Drug discovery

Protein Production and Characterisation (PPC) assists researchers with the expression, purification and analysis of their proteins of interest. We facilitate the production and characterisation of proteins, including those that may constitute major drug targets. Services include: 

• undertaking experiments to produce and characterise target proteins in state-of-the-art laboratories
• providing expert advice to users and training personnel (including students and staff). 

We have the expertise to express your protein in bacterial, insect, or mammalian cell host systems. We have access to highly specialised protein purification equipment and chromatography columns, and can tailor protocols to your target of interest.

Download Protein Production and Characterisation (pdf, 906 KB) for more information about our services and instruments. 

We have the equipment to undertake biochemical and biophysical characterisation of samples. Staff can collect measurements, or train users to collect data. Our instruments are described below or download Protein Production and Characterisation (pdf, 906 KB) for more information.

Prometheus Panta

Prometheus Panta is a protein stability screening platform. It combines four different measurement modes: nano differential scanning fluorimetry (nanoDSF), static light scattering (SLS), dynamic light scattering (DLS) and back reflection. This allows thermal unfolding, particle sizing, and aggregation measurements to be done simultaneously. The curated design and quality of the Prometheus Panta make it the current go-to instrument for screening protein stability.

UNCLE

UNCLE is a protein stability screening platform. It combines three different measurement modes: differential scanning fluorimetry (DSF, with or without a fluorophore like SYPRO Orange), static light scattering (SLS), and dynamic light scattering (DLS). This allows thermal unfolding, particle sizing, and aggregation measurements to be done simultaneously, which makes UNCLE one of the most popular instruments for screening protein stability.

Refeyn Two MP Mass Photometer

The Refeyn Two MP Mass Photometer is a relatively new method for molecular analysis. It measures the mass of single molecules in solution using light. It analyses individual molecules or complexes in their native state and label free. It has high sensitivity, a fast acquisition time, and low sample consumption (typically < 100 nM). It can measure proteins, antibodies, nucleic acids, lipids, and small viruses, with a detection range of 30 kDa – 5 MDa.

Circular Dichroism (CD)

CD can be used to assess protein secondary structure, as well as for protein stability studies. It has low sample consumption and a high degree of sensitivity. 

SEC-MALLS

We have access to and experience with running Multi-angle laser light scattering (MALLS) coupled to Size-Exclusion-Chromatography (SEC). An advanced and conformation-independent way of measuring the molar mass and size of species as they elute from a chromatography matrix. 

BioRad CFX Opus 96 Real-Time PCR machine

The CFX Opus 96 is Bio-Rad’s next-generation real-time PCR system, designed for high-performance, reproducible, and efficient qPCR analysis. Featuring six-channel multiplexing, fast thermal cycling, and intuitive CFX Maestro software, this system delivers accurate and consistent results with ease.

It has built-in Wi-Fi, Ethernet, and cloud connectivity allowing for remote monitoring and enhanced workflow flexibility. Whether you're performing gene expression analysis, genotyping, or pathogen detection, the CFX Opus 96 provides the speed, sensitivity, and reliability you need for modern qPCR applications.

Excitation Wavelength Range: 450 – 684 nm
Emission Wavelength Range: 515 – 730 nm

Protein X-ray crystallography is one of the most powerful methods to visualise the molecular structure of a protein at atomic resolution. The structure, in turn, provides a better understanding of a protein’s functionally important sites and its mechanism of action. This facilitates the development of efficient and specifically targeted drugs.

Sydney Analytical provides a platform for users to crystallise their proteins using state-of-the-art instruments. Our expert staff provide guidance and can assist researchers, especially those new to the field of X-ray crystallography, in determining the three-dimensional structure of their target protein.

Services offered include:

• crystallisation and structure solution (including training)
• data collection at the Australian Synchrotron*
  
• structure determination and refinement.

*Synchrotron X-rays are much more intense than in-house sources, allowing much smaller crystals to be measured much more quickly. Our partners at ANSTO operate three protein crystallography beamlines at the Australian Synchrotron (MX1 and MX2, with MX3 due to open shortly) tuned for different types of problems. We have access to the Australian Synchrotron X-ray facility through the Collaborative Access Program (CAP) which allows for the screening and data collection for crystals.

Download Macromolecular Crystallography (pdf, 417 KB) for more information about available Protein Crystallography equipment and expertise. 

Characterising the strength and nature of biomolecular interactions (e.g. protein-protein/peptide, protein-DNA/RNA, protein-drug) is fundamental to structural biology research, and drug discovery and development aims. Sydney Analytical has a range of specialised instruments, and staff expertise to assist researchers and companies in describing biomolecular interactions for both basic research and therapeutic-directed projects.

Our instruments are described below or download Macromolecular Interactions Analysis (pdf, 240 KB) for more information. 

BLitz (BiLayer InterferometryBLI)

Sydney Analytical currently has a Sartorius/ForteBio BLItz BLI instrument. BLI can be used to characterise biomolecular interactions. It is an optical, or light-based technique, but the interaction of the binding partners is monitored by a wavelength shift relative to a reference light beam, caused by the accumulation of material/compound on the surface of a fibre optic biosensor tip. In BLI, one binding partner (e.g. protein, antibody, peptide, DNA/RNA, etc) is immobilised on the functionalised biosensor tip surface, then the tip is consecutively placed in increasing concentration solutions of the analyte/other binding partner until saturated binding is approached. It can determine on-rates, off-rates, and the affinity constant (KD) of the binding interaction. BLI can be advantageous when complex or viscous samples (i.e. plasma/cell lysates or cell expression media) are to be tested, and when only small amounts of samples are available. Because BLI is a non-injection approach, samples can more easily be recovered for reuse.

Good for measuring: Protein:Protein, Protein:peptide, Protein:Nucleic Acids, antibody:antigen interactions

Biacore T200 and Biacore 8K+ (Surface Plasmon Resonance)

SPR is an invaluable tool to characterise the strength of interaction between one binding partner and another. With this method one binding partner is immobilised (the ligand) on the surface of a removable SPR chip, and the binding of the other partner (the analyte) monitored optically at increasing concentration. Saturating binding curves can then be established for a particular interaction and the affinity constant (KD) determined. This approach allows analysis of interactions between different proteins, domains, peptides or nucleic acids to be characterised.

For drug discovery, SPR can be used to screen libraries of compounds for therapeutic leads for diverse diseases as cancer, hypertension and stroke, and neurodegenerative and neuromuscular diseases. A wide variety of interaction types, such as antibodies and antigens, vaccines or viruses and antibodies, proteins and cyclic peptides, proteins and chemical fragments (small molecules) can all be conveniently explored.

SPR chips are also available that allow the assembly of model membranes, allowing protein-, and peptide-membrane interactions to be characterised, and the selectivity and action of potential antimicrobials to be investigated. These SPR chips can be used to immobilise liposome-reconstituted membrane proteins (e.g. G-protein coupled receptors), allowing key proteins of the signal transduction pathway, and a therapeutically targeted class of proteins, to be screened for drug leads.

Good for measuring: Protein:Protein, Protein:peptide, Protein:Nucleic Acids, Protein:Small Molecules, antibody:antigen interactions

PEAQ MicroCal ITC (ITC)

Isothermal Titration Calorimetry (ITC) measures the binding affinity between any two molecules that either release or absorb heat upon a binding interaction occurring.

The microcalorimeter instrument measures the heat difference between a sample cell and a reference cell (containing water or buffer) that occurs upon titration of increasing amount of a binding partner. ITC can be used to measure a variety of thermodynamic properties of biomolecular interactions, including affinity (KD), stoichiometry(n), as well as enthalpy (DH) and entropy (DS).

As a guide for users, the sample volumes we recommend for use with the instrument are below.
Sample Volume (for cell): 300 µL
Injection Syringe Volume: 50 µL

Good for measuring: Protein:Protein, Protein:peptide, Protein:Nucleic Acids, Protein:Small Molecules

Fragment-based drug discovery (FBDD) is a strategy that is growing rapidly in popularity. Rather than rely on large libraries of complex molecules, FBDD involves a small, carefully curated library of molecules that are about half the size of typical drugs. A drug target is screened against the library and ‘hits’ can then be chemically expanded to create lead compounds that bind with high affinity. The approach can be used to target enzymes as well as less traditional targets such as protein-protein or protein-nucleic acid interactions, and even membrane proteins.

Sydney Analytical use a fragment library curated by the medicinal chemists at the Monash Fragment Platform. Our primary screening methods are Nuclear Magnetic Resonance (NMR) and Surface Plasmon Resonance (SPR). Please download Fragment Based Drug Discovery (pdf, 154 KB) for more information about our FBDD workflow, as well as our equipment and expertise.

Our specialised Cyclic Peptide Screening service introduces you to the remarkable potential of small cyclic peptides in the realm of drug discovery. These compact yet powerful peptides are designed to adeptly disrupt interactions while embodying drug-like properties.

The efficiency of our Cyclic Peptide Display Screening (CPDS) service, a cutting-edge platform that seamlessly combines rapid parallel synthesis and screening. This innovative approach allows for the exploration of trillions of molecules against a wide array of expressible protein targets. The outcome? A curated collection of diverse ligands boasting exceptional affinity (typically low nM) and selectivity.

In the landscape of drug discovery, our service shines a spotlight on cyclic peptides, offering you a personalised and scientific approach. Uncover the potential of these molecular gems as we guide you through the intricacies of CPDS, paving the way for groundbreaking opportunities in the pursuit of tailored medications.

For more information, please download Cyclic Peptide Display Screening (pdf, 517 KB)

In vitro cell cultures are crucial tools for modelling diseases. 3D cell cultures more accurately model human physiology and provide better insights for oncology, drug discovery, and personalised medicine applications. We can assist with designing and developing automated 3D culture platforms for high-throughput drug discovery screening, personalised medicine screening, advanced therapeutics, and investigative biological studies.

Services

• Automate cell culture workflows for 2D iPSC cell lines, suspension and/or scaffold-based spheroids and/or organoids. 
• Produce 2D or 3D (spheroids, organoids, and organ-on-chip) cell models using secondary cell lines, primary cells and/or iPSC differentiated cell lines.
• Cell-based drug library screening using 2D or 3D cell models, available for FDA-approved drug library, Cancer compound library and Neuronal signalling compound library.
• Quantitative determination of cell-based permeability assay (for example Caco-2) using mass spectrometry analysis for drug/compound screening.

Equipment

We have a dedicated PC2 lab in G08 room 616 and instrumentation to assist with cell culture and cell-based assays. This includes three sets of Class II biosafety cabinets and incubators, fume hood, microscope, centrifuge, Countess cell counter, water bath, Neon transfection system, EVOM TEER measurement system, and Opentrons OT2 system. In particular:

• RASTRUM 3D cell bioprinter that auto-seed different/multiple cell types (primary cells and iPSCs) in a tunable 3D matrix (single or multiple models) that closely mimics the complexity of physiological and pathological in vivo microenvironments.
• Automated cell culture system that contains an incubator, imager, and liquid handler to standardize advanced in vitro tissue culture processes (such as iPSCs, spheroids, organoids, air-liquid interface, and organ-on-chip) including seeding, feeding, monitoring, AI-driven decision making and passaging to deliver consistent, unbiased, and biologically relevant results at scale.
  
  Capacity: 154 plates with CO2, temperature, and humidity control
  Light source: LED light
  Objectives: air 2X – 40X
  Filter cubes: DAPI, FITC, TRITC, TxRed, Cy5, Cy7, CFP, YFP
  Pipette head: Span 8
  Deck locations: plate cooling, heating, and tilting
• Spinning confocal imaging system has multi-laser light sources, a deep tissue penetrating confocal disk module, and machine learning analysis software that enables high-sensitivity detection and fast acquisition of 3D samples. Compatible with slides, and 1- to 1536-well microplates with CO2 and temperature control.
  
  Compatibility: Glass slides and 1- to 1536-well microplates with CO2 and temperature control
  Light source: Lasers 405nm, 445nm, 475nm, 520nm, 555nm, 640nm, and 730nm
  Channels: DAPI, CFP, FITC, YFP, TRITC, Cy5, Cy7, TxRed
  Objectives: air 2X, 4X, 10X, 20X, and water immersion 20X
  Spinning disk: 60 µm pinhole (single disk)
  Software: MetaXpress, IN Carta
• Hamilton Microlab^Ⓡ STAR – This liquid handler automates the pipetting workflows for in-process or endpoint procedures such as sample transfer, addition of reagent, serial dilution, replicates, and hit picking in a sterile controlled condition. It contains clean air protection system, UV light kit, and heater shaker.
  
  Pipetting Option: 1 – 8 channels
  Pipetting volume range: 1 µl – 5000 µl
  Sample tracking: Autoload barcode scanner
  Sterile controls: UV-lamp, HEPA filter
  Modules: Hamilton Heater Shaker automates the heating and shaking of microplates
• Multi-mode microplate readers that measure absorbance (Abs), luminescence (Lumi), fluorescence including fluorescence intensity, fluorescence polarization (FP), and time-resolved fluorescence (TRF). Compatible with 6- to 384-well microplates, and injector system is available.
  
  Monochromator (tunable in 1nm increments):
  - Abs: 230 – 1000 nm
  - FL Ex: 250 – 830 nm, FL Em: 270 – 850 nm
  - Lumi: 300 – 850 nm
  - FP Ex: 400 – 750 nm, FP Em: 400 – 750 nm
  - TRF Ex: 350 nm, TRF Em: 450 – 750 nm
  Optical filters:
  - FL: 440/480 (thioflavin)
  - FP: 485/520/520 nm (fluorescein), 540/590/590 nm (TAMRA/Cy3), 590/675/675 nm (Cy5)
  - HTRF: 337/665/620 nm
  - AlphaScreen: 680/570 nm
  - AlphaLISA: 680/615 nm
  - TRF: 350/490 nm (Terbium) or 616 nm (Europium)

The following is a complete list of all the equipment from the drug discovery node that is available to researchers. Contact us at sydney.analytical@sydney.edu.au for more information about any of the equipment listed below.

• Incushakers and incubators for bacterial, insect and mammalian culture
• Avestin Emulsiflex C3 homogeniser for cell lysis
• AKTA Start FPLC Purification system
• AKTA Pure M FPLC with Sample Pump (in refrigerated cabinet)
• AKTA FPLC Purification Systems (for RT purifications)
• Beckman Allegra Swing Bucket Centrifuge
• Biocomp Gradient station 
• Beckman Optima L-80XP ultracentrifuge 
• BioRad Trans-Blot Turbo transfer system 
• Apparatus for running DNA agarose gels
• Apparatus for running SDS-PAGE gels
• Bio-rad T100 thermal cycler 
• RotorGeneQ (qPCR machine)
• BioRad CFX Opus 96 Real-Time PCR machine
• Mic qPCR machine
• Illumina iSeq Nucleic Acid Sequencer
• Unchained Labs UNCLE for DLS/DSF
• NanoTemper Prometheus Panta for DLS and/or nanoDSF
• Jasco Circular Dichroism (CD) spectropolarimeter
• Refeyn Two MP Mass photometer
• Blitz (Bi-layer interferometry)
• Biacore T200 (Surface Plasmon Resonance)
• Biacore 8K+
• MicroCal PEAQ Isothermal Titration Calorimeter (ITC)
• Protein Crystallisation equipment:
  • Includes an NT8Ⓡ (Formulatrix), and access to a MosquitoⓇ LV (sptlabtech), Freedom Evo liquid handler (Tecan), Stereo Microscopes (Leica) and Incubators at various temperatures (Memmert)
• PC1 and PC2 Lab space 
• BioSafety Class II and Cytotoxic cabinets 
• Bio-Rad micropulser and neon electroporators 
• Countess cell counter  
• Cytation
• Equipment for automated 2D and 3D Cell culture
• High Content Imaging System
• Perkin Elmer Janus Liquid Handling Robot
• Rastrum 3D Cell Culture Platform
• Microplate readers with built-in absorbance (ABS), luminescence (LUM), fluorescence intensity, fluorescence polarization (FP), and time-resolved fluorescence (TRF) modes. Compatible with 6- to 384-well microplates.
  
  Detection technologies performance:
  - Absorbance (230 – 1000 nm)
  -  Luminescence (300 – 850 nm)
  - Fluorescence intensity Ex (250 – 830 nm) / Em (270 – 850 nm); FI filter 440/480 (thioflavin)
  - Fluorescence polarization Ex (400 – 750 nm) / Em (400 – 750 nm); FP filters 485/520/520 nm (fluorescein), 540/590/590 nm (TAMRA/CY3), 590/675/675 nm (Cy5)
  - Time-resolved fluorescence Ex filter 350 nm / Em (450 – 750 nm) or filter 490 nm (Terbium), 616 nm (Europium)
  - HTRF filter 337/665/620 nm
  - AlphaScreen filter 680/570 nm; AlphaLISA filter 680/615 nm