Cristina Croitoru
I completed my undergraduate studies at University of Bucharest in my home country, Romania, from where I obtained my bachelor’s degree in Chemistry. My project “Synthesis of novel alkylamino-pyrazole derivatives as antitumoral compounds” represented the reason beyond my desire of understanding better how medicines work in the human body, thus, afterwards I decided to continue with my postgraduate studies abroad. I obtained my master’s degree in Pharmacology and Drug Discovery from Coventry University, England. My project “Membrane proteins for drug discovery. Β-1 adrenergic receptor as a drug target” was about to represent the beginning of my journey in the study of membrane proteins.
In October 2020, I joined the MemTrain team and my PhD project focuses on De novo design of membrane protein channels, aiming to contribute to a better understanding of the rules that govern how proteins fold and the relationship between sequence, structure and function, which is still an enigma despite advances in the latest years in the field of structural biology.
Project: “De novo design of membrane protein channels using a multidisciplinary approach”
One aspect of Synthetic Biology is the de novo design of protein sequences that result in novel biological building blocks with innovative functions. A significant bottleneck in the development of de novo design is an understanding of the rules that govern how proteins fold. Traditionally, biophysical methods such as FRET, CD and NMR are used to understand the folding of membrane proteins. However, computational methods are becoming key, not only in the analysis of data but also generating meaningful predictions of the structure of proteins intractable by other methods. Multidisciplinary approaches that combine computational prediction, as well as lab-based experiments, provide a deep insight into the structure of membrane proteins which can, in turn, be used to design novel sequences.
This is a challenging project and will address both the de novo design of novel sequences as well as the re-design of naturally occurring scaffolds to form membrane protein channels. This multidisciplinary project will combine laboratory-based experiments (Molecular Biology, Protein Expression, Biophysics) with Computational Biology (Molecular Modelling and Membrane Protein Simulations) to generate a series of sequences which autonomously fold to act as ion channels. Furthermore, the experimental data discovered during the project will be used to further develop a novel, cutting edge computational structure prediction method with our industrial partner Syndial.
Overall, this is a challenging, multidisciplinary project that will explore the exciting area of de novo protein design.
Yanis Pantoja
I completed my BSc in Biomedical Science at Aston University, where I graduated with honours. I then completed my MSc in Biomedical Science at the University of Wolverhampton. Shortly after graduating I had the opportunity to work at the University of Miami. I worked for the Pulmonary Division where I was fortunate to form part of a project that looked at how sGC stimulators (Riociguat) modulated BK channel activity in human airway epithelial cells. I also had the great opportunity to work for ‘The Miami Project To Cure Paralysis’ at the University of Miami; the aim was to develop novel therapeutic interventions for traumatic brain injury. Now, I am on my way to complete my PhD degree and I am excited to be part of the MemTrain programme at Aston University.
Project: Understanding age and diabetes related changes in erythrocyte membrane
Diabetes is a metabolic disorder linked to cardiovascular disease risk and inflammation and is a huge threat to human health. Several studies have demonstrated that high glucose levels induce morphological and structural alterations in red blood cells. Aging and diabetes also alter the fluidity of erythrocytes and can lead to the modification of proteins by the formation of advanced glycation end products (AGEs) and advanced lipoxidation end products (ALEs). Aging also increases lipid and protein oxidation.
In this project the correlation between membrane fluidity, lipid composition and the formation of AGEs and ALEs on erythrocytes will be investigated. The aim is to understand how diabetes and aging lead to cellular dysfunction.
Afroditi Vaitsopoulou
I studied Biochemistry and Biotechnology in Greece where I also worked in the laboratory of bio-organic chemistry of my university. Then, I did an Erasmus + internship at Cancer Research Center of Marseille, in France. Moreover, I did my master in Marseille, on bioinformatics and structural biochemistry, where I did my internship in the laboratory of viral replicases. Always interested in different domains and multidisciplinary fields, I am happy to be in this team and to have the flexibility to move between the various fields. My project during this program is to find the best approach for stabilizing and characterizing structurally and functionally wild type membrane proteins. I am currently working on MRP4, a protein that is resistant to drugs including cancer chemotherapy, antivirals and antibiotics.
Project: Approaches for stabilising wild type membrane proteins for structural and functional characterisation
Membrane proteins are important drug discovery targets for a wide range of diseases. However elucidating the structure and function of native membrane proteins is notoriously challenging. Detergents have been used to solubilize membrane proteins from the lipid bilayer with varying degrees of success concerning protein stability. To try to improve stability many studies use mutagenesis approaches to further stabilise the protein, but this can often affect the structure and function of the protein. CALIXAR is a French SME which specialises in purification technologies for membrane proteins. They have developed a series of stabilising detergents and additives which have been shown to stabilise extracted membrane proteins, maintaining the native conformation in solution.
This collaborative project will include cryo-electron microscopy structural characterization of human transporter protein MRP4 (multidrug resistance protein 4/ABCC4), solubilised and purified using calixarene-based detergents and /or styrene maleic acid (SMA) polymers. In addition novel reconstitution approaches will be investigated to monitor MRP4 function. Finally the project will involve testing of novel polymers and additives developed by Calixar/Aston to evaluate their potential in terms of solubilisation efficiency, stabilization, function and compatibility with downstream techniques.
Carolina Almeida
Portuguese born and raised. I've been interested in molecular biology since a professor in Braga first remarked how exciting it would be to cross the plasma membrane and dive into a cell. I got my Masters in Applied Biochemistry at the University of Minho where I worked on a project that aimed to functionally express Prokaryotic membrane proteins in an Eukaryotic organism, further leading to an international pre-patent. After that I was involved in two other projects, one that explored the ability of two Pseudozyme spp species to synthetise Mannosylerythritol Lipids (MEL) with potential to replace traditional Jet-fuel. The last project aimed to assess the aerobic granular sludge bioreactors’ performance regarding textile wastewater toxicity removal. And now here I am, “diving” again!
Project: Strain optimisation for production of high value chemicals.
The global economy has an unsustainable dependence on fossil raw material and concerns about environmental sustainability are becoming more acute. Biotechnological processes using microorganisms as cell factories to produce valuable compounds from renewable biomass are an attractive alternative, and an increasing number of platform and high-value chemicals are being produced at industrial scale using this strategy. However, many microbial processes are not implemented at industrial level because the product yield is poorer and more expensive than achieved by chemical synthesis. It is well-established that microbes show stress responses during bioprocessing and one reason for poor product output from cell factories is production conditions that are ultimately toxic to the cells, often at the level of the cell membrane. Examples of stresses that are demonstrably membrane-centric are solvents, e.g. butanol production by Clostridia and ethanol production by yeast, and weak acids such a lactic acid produced by bacteria. This project will seek to alter the cell membrane of industrial microbes to increase tolerance to stresses during bioproces.
Biocleave have patented technology (CLEAVE™) for genome editing of Clostridial species. Clostridia have significant potential within bioproduction of both native compounds e.g. butanol, and to be engineered to make additional molecules. However, Clostridia have traditionally been difficult to manipulate on a genetic level. The introduction of CLEAVE technology, based on endogenous CRISPR, has the potential to be a game changer and provides an opportunity to greatly increase the utility of Clostridia in this field. This project will use a powerful combination of in vitro assays, microbial cell culture, and ‘omics technologies to identify the molecular targets suitable for overcoming stresses in bioprocessing e.g. lipids and transporters. Following this, CLEAVE will be used to create new strains, followed by strain characterisation to determine if the desired membrane alterations have been achieved and if tolerance to a particular stress (or stresses) has been increased. Iterative design-build cycles will be undertaken as appropriate to further improve the strains.
Ophelie Langlois
I completed a BSc in Biochemistry in Lyon, France and a MSc in Conception of Therapeutic and Diagnostic Tools in Bordeaux, France. As my studies made my interest focus on molecular mechanisms of life, and more particularly on protein functions, I undertook two internships during my Master’s degree that were focusing on proteins. The first one was at the University of Lyon 1 and ENS Lyon where I was studying the multi-scale dynamics of human transthyretin using network tools. During my second year, my project at INSERM in Bordeaux was focusing on the study of a new Fms-Like Tyrosine Kinase III receptor variant, which is involved in acute myeloblastic leukemia. I am glad to have a new challenge now that I am part of the MemTrain programme; my PhD project aims to understand the role of protein lipoxidation in cell membrane signalling.
Project: The role of protein lipoxidation in cell membrane signalling
During inflammation and metabolic imbalance, reactive oxygen species are formed, which leads to oxidative stress. This results in oxidative damage to phospholipids in cell membranes, producing a variety of short- and long-chain lipid oxidation products. The formation of reaction products between oxidized lipids and proteins (lipoxidation) can change the structure and activity of the protein, and the formation of these lipoxidation products has been demonstrated for a variety of metabolic, structural and signalling proteins. Although the result is often inhibition, in some cases detrimental gain of function is observed, and this is thought to relate to changes in cellular localization of the protein including targeting to membrane compartments.
This project will investigate the effect of lipoxidation of the membrane-associated signalling proteins HRas, a small G-protein, and the phosphatase phosphatase and tensin homolog (PTEN), both of which are central to key signalling pathways. Proteins will be treated with reactive lipid oxidation products in vitro and the protein isoforms will be characterized by novel chromatography approaches and ion mobility mass spectrometry. Cultured cell lines expressing wild type and mutant proteins will be treated with reactive lipid oxidation products and the effects on protein subcellular localization and activity will be monitored by fluorescence microscopy and western blotting respectively.
Lucas Unger
After completing the BEng in Biotechnology, I specialized in Pharma-Biotechnology in the following Master studies (Jena/Germany). For the master thesis I went abroad to Umeå/Sweden to work in the field of antifungal immunology studying the interaction between neutrophils and Candida albicans. Then I got the great offer to stay and work in collaboration with a biotech spin-off on a drug development project in the cross section between academia and industry. Finally, I wanted to move on and joined the MemTrain team in the UK for my PhD studies.
Project: Identification of new inhibitors of aquaporin water channel function.
With advisory input from our national and international partners, I am working on the development of new drugs that target the function of aquaporin water channels (AQP). AQPs control the flow of water in all forms of life; in humans their dysfunction is associated with diverse diseases. In order to meet the urgent need for medical treatment, I am aiming to set up a screening platform to identify potent pharmacological agents. Also, the project includes the expression of AQPs in mammalian cells and their biochemical and biophysical assessment. Furthermore computational modelling and simulation will be used to understand protein-protein-interactions and molecular docking. New aquaporin inhibitors will be benchmarked against existing molecules in novel functional assays.
Annaig Rozo
During my Bachelor degree I spent my final year as an Erasmus student at Aston University. I was awarded a Master's degree in Cancer Biology from the University of Lyon in 2019 during which I undertook two research internships. The first one was at the University of Tokyo where I was working on the role of inflammatory monocytes in the extravasation of breast cancer cell. The second internship was at the Aston University where I focused on the characterization of extracellular vesicles and their role in recruiting macrophages during inflammation.
Project: Characterisation of extracellular vesicles using microfluidic approaches
Extracellular vesicles (EV) are released from cells and act as a conduit for transfer of signals between them. However, relatively little is known about how EV act or the key modulators that underpin their function. Due to their small nature, traditional purification methods generally involve high-force regimes e.g. ultracentrifugation. Coupled to this, populations of EV are highly heterogeneous both in terms of size and composition. A key area for understanding is the varying functional effects of these different EV and the molecular basis underpinning their activity.
This project will utilise bespoke proprietary microfluidic chip technology to separate EV from cells and to sub-fractionate them by size under low-force regimes. These chips have been developed by the industrial partner, uFraction8, and have been demonstrated to be capable of separating biological particles on the nanoscale. Once separated, EV population will be subjected to rigorous biochemical (e.g. lipid and protein composition), biophysical (e.g. size, surface charge, membrane fluidity) and functional assays (e.g. control of inflammation). Taken together, these analyses will reveal the underlying properties of different EV populations that are responsible for their activities. This will pave the way to a better understanding of both normal and disease-state EV activity as well as the development of novel EV-based therapeutics.
Athanasios Kesidis
My studies began in Greece where I completed an undergraduate degree in Molecular Biology and Biotechnology Sciences at the University of Crete. During my research traineeships in Greece and England, I appreciated the significance of membrane proteins and their role in an incredible array of functions in the human body. For my undergraduate thesis, I investigated the role of cysteine 184 in the structure, function and the expression of the type 2 receptor (CRF2) of corticotropin-releasing factor. My future career goal is to become a world-leading expert in the pharmacology of membrane proteins and specifically G protein-coupled receptors. Furthermore, I want to be part of cutting-edge projects which will provide the world with all the information that is needed to find cures and treatments for major diseases which plague our society.
Project: Optimisation of membrane protein expression and purification
Peak Proteins Ltd. is involved in the production and supply of bespoke high-quality protein reagents to clients and the delivery of macromolecular structure solutions of client targets, largely to aid pharmaceutical and drug discovery research.
The student will be helping to expand Peak Proteins capabilities to handle membrane protein targets. They will be involved in the development of a rapid, simple and generic approach to membrane protein stability assessment using fluorescent protein tags. The project will include the expression of a number of therapeutically relevant membrane protein targets from different classes, with the initial focus on a serotonin receptor (GPCR) and an iron-sulphur cluster transporter (ABC transporter). Appropriate expression systems will be used, including E. coli, insect cell and HEK systems. New approaches will be benchmarked against traditional methods for assessing membrane protein quality, such as radioligand binding assays, protein activity assays and transport assays.
The student will gain a broad overview of protein production pipelines, from gene construct design, through expression, to protein purification methods. Furthermore, the student will gain specific skills such as tissue culture, membrane protein solubilisation, and biophysical assays for membrane protein assessment. Finally, the student will gain a unique perspective on a career in commercial research from a contract research organisation perspective, including risk management and business development skills.
Alexis Lode
I completed a BSc in Biology in Rennes, France, during which I was able to follow my final year in Erasmus exchange in Aston University in Birmingham. Then, I continued with a MSc in Conception of Therapeutic and Diagnostic Tools in Bordeaux, France. I am very interested in drug development against multiple targets, and I particularly liked my time in Birmingham, which is why I decided to join the AMPL team from October 2019 to do a PhD based on the use of membrane proteins as antifungal drug targets. This project aims to use innovative purification techniques (SMALPs) in order to purify membrane proteins that will have a certain affinity for potential antifungal drugs.
Project: Membrane proteins as antifungal drug targets
An estimated 1.5 million people die from invasive fungal infections each year. With limited treatment options and increasing resistance to available therapies, there is an urgent need for new antifungal drugs acting via novel mechanisms of action. To address this issue, this project will investigate membrane proteins as antifungal drug targets. F2G Ltd have antifungal programmes at different stages that target membrane proteins. The phase 2 antifungal compound olorofim acts by inhibiting the mitochondrial membrane protein dihydroorotate dehydrogenase. Additionally, a multi-spanning membrane protein has been identified as the target of a preclinical series of antifungals. Further potential membrane protein targets will also be assessed in this project. Traditionally, membrane proteins have been difficult to work with so that preparation of recombinant versions of potential drug targets for inhibitor screening has not always been possible. However, the use of innovative purification techniques including SMA lipid particles (SMALPs) has enabled difficult membrane proteins to be purified in their native form allowing their activity to be studied.
This project will apply cutting edge membrane protein technology to the exploration of antifungal drug targets, with the aim of supporting existing drug programmes and identifying potential novel targets.
Peer Depping
Peer studied chemistry at the university of Bonn in Germany where he received his bachelor’s degree in 2016 and his master’s degree in 2018. During his studies he worked on the crystallization of the trityl labelled cytochrome P450cam and the functional and structural analysis of the tripartite ATP-independent periplasmic (TRAP) transporter SiaPQM using nanodiscs and liposomes as membrane mimetic systems. His topic in the MemTrain programme is the development of antibody-based drugs targeting ion channels.
Project: Development of antibody-based drugs targeting ion channels
Ion channels represent the second largest family of human cell surface proteins and are implicated in a number of diseases including cancer, autoimmunity and chronic pain. To date, most of ion channel drug discovery focused on developing small molecules and peptides as therapeutics. These drug modalities often suffer from poor selectivity for the target ion channel leading to severe side effects and poor efficacy in patients. An attractive alternative is the use of antibody-based therapeutics which can demonstrate superior affinity, selectivity and in vivo half-life. However, the efforts to generate monoclonal antibodies against ion channels are hampered by the difficulties in expression and purification of ion channels in a format suitable for antibody isolation and screening.
Iontas is an innovative antibody-drug discovery company developing a novel platform technology (KnotBodyTM) targeting ion channels using antibody-like molecules. As part of the development of this technology, purified ion channels are extremely desirable. As such, this project will focus on expression, purification and functional analysis of ion channels, using cutting-edge polymer-based technology developed at Aston University. Following this, there will be the opportunity to undertake a substantial placement at Iontas to generate and validate antibodies against the ion channel(s) of interest using phage and/or mammalian display technology. Ultimately, this will aid the development of novel therapeutics.