Fragments vs IL17A: merging and linking

One of the talks at the Discovery on Target meeting last month described the discovery of small molecule inhibitors of IL17A, a pro-inflammatory cytokine. Antibody-based drugs against this protein are useful for psoriasis and other diseases, but they require regular injections. Also, because the antibodies stick around for a long time and dampen the immune response, they could leave patients less able to combat an infection. An orally available small molecule could solve both these problems, but blocking protein-protein interactions is generally difficult. Early progress towards this goal has been published (open access) in Sci. Reports by Eric Goedken and collaborators at AbbVie.

 

The researchers started by ¹³C-labeling the methyl groups of isoleucine, leucine, valine, and methionine. They then performed a 2D NMR screen ([¹H, ¹³C]-HSQC) of ~4000 fragments in pools of 12, with each fragment at 1 mM. This yielded multiple hits, including compound 4. Interestingly, the chemical shift perturbations (CSPs) caused by this fragment were distinct from those caused by known previously disclosed binders, suggesting a different binding site. In particular, one of these CSPs could be traced to a methionine residue. The full NMR assignment of the protein was not conducted, but modeling and mutagenesis narrowed the possibility down to a methionine near the C-terminus.

 

Surface plasmon resonance (SPR) experiments revealed that compound 4 had very low affinity, but two rounds of optimization led to compounds 5 and 6. At this point the researchers were able to solve the crystal structures of these molecules bound to IL17A. The protein exists as a homodimer, and the molecules bind symmetrically, with two copies per homodimer. Moreover, the two copies bind close to one another.

 

 

In addition to these fragments, the researchers had also identified compound 7, and a crystal structure revealed that this binds in a similar fashion. Merging compound 7 with compound 6 and linking two copies of the resulting monomer led ultimately to dimeric compound 10, with nanomolar affinity by both SPR and isothermal titration calorimetry (ITC). This molecule inhibited the binding of IL17A with its receptor in a biochemical assay and also showed low micromolar activity in a cellular assay.

 

This is a nice paper that bears some similarity to previous work we highlighted from AbbVie on a different cytokine, TNFα. There too fragment linking was used initially. As in the present case, that effort led to a drop in ligand efficiency and a significant increase in the size of the molecules, resulting in suboptimal pharmaceutical properties. Identifying drug-like small molecules has been an ongoing challenge for IL17A; peptide-based inhibitors and macrocycles have been found that bind to other sites on the protein, but many of these are also well beyond rule-of-five space. As the researchers conclude, “we look forward to seeing which of these sites prove to be the most amenable to producing optimized drug candidates.”