We have determined the three dimensional structure of human VAP-1 in complex with a set of novel inhibitors with X-ray crystallography. VAP-1 is a 180 kDa membrane-bound protein involved in leukocyte trafficking to sites of inflammation and, therefore, inhibition of the enzyme could be of great importance in chronic diseases like rheumatoid arthritis, asthma and psoriasis. However, despite extensive attempts no potent and specific reversible drug has successfully been developed. As our previous results showed a secondary binding site for an inhibitory imidazole in the active site channel of VAP-1, we have now designed and crystallized a novel set of pyridazinone inhibitors targeted to the active side channel to block the entrance to the deeply buried catalytic site. This is the first time VAP-1 has been crystallized with reversible inhibitors and our detailed characterization of their binding mode aids the future development of therapeutics for VAP-1 associated diseases.

Earlier studies have shown that the inhibitors designed for human VAP-1 often bind rodent VAP-1 with a lower affinity. Therefore, we have made homology models and structural comparisons of human and rodent VAP-1 to predict differences that affect the inhibitor binding. Based on our VAP-1-inhibitor complex structures we were able to make more accurate models and pinpoint differences that are important for the species-specific binding properties of these novel pyridazinone inhibitors. The information obtained from these studies will be of great importance for the development and design of drugs that block equally well the activity of human and rodent VAP-1, as mice and rats are often used for in vivo testing of candidate drugs.