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.

Nanostructures for sensors, electronics, energy and environment

Nanoscale science is growing evermore important on a global scale and is widely seen as playing an integral part in the growth of future world economies. The daunting energy crisis we are facing could be solved not only by new and improved ways of getting energy directly from the sun, but also by saving power thanks to advancements in electronics and sensors. New, cheap dye-sensitized and polymer solar cells hold the promise of environmentally friendly and simple production methods, along with mechanical flexibility and low weight, matching the conditions for a widespread deployment of this technology. Cheap sensors based on nanomaterials can make a fundamental contribution to the reduction of greenhouse gas emissions, allowing the creation of large sensor networks to monitor countries and cities, improving our quality of life. Nanowires and nano-platelets of metal oxides are at the forefront of the research to improve sensitivity and reduce the power consumption in gas sensors. Nanoelectronics is the next step in the electronic roadmap, with many devices currently in production already containing components smaller than 100 nm. Molecules and conducting polymers are at the forefront of this research with the goal of reducing component size through the use of cheap and environmentally friendly production methods. This, and the coming steps that will eventually bring the individual circuit element close to the ultimate limit of the atomic level, are expected to deliver better devices with reduced power consumption.

1,1,3,3-Tetraethylisoindolin-2-ium chloride

In the structure of the title compound C16H26N+ Cl-, the salt of a precursor in the synthesis of an isoindolin-2-yloxyl free-radical trapping agent, the cations and anions form discrete centrosymetric cyclic dimers through N---H...Cl hydrogen-bonding associations [graph set R2/4(8)].

Whelanite Ca5Cu2(OH)2CO3,Si6O17•4H2O – A vibrational spectroscopic study

Whelanite Ca5Cu2(OH)2CO3,Si6O17•4H2O is a hydrated hydroxy mixed anion compound with both silicate and carbonate anions in the formula. The structural characterisation of the mineral whelanite remains incomplete. Whelanite is probably a neosilicate with Cu2+ in square planar coordination. Two Raman bands at 1070 and 1094 cm-1 are assigned to the ν1 symmetric stretching modes of the CO32- units. The observation of two symmetric stretching modes supports the concept of two non-equivalent CO32- units in the whelanite structure. The intense sharp Raman band at 1006 cm-1 is assigned to the ν1 (A1g) symmetric stretching vibration of the Si6O17 units. The splitting of the ν3 vibrational mode offers support to the concept that the SiO4 tetrahedron in whelanite is strongly distorted. A very intense Raman band observed at 666 cm-1 with a shoulder at 697 cm-1 is assigned to the ν4 vibrational modes. Intense Raman bands at 3534, 3556, 3550 and 3595 cm-1 are assigned to the stretching vibrations of the OH units. Low intensity Raman bands at 2910, 3187 and 3453 cm-1 are assigned to water stretching modes. Thus, vibrational spectroscopy has been used to characterise the molecular structure of whelanite. Whelanite is a mineral that could be conceived as a healing mineral

The effect of hexagonal boron nitride additive on the effectiveness of grease-based lubrication of a steel surface

Purpose: The purpose of this paper is to study the sliding and the vibrating fretting tests mechanism of h-BN micro-particles when used as a lubricating grease-2 additive. Design/methodology/approach: The fretting tests were conducted on steel/steel contacts using both vibrating fretting apparatus and the shaftsleeve slide fitted tester. The wear scars were characterized with profilometry. The tribological properties of grease-2 compounded with h-BN additive were also compared to those obtained for the commercial product Militec-4. Findings: The experiment showed significant differences between the results obtained from the vibrating fretting and the shaft-sleeve sliding fitted tests. Adding h-BN to the lubricant leads to a better performance in the shaft-sleeve slide regime than in the steel/steel vibrating test condition. Originality/value: The results of the experimental studies demonstrate the potential of h-BN as an additive for preventing fretting sliding, and can very useful for further application of compound grease-2 with h-BN additive in industrial equipment.

rac-3-exo-Ammonio-7-anti-carboxytricyclo-[2.2.10.2,6]heptane-3-endo-carboxylate

The racemic title compound, C9H11NO4 . H2O, a tricyclic rearranged aminonorbornane dicarboxylic acid is a conformationally rigid analogue of glutamic acid and exists as an ammonium-carboxylate zwitterion, with the bridghead carboxylic acid group anti-related. In the crystal, intermolecular N-H...O and O-H...O hydrogen-bonding interactions involving the ammonium, carboxylic acid and water donor groups with both water and carboxyl O-atom acceptors give a three-dimensional framework structure.

Gas sensing characteristics of Fe-doped tungsten oxide thin films

This study reports on the gas sensing characteristics of Fe-doped (10 at.%) tungsten oxide thin films of various thicknesses (100–500 nm) prepared by electron beam evaporation. The performance of these films in sensing four gases (H2, NH3, NO2 and N2O) in the concentration range 2–10,000 ppm at operating temperatures of 150–280 °C has been investigated. The results are compared with the sensing performance of a pure WO3 film of thickness 300 nm produced by the same method. Doping of the tungsten oxide film with 10 at.% Fe significantly increases the base conductance of the pure film but decreases the gas sensing response. The maximum response measured in this experiment, represented by the relative change in resistance when exposed to a gas, was ΔR/R = 375. This was the response amplitude measured in the presence of 5 ppm NO2 at an operating temperature of 250 °C using a 400 nm thick WO3:Fe film. This value is slightly lower than the corresponding result obtained using the pure WO3 film (ΔR/R = 450). However it was noted that the WO3:Fe sensor is highly selective to NO2, exhibiting a much higher response to NO2 compared to the other gases. The high performance of the sensors to NO2 was attributed to the small grain size and high porosity of the films, which was obtained through e-beam evaporation and post-deposition heat treatment of the films at 300 °C for 1 h in air.

Characterisation of sugarcane juice particles that influence the clarification process

Problems associated with processing whole sugarcane crop can be minimised by removing impurities during the clarification stage. As a first step, it is important to understand the colloidal chemistry of juice particles on a molecular level to assist development strategies for effective clarification performance. This paper presents the composition and surface characteristics of colloidal particles originating from various juice types by using scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDX), X-ray photoelectron spectroscopy (XPS) and zeta potential measurements. The composition and surface characteristics of colloidal juice particles are reported. The results indicate that there are three types of colloidal particles present viz., an aluminosilicate compound, silica and iron oxide, with the latter two being abundant. Proteins, polysaccharides and organic acids were identified on the surface of particles in juice. The overall particle charge varies from –2 mV to –6 mV. In comparison to juice expressed from burnt cane, the zeta potential values were more negative with juice particles originating from whole crop. This in part explains why these juices are difficult to clarify.

Phenolics in sugar cane juice : potential degradation by hydrogen peroxide and Fenton's reagent

The presence of colour in raw sugar plays a key role in the marketing strategy of the Australian raw sugar industry. Some sugars are relatively difficult to decolourise during refining and develop colour during storage. A new approach that might result in efficient and cost-effective colour removal during the sugar manufacturing process is the use of an advanced oxidation process (AOP), known as Fenton oxidation, that is, catalytic production of hydroxyl radicals from the decomposition of hydrogen peroxide using ferrous iron. As a first step towards developing this technology, this study determined the composition of colour precursors present in the juice of cane harvested by three different methods. The methods were harvesting cane after burning, harvesting the whole crop with half of the trash extracted and harvesting the whole crop with no trash extracted. The study also investigated the degradation at pH 3, 4 and 5 of a phenolic compound, caffeic acid (3,4–dihydroxycinnamic acid), which is present in sugar cane juice, using both hydrogen peroxide and Fenton’s reagent. The results show that juice expressed from whole crop cane has significantly higher colour than juices expressed from burnt cane. However, the concentrations of phenolic acids were lower in the juices expressed from whole crop cane. The main phenolic acids present in these juices were p-coumaric, vanillic, 2,3–dihydroxybenzoic, gallic and 3,4–dihydroxybenzoic acids. The degradation of caffeic acid significantly improved using Fenton’s reagent in comparison to hydrogen peroxide alone. The Fenton oxidation was optimum at pH 5 when up to ~86 % of caffeic acid degraded within 5 min.

Phenolics in sugar cane juice : potential degradation by hydrogen peroxide and Fenton’s reagent

The presence of colour in raw sugar plays a key role in the marketing strategy of the Australian raw sugar industry. Some sugars are relatively difficult to decolourise during refining and develop colour during storage. A new approach that might result in efficient and cost-effective colour removal during the sugar manufacturing process is the use of an advanced oxidation process (AOP), known as Fenton oxidation, that is, catalytic production of hydroxyl radicals from the decomposition of hydrogen peroxide using ferrous iron. As a first step towards developing this technology, this study determined the composition of colour precursors present in the juice of cane harvested by three different methods. The methods were harvesting cane after burning, harvesting the whole crop with half of the trash extracted and harvesting the whole crop with no trash extracted. The study also investigated the degradation at pH 3, 4 and 5 of a phenolic compound, caffeic acid (3,4–dihydroxycinnamic acid), which is present in sugar cane juice, using both hydrogen peroxide and Fenton’s reagent. The results show that juice expressed from whole crop cane has significantly higher colour than juices expressed from burnt cane. However, the concentrations of phenolic acids were lower in the juices expressed from whole crop cane. The main phenolic acids present in these juices were p-coumaric, vanillic, 2,3–dihydroxybenzoic, gallic and 3,4–dihydroxybenzoic acids. The degradation of caffeic acid significantly improved using Fenton’s reagent in comparison to hydrogen peroxide alone. The Fenton oxidation was optimum at pH 5 when up to ~86% of caffeic acid degraded within 5 min.

Prevention of pelvic sepsis in major open pelviperineal injury

Compound pelvic fractures are deemed to be one of the most severe orthopaedic injuries with an extremely high morbidity and mortality. After the initial resuscitation phase the prevention of pelvic sepsis is one of the main treatment goals for patients with an open pelvic fracture. If there is a suspicion of a rectal injury or if the wounds are in the perineal area, The Princess Alexandra Hospital's management plan includes early faecal diversion combined with vigorous soft tissue debridement, VAC(®) therapy and (if indicated) external fixation of the pelvic fracture. We present our flowchart for the treatment of trauma patients with compound pelvic fractures illustrated by a case report describing a 32 year old patient who sustained an open pelvic ring injury in a workplace accident. The aim of this paper is to underline the importance of a safe, straightforward approach to compound pelvic fractures.

Resolution of the chiral (1R,2S) enantiomer of cis-cyclohexane-1,2-dicarboxylic acid in the brucinium salt 2,3-dimethoxy-10-oxostrychnidinium (1R,2S)-2-carboxycyclohexane-1-carboxylate dihydrate

The structure of the 1:1 brucinium salt of cis-cyclohexane-1,2-dicarboxylic acid, 2,3-dimethoxy-10-oxostrychnidinium (1R,2S)-2-carboxycyclohexane-1-carboxylate dihydrate, has revealed the resolved (1R,2S) enantiomer of the acid. Crystals of the compound are orthorhombic, space group P212121, with unit cell dimensions a = 8.1955(3), b = 12.4034(3), c = 29.9073(9)Å, and Z = 4. The asymmetric unit comprises the brucinium cation, the hydrogen cis-cyclohexane-1,2-dicarboxylate cation, in which the carboxylate group is disordered over two sites (58, 42%), and two water molecules of solvation, one of which is occupies two 50% occupancy sites. The classic undulating brucinium cation substructures are present with the anion and the water molecules occupying the interstitial cavities and are hydrogen-bonded to them in a two-dimensional network structure.

A decision table method for randomness measurement

Data quality has become a major concern for organisations. The rapid growth in the size and technology of a databases and data warehouses has brought significant advantages in accessing, storing, and retrieving information. At the same time, great challenges arise with rapid data throughput and heterogeneous accesses in terms of maintaining high data quality. Yet, despite the importance of data quality, literature has usually condensed data quality into detecting and correcting poor data such as outliers, incomplete or inaccurate values. As a result, organisations are unable to efficiently and effectively assess data quality. Having an accurate and proper data quality assessment method will enable users to benchmark their systems and monitor their improvement. This paper introduces a granules mining for measuring the random degree of error data which will enable decision makers to conduct accurate quality assessment and allocate the most severe data, thereby providing an accurate estimation of human and financial resources for conducting quality improvement tasks.

Ozone-initiated particle formation, particle aging, and precursors in a laser printer

An increasing number of researchers have hypothesized that ozone may be involved in the particle formation processes that occur during printing, however no studies have investigated this further. In the current study, this hypothesis was tested in a chamber study by adding supplemental ozone to the chamber after a print job without measurable ozone emissions. Subsequent particle number concentration and size distribution measurements showed that new particles were formed minutes after the addition of ozone. The results demonstrated that ozone did react with printer-generated volatile organic compounds (VOCs) to form secondary organic aerosols (SOAs). The hypothesis was further confirmed by the observation of correlations among VOCs, ozone, and particles concentrations during a print job with measurable ozone emissions. The potential particle precursors were identified by a number of furnace tests, which suggested that squalene and styrene were the most likely SOA precursors with respect to ozone. Overall, this study significantly improved scientific understanding of the formation mechanisms of printer-generated particles, and highlighted the possible SOA formation potential of unsaturated nonterpene organic compounds by ozone-initiated reactions in the indoor environment. © 2011 American Chemical Society.