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 ...
Analyzing SAR and property data is a core expertise for Cresset Discovery Services (CDS). We have experience working with a wide range of different targets, including fragrances, flavors, standard pharmaceutical reagents and anti-fungal agents.
Our XED force field analysis of molecules gives you unique insight into the source of activity of your molecules. When we combine this with state of the art data analysis tools you can be sure that you are getting the best possible value from the data you own.
Usually customers come to us with a chemical asset. Their immediate objective may be to optimize a molecule to its maximum potential, or come up with a backup chemotype. Whatever the goal, they need to be able to understand the system and gain the maximum amount of information from it so that they can exploit it to the fullest extent.
A comprehensive analysis of SAR and property data is a fundamental prerequisite to most of the other work that we do. Whatever the project, we will start by looking at the activity data along with any known target information, such as sequence information or X-ray data. We investigate the different chemotypes and essentially get to know the project. For example, virtual screening often starts with some field based analysis of the active molecules to define the bioactive conformation. This analysis is fundamental to any computational chemistry work.
Cresset scientists work in 3D. Moving from a 2D to 3D structure always reveals something new about a project and it usually gives very helpful insights. In order to know how to translate from 2D to 3D it is vital to understand the system. For example, one key determinant in finding a bioactive conformation is the inherent flexibility of the active molecules.
A customer purchased our expertise to get the most from their molecules. They had 1,000 molecules in their active set and were looking to understand and extract the most useful information from that data. The fields, in other words the electrostatics of molecules, are mostly invisible to most software packages which typically look at H bonds and features rather than the overall shape. However, some quite subtle interactions come from the electrostatics and shape of the molecules, such as the electrostatics in aryl and hetero aryl rings, which are dependent on specific substitution.
In this project we were able to find a binding hypothesis that interpreted how their molecules were likely to be interacting with the protein target. This was a great help to the customer’s subsequent design rounds. We also carried out a more traditional sequence alignment based analysis, which backed up the binding hypotheses with specific mutations to conduct. This analysis supported the binding hypothesis.
This collaboration is ongoing. As a result of the proven value of our work we have carried out many additional projects with this client.
Contact us for a free, confidential discussion to find out how Cresset Discovery Services can help you to get the best possible value from your SAR and property data.