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Enhanced force fields for computational drug design and materials research. This project aims to improve the atomic interaction functions used to calculate the structural, dynamic and thermodynamic properties of molecules that alter net charge or structure in different environments. Predicting the stability of alternative protonation and tautomeric states for molecules bound to therapeutic targets is a major challenge in computational drug design. It is key to identifying the therapeutically act ....Enhanced force fields for computational drug design and materials research. This project aims to improve the atomic interaction functions used to calculate the structural, dynamic and thermodynamic properties of molecules that alter net charge or structure in different environments. Predicting the stability of alternative protonation and tautomeric states for molecules bound to therapeutic targets is a major challenge in computational drug design. It is key to identifying the therapeutically active chemical species as well as understanding drug transport and off-target effects. The work will expand the utility of modelling software used by over 13,000 researchers worldwide. In addition, the improved interaction functions will also help in the understanding of a wide range of other materials at an atomic level.Read moreRead less
Ultrasound-assisted fabrication of biofunctional materials. The project aims to develop a fundamental understanding of the mechanism involved in the synthetic process in order to control the physical and functional properties of core-shell biomaterials. Biofunctional core-shell materials are of scientific interest due to their potential use in a variety of applications including food manufacturing. Among existing methodologies for the synthesis of core-shell biomaterials, ultrasonic technology o ....Ultrasound-assisted fabrication of biofunctional materials. The project aims to develop a fundamental understanding of the mechanism involved in the synthetic process in order to control the physical and functional properties of core-shell biomaterials. Biofunctional core-shell materials are of scientific interest due to their potential use in a variety of applications including food manufacturing. Among existing methodologies for the synthesis of core-shell biomaterials, ultrasonic technology offers versatility and a wider choice of core and shell materials possessing specific biofunctionality. The outcomes of this project may include the establishment of a versatile technology for the fabrication of tailor-made biofunctional materials suitable for specific applications.Read moreRead less
Pushing The Boundaries Of Flow Chemistry – Towards New Anti-Viral Agents. Synthetic chemistry approaches to new drugs rely on access to robust reliable reactions. Traditionally these approaches are highly wasteful with the pharmaceutical industries producing five to a hundred kilograms of waste per kilogram of product. Total flow chemistry approaches will significantly reduce waste, allow rapid reaction sequence optimisation, and seamless scale up. In a collaborative effort spanning Australia, G ....Pushing The Boundaries Of Flow Chemistry – Towards New Anti-Viral Agents. Synthetic chemistry approaches to new drugs rely on access to robust reliable reactions. Traditionally these approaches are highly wasteful with the pharmaceutical industries producing five to a hundred kilograms of waste per kilogram of product. Total flow chemistry approaches will significantly reduce waste, allow rapid reaction sequence optimisation, and seamless scale up. In a collaborative effort spanning Australia, Germany and the USA, in an exemplar of a real world application, this project will produce benefits not only in enhanced and greener synthetic approaches, but also in the development of strategies for the identification of small molecules, the precursors to a new mode of action class of anti-viral drugs.Read moreRead less
Protein design. This project aims to design binding specificity in proteins in a rational way. Extending the existing repertoire of protein specificity using engineering principles should harness the catalytic power and high binding affinities of natural proteins. By building upon protein design algorithms, this project will develop biosensors for neurotransmitters and specialist enzymes to incorporate unnatural amino acids. It will iteratively improve the designs and algorithms by computational ....Protein design. This project aims to design binding specificity in proteins in a rational way. Extending the existing repertoire of protein specificity using engineering principles should harness the catalytic power and high binding affinities of natural proteins. By building upon protein design algorithms, this project will develop biosensors for neurotransmitters and specialist enzymes to incorporate unnatural amino acids. It will iteratively improve the designs and algorithms by computational and experimental characterisation. The outcomes should address the long-standing need in synthetic biology for a facile route to designer proteinsRead moreRead less
Making peptides orally bioavailable. Bioactive peptides are exceptionally useful molecules, however to fully realise their exciting applications key limitations need to be overcome: they can't be delivered orally and they do not last long in the body. This project aims to develop a molecular tag that can dramatically enhance both the oral absorption and time in the body of a peptide. This will include identifying the key elements of the tag required for function, the breadth of peptide cargoes i ....Making peptides orally bioavailable. Bioactive peptides are exceptionally useful molecules, however to fully realise their exciting applications key limitations need to be overcome: they can't be delivered orally and they do not last long in the body. This project aims to develop a molecular tag that can dramatically enhance both the oral absorption and time in the body of a peptide. This will include identifying the key elements of the tag required for function, the breadth of peptide cargoes it can be applied to and the mechanisms underlying this technology. The outcomes of this project will facilitate the future development of peptides for biotechnology, pharmaceutical and veterinary applications.Read moreRead less
Discovery Early Career Researcher Award - Grant ID: DE140100550
Funder
Australian Research Council
Funding Amount
$358,248.00
Summary
Quantum refinement of DNA X-ray structures. DNA carries the genetic map of life and refinement of its x-ray structures is a key tool to understand its functions. Standard refinement, however, relies strongly on empirical geometry constraints, and it is known that these can induce unphysical features. Quantum mechanical (QM) methods have now evolved to a level that offers an intriguing way out of this dilemma. In this project, state-of-the-art QM methods will be applied to DNA x-ray structures, a ....Quantum refinement of DNA X-ray structures. DNA carries the genetic map of life and refinement of its x-ray structures is a key tool to understand its functions. Standard refinement, however, relies strongly on empirical geometry constraints, and it is known that these can induce unphysical features. Quantum mechanical (QM) methods have now evolved to a level that offers an intriguing way out of this dilemma. In this project, state-of-the-art QM methods will be applied to DNA x-ray structures, and a unique quantum refinement scheme will be developed. Such a scheme will provide crystallographers with a new tool to determine DNA structures with greater accuracy and it will offer benefits to many areas of the life sciences that depend on such accurate structures.Read moreRead less
Understanding the molecular basis of heparanase activity. This project aims to advance our understanding of the structure and impact on biological processes of heparanase (HSPE), an enzyme of critical importance. HSPE’s ability to interact with heparan sulfate (HS), a key component of the extracellular matrix and basement membranes, makes HPSE a pivotal enzyme in many important physiological and disease-related processes ranging from angiogenesis, tumour metastasis, inflammation, hair follicle ....Understanding the molecular basis of heparanase activity. This project aims to advance our understanding of the structure and impact on biological processes of heparanase (HSPE), an enzyme of critical importance. HSPE’s ability to interact with heparan sulfate (HS), a key component of the extracellular matrix and basement membranes, makes HPSE a pivotal enzyme in many important physiological and disease-related processes ranging from angiogenesis, tumour metastasis, inflammation, hair follicle development to wrinkle formation. The knowledge gained through this project is expected to provide new insight into the interaction between HSPE and HS/HSPG to reveal new pathways to the development of inhibitors to treat diseases such as cancer and diabetes.Read moreRead less
Exploring the novel structural features of influenza virus sialidase. The outcomes of this project will provide a deeper mechanistic understanding of influenza virus sialidase and the importance of the enzyme's flexible loops in carbohydrate recognition. Specifically, this project will improve our understanding of fundamental aspects of inhibitor binding by influenza virus sialidases.
Engineered plant receptors as orthogonal neuronal switches. This project aims to develop synthetic biology methods to study brain function by utilising engineered plant receptors. This project will expand our ability to manipulate nerve cell function with high specificity and without side effects in freely behaving animals. Plant receptors will be developed into molecular tools in an iterative process that improves key properties using rational protein design. Expected outcomes include innovativ ....Engineered plant receptors as orthogonal neuronal switches. This project aims to develop synthetic biology methods to study brain function by utilising engineered plant receptors. This project will expand our ability to manipulate nerve cell function with high specificity and without side effects in freely behaving animals. Plant receptors will be developed into molecular tools in an iterative process that improves key properties using rational protein design. Expected outcomes include innovative and broadly-applicable neuroscience methods and an understanding of receptors involved in plant growth and defense. Benefits of this project include an enhanced capacity to generate knowledge, multidisciplinary training opportunities and patentable synthetic biology technologies.Read moreRead less
Natural product scaffolds: an approach to privileged structures. Based on the fact that nature has provided approximately 50 per cent of current drugs, the purpose of this project is to identify scaffolds that are critical for the biological interactions. The expected outcome is to build libraries based on the scaffolds and identify new privileged structures for application in drug discovery.