Non-substrate-like inhibitors do not take after dipeptidic nature of DPP-4 substrates. They are non-covalent inhibitors and usually have an aromatic ring that occupies the S1-pocket, instead of the proline mimetic.
In 1999, Merck started a drug development program on DPP-4 inhibitors. When they started internal screening and medicinal chemistry program, two DPP-4 inhibitors were already in clinical trials, isoleucyl thiazolidide (P32/38) and NVP-DPP728 from Novartis. Merck in-licensed L-threo-isoleucyl thiazolidide and its allo stereoisomer. In animal studies, they found that both isomers had similar affinity for DPP-4, similar in vivo efficacy, similar pharmacokinetic and metabolic profiles. Nevertheless, the allo isomer was 10-fold more toxic. The researchers found out that this difference in toxicity was due to the allo isomer's greater inhibition of DPP-8 and DPP-9 but not because of selective DPP-4 inhibition. More research also supported that DPP-4 inhibition would not cause compromised immune function. Once this link between affinity for DPP-8/DPP-9 and toxicity was discovered, Merck decided on identifying an inhibitor with more than a thousandfold affinity for DPP-4 over the other dipeptidases. For this purpose, they used positional scanning libraries. From scanning these libraries, the researchers discovered that both DPP-4 and DPP-8 showed a strong preference for breaking down peptides with a proline at the P1 position but they found a great difference at the P2 site; i.e., they found that acidic functionality at the P2 position could provide a greater affinity for DPP-4 over DPP-8. Merck kept up doing even more research and screening. They stopped working on compounds from the α-amino acid series related to isoleucyl thiazolidide due to lack of selectivity but instead they discovered a very selective β-amino acid piperazine series through SAR studies on two screening leads. When trying to stabilize the piperazine moiety, a group of bicyclic derivatives were made, which led to the identification of a potent and selective triazolopiperazine series. Most of these analogs showed excellent pharmacokinetic properties in preclinical species. Optimization of these compounds finally led to the discovery of sitagliptin.