcomes. Conclusions Patient expectations have little bearing on final outcome and satisfaction.

Attitudes and expectations of technologies to manage high risk wandering and elopement in persons with dementia : an Australian perspective

Wandering is aimless and repetitive locomotion that may expose persons with dementia (PWD) to elopement, getting lost and death. This study is an Australian replication of a US study. Cross-disciplinary consensus- based analysis was applied to data from five focus groups (N =47: cognitively intact LTC residents (5), carers of PWD (11), home care workers (13) allied health professionals and health-focused engineers (7) and RNs (11). Groups received briefing about wandering monitoring and elopement management systems. Consistent with US attitudes, participants in all groups agreed on what a wandering technology should do, how it should do it, and necessary technical specifications. Within each group participants raised the need for a continuum of care for PWD and the imperative for early recognition of potentially dangerous wandering and getting lost when they occur. Global Positioning System elopement management was the preferred option. Interestingly, the prospective value of GPS to recover a lost or eloped wanderer far outweighed privacy concerns, as in the US. A pervasive theme was that technologies need to augment, but cannot replace, attentive, compassionate caregiver presence. A significant theme raised only by Australian carers of PWD was the potential for development of implantable GPS technologies and the need for public debate about attendant ethical issues. Given that 60% or more of over 200,000 Australians and 4.5 million Americans with dementia will develop wandering, there is a pressing need to develop effective locator systems that may delay institutionalization, help allay carer concern and enhance PWD safety.

Indian students at QUT : expectations and experiences

India currently ranks among the top source countries for the Australian education industry and therefore, a better understanding of the concerns and challenges confronted by Indian students is essential. This study was undertaken to assess the needs and expectations of Indian students enrolled at Queensland University of Technology (QUT) that would inform the formulation of strategies to provide superior service to the current and future cohorts of students coming from India. Data collection was undertaken through surveys and focus group meetings. The findings reveal the acute need for more effective dissemination of information prior to the students commencing their programs on both academic and non-academic aspects of university life as well as the resources and support available at QUT. Usage of English in an academic setting, career related services, accommodation, and networking opportunities were identified as some of the key areas of concern by the participants.

Successful outcomes in vocational education and training courses : how pedagogy and expectations influence achievement

This paper reports on a four year Australian Research Council funded Linkage Project titled Skilling Indigenous Queensland, conducted in regional areas of Queensland, Australia from 2009 to 2013. The project sought to investigate vocational education, training (VET) and teaching, Indigenous learners’ needs, employer cultural and expectations and community culture and expectations to identify best practice in numeracy teaching for Indigenous VET learners. Specifically it focused on ways to enhance the teaching and learning of courses and the associated mathematics in such courses to benefit learners and increase their future opportunities of employment. To date thirty-nine teachers/trainers/teacher aides and two hundred and thirty-one students consented to participate in the project. Nine VET courses were nominated to be the focus on the study. This paper focuses on questionnaire and interview responses from four trainers, two teacher aides and six students. In recent years a considerable amount of funding has been allocated to increasing Indigenous Peoples’ participation in education and employment. This increased funding is predicated on the assumption that it will make a difference and contribute to closing the education gap between Indigenous and non-Indigenous Australians (Council of Australia Governments, 2009). The central tenet is that access to education for Indigenous People will create substantial social and economic benefits for regional and remote Indigenous People. The project’s aim is to address some of the issues associated with the gap. To achieve the aims, the project adopted a mixed methods design aimed at benefitting research participants and included: participatory collaborative action research (Kemmis & McTaggart, 1988) and, community research (Smith, 1999). Participatory collaborative action research refers to a is a “collective, self-reflective enquiry undertaken by participants in social situations in order to improve the rationality and justice of their own social and educational practices” (Kemmis et al., 1988, p. 5). Community research is described as an approach that “conveys a much more intimate, human and self-defined space” (p. 127). Community research relies on and validates the community’s own definitions. As the project is informed by the social at a community level, it is described as “community action research or emancipatory research” (Smith, 1999, p. 127). It seeks to demonstrate benefit to the community, making positive differences in the lives of Indigenous People and communities. The data collection techniques included survey questionnaires, video recording of teaching and learning processes, teacher reflective video analysis of teaching, observations, semi-structured interviews and student numeracy testing. As a result of these processes, the findings indicate that VET course teachers work hard to adopt contextualising strategies to their teaching, however this process is not always straight forward because of the perceptions of how mathematics has been taught and learned historically. Further teachers, trainers and students have high expectations of one another with the view to successful outcomes from the courses.

Discussion paper and working paper series : Motivations, expectations and experiences of Australian rural and regional planners

Despite playing an extremely important role in shaping communities, the role and contribution of planners is not widely understood or acknowledged. At the same time, there is a shortage of planners in Australia, especially in non-urban areas. Thus, though an online survey of 185 rural and regional planners, this research explores their motivations, expectations and experiences. Most enjoyed and felt confident in their role, explaining that they valued the relaxed family orientated rural lifestyle and the varied nature of the planning work. Although they sometimes felt isolated, the non-urban location provided quicker progression to senior roles, the ability to engage directly with the community and to see the consequences of their decisions. Only half felt their education had prepared them well for their role, citing gaps in terms of computerised modelling, team leadership and conflict resolution skills. Their feedback centred on providing a more practical course, focussing more on regional planning, and encouraging urban and rural experience placements. As the first study to quantifiably explore rural and regional Australian planners perceptions of their role and challenges, the findings illustrate current experiences, key planning challenges, perceived educational gaps and future priorities.

Perceptions and expectations for learning and development for older workers within Queensland local government councils : a case study

Current literature warns organisations about a global ageing phenomenon. Workplace ageing is causing a diminishing work pool which has consequences for a sustainable workforce in the future. This phenomenon continues to impact on local government councils in Australia. Australia has one of the world’s most rapidly ageing populations, and there is evidence that Australian local government councils are already resulting in an unsustainable workforce. Consequently, this research program investigated the role of older workers in the Queensland local government workplace in enabling them to extend their working lives towards transitional employment and a sustainable workforce in the future. Transitional Employment is intended as a strategy for enabling individuals to have greater control over their employment options and their employability during the period leading to their final exit from the workforce. There was no evidence of corporate support for older workers in Queensland local government councils other than tokenistic government campaigns encouraging organisations to "better value their older workers". (Queensland Government, 2007d, p.6). TE is investigated as a possible intervention for older workers in the future. The international and national literature review reflected a range of matters impacting on current older workers in the workforce and barriers preventing them from accessing services towards extending their employment beyond the traditional retirement age (60 years) as defined by the Australian Government; an age when individuals can access their superannuation. Learning and development services were identified as one of those barriers. There was little evidence of investment in or consistent approaches to supporting older workers by organisations. Learning and development services appeared at best to be ad hoc, reactive to corporate productivity and outputs with little recognition of the ageing phenomenon (OECD, 2006, p.23) and looming skills and labour shortages (ALGA, 2006, p. 19). Themes from the literature review led to the establishment of three key research questions: 1. What are the current local government workforce issues impacting on skills and labour retention? 2. What are perceptions about the current workplace environment? And, 3. What are the expectations about learning and development towards extending employability of older workers within the local government sector? The research questions were explored by utilising three qualitative empirical studies, using some numerical data for reporting and comparative analysis. Empirical Study One investigated common themes for accessing transitional employment and comprised two phases. A literature review and Study One data analysis enabled the construction of an initial Transitional Employment Model which includes most frequent themes. Empirical Study Two comprised focus groups to further consider those themes. This led to identification of issues impacting the most on access to learning and development by older workers and towards a revised TEM. Findings presented majority support for transitional employment as a strategy for supporting older workers to work beyond their traditional retirement age. Those findings are presented as significant issues impacting on access to transitional employment within the final 3-dimensionsal TEM. The model is intended as a guide for responding to an ageing workforce by local government councils in the future. This study argued for increased and improved corporate support, particularly for learning and development services for older workers. Such support will enable older workers to maintain their employability and extend their working lives; a sustainable workforce in the future.