Auer lab

University of Edinburgh



Professor Manfred Auer - Group leader

In his lab Manfred Auer links basic research and applied science by developing and running new miniaturized target, compound and technology platforms comprising all steps from design, theoretical and experimental target analysis, high throughput chemical synthesis and screening, to quantitative mechanistic studies of compound action in cells and model organisms. These integrated projects result in small molecular and peptidomimetic tool compounds and chemical probes used to validate proteins as drug targets and in hit and lead compounds progressed into drug discovery in industrial collaborations.
Manfred is responsible for the Biochemical Techniques course in Biochemistry Honours for which also acts as a member of the Exam Board. He also teaches in the following courses: Structure and Function of Proteins (Year 3), Biotechnology Honours (Year 4), Next Generation Drug Discovery” Distance Learning PG Programme, MSc Protein Structure Determination, MSc Commercial Aspects of Drug Discovery. At the University of Salzburg, Austria, he teaches a 15 lectures comprising course in “Current Trends in Drug Discovery, Assays and Screening” as Adjunct Professor.

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Dr Nhan T Pham - Postdoctorial researcher and Lab manager

Nahn is responsible for management of equipment and laboratories as well as all screening platforms utilised in the Auer lab. Biophysical characterisation of protein targets. Screening small molecule compounds/libraries against proteins. Performing fluorescence imaging, phenotypic screening, single molecule and ensemble averaging spectroscopic measurements.

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Dr Steven Shave - Postdoctorial researcher

Steven comes from a computational background and entered the field of drug discovery during his Ph.D specialising in virtual screening techniques and HPC/parallel computing. His work involves the development of new software and algorithms for virtual screening and their application to validated drug targets. The interdisciplinary crossover between computing, biology and chemistry requires close alignment with chemists and biologists within the Auer group. Since joining the Auer group, focus has shifted to the support of combinatorial chemistry and screening efforts with both structure and ligand-based virtual screening techniques along with the development of a systematic approach to the disruption of protein-protein interfaces using peptidomimetics.

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Dr David Evans - Postdoctorial researcher

In 2004, David obtained an MEng in Electronic and Photonic Engineering with a final specialization in biophotonics and in 2009 a PhD at the Life Science / Physical Science Interface, at the School of Physics and Astronomy at the University of Leeds. His primary research during the PhD was the development of electronic-bio-hybrid devices. The research involved fabrication, patterning and electronic detection of biological molecules on nanostructured surfaces with minimum crosstalk and without loss of biological function. Following this period, he moved to Karlsruhe Institute for Technology, where he worked on single molecule FRET including the design and fabrication of microfluidic devices for single molecule FRET measurements, fabrication of zero mode waveguides and the development of photothermal imaging and correlative AFM and fluorescence techniques which add an extra dimension to the analysis of biomaterial surfaces. In October 2011 he moved to a position in SESMOS Ltd, a startup company based at the University of Edinburgh. His primary role was the development of a biosensor system based on a thin film bulk acoustic resonator (FBAR), including the development of improved hardware, a complete control software package and surface functionalization processes. In 2013, he moved to a position in the Auer lab, where his primary role has been the design and development of a custom built single molecule TCSPC microscope and single molecule fluorescence assays. He has also been heavily involved in software development for many other projects.

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Dr Joanna Koszela - Postdoctorial researcher

Joanna started her adventure with ubiquitination - a regulatory modification of proteins which controls virtually all cellular processes - during a Masters project on p53 neddylation with Dimitris Xirodimas at the Wellcome Trust Centre for Gene Expression and Regulation in Dundee, UK. She obtained her Masters diploma in Biosciences at the Ecole Normale Supérieure de Lyon in France. She then joined a 4-year Wellcome Trust PhD Programme in Cell Biology at the University of Edinburgh, UK in Mike Tyers’ and Manfred Auer’s groups, where she had been developing new methods for identification of ubiquitination modulators. Currently a postdoc in Manfred Auer’s lab, she is a co-inventor of a novel in-vitro assay technology, UPS-CONA, and a co-author of a patent application. With a strong background in cell and molecular biology and increasing interest in systems biology approaches, Joanna’s future research plans include unravelling the molecular details of polyubiquitin chain formation and exploring specificity in the ubiquitination system with an ultimate goal to identify key players contributing to development of cancer, neurodegeneration and other diseases.

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Dr Stefan Mann - Postdoctorial researcher

Stefan started as a biochemist at the Biozentrum in Basel, Switzerland and obtained his MSc in biotechnology at the École Supérieure de Biotechnologie de Strasbourg in France. He continued with a 4-year Marie Curie funded Phd in molecular microbiology with the research group of Professor Tracy Palmer at the John Innes Centre in Norwich. The subject of his PhD studies was the role the TAT (Twin Arginine) secretion system plays in the virulence of phytopathogenic Streptomycetes bacteria. This was followed by a postdoctoral position in epigenetics researching the influence of non-digestible carbohydrates on promoter methylation levels of colorectal cancer marker genes. He then joined the Wellcome Trust Centre for Cell Biology in Edinburgh as a liaison between cell biology and drug discovery. He currently is working as a postdoctoral researcher in Professor Auer’s group where his role primary role encompasses all aspects of molecular biology as well as the development and application of phage display based methods for drug discovery.

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Nicholas Fethers - PhD student

Nick studied his Bachelor’s degree at the Keele University in Medicinal Chemistry and Biochemitry before finishing a Master’s degree in Pharmaceutical Science and Medicinal Chemistry at Loughborough University. He currently studies WD40 domains and their interactions at the University of Edinburgh in the Auer lab. His work includes the collection and curation of data on human WD40 domain containing proteins, the expression and purification of WD40 domains, screening of small molecules against target proteins using label free affinity techniques, the synthesis of chemical tools, and the synthesis and screening of fluorescently labelled peptides against protein targets.

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Irene Pérez Pi - PhD student

Irene was born in Pamplona, in the north of Spain. She did her undergraduate in chemistry at University of Navarra. After completing her master’s degree in IQS in Barcelona focusing on the dehydrogenation of pyrido-pyrimidines, she worked as an analytic chemist for the research and development in the application of additives for artificial sausage casings. Subsequently she went with an international internship to London to work on the synthesis and biophysical characterization of peptides. Currently Irene is finishing her PhD in the Auer group in University of Edinburgh, focusing on her interest in alpha-synuclein, a protein whose aggregation is involved in Parkinson’s disease, and the development of novel chemical tools, fluorescent assays and inhibitors of the process.

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Ian Spink - PhD student

Ian completed his undergraduate Master’s degree at the University of Edinburgh in Medicinal and Biological Chemistry. He completed his Masters project under the supervision of Prof. Paul Barlow, studying methods of protein production, purification, bio-conjugation and protein NMR. Ian is currently studying for his PhD focussing on the proteins involved in the ubiquitin proteasome system, particularly the autoimmune disease associated protein UbE2L3. The main focus is on fragment based screening techniques using 19F NMR methods to identify small molecule and peptidomimetic inhibitors of this pathologically relevant disease pathway.

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Antonia Peter - Project student

Antonia was born in Krems in Austria and moved to Vienna after secondary school for a Bachelor’s degree in Microbiology and Genetics, which she finished in July 2015. She did the research work for her thesis at the Veterinary University of Vienna, analysing gene expression of the cereulide synthetase of different Bacillus cereus strains. In the course of her Master’s degree in Molecular Medicine she completed several internships at the Medical University of Vienna, the General Hospital of Vienna, and the Austrian Institute of Technology. Antonia has joined our group in January for her Master’s project and will stay in Edinburgh until the end of July. Until then she will work on finding a binder for the Ska1 microtubule-binding domain and evaluating this protein as a novel target in cancer therapy.

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Emily Robson - Project student

Emily is a fourth year undergraduate student at the University of Edinburgh, studying for a BSc (Hons) in Biochemistry. She is currently working on her Honours project with Stefan Mann in the Auer Lab using Phage-CONA technology as a tool for drug discovery. In 2016 she completed an eight-week summer internship at Edinburgh Napier University through the Equate Scotland organisation, which aims to encourage women to pursue careers in STEM fields. As part of her internship she worked with Salmonella to investigate a potentially antimicrobial protease that could be used to fight Salmonella infections. After graduation, she plans on pursuing a PhD in a field related to human health, such as cancer, neurodegenerative diseases, or antimicrobial drug development, with the aim to follow a career in medical research.

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Cecilia Ayala - Project student

Cecilia Ayala is an MSc Biotechnology student at the University of Edinburgh. She holds a Bachelor in Biological Pharmaceutical Chemistry by the National Autonomous University of Mexico. The research work for her thesis was on the N-glycosylation on a renal ion channel. Moreover, she has participated in several internships in the areas of molecular biology, cell biology, genomics applied to the study of different diseases. Currently, she is doing her dissertation project in the Auer group using Phage-CONA technology to identify peptides binding to ovotransferrines which have the potential to treat infectious diseases. After completing her master’s degree Cecilia plants to study a PhD in medical research.

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Chia-Yin Ho – Project student

Chia-Yin was born in Taiwan. She did her undergraduate in Life Science at National Cheng Kung University. And then she completed her master’s degree in Molecular Medicine at the same university, focusing on a project of the interaction of influenza viral proteins with host cells by analyzing its protein-protein interaction and viral function. After finishing her project, Chia-Yin did her work as a research assistant in China Medical University on a thesis of the function of ubiquitination on influenza viral proteins. Currently, Chia-Yin did her second master’s degree in Drug Discovery at the University of Edinburgh, and she will work on the project of comparison of wild-type and GFP-fused E2 proteins by purifying proteins and using several in vitro ubiquitination assays.

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Yan-Kai Chen – Project student

Yan-Kai obtained his Master’s degree at National Yung-Ming University in Taiwan. He completed research work for his Master’s thesis, focusing on the mechanism of Amyloid Beta peptide aggregation by molecular dynamics simulation. After finishing his studies in Taiwan, he worked as a R&D assistant at Taiwan Centers for Disease Control (TCDC), analysing statistical data of communicable diseases and establishing disease prevention policies. Subsequently, he was employed as an engineer by a microarray manufacturer responsible for probe design and data analysis. He is currently studying for a Master’s degree in Bioinformatics at the University of Edinburgh and performing a cheminfomatic project predicting physiochemical properties using machine learning techniques.

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Adam Gaffney – Project student

Adam Gaffney completed his undergraduate Bachelor’s degree in Biomedical science with a focus on pharmacology from the National University of Ireland, Galway. For his undergraduate thesis, he examined aberrant inflammasome activation within monocytes of chronic kidney disease patients. He is currently completing a Masters degree in Drug Discovery and Translational Biology here, at the University of Edinburgh. For his Masters Thesis, he is attempting to develop and optimise a novel on-bead assay utilising the CONA technology available in the Auer lab for the assessment of ubiquitin free chain formation.

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