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.

A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate

Evidence for a two-metal ion mechanism for cleavage of the HH16 hammerhead ribozyme is provided by monitoring the rate of cleavage of the RNA substrate as a function of La3+ concentration in the presence of a constant concentration of Mg2+. We show that a bell-shaped curve of cleavage activation is obtained as La3+ is added in micromolar concentrations in the presence of 8 mM Mg2+, with a maximal rate of cleavage being attained in the presence of 3 microM La3+. These results show that two-metal ion binding sites on the ribozyme regulate the rate of the cleavage reaction and, on the basis of earlier estimates of the Kd values for Mg2+ of 3.5 mM and > 50 mM, that these sites bind La3+ with estimated Kd values of 0.9 and > 37.5 microM, respectively. Furthermore, given the very different effects of these metal ions at the two binding sites, with displacement of Mg2+ by La3+ at the stronger (relative to Mg2+) binding site activating catalysis and displacement of Mg2+ by La3+ at the weaker (relative to Mg2+) (relative to Mg2+) binding site inhibiting catalysis, we show that the metal ions at these two sites play very different roles. We argue that the metal ion at binding site 1 coordinates the attacking 2'-oxygen species in the reaction and lowers the pKa of the attached proton, thereby increasing the concentration of the attacking alkoxide nucleophile in an equilibrium process. In contrast, the role of the metal ion at binding site 2 is to catalyze the reaction by absorbing the negative charge that accumulates at the leaving 5'-oxygen in the transition state. We suggest structural reasons why the Mg(2+)-La3+ ion combination is particularly suited to demonstrating these different roles of the two-metal ions in the ribozyme cleavage reaction.

Adsorption of carbon dioxide and nitrogen on single-layer aluminum nitride nanostructures studied by density functional theory

The adsorption of carbon dioxide and nitrogen molecules on aluminum nitride (AlN) nanostructures has been explored using first-principle computational methods. Optimized configurations corresponding to physisorption and, subsequentially, chemisorption of CO2 are identified, in contrast to N2, for which only a physisorption structure is found. Transition-state searches imply a low energy barrier between the physisorption and chemisorption states for CO2 such that the latter is accessible and thermodynamically favored at room temperature. The effective binding energy of the optimized chemisorption structure is apparently larger than those for other CO2 adsorptive materials, suggesting the potential for application of aluminum nitride nanostructures for carbon dioxide capture and storage.

Addition of diazomethane to armchair single-walled carbon nanotubes and their reaction sequences : A computational study

The sidewall additions of diazomethane to (n, n), n = 3–10 armchair single-walled carbon nanotubes (SWCNTs) on two different orientations of C–C bonds have been studied using the ONIOM(B3LYP/6-31G(d):PM3) approach. The binding energies of SWCNTs complexes with CH2N2, CH2 and their transition-state structures were computed at the B3LYP/6-31G(d) level. The effects of diameters of armchair SWCNTs on their binding energies were studied. Relative reactivities of all the SWCNTs and their complexes based on their frontier orbital energies gaps are reported.

Porous graphene and nanomeshes

This chapter briefly introduces the concepts and modeling of gas/isotope separation by two dimensional carbon frameworks, i.e. porous graphene and carbon nanomeshes, on the basis of reviewing recent literatures. The small size of evenly distributed pores on these carbon frameworks make them ideal not only for the separation of small gas molecules but also for isotope separation by utilizing the different zero point energies induced by confinement of the pores. The related simulations were treated by transition state theory, an affordable yet precise method that could be adopted in combination with different levels of theory. Such method could be employed to evaluate the performance, as well as to aid the design, of other 2D carbon frameworks toward the goal of gas/isotope separation in the future.

The loss of CO from the ortho, meta and para forms of deprotonated methyl benzoate in the gas phase

The ortho, meta and para anions of methyl benzoate may be made in the source of a mass spectrometer by the S(N)2(Si) reactions between HO- and methyl (o-, m-, and p-trimethylsilyl)benzoate respectively. All three anions lose CO upon collisional activation to form the ortho anion of anisole in the ratio ortho>>meta > para. The rearrangement process is charge directed through the ortho anion. Theoretical calculations at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory indicate that the conversion of the meta and para anions to the ortho anion prior to loss of CO involve 1,2-H transfer(s), rather than carbon scrambling of the methoxycarbonylphenyl anion. There are two mechanisms which can account for this rearrangement, viz. (A) cyclisation of the ortho anion centre to the carbonyl group of the ester to give a cyclic carbonyl system in which the incipient methoxide anion substitutes at one of the two equivalent ring carbons of the three membered ring to yield an intermediate which loses CO to give the ortho anion of anisole, and (B) an elimination reaction to give an intermediate benzyne-methoxycarbonyl anion complex in which the MeOCO- species acts as a MeO- donor, which then adds to benzyne to yield the ortho anion of anisole. Calculations at the B3LYP/6-311++G(d,p)//HF/6-31+G(d) level of theory indicate that (i) the barrier in the first step (the rate determining step) of process A is 87 kJ mol(-1) less than that for the synchronous benzyne process B, and (ii) there are more low frequency vibrations in the transition state for benzyne process B than for the corresponding transition state for process A. Stepwise process A has the lower barrier for the rate determining step, and the lower Arrhenius factor: we cannot differentiate between these two mechanisms on available evidence.

Photoelectron spectroscopic study of the oxyallyl diradical

The photoelectron spectrum of the oxyallyl (OXA) radical anion has been measured. The radical anion has been generated in the reaction of the atomic oxygen radical anion (O center dot-) with acetone. Three low-lying electronic states of OXA have been observed in the spectrum. Electronic structure calculations have been performed for the triplet states (B-3(2) and B-3(1)) of OXA and the ground doublet state ((2)A(2)) of the radical anion using density, functional theory (DFT). Spectral simulations have been carried out for the triplet statics based on the results of the DFT calculations. The simulation identifies a vibrational progression of the CCC bending mode of the B-3(2) state of OXA in the lower electron binding energy (eBE) portion of the spectrum. On top of the B-3(2) feature, however, the experimental spectrum exhibits additional photoelectron peaks whose angular distribution is distinct from that for the vibronic peaks of the B-3(2) state. Complete active space self-consistent field (CASSCF) method and second-order perturbation theory based on the CASSCF wave function (CASPT2) have been employed to study the lowest singlet state ((1)A(1)) of OXA. The simulation based on the results of these electronic structure calculations establishes that the overlapping peaks represent the vibrational ground level of the (1)A(1) state and its vibrational progression of the CO stretching mode. The A, state is the lowest electronic state of,OXA, and the electron affinity (EA) of OXA is 1.940 +/- 0.010 eV. The B-3(2) state is the first excited state with an electronic term energy of 55 +/- 2 meV. The widths of the vibronic peaks of the (X) over tilde (1)A(1) state are much broader than those of the (a) over tilde B-3(2) state, implying that the (1)A(1) state is indeed a transition state. The CASSCF and CASPT2 calculations suggest that the (1)A(1) state is at a potential maximum along the nuclear coordinate representing disrotatory motion of the two methylene groups, which leads to three-membered-ring formation, i.e., cydopropanone. The simulation of (b) over tilde B-3(1) OXA reproduces the higher eBE portion of the spectrum very well. The term energy of the B-3(1) state is 0.883 +/- 0.012 eV. Photoelectron spectroscopic measurements have also been conducted for the other ion products of the O center dot- reaction with acetone. The photoelectron imaging spectrum of the acetylcarbene (AC) radical anion exhibits a broad, structureless feature, which is assigned to the (X) over tilde (3)A '' state of AC. The ground ((2)A '') and first excited ((2)A') states of the 1-methylvinoxy (1-MVO) radical have been observed in the photoelectron spectrum of the 1-MVO ion, and their vibronic structure has been analyzed.

Base-induced decomposition of alkyl hydroperoxides in the gas phase. Part 3. Kinetics and dynamics in HO-+CH3OOH, C2H5OOH, and tert-C4H9OOH reactions

The E-CO(2) elimination reactions of alkyl hydroperoxides proceed via abstraction of an (x-hydrogen by a base: X- + (RRHCOOH)-R-1-H-2 -> HX + (RRC)-R-1-C-2=O + HO-. Efficiencies and product distributions for the reactions of the hydroxide anion with methyl, ethyl, and tert-butyl hydroperoxides are studied in the gas phase. On the basis of experiments using three isotopic analogues, HO- + CH3OOH, HO- + CD3OOH, and H18O- + CH3OOH. the overall intrinsic reaction efficiency is determined to be 80% or greater. The E(CO)2 decomposition is facile for these methylperoxide reactions, and predominates over competing proton transfer at the hydroperoxide moiety. The CH3CH2OOH reaction displays a similar E(CO)2 reactivity, whereas proton transfer and the formation of HOO- are the exclusive pathways observed for (CH3)(3)COOH, which has no (x-hydrogen. All results are consistent with the E-CO(2) mechanism, transition state structure, and reaction energy diagrams calculated using the hybrid density functional B3LYP approach. Isotope labeling for HO- + CH3OOH also reveals some interaction between H2O and HO- within the E(CO)2 product complex [H2O center dot center dot center dot CH2=O center dot center dot center dot HO-]. There is little evidence, however. for the formation of the most exothermic products H2O + CH2(OH)O-, which would arise from nuclephilic condensation of CH2=O and HO-. The results suggest that the product dynamics are not totally statistical but are rather direct after the E-CO(2) transition state. The larger HO- + CH3CH2OOH system displays more statistical behavior during complex dissociation.

H2 purification by functionalized graphdiyne – role of nitrogen doping

A nitrogen modified graphdiyne is investigated concerning its performance for hydrogen purification from CH4 and CO by density functional theory with dispersion correction and transition state theory. After nitrogen doping, the porous N-graphdiyne nano-mesh shows a reduced H2 diffusion barrier and increased CH4/CO diffusion barriers, hence leading to an enhanced hydrogen purification capability.

Transition to intensive care nursing: A state-wide, workplace centred program-12 years on

In November 1999, the Queensland Health (QH) Transition to Practice Nurse Education Program - Intensive Care (TPNEP-IC) was initiated in QH Intensive Care Units (ICUs) across Queensland. This 12-month, state-wide, workplace based education program has set minimum standards for intensive care nursing education and therefore minimum standards for intensive care nursing practice in QH. In the 12 years of operation, 824 nurses have completed TPNEP-IC, 761 achieving academic credit status and 453 utilising this academic credit status to undertake postgraduate study in critical/intensive care nursing at three Queensland universities. These outcomes were achieved through the appointment of nurse educators within ICUs who, through a united and strong commitment to this state-wide approach formed collaborative professional networks, which resulted in the development, implementation and maintenance of the program. Furthermore, these networks enabled a framework of support for discussion and dissemination of evidence based practice, to endorse quality processes for TPNEP-IC and to nurture leadership potential among educators. Challenges to overcome included obtaining adequate resources to support all aspects of the program, gaining local management and administrative support, and embedding TPNEP-IC within ICU culture. The 12 years of operation of the program have demonstrated its long term sustainability. The program is being launched through a new blended learning approach utilising e-learning strategies. To capitalise on the current success, a strong commitment by all stakeholders will be required to ensure the ongoing sustainability of the program.

Molecular dynamics investigation on edge stress and shape transition in graphene nanoribbons

Graphene nanoribbon (GNR) with free edges demonstrates unique pre-existing edge energy and edge stress, leading to non-flat morphologies. Using molecular dynamics (MD) methods, we evaluated edge energies as well as edge stresses for four different edge types, including regular edges (armchair and zigzag), armchair edge terminated with hydrogen and reconstructed armchair. The results showed that compressive stress exists in the regular and hydrogen-terminated edges along the edge direction. In contrast, the reconstructed armchair edge is generally subject to tension. Furthermore, we also investigated shape transition between flat and rippled configurations of GNRs with different free edges. It was found that the pre-existing stress at free edges can greatly influence the initial energy state and the shape transition.

Electrochemical and photochemical routes to semiconducting transition metal-tetracyanoquinodimethane coordination polymers

TCNQ·− radical anions (TCNQ = 7,7,8,8,-tetracyanoquinodimethane) form a wide range of semiconducting coordination polymers when coordinated to transition metals. Some such as CuTCNQ and AgTCNQ exhibit molecular switching and memory storage properties; others have intriguing magnetic properties and for example may behave as molecular magnets at low temperature. In this review, the electro- and photo-chemical synthesis and characterization of this important class of material is reviewed. In particular, the electrochemistry and the redox properties of TCNQ derivatives of coordination polymers based on Cu, Ag, Mn, Fe, Co, Ni, Zn and Cd transition metals are surveyed, with an emphasis on the mechanistic aspects of their electrochemical formation via nucleation–growth processes. Given that TCNQ is an extremely good electron acceptor, readily forming TCNQ•− and TCNQ2-, electrochemical reduction of TCNQ in the presence of a transition metal ion provides an ideal method for synthesis of metal-TCNQ materials by electrocrystallization from organic solvents and ionic liquids or solid-solid transformation using TCNQ modified electrodes from aqueous media containing transition metal electrolytes. The significance of the reversible formal potential (E0f) in these studies is discussed. The coupling of electrocrystallisation on electrode surfaces and microscopic characterization of the electrodeposited materials reveals a wide range of morphologies and phases which strongly influence their properties and applications. Since TCNQ also can be photo-reduced in the presence of suitable electron donors, analogous photochemical approaches to the synthesis of TCNQ-transition metal derivatives are available. The advantages of electrochemical and photochemical methods of synthesis relative to chemical synthesis are outlined.

The importance of agency in facilitating the transition to a multifunctional countryside

We appreciate Holmes' body of work relating to transitions within the Australian landscape, and welcome the opportunity to engage in a discussion on this topic. The paper to which Holmes refers (Bjørkhaug and Richards, 2008) examined the application of agricultural (rather than landscape) multifunctionality in both Norway and Australia. Of specific focus was how non-tradeable concerns, such as environmental sustainability, faired under these divergent systems. We argued that Norway's multifunctionality was strong, due to it being embraced at both the policy and actor level, whereas Australia's could be described as weak. This ‘weak multifunctionality’ that we observed in Australia was due to an emerging bi-lateral (state and federal) policy framework that advocated the importance of environmental values which was rarely embraced by landholders who found themselves trapped on the ‘agricultural treadmill’. The nature of the treadmill is that alternative forms of land use are unthinkable when on-farm investments have been made that support the status quo – to get bigger and/or more efficient. For many of the Australian landholders interviewed in relation to this study, efficiency in production was at odds with the values necessary to effect a transition toward multifunctionality. For instance, graziers in Central Queensland were unconvinced of the value of conserving native flora and fauna when economic viability can be better assured through clear felling native forests to increase the productive capacity of the land.