Therapeutic protein degradation by design?
The old problem and the new paradigm Classical small molecule drug paradigms generally involve intervention at a ligand protein binding ...
An academic group had identified a molecule that was active in a phenotypic assay. Due to its similarity to other compounds, they initially thought it was acting through a known pathway. However, further work revealed it was acting through a different pathway. The challenge was to identify the protein target. They chose a computational method and outsourced the project to Cresset Discovery Services (CDS).
There are a number of ways to go about identifying possible protein targets. The biological route is the standard method of trying to de-convolute the target from the cellular context. However, it involves a lot of time and work. Taking a computational approach can be a very efficient shortcut that narrows the search down to a few likely candidates.
The academic group choose to take the computational route and they decided to outsource this sophisticated project to CDS. Cresset was the ideal choice for a number of reasons.
Firstly, it was far quicker and cost effective to outsource the project rather than trying to do it in-house. To do the work in-house would have needed to recruit an expert and to purchase the software and hardware. There would have been steep learning curves for using the software and methods. Added to this, they would potentially have been left with these overheads at the end of the project.
By contrast, for an outsourced project CDS supplies both the expertise and the infrastructure. This makes it far quicker to get up and running. It is also far more cost effective since the resources are only paid for the duration of the project.
Added to these advantages, CDS has specific expertise in this field. Our software calculates the interaction potentials of molecules by analysing their shape, electrostatic fields and hydrophobicity relative to atomic probes. These values are used to create a unique representation of
molecules, making it possible to build up a ‘protein’s eye view’ of a compound. This gives a quantitative basis for comparing compounds based on how they are likely to interact with a protein.
We had already encoded the PDB ligands into Cresset field space, which translated to a head start in identifying the possible protein targets.
CDS took the active molecule as a starting point and found a number of conformations for it. We used the field patterns to search the PDB for similar molecules in order to find potential pharmacological matches. These matches revealed which proteins were worth investigating further.
From this work, CDS provided a list of potential targets to the customer. The academics worked through this short list in order to identify the actual target. This outsourced project was a very cost effective way of cutting down the list of potential targets and was certainly far more efficient than taking a purely biological route.
Contact us today to find out how Cresset Discovery Services can use their expertise to help with new approaches for your project.