2024 Studentships

Student

Konstantina Arvaniti

Title

Systematic prediction, validation, prioritization and on-target lead discovery for next-generation antimicrobials

This project is funded by the Institute of Chemical Biology EPSRC Centre for Doctoral Training and The NIHR Imperial Biomedical Research Centre (BRC)

Supervisors

• Dr Matthew Child (Department of Life Sciences, Imperial)
• Professor Sophia Yaliraki (Department of Chemistry, Imperial)
• Professor Ed Tate (Department of Chemistry, Imperial)
• Professor Mauricio Barahona (Department of Mathematics, Imperial)

Abstract

Antimicrobial resistance constitutes one of the biggest global challenges facing modern medicine. Yet antimicrobial discovery is impeded by the limited number of validated microbial targets, and the rapid development of resistance by pathogens to existing frontline therapeutics. Chemically sensitive amino acids on proteins are targets for covalent-mechanism drugs. These are potential Achilles' heels of pathogens, yet are underexploited as antimicrobial targets. Chemoproteomic approaches identify chemically sensitive residues via their intrinsic reactivity towards probe molecules, but do not integrate functional prioritization. This results in most of these chemically tractable protein targets being overlooked. A new cross-disciplinary functional chemoprotegenomics platform enables unbiased discovery and validation of chemically sensitive residues on proteins. This project will integrate emerging computational and experimental technologies from our labs to establish a high-throughput approach for discovering, validating, and selectively targeting chemically tractable residues in any pathogen, presenting a new paradigm for on-target antimicrobial drug discovery. 

Student

Max Barnett

Title

Phosphine Oxides as Rising Stars in Drug Discovery

This project is funded via the Institute of Chemical Biology and co-sponsored by UCB

Supervisors

• Dr James Bull (Department of Chemistry, Imperial)
• Dr Jeffrey Bruffaerts (UCB)

Abstract

Phosphine oxides represent a noticeably underrepresented chemotype in drug discovery. However, the clinical validation of Brigatinib, containing dimethyl phosphine oxide, and the disclosure of other therapeutic preclinical compounds featuring these polar and hydrophilic functional groups have sparked a revived interest across the pharmaceutical sector. The surge in relevant publications have further highlighted an untapped potential in drug-like chemical space, as these analogues were shown to present beneficial physicochemical and ADMET properties. Phosphine oxides notably exhibit a highly polarized P=O bond, translating in enhanced hydrophilicity, and thus aqueous solubility and enhanced metabolic stability. 

Acknowledging the current synthetic knowledge gap, enabling new synthetic methodologies to access this vastly uncharted chemical space is thus critical to capture the potential of phosphine oxides more extensively in drug design. This project will combine synthetic chemistry and ADME studies. Phosphine oxides motifs in new chemical space will be designed and prepared aiming to maximise the understanding of how this highly polar functional group can be best exploited in medicinal chemistry.

Student

Hayden Jit Hei Cheung

Title

Understanding and optimising RNA therapeutic delivery, efficacy, and toxicity with chemical biology

This project is funded via the Institute of Chemical Biology and co-sponsored by AstraZeneca

Supervisors

• Professor Ed Tate (Department of Chemistry, Imperial)
• Dr Santiago Vernia (MRC Laboratory of Medical Sciences)
• Laurent Knerr (AstraZeneca)

Abstract

Chemically modified RNAs have recently emerged as a unique and powerful therapeutic approach since they can be designed to address almost any disease state by directly and specifically modulating gene expression. These molecules operate through a diverse range of mechanisms, and include antisense oligonucleotides (ASOs), small interfering RNA (siRNA), micro-RNA (miRNA), messenger RNA (mRNA) and RNA vaccines, and splice-switching oligonucleotides (SSOs). However, these advanced therapeutics are currently limited by lack of understanding of mechanisms of uptake and delivery to target disease, whilst avoiding toxicity and non-specific delivery to off-target tissues.

In this project you will develop and apply a platform of chemical biology technologies to explore the interactome of any oligonucleotide therapeutic in living cells, combining synthetic oligonucleotide probes with quantitative proximity labelling proteomics. Your platform will be used to discover and explore the interacting partners of diverse oligonucleotide modalities, establishing mediators of delivery, uptake, and mechanisms of action in cells and in plasma. You will then proceed to explore the impact of chemical modifications commonly used to modulate delivery, providing a framework for knowledge-led optimisation of next generation oligonucleotide therapies.

You will benefit from a unique supervision team and access to state-of-the-art facilities, including expertise in chemical biology and proteomics (Tate, Imperial/Crick), RNA biology and therapeutics (Vernia, MRC Laboratory of Medical Sciences), and RNA therapeutic discovery (Knerr, AstraZeneca Sweden).

Student

Ido Dan

Title

Transforming our understanding of electron transfer in membrane proteins through automation, additive manufacturing and spectroelectrochemistry

Supervisors

• Dr Maxie Roessler (Department of Chemistry, Imperial)
• Professor Oscar Ces (Department of Chemistry, Imperial)
• Dr James Hindley (Department of Chemistry, Imperial)

Abstract

Electron transfer processes in membrane proteins underpin fundamentally important biological processes, such as respiration and photosynthesis. Capturing paramagnetic reaction intermediates is key to understanding how these proteins function. However, capturing truly catalytic intermediates (rather than resting or off-cycle states), while harnessing information on both reactivity and structure, has remained a holy grail. We will enable the generation and interrogation of such catalytic intermediates in two exemplary and important membrane-bound oxidoreductase enzymes through the development of film-electrochemical EPR (FE-EPR) for membrane proteins. The challenging physical sciences innovation required to unlock the ability to study the time-dependent nature of these molecular interactions is timely and made possible by developing automated platforms for placing membrane proteins into artificial vesicles which incorporate in situ measurement of protein activity and computer-guided optimization processes, as well as additive manufacturing of tailored electrodes. Another crucial element is our recent proof-of concept demonstration that small-molecular catalysts can be interrogated with real-time FE-EPR (Nature Chemistry 2024). The advances in understanding the molecular interactions that underpin respiration and photosynthesis will pave the way to healthy ageing and sustainable agriculture, whilst the methodologies developed will be widely applicable in chemical biology and beyond. 

Student

Bracha Lawrence

Title

Target-directed Synthesis of Protein-Protein Interaction Inhibitors

This project is funded via the Institute of Chemical Biology and The NIHR Imperial Biomedical Research Centre (BRC)

Supervisors

• Dr Anna Barnard (Department of Chemistry, Imperial)
• Professor Alan Armstrong (Department of Chemistry, Imperial)
• Dr David Mann (Department of Life Sciences, Imperial)

Abstract

Protein-protein interactions (PPIs) play critical roles in many biological pathways, the mis-regulation of which can result in disease. Therefore, PPIs have long been considered attractive drug targets, but the number of successful inhibitors generated remains limited. Current screening methods using established compound libraries often lack the structural properties necessary to identify inhibitors of the characteristically large and flat interfaces of most PPIs. We will combine the advantages of robotically enabled screening and a novel assay developed in the Armstrong and Mann groups to establish a high-throughput technology for the identification of PPI inhibitors with the target protein present in the screening conditions to enable it to select for its preferred ligands. This will enable the rapid identification of either peptide or small molecule ligands for any target PPI.

We are no longer acceping applications for this studentship; shortlisting is underway.

Posted: 6 March 2024

Student

Chelsie (Xinran) Li

Title

Unravelling the role of G-quadruplex structures in brain ageing and neurodegeneration.

Supervisors

• Dr Marco Di Antonio (Department of Chemistry, Imperial)
• Dr Raffaella Nativio (Department of Brain Sciences, Imperial)
• Dr Silvia Galli (Department of Chemistry, Imperial)

Abstract

The increasing incidence of neurodegenerative disorders is posing a significant threat to the NHS and public health services world-wide. Epigenetic regulation has emerged as a critical player in ageing of model organisms and because of its role in integrating environmental stimuli into the genome, represents a therapeutically tractable player in brain ageing and neurodegeneration. Studies from Nativio et al. (Nat. Neuro 2018, Nat. Genet. 2020) have revealed that different epigenetic modifications are differently associated with healthy ageing and Alzheimer’s, driving distinct functional pathways. The Di Antonio group has recently demonstrated that the formation of DNA secondary structures known as G-quadruplex (G4) is linked to neurodegeneration (Nat. Commun. 2023) and that the mutation of key proteins that resolve G4s leads to accelerated ageing (J. Am. Chem. Soc. 2021). In this project, we propose to leverage this knowledge to systematically investigate the role of G4-formation in ageing neuron models that are established in the Nativio’s group. To achieve this, we plan to combine genome-wide mapping strategies to assess the changes in G4-distribution in ageing neurons with the development of chemical-biology probes to disrupt G4-structures and assess their potential as anti-ageing targets. We anticipate that this project will lead to the identification of G4s that could be targeted to prevent epigenetic dysregulation associated with neurodegeneration.

Student

Fawaz Raja

Title

Visualising the effects of pollution nanoparticles on respiratory epithelial cells at air-liquid interface

This project is funded via the Institute of Chemical Biology and The NIHR Imperial Biomedical Research Centre (BRC)

Supervisors

• Professor Marina Kuimova (Department of Chemistry, Imperial)
• Professor Alexandra Porter (Department of Materials, Imperial)
• Professor Fan Chung (National Heart & Lung Institute, Imperial)
• Professor Ian Adcock (National Heart & Lung Institute, Imperial)

Abstract

Pollution nanoparticles, termed particulate matter (PM), carry enormous population health burden, through direct and indirect effects that are thought to involve oxidation and inflammation. However, currently there is no single imaging or biochemical technique available to unequivocally assign the exact timing and the (bio)-chemical effects of PM components, thus preventing the implementation of solid strategies for the mitigation of their deleterious effects. This proposal will establish the exact site, sequence and timings of PM interaction with human airway epithelial cell and organelles. By establishing the relationship between these events this work will pinpoint the crucial subcellular processes that lead to oxidative stress and inflammation both at a single cell level and in whole cell populations. We will develop protocols to assess localisation via analytical cryo-electron microscope (cryo-EM) and direct oxidation pathways via fluorescence lifetime imaging microscopy (FLIM) in primary human bronchial epithelial cells (HBECs) grown in submerged culture and at air-liquid interface (ALI), which is the only model that accurately reflects airway pathophysiology, for the first time. 

Student

Rie Rønnow

Title

Developing novel transition metal complexes to enhance crop yields

Supervisors

• Dr Laura Barter (Department of Chemistry, Imperial)
• Dr Rudiger Woscholski (Department of Chemistry, Imperial)
• Professor Nicholas Long (Department of Chemistry, Imperial)

Abstract

This studentship will explore novel synthetic chemistry and chemical biological routes to tackle the global challenge of food security, by developing molecular tools, with the potential to transform crop security across the globe. It will enable plants to exceed performance levels that are limited by in-built pathway inefficiencies, currently only being addressed via expensive & often perceived as controversial genetic engineering approaches. This novel form of crop enhancement will enable plants to function at levels beyond that set by their natural performance and will target the inefficient process of photosynthesis and in particular the wasteful photorespiration reactions, where O2 competes with CO2, lowering photosynthetic efficiency by ~50%. It will mitigate this by increasing local CO2 concentrations, minimising photorespiration & thereby increase photosynthetic efficiencies and crop yields. This studentship will design, synthesise (transition metal complexes of multidentate ligands), test & optimise (in an iterative manner) a suite of these novel, molecular CO2 delivery vehicles, to investigate their mode of action. This will support the rational optimisation of efficacy, solubility and bioavailability and demonstrate their potential as a viable, scalable & cost-effective tool able to supercharge photosynthesis, resulting in increased crop yield.

Student

Seshagiri Sakthimani

Title

Highly multiplexed detection of cancer biomarkers from clinical samples using nanopore sequencing

This project is funded via the Institute of Chemical Biology and is co-sponsored by Oxford Nanopore Technologies

Supervisors

• Professor Joshua Edel (Department of Chemistry, Imperial)
• Dr Aleksandar Ivanov (Department of Chemistry, Imperial)
• Caroline Koch (Department of Chemistry, Imperial)
• Dr Nadia Guerra (Department of Life Sciences, Imperial)
• Dr Richard Gutierrez (Oxford Nanopore Technologies)
• Dr Mark Bruce (Oxford Nanopore Technologies)
• Dr Lakmal Jayasinghe (Oxford Nanopore Technologies)

Abstract

The unmet need in cancer diagnostics lies in the discovery and detection of novel biomarkers with both prognostic and predictive value. This is essential for enhancing early detection, optimizing treatment strategies and improving patient outcomes through personalized care. Currently, the majority of blood tests are conducted within a clinical environment and only examine a limited number of indicators. The potential for clinical diagnostics to progress beyond the customary single biomarker model lies in developing an inexpensive, rapid, and highly multiplexed platforms. To this end, we propose the creation of a novel technology that leverages nanopore sequencing and barcoded molecular probes building on work from our groups as shown in Koch et al. Nature Nanotechnology, 18, 1483 (2023). This innovative approach will facilitate the simultaneous multiplexed detection of analytes implicated in liver cancer within a single sample. The platform will allow for precise de-multiplexing of single molecule detection, enabling the simultaneous quantitative detection of hundreds of miRNAs and proteins and the generation of large single molecule data sets to build Modified Hidden Markov ML models. This adaptable method can also be expanded to detect a vast array of molecules, depending on the specific application required. To ensure the success of this project, we have assembled a team composed of Imperial physical and life scientists as well as an industrial partner, Oxford Nanopore Technologies (ONT), who we will collaborate with to deliver proof of concept and preclinical studies.

Student

Rohan Sekhri

Title

3D printed synthetic tissues for patterned interactions with cellular populations

This project is funded via the Institute of Chemical Biology and The NIHR Imperial Biomedical Research Centre (BRC)

Supervisors

• Dr Ravinash Krishna Kumar (Department of Infectious Disease, Imperial)
• Dr Yuval Elani (Department of Chemical Engineering, Imperial)
• Professor Karen Polizzi (Department of Chemical Engineering, Imperial)

Abstract

Cellular communities, consisting of cells (microbial and/or eukaryotic) living and interacting in various environments, are starting to be used in applications ranging from environmental remediation, agriculture, food science, bioproduction, and biomedicine. Moreover, it is increasingly being realized that communities of interacting cells underpin many aspects of human health (i.e. microbiomes). A global research priority therefore is to understand and engineer these communities for our own goals. Patterned population gene expression in cellular communities is critical for the establishment and development of both microbial communities and eukaryotic tissues. However, external control over target-cell populations is hugely limited due to the lack of smart-patterned release systems that can integrate and deliver effector molecules to cells when required. Here we propose to solve this, by using a custom-built 3D printer to build a smart-patterned release system for controlling population gene expression in cells with high spatial and temporal resolution. These printed systems will comprise of 100s of pL-sized aqueous droplets networked by interfaced lipid bilayers, of which we call synthetic tissues. Critically, we will develop these synthetic tissues to function in aqueous environments where encapsulated effector molecules will be released through membrane proteins present in the connected bilayers. Further, we will develop these 3D printed patterned release systems to be robust and adaptive to their external environment, and validate our system by interrogating patterned gene expression in both defined bacterial and mammalian cell populations. 

Student

Jak Soon

Title

Unlocking a new generation of antimicrobial resistance targets by high-throughput lipidomics drug discovery

This project is funded by the Institute of Chemical Biology EPSRC Centre for Doctoral Training and The NIHR Imperial Biomedical Research Centre (BRC)

Supervisors

• Dr Gerald Larrouy-Maumus (Department of Life Sciences, Imperial)
• Dr Andrew Edwards (Department of Infectious Disease, Imperial)
• Professor Ed Tate (Department of Chemistry, Imperial)

Abstract

Escherichia coli is the leading cause of death associated with drug-resistant bacterial infections and is one of the World Health Organisation’s highest priority pathogens for which new treatments are desperately needed. Focussing on the mechanism of assembly of the outer membrane of Escherichia coli and capitalising on the new drug discovery hub at Imperial, this project will develop and implement a high-throughput mass-spectrometry-based approach to identify new compounds that target the Gram-negative cell envelope via novel modes of action. Taking an interdisciplinary approach to drug discovery, hits will be optimised for potency, spectrum of activity, and therapeutic index. Hits with the best profiles will be subjected to target identification approaches which employ lipidomic, genetic, chemical biology and proteomic approaches, with the ultimate goal of developing novel antibiotics for use in the clinic.

Student

David Tsang

Title

Engineering synthetic cells using next-generation robotics and machine learning

Supervisors

• Dr James Hindley (Department of Chemistry, Imperial)
• Professor Oscar Ces (Department of Chemistry, Imperial)
• Dr Antonio Del Rio Chanona (Department of Chemical Engineering, Imperial)

Abstract

Bottom-up synthetic biology has ushered in a new era of synthetic cell science where biomimetic entities including microrobots are constructed from non-living and living components to create tailorable structural elements and complex life-like behaviours. Synthetic cells can model systems to unravel biological processes including signal transduction and have the potential to act as microrobots for therapeutics, agrochemical delivery, diagnostics and regenerative medicine. Although significant progress has been made in developing synthetic cells with individual behaviours such as motility, biosynthesis and communication, a crucial lack of high-throughput production and screening technologies hinders the design of next generation systems.

Here, we propose to unlock this potential by developing robotic synthetic cell production methods and coupling these with machine learning-powered feedback. Such methods will be used to design and develop a suite of new synthetic cells that are capable of sensing, computation and biosynthesis using a variety of molecular parts from membrane proteins to DNA circuitry. Integration of machine learning methods will facilitate rapid data analysis and inform future experimental design, unlocking new high-throughput production workflows. Such processes will be critical in translating fundamental synthetic cell technologies to tackle societal challenges in medicine and industry, acting as new delivery systems, microreactors and diagnostics.

Student

Athos Vacanas

Title

A systems biology approach to understand the role of skin microbiome in healing of micro-wounds on the face and neck

This project is funded by the Institute of Chemical Biology EPSRC Centre for Doctoral Training and Procter & Gamble

Supervisors

• Dr Claire Higgins (Department of Bioengineering, Imperial)
• Professor Reiko Tanaka (Department of Bioengineering, Imperial)
• Dr Ben Almquist (Department of Bioengineering, Imperial)
• Dr Leigh Knight (Procter & Gamble)
• Dr Kous Shah (Procter & Gamble)

Abstract

The human skin microbiome plays a critical role in maintaining skin health. For example, skin microbiota speeds up skin regeneration and repair of acute wounds. Skin healing after micro-wounding varies between body sites – specifically two notable locations where healing rates vary are the skin on the face and the skin on the neck. While healing is faster on the neck, shaving this location also results in more ingrown hairs than the face. Ingrown hairs are problematic because they elicit inflammation and cause bumps, which razor blades can cut upon the next shave, creating an ongoing cycle of skin damage and irritation. 

This MRes + PhD project aims to understand the skin microbiome's roles in healing micro-wounds on the face and neck and propose solutions that leverage the skin microbiome to enhance skin healing to address shave-induced nicks and cuts. We will take an interdisciplinary approach first developing computational models that describe an intricate dynamic interplay between skin microbes and cells, then subsequently we will experimentally evaluate model predictions in vitro. 

Specifically, we will first develop a computational model of stable communities of dominant microbes from healthy skin that describes the dynamic interactions between skin microbes and cells, considering the effects of environmental factors (pH, humidity, immune response and nutrients). These computational models will be based on metabolomics and microbiome profiling data that will be collected by the student, from hair follicles on the face and neck at the start of the PhD. We will use the mathematical model to decide how the skin microbiome and environmental factors impact micro-wounds healing processes by evaluating the intrinsic healing properties of epithelial cells isolated from hair follicles on the face and neck. This research will allow us to devise therapeutic strategies to mitigate or augment both micro-wounds healing and trapped hairs after shaving.

Student

Daisy Williams

Title

Chemical proteomic discovery of covalent ligands for novel drug targets in Myc-deregulated cancers

This project is co-funded by the EPSRC Centre for Doctoral Training in Chemical Biology and Merck KGaA

Supervisors

• Professor Ed Tate (Department of Chemistry, Imperial)
• Dr Pedro Ballester (Department of Bioengineering, Imperial)
• Dr James Bull (Department of Chemistry, Imperial)
• Dr Oliver Schadt (Merck KGaA)
• Dr Ingo Kober (Merck KGaA)

Abstract

Myc oncogenes (such as c-MYC) are deregulated in >70% of all cancers, where they promote transcriptional activation of genes involved in protein synthesis and cancer metabolism. c-MYC is among the most important oncogenes (drivers of cancer) and one of the most sought-after cancer drug targets. However, c-MYC exemplifies the features of an “intractable” drug target, being largely disordered and lacking clearly identifiable ligand binding sites, and despite decades of research it has yet to yield to small molecule drug discovery.

In this project, we will develop a new approach to targeting Myc-deregulated cancers by discovering changes in the reactivity and covalent ligandability of cysteine residues caused by c-MYC actively driving tumorigenesis. Using chemical proteomics, which exploits chemical probes for cysteine ligandability coupled to enrichment and high-throughput mass spectrometry proteomics, we can discover and quantify c-MYC-dependent changes across the entire proteome, including but not limited to c-MYC itself. These alterations represent potential novel drug targets for Myc-deregulated cancers and may be driven by differences in post-translational modification (e.g. modifications at cysteine such as oxidation or acylation), protein interactions (e.g. shielding or exposure of cysteines due to gain or loss of a binding partner or protein-DNA interaction), or changes in protein expression. In parallel we will also examine the scope for degradation and stabilisation of targets through covalent modification, encompassing the rapidly emerging field of covalent molecular glues.

You will develop chemical proteomic technologies at the cutting edge of chemical biology, using synthetic chemical probes bearing a cysteine-reactive group (or “warhead”) and recent advances in high-throughput proteomics, to enable both identification of altered cysteine reactivity and high-throughput proteomic screening against a carefully designed library of diverse covalent ligands. You will apply this platform to cancer cells as they transition from low to high c-MYC states, to identify critical novel vulnerabilities in the Myc-deregulated cancer proteome; these rich datasets will provide the basis for understanding the biology of Myc-deregulated cancers, and potential starting points for covalent drug discovery.

Student

Pietra Cerqueira Diaz

Title

Modelling hair lubrication in the presence of additives

This project is co-sponsored by the Institute of Chemical Biology EPSRC Centre for Doctoral Training and Procter & Gamble

Supervisors

• Professor Daniele Dini
• Dr James Ewen
• Dr Stefano Angioletti-Uberti
• Professor Nick Brooks

Abstract

This project will study the molecular-level interactions and fundamental mechanisms responsible for wet friction in hair-to-hair contacts in the presence of new additives used in silicone-free conditioners and sulfate-free shampoos. Particular emphasis will be placed upon natural products with lower environmental impact. Molecular Dynamics (MD) and Non-Equilibrium Molecular Dynamics (NEMD) simulations will be used to study changes on the hair surface chemistry in presence of surfactants, polymers, and natural products and their impact on hair-hair lubrication. We will also explore the use of continuum-based models and hybrid molecular-continuum simulations to capture the impact of the surface changes induced by the improved formulations on macroscale friction.

Student

Saskia Pieters

Title

Research Assistant in Chemical Glycobiology - "Unraveling how viral glycosylation machineries affect host glycoproteins"

Supervisor

• Dr Benjamin Schumann (Department of Chemistry, Imperial; Francis Crick Institute)

Summary

A pre-doctoral scientist with a background in biochemistry, chemical biology, chemistry or related areas will help us on our mission to develop and use novel “precision tools” to understand the roles of glycans in biological processes (Curr Opin Struct Biol, 2021). In a multidisciplinary collaboration, we have pioneered the tactic of glycosyltransferase “bump-and-hole engineering”, generating reporter tools for the activity of individual glycosyltransferases in the living cell (Nat. Commun. 2022, ACS Chem Biol, 2021, PNAS, 2020, Mol Cell, 2020).

In our work, we are routinely applying Nobel Prize-winning bioorthogonal chemistry. We have developed tools that enhance our ability to probe and understand glycans in relevant biological settings (ACS Cent. Sci, 2023, JASMS, 2021). For this work, we have been awarded a number of awards including the 2021 RSC Horizon Prize in Chemical Biology.

We are currently implementing new bioorthogonally tagged monosaccharide analogues into our toolbox, applying these compounds in highly exciting collaborative projects in vitro and in vivo, and employing metabolic engineering to guide their incorporation into defined subsets of the glycoproteome. Within these multidisciplinary efforts, our lab has developed a keen interest for the glycobiology of viruses, as part of the Marie Sklodowska Curie Network “GLYCOprotein N-glycosylation from non-life to eukaryotes” (GLYCO-N; https://glyco-n.eu/).