2020 projects list

The studentship projects that have formed our second cohort of the CDT in Chemical Biology: Innovation in Life Sciences, which started in autumn 2020, are listed below.

Filled studentships

Cell-engineered synthetic chylomicrons for oral drug delivery applications

Student

Jake Samuel

Title

Cell-engineered synthetic chylomicrons for oral drug delivery applications

Supervisors

  • Nazila Kamaly
  • Oscar Ces

Abstract

The delivery of biological drugs such as therapeutic peptides and proteins via the oral route is an important area of research. However, successful peptide delivery via any administration route is currently highly challenging. The oral delivery of peptides is hampered due to their low bioavailability, which results from low absorption and high rates of first-pass extraction, due to enzymatic and pH mediated hydrolysis in the gastrointestinal (GI) tract and liver. Given the successful generation of antidiabetic peptides and insulin-like peptides (such as glucagon-like peptide-1 (GLP-1), there is great interest in developing oral peptide delivery methodologies due to high patient compliance and market potential.

Chylomicrons are lipoproteins (a group of soluble proteins that combine with and transport fat or other lipids in the blood plasma) formed in enterocytes via the packaging of nascent triacylglycerols, cholesterol, cholesterol esters, at least one fat soluble vitamin, and apolipoprotein B48 (ApoB48). Chylomicrons are secreted from the enterocyte into the mesenteric lymph. Incorporation of hydrophobic molecules and drugs into chylomicrons can exploit this pathway for drug delivery to the lymphatics. In this project, we aim to create a new paradigm for lipophilic peptide delivery across the gut by hijacking and exploiting chylomicron cellular machinery in enterocytes with the chylomicrons in effect acting as stealth shields for the peptide of interest. By combining droplet-based microfluidics with robotics we will able to manufacture synthetic chylomicrons for the first time (termed chylosomes) enabling us to systematically vary their composition and study the molecular interactions that underpin their stability. Using the resulting molecular engineering rules that will emerge from these studies we will design de-novo chylomicrons that can onboard user-defined peptides. Using organon-a-chip technologies coupled with super-resolution microscopy (nanoscopy) we will then study the mechanism of interaction between the chylomicrons and the gut lining.

Ultrasensitive prostate cancer screening based on miRNA sensing from whole blood

Student

Charlotte Hudlerova

Title

Ultrasensitive prostate cancer screening based on miRNA sensing from whole blood

Supervisors

  • Joshua Edel
  • Sylvain Ladame
  • Aleksandar Ivanov
  • Charlotte Bevan

Abstract

Current tests for the diagnosis, prognosis and stratification of prostate cancer suffer from two main drawbacks, being either invasive (requiring tissue biopsies) or inaccurate and therefore unreliable. Recent studies have highlighted the potential of microRNA (miRNA) as a minimally-invasive diagnostic and prognostic biomarker for various cancer types, including prostate. The main challenges with current miRNA sensing strategies relate to the naturally low abundance of these biomarkers in bodily fluids and high sequence homology between fragments. Besides, most technologies available to date cannot detect such biomarkers directly from whole blood and require heavy sample processing, which in the absence of standardised protocols can be a major source of error. While miRNAs have been reported as promising diagnostic biomarkers for prostate cancer, the lack of technologies enabling their direct and accurate detection from blood has prevented their broader use in new screening tests. As part of this project, we propose to improve diagnostic specificity beyond the PSA test by performing multiplexed detection of up to 5 miRNA biomarkers. This innovative technology has the potential to enable new blood tests for prostate cancer and future point-of-care devices, decreasing diagnostic uncertainty and improving quality of life.

Next-generation biosensors for real-time, enhanced sensitivity antigen detection

Student

Oliver Burman

Title

Next-generation biosensors for real-time, enhanced sensitivity antigen detection

Supervisors

  • Aleksandar Ivanov
  • Sarah Goodchild
  • Joshua Edel

Abstract

The ability to measure biomarkers and trace analytes both specifically and selectively at the single-molecule level in biological fluids has the potential to transform the diagnosis, real-time screening, analyte seining for specific hazardous materials of high-profile defence interest. Strategies such as the use of nanopore sensors combined with functional molecular probes have been gaining in prominence not only for sequencing but more recently in screening applications. However, substantial challenges remain in achieving sufficient resolution to distinguish bound from unbound target analytes or in reaching detection of critical analytes that may be present at a very low level in biofluids. The proposed CDT project addresses the above limitations by delivering a new class of biosensors, of importance to the DstL, the research arm of the Ministry of Defence. The platform combines custom molecular probes and dielectrophoretic nanopore sensors, that are capable of selective analyte discrimination in near real-time at sub-pM and fM concentrations.

Smart Bioisosteres: Beyond a spatial mimic to improved plant biology

Student

Hannan Seyal

Title

Smart Bioisosteres: Beyond a spatial mimic to improved plant biology

Supervisors

  • James Bull
  • James Murray
  • William Whittingham

Abstract

Bioisosteres are essential alternative design options in the development of new agrochemicals, to retain or improve overall biological properties of an active ingredient, such as activity, biokinetics, and metabolic stability. However, the development of bioisosteric replacements for linking groups (not directly involved in binding to the protein target) has to date focused exclusively on their scaffolding properties, to mimic topology, and neglected the effect on the properties of the substituents directly attached to the scaffold (e.g. pKa or H-bonding potential, hybridisation). In developing new agrochemicals, these substituent features are crucial to the progress of a compound, and notably the potential to reach the relevant site of activity. This project will design, synthesise and assess new bioisosteres for ortho-substituted phenyl derivatives, for which there are currently no established replacement options. With the designed scaffolds a series of 'matched molecular pairs' will be prepared, to examine systematically the change in the physicochemical and ADME properties of the compound as a whole (logP, solubility, metabolic stability), as well as the particular changes to the key functional substituents on the scaffold, providing new insights to these materials. Advantageous scaffolds will be incorporated into known agrochemical compounds, for which 3 herbicides have been identified for this proposal. The designed bioisosteric compound will be prepared and the biological response will be investigated (from in vitro enzyme assays, to whole plant studies in the glasshouse, docking and X-ray studies, physical / metabolic stability), and compared to that of the ortho-phenyl containing compounds. These studies will provide new understanding and new design options for the development of new agrochemicals.

A multifunctional biomimetic lab-on-a-chip assault course for agrochemical bioavailability screening

Student

Tom Kitto

Title

A multifunctional biomimetic lab-on-a-chip assault course for agrochemical bioavailability screening

Supervisors

  • Oscar Ces
  • Laura Barter
  • Yuval Elani
  • Nazila Kamaly

Abstract

A current challenge with the delivery of agrochemicals is their non-specific distribution throughout the plant. This is compounded by the lack of a systematic fundamental physicochemical based set of rules to effectively predict agrochemical bioavailability. This proposal aims to address this challenge by designing and establishing a modular on-chip model transport system that can mimic the various compartments and layers an agrochemical needs to traverse to gain access to its active-site within the plant. We propose to do this using automated droplet-based microfluidics that will enable the user to "dial up" in-vitro biologically relevant mimics of plant compartments and barriers. The resulting biomimicry toolkit will capture the key features of the molecular environments (molecular interactions, degree/length scale of compartmentalization, sequencing of barriers, types of barriers (e.g waxy cuticle vs biomembrane) at each phase of the bioavailability pathway. This will involve plugging together novel motifs including vesicles, multisomes, droplet interface bilayers, phase-separated domains and vesicle interface bilayers. Control of the end-to-end connectivity of motifs and being able to embed one motif within another motif will be features engineered into the resulting device. The fully integrated system will have added functionalities of dynamic and real-time molecule tracking across key stages of the assault course with read outs facilitated by fibre-optic based UV Vis, Raman Imaging, Mass Spec and HPLC depending on the assault course element under study. The device will enable us to screen a library of Syngenta's existing agrochemicals with defined physicochemical properties and to identify those molecules that can successfully cross key barriers in plants. Knowledge gained will facilitate the design of more effective agrochemicals that can cross plant structures beyond simple diffusion or ion trapping mechanisms and allow sitetargeted distribution of agrochemicals, leading to a more sustainable, economical and environmentally green approach to agrochemical use in agriculture.

Directing protein modification in living systems with bifunctional molecules

Student

Vincent Saverat

Title

Directing protein modification in living systems with bifunctional molecules

Supervisors

  • Ed Tate
  • Mark Rackham
  • Louise Walport

Abstract

Protein post-translational modifications (PTMs) are chemical changes to the structure of a protein after it has been made in the cell and are typically introduced and/or removed by enzymes. There are over 1000 classes of PTM in the human proteome introduced at over 1 million distinct sites on proteins. PTMs often have a profound effect on protein function and regulate all aspects of biology and underlie or represent opportunities for intervention in every type of disease. Recently, a new drug discovery paradigm has emerged whereby bifunctional molecules induce assembly of complexes which catalyse PTMs de novo, most prominently to induce ubiquitination and degradation of a target protein (so-called 'PROTACs'), a modality recently progressed into clinical trials. Since they co-opt enzyme catalytic functions already present in cells, such drugs can deliver potent biological effects at low occupancy and at sites unrelated to protein function, overturning previous assumptions about what can be achieved with small molecules. Drawing on the deep expertise of the Tate group in the design of chemical tools to understand and exploit PTMs in living systems, a powerful peptide selection platform in the Walport lab, and the world-leading capabilities at MSD in drug discovery and development, you will design, synthesize and develop a new class of bifunctional molecules capable of inducing dramatic changes in protein function and localisation, with profound potential for manipulating biology and modulating disease outcomes.

Biomechanical regulation of cell extrusion and migration during metastasis

Student

Rachel Healy

Title

Biomechanical regulation of cell extrusion and migration during metastasis

Supervisors

  • Vania Braga
  • Sam Au

Abstract

Most adult tumours are comprised of tightly bound epithelial cells organised into continuous sheets. The extrusion of cancer cells from these sheets is an important initial step in metastasis. It was previous believed that tumour cell extrusion is driven by epithelialmesenchymal transition (EMT) whereby cancer cells lose epithelial phenotypes and adhesions to neighbouring cells. However, recent evidence has suggested a more complex behaviour, where different cancer subtypes perform varying degrees of EMT and in certain cases, EMT may not be required at all. Furthermore, tumour cells often disseminate via collective migration where group of cells migrate together with intact adhesions among neighbours. Cell collectives can then enter the bloodstream as circulating tumour cell clusters, which are "the most likely harbingers of metastases" due to their 50-100X greater metastatic potential than equal numbers of individual circulating cells.

We currently do not fully understand how cell-cell and cell-ECM adhesions, intrinsic forces (cortical tension) or extrinsic biomechanical forces (extracellular environment) contribute to the a) extrusion of cells from epithelial sheets and b) individual vs. collective migration. Our lack of physiologically-relevant models capable of isolating these variables severely hampers our ability to study their contributions and interactions during tumour cell dissemination. In this work, we aim to use novel microfabricated devices to explore how cell-cell contacts, cell-cell interfacial tension and "squeeze" forces applied by neighbouring tissues drive tumour cell extrusion and detachment.

Confinement of doublets into geometric shapes (2D micropatterned substrates) has a dramatic influence on intercellular boundaries, cortical tension and cell motility. Depending on the tensional level, cells displayed undulated, weak junctions and migrate faster (circular shapes) or strong junctions and less motility (triangular shapes), resembling healthy epithelial tissues. This indicates an essential role of cell cortex stiffness and intracellular mechanics to influence the ability to stick together or to migrate faster, and that these can be controlled via geometric confinement.

We hypothesize that (i) the lower cortical tension seen in tumour cells increases tumour cell dissemination by weakening cohesion among neighbours and (ii) biomechanical forces and the balance between cell-cell & cell-ECM adhesions control the detachment and dissemination of cancer cells as individual vs. clusters from benign tumours.

As a model of carcinoma development, we will use a panel of cells: primary keratinocytes, immortalized keratinocytes, and two sets of primary tumour and metastatic head and neck carcinoma cells from patients (available in the Braga lab; keratinocyte-derived tumours). We will design novel platforms to provide high controllability of mechanical stress. We aim to: Design next generation 3D-microwell arrays and microchannels to evaluate the influence of cell geometry and external mechanical forces on adhesive properties and migration; Define the response of cells at various stages of transformation to variations in intrinsic cortical tension and external mechanical forces; Compare the oncogenic signalling in the various geometric challenges (3D cellular microwell) and cell detachment/motility as cohorts (microchannels).

Outcomes: This project will accelerate our understanding of the factors that drive tumour cell extrusion and motility, enabling us to devise novel anti-metastatic strategies to inhibit tumour cell invasion. The project will generate comprehensive knowledge of mechanical force regulation of metastasis, how different states of tumour progression respond to tensional challenges, molecular regulators and screening platforms to interfere with the process.

Engineering synthetic cell translators to mediate human-cell communication

Student

Karen Zhu

Title

Engineering synthetic cell translators to mediate human-cell communicaation

Supervisors

  • Yuval Elani
  • Oscar Ces

Abstract

Synthetic biology can be divided into two distinct approaches. The first is the top-down approach, where cells are modified using metabolic and genetic engineering techniques. The second is concerned with the bottom-up construction of membrane-bound microsystems - artificial cells - that resemble biological cells in form and function. The current state-of-the-art involves using lipid vesicles as chassis that are functionalised with biomolecular machinery allowing cellular processes to be mimicked. Until now, these approaches have largely evolved in isolation from one another. The aim of this project is to bridge this divide by chemically networking synthetic cells with engineered biological ones on a population level using through-space communication. In this project we will design a suite of stimuli-responsive synthetic cells that can induce activation of a DNA programme in living E. coli in response to external stimuli. The artificial cells will act as intermediaries between a human user and a living cell, capable of 'translating' a signal (heat, light, magnetic field, acoustic field) into a language that living cells can understand (IPTG) and act upon (synthesizing a protein of interest). This new conceptual framework in biotechnology will allow the creation of responsive systems in a way that is not possible using living systems alone, a strategy that is directly aligned with the remit of the CDT. This approach will effectively lead to expanded sensory range of bacteria, allowing then to respond to cues that are entirely different from the ones they have evolved to respond to.

Compartmentalised biomembrane capsules as novel vaccine technologies

Student

Hannah Cooke

Title

Compartmentalised biomembrane capsules as novel vaccine technologies

Supervisors

  • Yuval Elani
  • Oscar Ces

Abstract

The development of new vaccine technologies that are targeted, effective, and programmable is increasingly being recognised as one of the key industrial challenges in chemical biology. The packing of vaccines , both protein- and RNA-based, inside a lipid-bound compartment is currently at the forefront of approaches to a more effective delivery mode of the active agents. The majority of vaccine delivery vehicles share a common structural motif, namely that of a single compartment encased by a lipid layer; this lack of architectural diversity has hindered their technological potential.

We know from biology that step changes in sophistication of chemical microsystems can be achieved by having non-uniform spatial organisation; this is achieved through compartmentalisation of content in discrete spatial locations. In this project, novel vaccine delivery vehicles will be developed using novel microfluidic technologies, where the size, membrane composition, encapsulated cargo, and number of compartments can be 'dialled-in' on demand. To do this, the student will develop underlying microfluidic platforms for the layer-by-layer assembly of a suite of lipid membrane motifs using a molecular assembly line. The ability of these structures to house both the antigen and adjuvant in different compartments will be explored, together with their potential for multi-stage release of a vaccine payload.

Target-directed synthesis of protein-protein interaction inhibitors

Student

Sachi Sharma

Title

Target-directed synthesis of protein-protein interaction inhibitors

Supervisors

  • Anna Barnard

Chemical biology approaches to study the ubiquitin system

Student

Katherine McPhie

Title

Chemical biology approaches to study the ubiquitin system

Supervisors

  • Katrin Rittinger
  • Louise Walport

A multidisciplinary approach to target MYC-driven childhood cancers

Student

James Zhang

Title

A multidisciplinary approach to target MYC-driven childhood cancers

Supervisors

  • Ed Tate
  • Louis Chesler

Abstract

Multidisciplinary collaboration to understand the mode of action of inhibitors targeting PTM pathways in MYCN-driven childhood cancers, with additional broad applications in a range of MYC-driven cancers. You will apply chemical proteomic tools and novel drugs currently in preclinical development to drive validation of drug targets in these pathways.

Roles of post-translational modifications in neurodegenerative protein aggregation

Student

Rebecca Thrush

Title

Roles of post-translational modifications in neurodegenerative protein aggregation

Supervisors

Francesco Aprile

Abstract

Identifying and characterising PTMs, which are able to redirect, delay, or accelerate the formation of amyloids of the protein alpha-synuclein, which are linked to Parkinson's disease and other forms of dementia. During her project, she will use a highly multidisciplinary approach, involving chemical biology for generating PTM-amyloids, antibody production techniques, and biophysical structural and functional analysis of proteins.

Using chemical tools to understand the glycobiology of metastatic breast cancer

Student

Beatriz Calle

Title

Using chemical tools to understand the glycobiology of metastatic breast cancer

Supervisors

  • Ben Schumann
  • Ilaria Malanchi

Abstract

Aberrant glycosylation is a hallmark of cancer. Glycans are recalcitrant to classic genetic engineering, calling for alternative methods to understand their physiological function during tumorigenesis. This project will focus on the development of chemical tools to dissect the role glycans play in the metastatic behaviour of breast cancer.

A DNA-nanotechnology toolkit for artificial cell design

Student

Diana-Alexandra Tanase

Title

A DNA-nanotechnology toolkit for artificial cell design

Supervisors

Lorenzo Di Michele

Abstract

The project consists of constructing synthetic cellular systems in which both structural and functional elements are mainly reliant on synthetic DNA nanostructures. Diana will be focusing on the embedding novel functionalities in the DNA-baed synthetic cells, including sensing and stimuli-responsiveness, materials synthesis, coupling between structure and information processing.

Developing new tools to investigate complex redox-active proteins

Student

Fang Fang

Title

Developing new tools to investigate complex redox-active proteins

Supervisors

Maxie Roessler

Abstract

I intend to investigate the elusive mechanism of respiratory enzyme complex I, a protein that is essential for ATP synthesis and whose malfunction is associated with ageing and numerous neurodegenerative disorders including Parkinson's disease. In order to acquire cutting-edge insight into large metalloenzymes such as the complex I, a novel technique developed by Roessler lab will be applied and developed further, which involves the combination of electron paramagnetic resonance (EPR) spectroscopy and protein film electrochemistry (PFE).

Development and application of QM/MM/MD to modelling Rubisco

Student

Zhili Chen

Title

Development and application of QM/MM/MD to modelling Rubisco

Supervisors

  • Ian Gould
  • Laura Barter

Abstract

Rubisco is the world's most abundant protein and yet is highly inefficient. The highly symmetrical geometry of Rubisco provides for 8 active sites; however, it is estimated experimentally that only 6 are active in the catalytic cycle. Due to the extremely large size, ca. 74 thousand atoms, of Rubisco it has been difficult to investigate its reactivity using conventional computational chemistry techniques. This project is aimed at developing and applying hybrid QM/MM MD techniques to ascertain the origins of the catalytic inefficiency of Rubisco. Successful development and application of such methods will facilitate the modelling of mutated variants of Rubisco to predict if mutations would be appropriate experimental targets to improve its efficiency.

Optical Control in a Single-molecule Electrochemical Sensor

Student

Yilin Li

Title

Optical Control in a Single-molecule Electrochemical Sensor

Supervisors

  • Joshua Edel
  • Alex Ivanov

Abstract

Single-molecule detection technique provides a powerful platform for scientists to observe biomolecular function that is difficult to sense using conventional techniques. Quantum tunnelling, combined with biosensors has raised broad interests recently due to its advantages in high spatial resolution and sensitivity. However, it is still challenging to controllably fabricate a tunnelling device with ease and low cost. This project aims to develop a novel method for fabrication of tunnelling device by electrochemical feedback-control deposition of platinum. Such electrochemically fabricated tunnelling junctions will likely have extended long term stability and will be ideally suited for continuous monitoring in complex samples. Single-molecule techniques have attracted great attention because of their ability to conduct studies of molecules at the nanoscale. Tunnelling sensors are a class of single-molecule detection techniques that possess extremely high spatial resolution and sensitivity. However, an obstacle during detection is the poor temporal resolution. One promising route to overcome this challenge is to combine ultrafast spectroscopy with tunnelling detection. In this project, the combination of electrochemical deposition and electromigration breakdown is applied to fabricate a new type of tunnelling sensors that are based on dual-barrel nanopipettes.