Case study: Tackling CYP 2C9 inhibition challenges

The Problem:

• Active compounds in a project were found to be highly potent inhibitors of CYP 2C9
• The compounds selectively inhibited CYP 2C9 with IC50 values <100 nM
• There was no considerable inhibition of the other CYP isoforms

Our Mitigation Approach:

• CYP 2C9 inhibition data was generated for a larger set of compounds with diverse moieties irrespective of their biochemical potency towards the target
• SAR was derived with respect to the CYP 2C9 inhibition

Our Observations:

• Compounds without ‘Linker 2’ were found to have lower CYP 2C9 inhibition potential
• However, ‘Linker 2’ was critical for primary activity towards the target

Replacement of the tetrahydropyron with N-methyl piperidine yielded high CYP 2C9 selectivity, while maintaining the potency towards the target

Our Solution:

Understanding the interaction of the inhibitor with CYP 2C9 was important to mitigate this problem

• CYP 2C9 inhibitors are reported to be involved in a key binding interaction with an Arginine (Arg 108), a cationic residue in the active site of the protein
• This binding site is unique to CYP 2C9 and not present in the other CYP isoforms
• It would require an anionic moiety on the molecule to make this interaction with Arg 108 in CYP 2C9
• Systematic SAR was built on this hypothesis by modifying the anionic groups in different regions of the molecule, meanwhile retaining the primary activity

Corroboration:

The in-silico docking studies which followed this project support our above-mentioned finding/hypothesis