Drug Discovery Research

We work with the wider cancer community to identify and validate targets in cells that drive cancers. We work with clinical colleagues and both fundamental and translational biologists.

Identifying and validating therapeutically-relevant drug targets is particularly challenging in oncology. There are over 200 types of cancer that originate from different tissues. Furthermore, there is significant variation in the abnormalities that promote their unrestrained growth and malignant behaviour.

We use a wide variety of methods to identify and validate prospective targets in human cells. This allows us to determine whether they are likely to be suitable for drug discovery. Our methods include:

• Quantifying RNA, DNA and protein
• Sorting cells based on markers
• Analysing biological endpoints such as tumour cell proliferation and survival
• Visualising endpoints in cells using advanced microscopy

We only use authenticated tumour cell lines. We examine them under well-defined culture conditions. Target expression of function is manipulated using techniques such as gene silencing or by treatment with tool compounds. The consequences of target modulation are then assessed by examining cellular signalling and biological endpoints in multiple tumour cell lines.

It is through these studies that we aim to provide insights into whether a given target is critical for some cancers. We also aim to determine which patients might be likely to benefit most were a new treatment to be developed against it.

We develop new ways to find hit molecules that interact with a target. We then develop these iteratively through synthetic strategies.

Our group of experienced medicinal chemists use state-of-the-art methods for:

• Identifying early hit molecules that bind to a target. There is an emphasis on using fragment-based lead generation
• Undertaking structure-guided development of hit molecules to develop chemical lead series
• Further optimising leads to ensure the compounds produced have the desired features to make them suitable for use as drugs

We enjoy generous lab space. Our labs are fully equipped to perform synthetic chemistry on a small to multi-gram scale.

We have 40 fume hoods dedicated to Medicinal Chemistry across three adjoining laboratories. These areas are fully modernised and well equipped for undertaking contemporary chemistry. We also have a dedicated toxic/special operations lab. It houses a glovebox for manipulating reagents where an inert atmosphere is required.

We develop innovative chemical synthesis and optimise reactions. To do this we use three Biotage® microwave synthesisers. We also use a ThalesNano H-cube® to perform catalytic hydrogenations. Reactions can be promptly monitored using a Waters Acquity LC-MS. High boiling point solvents can be readily removed from compounds. We do this using either a Biotage® V-10 or Genevac evaporation system. We can use a freeze dryer to further remove water from samples. Purification of compounds are routinely carried out on one of four automated flash chromatography systems. Those compounds requiring a higher purity can undergo purification using one of our two Agilent preparative HPLC systems.

We also have privileged use of the Roger Griffin Molecular Graphics Suite. This supports computer-aided drug design activities.

We synthesise target proteins. We then use them in a wide range of biochemical and biophysical assays or X-ray crystallography.

We assess, qualify and quantify the interactions of targets with binding partners and inhibitors. Some technologies have also been optimised to permit screening of novel compounds. This assists in our search for new, active molecules against our targets.

We produce target proteins recombinantly in either bacterial or insect cell expression systems.

For new targets, we typically screen multiple expression constructs, bacterial strains, and culture media. We do this on a small-scale prior to scale-up. This is to optimise protein production for use in assays and crystallography.

We utilise a variety of expression tags including GST and poly-histidine. We have also incorporated several assay-relevant tags such as FLAG and SBP within our customised vector sets.

Automated protein purification is conducted at both room temperature and under refrigerated conditions. This allows a range of conditions to be examined rapidly. Reagents are quality-controlled using mass spectrometry.

We use a wide variety of assay methods and platforms to screen, confirm and characterise ligand binders. Often they have been optimised toward high-throughput usage.

Our equipment includes:

• Labcyte Echo Acoustic Handler and dispensing instrument: This rapidly and accurately dispenses compounds. Using sound waves, the Echo can transfer volumes as low as 2.5 nL into plates for assay and crystal soaking
• Biacore S200: Surface plasmon resonance (SPR) screening and characterisation
• MicroCal PEAQ-ITC: Thermodynamic assessment of binding

We also have a Pherastar FS and QuantStudio 7. This allows us to use fluorimetric assays including:

• Differential scanning fluorimetry
• Fluorescence polarisation
• Homogenous time-resolved fluorescence for binding and stability studies

Our approach is anchored by structure-based drug design. This is driven primarily by X-ray crystallography. From identification to characterisation, we have a suite of techniques for exploring our targets.

We recently invested in an in-house state-of-the-art X-ray source and detector. This made us the UK’s first academic institution to host a Bruker Liquid METALJET D2. The METALJET uses a high-speed jet of liquid metal, gallium, to produce X-rays.

Our set-up also includes a sample robot. This assists with high-throughput testing and data collection.

For crystal screening, we use a TTP Labtech Mosquito liquid handler for protein crystallisation. This is equipped with a humidifier for complex samples and reduced sample loss. Plates are housed in one of:

• A temperature-controlled crystallisation room
• Dedicated incubators
• Our Rigaku Minstrel providing flexibility in crystallisation conditions

We also have routine access to Diamond Light Source, the UK national synchrotron. This gives us access to a wider range of X-ray based experimentations. This includes the XChem service for fragment-based crystallographic screening. We can also access Diamond facilities for small-angle light scattering and cryo-electron microscopy.

Several of our research interests also involve characterising our targets in functional complexes. Cryo-electron microscopy is becoming an integral part of that exploration. We recently acquired a Hitachi 120kV microscope and plunge freezer. This allows us to routinely screen and optimise samples for cryo-EM.

Our University's NMR facility also hosts four spectrometers. This includes a Bruker Avance 700 MHz equipped with nitrogen-cooled cryoprobe and autosampler. This allows us to explore binding events by both:

• Natural abundance
• Isotopic labelling of proteins.

We use bioinformatic and computational chemistry approaches. This allows us to examine target expression and contribute to chemistry design strategies.

We use various computational methods for assessing target biology. This also assists the chemical design process.

BioInformatics

We have an experienced bioinformatician. They use custom-made algorithms and visualisation tools to interrogate candidate targets in silico. Such work also helps us to identify genetic-based predictors of drug sensitivity​.

Computational chemistry

We use a wide range of computational modelling techniques, with a focus on:

• Virtual screening for hit identification.
• Classical molecular dynamics and quantum mechanics for probing protein and small molecule structure and function
• Free energy calculations for protein-ligand binding affinity prediction.

We make extensive use of our University's high performance computing facilities. We also collaborate with computational groups.

We have expertise in translational and clinical oncology. This enables us to examine patient materials and design appropriate clinical studies.

Our Centre for Cancer incorporates a leading UK Oncology Phase I trials Unit. Professor Ruth Plummer leads the unit. Drug Discovery is a key integral part of the Centre vision.

Being embedded in an active clinical centre is a great advantage. Clinicians working directly with cancer patients and examining new therapies provides great insight.

The Newcastle Cancer Biobank provides access to patient samples. This supports experimental work and drug-positioning studies.

We also work alongside clinical pharmacology (pharmacokinetic and biomarker research). This provides access to a range of technologies and approaches for biomarker development:

• Measurement of circulating free tumour DNA
• The analysis of circulating tumour cells
• Target protein quantification using automated immunohistochemistry and image analysis