Protein ligand interactions
Our experience in ligand – target discovery and analysis
We provide expertise in various methods to identify the ligand – protein interactions, using both label-free as well as methods requiring labeling of the interacting molecules. Interacting proteins can be discovered by nanoLC-MS/MS based proteomics methods (also label-free) and by using comprehensive commercial protein arrays.
For more in depth interaction analysis, we use mainly surface plasmon resonance technology (SPR; BiaCORE). We have also an ability to identify the interacting proteins from a complex mixture of analytes, by combining the SPR with MS-based protein identification.
Oud ligand interaction studies are tailored to each project, contact us for more information from this link.
Proteomics for biologics discovery
We offer our proteomics expertise also for customers discovering protein based biological drugs. We provide customized services in e.g.
- Protein stability and kinetics in different biological fluids and tissue extracts
- Protein bioavailability and translocation like placental perfusion transport
- Analysis of microheterogeneities in manufactured proteins, like antibodies
- Quantitative targeted bioanalytics for proteins
These studies are always tailored to each project, contact us for more information from this link.
Other proteomics services
We provide expertise in many other proteomics services. Please follow these links to find out more:
- Proteomics – protein identification, quantitative proteomics, intact protein analysis, analysis of post translational modifications etc.
- Protein biomarkers – protein biomarker discovery, biomarker verification and biomarker project planning
Background
Target deconvolution
Phenotypic or cell based high-content screening campaigns have again gained popularity in many drug discovery projects. Whilst the hits obtained from phenotypic screening campaigns are often of better quality than from target based approaches, the question of identifying the binding target(s) remain.
We offer our proteomics expertise to these studies and may utilize many different technologies, like ligand-coupling pull-downs followed by LC-MS protein identification, drug affinity responsive target stability followed by LC-MS protein identification or comprehensive protein array technologies.
Protein-ligand interaction analysis
Understanding the nature of the protein – drug interaction is very important in drug discovery. Currently there are label-free technologies available to analyze the biomolecule interactions in detail, including NMR, X-ray crystallography and surface plasmon resonance technology (SPR).
SPR may be the most robust analysis method, giving the direct affinity, association and dissociation speed data for the interaction. Using SPR, also competitive study settings is possible, like whether an antagonist drug molecule is able to replace or prevent the binding of the natural ligand to its receptor. In SPR, one interaction partner is bound to the sensor chip via e.g. a chemical linkage like biotin-avidin or covalently to the dextran molecules on this chip using -NH2, -SH, -CHO and -COOH moieties of the biomolecule. The other analyte (interacting protein or small molecule ligand etc.) or a mixture of analytes, is introduced to the chip in solution by microfluidistics and the interaction (association and dissociation) is monitored in real time. Interaction is measured in arbitrary RU-units and presented in a sensongram, where Y-axis is te interaction strength and X-axis is the time line. Because the measurement happens in real time, a more complex study setups can be done, where e.g. a small molecule is bound to the target and its affinity is compared to the affinity of the natural ligand.
In addition also the potential of the small molecule to replace the natural ligand from the receptor and block binding of the natural ligand can be studied (antagonist settings). Also the association and dissociation rates can be studied in real time, i.e. how quickly the ligand-target association happens and how soon the interaction breaks.
In drug discovery, these setups can be used to analyze the binding interaction and rank the compounds. Also ranking of the compounds for non-specific binding can be accommodated with the SPR method. In addition, the SPR technology is not limited to just protein-protein, peptide-protein, small molecule-protein interactions, but rather interactions with other molecules, like DNA – DNA, DNA – protein, lipid – protein etc. can be also studied.
