NIHRDataInsights/HRCSData huggingface dataset:
Title: Rapid Evolution of Enzymes and Synthetic Micro-organisms for the Development of Industrial Biocatalysts
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Industrial Biotechnology is the use of biological resources, such as algae, plants, marine organisms, fungi and micro-organisms, for the production and processing of chemicals, energy and materials. The use of biocatalysts, both as enzymes and also engineered whole cells, in the manufacture of chemicals presents significant advantages in terms of enhanced reaction selectivity, reduced cost of raw materials, lower energy costs, safety and importantly sustainability. The recent explosion in sequence information available from microbial gene sequencing, coupled with a suite of technologies underpinning protein expression, protein engineering, high-throughput screening and bioprocess development, have stimulated chemical companies to consider alternative biotechnology based routes to their products which to date have been produced using traditional chemical feedstocks, reagents and catalysts. A major limitation at present is the length of time required to develop biocatalysts and biocatalytic processes such that they are fit-for-purpose. From initial identification of enzyme activity, to development of a pilot-scale process, takes at best several months and more likely 1-2 years. This timescale currently restricts the application of biocatalysts mainly to 2nd or 3rd generation manufacturing processes. In this context, recent successes have been achieved in the area of APIs, platform chemicals specialty chemicals and agrochemicals. In order for biocatalysis to be more widely embraced, development times must be reduced to weeks/months thereby bringing this technology in line with existing chemical based technologies. This proposal seeks to develop an accelerated laboratory evolution platform for rapid optimisation of biocatalysts such that they are fit-for-purpose, particularly in the context of industrial application. We shall demonstrate the value of this platform by evolving six different classes of biocatalyst for applications in target molecule synthesis.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE
Title: Cyclization specificity in terpene synthases by residue interaction networks
Funder: Biotechnology and Biological Sciences Research Council

Abstract: An emerging theme in our understanding of enzyme function is that outer tiers of protein structure clearly exert profound influence on enzyme function. This has been demonstrated in directed evolution studies and in naturally evolved terpene synthases (TPSs), enzymes that make diverse bioactive natural products. We previously found outer tier mutations were essential to achieve high product specificity in TPSs. Results from theses studies indicate that outer tier mutational effects are transmitted to the active site through residue interaction networks in the protein structure. We will use farnesene synthase (FS) from Artemisia annua, a linear product-producing TPS, as a model system to study the interplay of active site and outer tier mutations in the emergence and refinement of cyclization specificity. Considering a folded protein as a network, this proposal will exploit well-developed graph theory tools to predict functionally important outer tier residue positions from network analysis of protein structure. We will first biochemically characterize FS active site mutants that produce cyclic products from preliminary investigations to identify progenitor mutant enzymes with catalytically-robust activities. We will apply SCOPE to diversify predicted outer tier residues in progenitor enzymes and then distill minimal combinations of mutations that modulate cyclization specificity as measured by GC-MS analysis. These investigations will test predictions from graph theory and enable us to dissect the residue interaction networks linking outer tier and active site mutations. Therefore, this proposal will deliver new fundamental knowledge on how enzymes function as an integrated unit while generating new 'parts' for synthetic biology and industrial biotechnology applications.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Dynamic surfaces to mimic mesenchymal stem cell niche functions
Funder: Engineering and Physical Sciences Research Council

Abstract: The stem cell niche acts to control stem cell growth (control self-renewal) and differentiation in a dynamic manner. Current developments in materials science, focused on a key regenerative stem cell type, the mesenchymal stem cell, have allowed us to regulate both self-renewal (to allow us to grow multipotent populations by preventing phenotypical Dr.ift to e.g. fibroblasts) and to target differentiation to desired functional cell types. The materials do this by controlling cell adhesion and intracellular tension important for regulation of biochemistry and transcription. However, the materials are designed either for growth or for differentiation and lack the flexibility to support both stem cell functions. We have developed enzyme switchable surfaces that can be used to control cell adhesion in an on-demand manner and will exploit this technology to develop dynamic materials for stem cell culture. In the proposal, we will create an initial surface that control adhesion to promote self-renewal and hence growth as multipotent stem cells allowing us to achieve large numbers of true stem cells. This will be achieved by controlling the length of polyethyleneglycol (PEG) chains that block cells from adhering to the underlying differentiation surface (e.g. RGD, t-butyl, single peptides). Enzymatic cleavage of the PEG chains will then expose the differentiation surface to the mesenchymal stem cells on demand. Hence we will have fabricated surfaces that allow the cells to grow to large numbers and then change to functional cells in a controllable manner mimicking niche dynamics. Finally, we will explore the possibility of using secreated enzymes (e.g. matrix metalloproteases) which have changes expression profiles in dense cultures to switch the surfaces as the cells grow more confluent (i.e. the enzymatic switch would automatically happen when enough stem cells were present).


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE
Title: The evolution and molecular basis of adaptations to Telomere Biology in immortal worms
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Current invertebrate systems for studying molecular and cellular processes of aging are mainly limited to C. elegans and D. melanogaster. These species are from the same major protostome branch of the animal tree (Ecdysozoa), are relatively short lived and are essentially post-mitotic as adults. These features might suggest they may not be useful as a model of aging in mammals. However, this could not be further from the truth as the genetic power and simplicity of these model organisms has been absolutely key in establishing key insights into conserved aspects of aging biology. This suggests that other invertebrates from alternative parts of the animal tree and with starkly contrasting life histories may also contribute to our fundamental understanding of the aging process. Animals that are relatively longer lived, utilize an adult stem cell system and are amenable to molecular genetic studies as adults might be particularly useful. Here we will investigate this proposal by studying telomere biology in planarians. Our preliminary work has ported existing tools for studying telomeres and telomere biology to the model planarian S. mediterranea and suggests planarians will be an excellent system for these studies. We can now measure telomere length, telomerase activity, assess karyotype instability and investigate the function of other components of the telomere protein complex. This work suggests that asexual planarians may potentially be immortal and avoid the aging process at the organismal level altogether. We will investigate the replicative capacity of planarian adult stem cells in relation to telomere biology and study how the regulation of telomere biology has evolved. Finally we will study telomere biology in planarians that have reduced regenerative capacity and a finite lifespan despite having a population of pluripotent stem cells. Together these studies will provide novel insights into telomere biology and aging in animal pluripotent stem cells.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: To benchmark the utility of E06: A half-life extension, single-domain, shark antibody bio-tool, and progress it to a Phase 1 ready candidate clone
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Scientifically we are developing a "bio-tool" that could be fused to a range of different therapeutic proteins/peptides to extend their serum half-life from hours to weeks, with the potential of greatly increasing their therapeutic potency. It works by hitching a ride on other long-lived proteins in the blood. Commercially, our medium-term goal is to create a Drug Discovery company, based on our unique, single-domain shark antibody (VNAR) platform, which will develop therapeutic agents in-house or in partnership with larger companies. To achieve this, meeting of scientific milestones is key, and in particular confirming non-immunogenicity (not seen by the human immune system & safe for use), and validate the most advanced of our products (E06 VNAR half-life extension bio-tool). Progress towards this goal will also provide a platform for NewCo formation and equity raising, and will deliver an asset capable of securing multiple revenue streams of licensing and partnered income.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE
Title: Investigation of optimal gel conditions for stem cell preservation at room temperature and scaling up of selected methodology
Funder: Engineering and Physical Sciences Research Council

Abstract: Successful outcome from this project will significantly advance regenerative medicine product development as it will solve the control of distribution/thawing/administration of these complex cellular medicines. Implementing such a step-change in the way cell therapies are distributed will open up novel opportunities and encourage big-pharma's interest in the sector (as a major bottleneck in the product value-chain is reduced). There is currently an unmet need. Our solution - a simple hyDr.ogel capable of encapsulating and holding stem cells in suspension for up to 1 week at room temperature and atmospheric carbon dioxide. Therefore no need for complicated freezing/thawing systems or the inconvenience of shipping at low temperatures. With the assistance of chemical engineers we will explore the manufacturing process of hyDr.ogels for stem cell encapsulation in biopolymers with controlled porosity and mechanical properties using an aqueous-in-oil emulsification approach (in which the Co-I is a leading expert). Parallel to this we will investigate the underlying mechanisms that allows for the excellent preservation of stem cells at room temperature once encapsulated within a biopolymer hyDr.ogel. Building upon our exciting (BRIC enabling funded) proof-of-concept results, which have demonstrated the potential of this technology in the regenerative medicine field, we aim to explore its application in commercial settings with the collaboration of BRIC members.


Research activity codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE
Title: Commercializing Abysis - an integrated resource for storing and analyzing antibody sequence and structure
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Around 1/3rd of drugs in development are now monoclonal antibodies (mAbs) with >30 clinically approved. However many fail during development often because they create an immune reaction in the patient. Even newer 'fully human' mAbs can be immunogenic. We will enhance Abysis, our prototype software for storing and analyzing antibody sequence and structure, to allow wide used by pharmaceutical companies enabling production of better antibody-based biotherapeutics. The resource links DNA and protein sequence and structure to aid in developing therapeutic antibodies. We will enhance the interface and underlying code to make the system easier to maintain and install. The software will be modified to work more effectively with unusual antibodies from camel, llama, shark and chicken, which are now of interest to drug companies. We will link unusual sequence features to structure allowing identification of regions of antibodies that may be responsible for generating an immune response.


Research activity codes: 5.1 PHARMACEUTICALS;5.9 RESOURCES AND INFRASTRUCTURE (TREATMENT DEVELOPMENT)
Health categories: GENERIC HEALTH RELEVANCE
Title: Inquire: Software for real-time analysis of binding
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Recent breakthroughs in hardware and software development allow condensed-phase molecular dynamics simulations of biomolecular systems to access biochemically relevant timescales (microseconds to milliseconds). Using molecular dynamics, it is now possible to simulate biochemically important events, such as protein folding and drug binding and unbinding. While the ability to perform such dynamics simulations is a leap forward for the field of computational biochemistry, the ability to watch something happening does not provide enough information about why it happens, or the mechanism behind that action. Watching a drug unbind during a dynamics trajectory can suggest that a particular protein mutant is drug resistant, but provides little detail as to how this resistance has been conferred. How has the binding affinity of the drug been reduced? How has the mutation changed the structure of water in the active site to displace the drug? Medicinal chemists need detailed answers to these questions at the molecular scale to enable them to design new features into the drugs to encourage binding and to overcome resistance. Binding free energy calculations provide exactly this type of information. The aim of this project is to develop software that is capable of near real-time analysis of protein-drug binding. The software will calculate binding free energies, globally, locally (with respect to time) and also decomposed to per-residue and per-active-site water molecule components. The result will be animations and visualisations of protein-drug binding that reveal the molecular detail behind specific interactions between the drug, active-site residues and water molecules. This will guide drug designers by revealing the mechanisms by which a drug achieves a strong binding affinity, and revealing why emerging mutations in protein targets lead to drug resistance.


Research activity codes: 5.1 PHARMACEUTICALS;8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: GENERIC HEALTH RELEVANCE
Title: Regulation of DNA damage signaling by autophagy in senescence.
Funder: Biotechnology and Biological Sciences Research Council

Abstract: This application investigates cellular and molecular mechanisms that control cell and tissue ageing. Cellular senescence is an important tumor suppression mechanism, but also contributes to tissue and organismal ageing. DNA damage signaling, dysfunctional mitochondria and reactive oxygen species (ROS) are established triggers and effectors of the senescence program. Autophagy is a cellular recycling process, whereby double membrane vesicles, called autophagosomes, sequester cytoplasmic content and organelles and deliver it to lysosomes for degradation. Like senescence, autophagy is implicated in control of tumor suppression and ageing. In fact, recent studies have demonstrated a role for autophagy in control of cell senescence. However, the precise role played by autophagy and whether it serves as an activator or repressor of senescence is unclear. To understand the contribution of autophagy to tumor suppression and ageing, it is essential to understand its role in cell senescence. Building on extensive preliminary data from the labs of Drs. Adams and Passos, we propose that autophagy antagonizes the senescence program in at least two ways. First, we hypothesize that autophagy suppresses accumulation of dysfunctional mitochondria, thereby suppressing accumulation of ROS and DNA damage. Second, we hypothesize that autophagy degrades fragments of DNA damage-containing chromatin that accumulate in the cytoplasm of senescent cells. By suppressing such DNA damage signals, autophagy antagonizes onset or maintenance of cell senescence and tissue aging. We will investigate these hypotheses through the following two Aims Aim 1. Investigate the role of autophagy in suppression of DDR via elimination of dysfunctional mitochondria and ROS. Aim 2. Investigate the role of autophagy in degradation of senescence-inducing cytoplasmic chromatin fragments (CCF) containing damaged DNA.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Unravelling and engineering the role of trace metals on recombinant therapeutic protein synthesis and heterogeneity from Chinese hamster ovary cells
Funder: Biotechnology and Biological Sciences Research Council

Abstract: This application details a novel approach towards understanding and exploiting trace metal biology in underpinning mammalian cell growth and therapeutic recombinant protein (rP) production, quality and heterogeneity in the industrially important Chinese hamster ovary (CHO) cell line. The proposal balances the long-term goals of cell engineering to exploit metal homeostasis with the more immediate deliverables of developing a better process understanding with regard to trace metals that will lead to improved process control and impact upon the consistency and safety of the drug substance. The programme of work will test the hypothesis that 'extra- and intra-cellular metals, including those introduced as impurities in raw materials, and the maintenance of their homeostasis during the culturing of CHO cells engineered to produce rPs is critical in determining cell growth, product yield and product heterogeneity and these can be manipulated directly in the media or indirectly intra-cellularly by engineering approaches to improve cell growth and reduce product heterogeneity'. In addressing this hypothesis we will characterise the variation in total metal ion concentrations in key raw materials and the extra- to intra-cellular flux of trace metal ions, determine the effect of extra- and intra-cellular metal ion concentrations on rP product quality, investigate intracellular metal compartmentalisation and how this relates to cell growth and product quality, determine the effect of manipulating cell culture metal concentrations on the CHO cell proteome, and develop a 'ranking' of total metal ion concentration impurities and impact so that target screening of raw materials can be used to assess risk. The outcomes will be (i) novel process control and engineered CHO cell lines that exploit metal biology underpinning cell growth and rP production, quality and heterogeneity, and (ii) an understanding of how metals impact upon safety and efficacy of the drug substance.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: GENERIC HEALTH RELEVANCE
Title: Solution NMR spectroscopy studies of an adrenergic receptor b1AR
Funder: Biotechnology and Biological Sciences Research Council

Abstract: Although crystal structure determination of GPCRs has become increasingly available over the last years, there is a distinct lack of insight on the dynamic nature of these highly mobile signaling proteins. Downstream signal transduction events follow from extracellular ligand-induced interactions that dynamically change the functional state of the receptor. Information on this functional receptor plasticity is not accessible through crystal structure snapshots obtained in often non-native detergent environments. Considering predominantly structure based static arguments therefore is unlikely to reveal all the essential aspects of how GPCRs function. Hence, investigation through complementary techniques that can provide information on receptor dynamics is urgently required. NMR is well suited to provide such information, however, until now the success of extensive NMR studies on GPCRs has been obstructed by the unfavourable properties of these proteins; sample preparation being a major bottleneck for structural studies of GPCRs. We intend to pursue comprehensive solution NMR studies of a class A GPCR. Our study will concentrate on a conformationally thermostabilized mutant of turkey b1AR which has been extensively used in X-ray crystallography studies and which provides beneficial sample characteristics to enable extensive NMR studies. The receptor is stabilized predominantly in one conformation, which results in superior NMR spectral quality due to improved sample homogeneity. In addition, spin relaxation dispersion techniques can probe the presence of 'invisible' low-populated receptor states and will provide the missing information on the conformational dynamics of the receptor. Using uniform and selective isotope labelled b1AR samples we will utilise this approach to study what effect ligands of different efficacies have on the conformational dynamics of the receptor, which regions of the GPCR are affected and how the changes depend on the type of ligand bound.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: GENERIC HEALTH RELEVANCE
Title: Manufacture and applicator technologies for commercialisation of polymeric microneedle arrays
Funder: Biotechnology and Biological Sciences Research Council

Abstract: We have developed a novel type of transdermal patch with tiny needles on its surface that painlessly and without causing bleeding by-pass the skin's stratum corneum barrier. These needles either dissolve quickly, leaving tiny holes in the skin, which will let proteins and peptides enter the body, or swell, turning into a jelly-like material that keeps the holes open and allows continuous delivery. Our technology is unique and could potentially revolutionise delivery of medicines. Interestingly, we have also found that our swellable microneedles can extract fluid from the skin. This permits us to monitor the levels of drugs in a person's blood without actually taking blood samples, meaning that adverse events and complications arising from blood sampling could be prevented, to the benefit of patients Worldwide. In this project, we will focus on moving our microneedle production from laboratory scale to industrial scale and design and validation of a low-cost user friendly applicator.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;5.1 PHARMACEUTICALS
Health categories: GENERIC HEALTH RELEVANCE