NIHRDataInsights/HRCSData huggingface dataset:
Award Title: Structural Investigations of Sodium Channel Mutations Associated with Neurological Diseases
Funder: Wellcome Trust

Abstract: Sodium channels (Navs) are proteins which are found in cells around the body, including the central and peripheral nervous system and heart muscles. These proteins span the cell membrane and form channels which specifically allows sodium ions to cross the membrane under certain conditions. This influx of sodium ions in neurons is responsible for information processing and is critical for nervous system function. Genetic mutations in Navs can cause multiple diseases including epilepsy, chronic pain and cardiac arrhythmias. Generally, these mutations reduce the function of Navs, disrupting the balance of information, for example in the brain sometimes resulting in epilepsy. Specific drugs therefore need to be developed in order to re-establish this balance either by adding to Navs’ functionality or reducing it. We aim to use structural biology techniques, including x-ray crystallography and potentially cryo-EM to visualise potential drug binding sites. We will also look at common disease-causing mutations allowing us to identify drugs which will not only target a specific subtype of Nav but also a specific mutation. In particular we will be looking at repurposing already commercially available drugs. This work has the potential to identify drugs for Nav related diseases and provide new treatment options for patients.


Research Activity Codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health Categories: GENERIC HEALTH RELEVANCE;NEUROLOGICAL
Award Title: Structural and functional characterisation of the fungal proton pump Pma1
Funder: Wellcome Trust

Abstract: Fungi fuel their nutrient uptake through generating a proton-motive force across their plasma membrane via the membrane protein proton pump Pma1. This proton-motive force is used as an energy source to import nutrients for the cell, and fungi die without the activity of Pma1. To date, knowledge on the molecular structure and function of this protein is limited. I therefore aim to study the structure of Pma1 and understand its molecular function, through the use of structural analyses, including cryoEM and X-ray crystallography and biophysical assays. I will be using protein isolated from the fungus Neurospora crassa and a set of known small molecules that lock the protein in different catalytic conformations to investigate its catalytic cycle. I will also establish a way to produce Pma1 in baker's yeast, allowing me to generate variants of the native protein for functional and structural studies. My findings will broaden our understanding of the structure and function of the protein, opening the possibility of a wide range of secondary research including protein-lipid interaction studies and the possibility of designing novel antifungal agents.


Research Activity Codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health Categories: GENERIC HEALTH RELEVANCE;INFECTION
Award Title: Structural and mechanistic studies of proteins involved in human DNA double-strand break repair
Funder: Cancer Research UK

Abstract: 1) Background
DNA damage results in mutations that can lead to cancer. DNA can be damaged in many ways but one of the potentially most serious is double-strand breaks.
If these breaks are not repaired correctly, point mutations and/or deletions can occur. In worst cases, re-joining of ends incorrectly can lead to chromosome translocations and other forms of genomic instability that give rise to cancer. Several genes implicated in genome instability are associated with syndromes that have cancer predisposition (e.g. Bloom’s, Werner’s, Fanconi’s).

2) Aims
 The aims of this proposal are to understand the structure and mechanism of the processing of double-strand DNA breaks as a prelude to recombination repair. Defects in this process cause problems with the repair of DNA damage leading to genomic instability that results in cancer. Our previous work on the RecBCD/AddAB systems have revealed insights into this process in bacteria. Although the RecBCD/AddAB proteins themselves are not conserved in humans, there is an underlying similarity between the process of double-strand break repair in bacteria and humans. Indeed, proteins with the same activities found in the bacterial proteins are present in humans but located within different proteins and protein complexes.

 This research proposal will be to extend what we have learned from RecBCD/AddAB to the human double-strand break repair system. In particular, I wish to understand how the large human protein complexes interact and cooperate with one another to achieve DNA break repair. which is even more complex and presents some challenging problems in structural biology. However, meeting these challenges is essential if we are to understand fully how these multi-component systems cooperate to repair DNA damage, and hence prevent cancer, in humans.

 3) Methods
The primary methods used in this study will be structural techniques particularly single particle cryo-electron microscopy but also X-ray crystallography as well as other biophysical techniques such as Small Angle X-ray Scattering (SAXS) and Fluorescence Resonance Energy Transfer (FRET). In addition, biochemical characterisation of the proteins will involve a variety of standard techniques including DNA footprinting, ATPase and helicase assays, site-directed mutagenesis, isothermal titration calorimetry, protein cross-linking and mass spectrometry analysis.

4) How the results of this research will be used
The results of this research will be used to improve our understanding of how the interplay between the various protein components leads to double strand-break repair in humans.


Research Activity Codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health Categories: CANCER AND NEOPLASMS;GENERIC HEALTH RELEVANCE
Award Title: Structural cell biology of transport vesicle and organelle biogenesis
Funder: Wellcome Trust

Abstract: Integral membrane protein cargo are constantly moved in coated tubular/vesicluar carriers between the cell's organelles and its limiting membrane in order to maintain membrane identity and function. That these transport processes are of fundamental importance is reflected by the fact that ~30% of mammalian proteins are either components of the vesicle/tubule transport machinery or are its cargo. Coated vesicular/tubular carrier formation including cargo selection requires the interplay of a network of peripheral membrane proteins and membrane components including phospholipids, small GTPases, docking proteins and the cargo itself. The coat must also prepare and facilitate the carrier for fusion with its target. AP2, AP3, COPI and retromer/VARP based coats along with their accessory/regulatory factors are vital for producing a fully functional endosomal system. We will use a combination of X-ray crystallography, NMR and the fast developing techniques of single particle cryoEM and cryo electron tomography allied with biochemical/biophysical studies to formulate theories concerning the architecture, assembly routes and control/regulation of the formation of these four key tubular/vesicular transport carriers. Specific function abolishing mutations designed on the basis of these studies will allow us to test and further explore our theories in cells using a wide range of in vivo techniques.

Lay Abstract: Every one of the trillions of cells in a human are surrounded by a lipid membrane and contain membrane-bound compartments. Proteins embedded in these membranes mediate cell interactions with the blood and the immune system. They also permit signals and small molecules to cross these membrane barriers. These embedded proteins are moved in the right quantities at the right times to the right membranes in transport vesicles. These are formed when a portion of a donor membrane, into which the correct embedded proteins have been sorted, is pinched off, transported to and fused with its target membrane. Failures in vesicle transport can result in cell death or malfunction leading to diseases including Alzheimers, Parkinsons and cancers. The transport vesicle system can be ‘hijacked’ by pathogens to facilitate their entry into host cells. We aim to determine atomic resolution structures of various protein nano-machines that are recruited onto membranes from inside the cell to drive a transport vesicle’s formation, transport and fusion. This will allow us to explain how these proteins function correctly and how they can go wrong. It will also allow us to design highly specific mutant forms of them to help test theories of vesicle formation/destruction in cells.

Research Activity Codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health Categories: GENERIC HEALTH RELEVANCE;INFECTION;NEUROLOGICAL
Award Title: Structural mechanics in subcellular structure formation
Funder: Wellcome Trust

Abstract: A failure to properly build and maintain cellular structures leads to cell-death or disease. Yet, the regulation and mechanisms of the machinery that coordinate such structures are generally poorly understood. The formation and maintenance of many cellular substructures is dependent on the receipt and retention of specific components, selected through tethering complexes. Of particular interest is the exocyst complex, whose role in polarized trafficking leads in part to the spatially and physically distinct cilia and tight junction membrane substructures. I hypothesize that membranes and combinations of their signaling proteins coordinate the mechanics of the polarized trafficking machinery through the exocyst. I will determine how this complex assembles and targets specific membranes through an innovative reconstitution combining biophysical and cell biological approaches. Through synergy with structural methods, the outcome of this approach will be information on the relationship between structure and functional mechanism on membranes, and the cellular consequence of exocyst spatiotemporal regulation. The imbalances of polarized trafficking in both aberrant development and cancers urge a program aimed at resolving the molecular mechanics of this pathway.

Lay Abstract: Cells harbor structures that define their function. Yet the regulation and mechanisms of the machinery that coordinate such structures are generally poorly understood. I aim to understand the mechanics of this machinery. I will use a reconstitution approach, building the system from minimal components through to its full complexity. This approach harnesses state-of-the-art protein biochemistry and membrane biophysical methods in a unique way, aimed at broad and high-throughput experimentation. I will build synergy of this strategy with experimental cell biology, which provides both validation and new avenues exploring cellular consequences of perturbations to the coordinating machinery. The outcome of these studies will be a comprehensive model for regulation and the structural basis for coordination of subcellular structures. Signaling in both development and cancers result in drastic changes to this aspect of biology, and an understanding of the basic mechanisms has the long-term potential for new opportunities in treatment.

Research Activity Codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health Categories: GENERIC HEALTH RELEVANCE
Award Title: Structure, mechanism and dynamics of recoding in viral infection
Funder: Wellcome Trust

Abstract: Many RNA viruses (e.g. SARS-CoV-2, HIV-1) have evolved ways of reprogramming translation to expand the coding capacity of their small genomes. ‘Recoding’ events such as -1 frameshifting, stop codon read-through and StopGo peptide release are necessary for viral replication, producing viral proteins in optimal ratios for efficient assembly. Recoding is regulated by a complex interplay between the elongating ribosome, cis-acting elements in the mRNA or nascent peptide, and trans-acting protein factors. Elucidating the structural basis of recoding is essential to understand viral pathogenesis. However, classical biochemical approaches cannot accurately capture kinetics or per-ribosome heterogeneity, making it difficult to define a "window of opportunity" for structure determination. Recent technological advances allow single-molecule fluorescent imaging of translation in real-time. I will apply these methods to study recoding in vitro and in live cells, starting with -1 frameshifting in SARS-CoV-2, HIV-1 and EMCV, which utilise topologically-distinct stimulatory elements. I will determine the structure of key ribosomal states by time-resolved cryo-EM, and investigate the structure and stability of stimulatory elements using crystallography, single molecule FRET and optical tweezers. Longer-term, this approach will be applied to investigate other recoding events, thus revealing universal and case-specific mechanistic principles, and highlighting new avenues for therapeutic intervention.

Lay Abstract: Accurate translation of mRNA by the ribosome is essential for all life. It is therefore a high-fidelity process, with spontaneous error rates of only ~ 1 in 100,000 codons. When RNA viruses infect cells they frequently make proteins that differ from the genetically encoded sequences. These highly-regulated ‘recoding’ events are vitally important to viral gene expression, and if disrupted many viruses (e.g. SARS-CoV-2, HIV-1) fail to complete their replication cycles. I aim to use a multidisciplinary approach to better understand recoding, initially focussing on -1 programmed ribosomal frameshifting (PRF) in SARS-CoV-2, HIV-1 and EMCV. Using single-molecule fluorescence microscopy, I will observe PRF in real-time both in vitro and in live cells. I will also reveal mechanistic details by time-resolved cryo-EM, crystallographic and biophysical studies. Together, this work will reveal universal structural and mechanistic principles that govern mammalian recoding, laying the foundations for developing a new class of antiviral drugs.

Research Activity Codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health Categories: GENERIC HEALTH RELEVANCE;INFECTION
Award Title: SureChEMBL: open patent data for all
Funder: Wellcome Trust

Abstract: SureChEMBL is a large-scale, fully automated, chemical-structure-enabled database providing the research community with open, free and FAIR access to the patent literature. SureChEMBL contains ~140 million patents with ~50,000 added monthly. Of these, ~50 million patents are chemically annotated with more than 20 million unique chemical structures. Around 80,000 new compounds are extracted and stored monthly. The data in SureChEMBL can currently be accessed via a web interface that enables users to perform text and chemical structure queries, filter the output and then display the results. The complete set of chemical structures and patent associations are also available for download.  In this proposal we plan to significantly enhance SureChEMBL, enabling a wider selection of questions and use cases to be addressed, by: expanding annotations to include biological entities; developing methods to assess the relevance of information identified in patents and enable more accurate data retrieval and analysis; significantly improving the technical infrastructure and web interface with enhanced stability and usability; providing programmatic access through development of a RESTful application programming interface (API). The new, upgraded SureChEMBL will provide the broader life sciences research community with unparalleled access to a large and rich source of information and knowledge.

Lay Abstract: Understanding the activity and properties of drug-like molecules is key to the discovery of new medicines. Patents are a valuable source of such information, yet are difficult for many scientists to access. SureChEMBL is a database that enables the scientific community to obtain and analyse data and information from patents. This is important because significant amounts of drug discovery information are first disclosed in patent form and may never be written up in the “traditional” scientific literature. We will make it much easier for scientists to access and use patents for their own projects. We will extend and enhance our annotations of key terms, enabling users to identify those patents most relevant to their research. We will make major improvements to the website and the underlying software infrastructure. All data will be freely accessible to enable drug discovery scientists to be even more effective in their quest for new medicines.

Research Activity Codes: 1.3 CHEMICAL AND PHYSICAL SCIENCES;2.4 SURVEILLANCE AND DISTRIBUTION
Health Categories: GENERIC HEALTH RELEVANCE
Award Title: Synaptic and neuronal compensation in Alzheimer’s disease
Funder: Medical Research Council

Abstract: Alzheimer’s disease (AD) is characterized by synaptic and neuronal loss at early and late stages in the disease progression, respectively. One of the most puzzling aspect of AD is that the accumulation of amyloid and tau pathology precedes by several decades the onset of clinical dementia. Our research program rests on the notion that this gap corresponds to compensatory mechanisms implemented at all levels: first, at the synaptic level following synapse loss, and then at the neuronal and circuit level - and that the saturation of all these compensatory mechanisms mark the onset of dementia. In this research program, we aim to investigate the nature of these compensatory protective mechanisms, in particularly those implemented at the synaptic and neuronal level. Although much is known about the mechanisms underlying synaptic loss in AD, the compensatory mechanisms implemented following synaptic loss remain unexplored. This is probably due to the inability to predict which synapses will be lost and consequently, which will be compensated. To overcome this hurdle, we are developing optogenetic and chemogenetic tools to artificially eliminate synapses with complete spatio-temporal control in order to monitor the emergence of synaptic compensation over time (days and weeks) both at the structural and functional level using in-vitro and in-vivo two-photon microscopy.   Using this targeted approach, we aim to investigate i) the nature of synaptic compensation (e.g., enlargement of surviving synapses and/or synaptic regrowth), ii) the molecular mechanisms underlying compensation using transcriptomics and proteomics approaches, iii) the role of astrocytes and microglia in modulating synaptic compensation, and more importantly iv) the role of synaptic compensation in delaying the onset of cognitive deficits in well-characterized AD animal models (e.g., APP/PS1). As a neurodegenerative disease, AD is also characterized by neuronal loss at the later stages of the disease. In the second part of our research program, we will investigate the compensatory mechanisms implemented at the level of neuronal ensembles following neuronal loss. Using in-vivo two-photon microscopy to identify neuronal ensembles, we will investigate i) the ensemble compensation following the selective photoablation of constituents of the ensemble, ii) the molecular mechanisms underlying neuronal compensation and ultimately, iii) the role of neuronal compensation in improving cognition in AD models associated to neuronal loss.  We strongly believe that understanding the molecular mechanisms underlying synaptic and neuronal compensation will be crucial for developing alternative therapeutics to delay the onset of clinical dementia.


Research Activity Codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health Categories: NEUROLOGICAL
Award Title: Synthesis and evaluation of novel antagonists and fluorescent ligands for the human P2Y2 receptor
Funder: Wellcome Trust

Abstract: The human P2Y2 receptor is one of a large and diverse family of disease-relevant drug targets called G protein-coupled receptors. The P2Y2 receptor is a promising therapeutic target for important conditions, including metastatic cancer. However, no drugs which block the P2Y2 receptor have ever entered clinical trials. The research group recently published an initial study where novel P2Y2 receptor inhibitors, that prevent the action of the receptor, with good biological activity were produced. The project will build on this previous work to design, synthesise and evaluate further inhibitors with improved biological activity and "drug-like" properties to make them more clinically viable. The design of these inhibitors will be driven by visualisation of key interactions with the P2Y2 receptor in computational models. Another subsequent part of the project will involve equipping these novel inhibitors with a light emitting fluorescent dye that can be used to investigate their interaction with the P2Y2 receptor in cell and tissue-based experiments with state of the art imaging equipment.  Novel, high affinity and drug-like P2Y2 receptor inhibitors and their fluorescently-labelled counterparts would provide a vital tool to further validate the role of P2Y2 in disease and aid in the development of clinically viable drugs.


Research Activity Codes: 5.1 PHARMACEUTICALS
Health Categories: CANCER AND NEOPLASMS
Award Title: Systemic Inflammation and Growth following Acute Illness in Children.
Funder: Wellcome Trust

Abstract: Medical and nutritional management in acutely-ill undernourished children in developing countries aim to support rapid weight gain. However, such children remain at risk of death and poor catch-up growth post-hospital discharge. Little is known about mechanisms regulating childhood growth after acute illness. I hypothesise that persistent systemic inflammation (SI) is a key determinant of growth post-discharge among undernourished children. SI is associated with reduced linear growth in community cohorts, and is demonstrable at hospital discharge among undernourished children, potentially indicating untreated infections, microbiota dysbiosis, gut-circulation microbial product translocation, or enteric inflammation. My proposed work is nested within the CHAIN cohort that aims to characterise modifiable risks for mortality among acutely-ill children <2 years old in six countries in Africa and Asia. I aim to investigate whether persistent SI is a key determinant of catch-up growth among undernourished children and investigate its causes. I will examine relationships between growth and markers of SI, blood metabolomic profile, growth mediators, and microbial exposures comparing with well community children through a collaborative network between KEMRI-Wellcome; Kenya, the University of Oxford and the Wellcome Sanger Institute. Better understanding of relationships between SI and post-discharge growth is expected to inform therapeutic strategies to improve recovery.

Lay Abstract: Undernutrition remains a major global health problem that increases risks of infectious diseases, and affects brain development, immunity, cardiovascular and metabolic health. Systemic inflammation (SI) is a natural response to infections and should resolve with recovery. In pilot studies, I have observed high levels of SI among undernourished children when they appear well at the time of discharge from hospital linked to the risk of subsequent death and poor growth. In community studies and in inflammatory diseases, SI has been seen to impair child growth. In this fellowship, I aim to determine whether SI persists after hospital discharge, is greater among undernourished children, if it affects post-discharge growth and identify causes of SI. I will utilise a large set of existing high-quality data and biological samples from a recent large study of children admitted to hospitals in sub-Saharan Africa and South Asia and followed up for 6 months after discharge.

Research Activity Codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health Categories: INFECTION