Mapping the S1 and S1’ subsites of cysteine proteases with new dipeptidyl nitrile inhibitors as trypanocidal agents

Abstract

The cysteine protease cruzipain is considered to be a validated target for therapeutic intervention in the treatment of Chagas disease. A series of 26 new compounds were designed, synthesized, and tested against the recombinant cruzain (Cz) to map its S1/S1ś ubsites. The same series was evaluated on a panel of four human cysteine proteases (CatB, CatK, CatL, CatS) and Leishmania mexicana CPB, which is a potential target for the treatment of cutaneous leishmaniasis. The synthesized compounds are dipeptidyl nitriles designed based on the most promising combinations of different moieties in P1 (ten), P2 (six), and P3 (four different building blocks). Eight compounds exhibited a K i smaller than 20.0 nM for Cz, whereas three compounds met these criteria for LmCPB. Three inhibitors had an EC 50 value of ca. 4.0 μM, thus being equipotent to benznidazole according to the antitrypanosomal effects. Our mapping approach and the respective structure-activity relationships provide insights into the specific ligand-target interactions for therapeutically relevant cysteine proteases.

Predicting the Relative Binding Affinity for Reversible Covalent Inhibitors by Free Energy Perturbation Calculations

“…Figure shows the putative binding mode of 2a–c , where essential hydrogen bonds are observed between the ligands and the main chain from Gly68 and Asp162 in the hCatL active site. These fundamental interactions are commonly observed for peptidomimetics interacting with hCatL . It is also worth mentioning that the single-atom modification observed in 2a–c is located at the P3 group (Figure ), where the aromatic ring is to a large extent exposed to the solvent environment.…”

“…These fundamental interactions are commonly observed for peptidomimetics interacting with hCatL. 66 It is also worth mentioning that the single-atom modification observed in 2a−c is located at the P3 group (Figure 2), where the aromatic ring is to a large extent exposed to the solvent environment. Therefore, one can assume that the P3 group is not involved in critical interactions in the active site of hCatL.…”

“…Our research group reported several peptidomimetic inhibitors of hCatL and other cysteine proteases in recent publications. ,,, These studies demonstrated that compounds bearing a halogen atom at the meta position of the P3 benzyl ring (Figure ) presented selectivity for hCatL over other CPs and showed a good affinity for the enzyme. Compounds with the biphenyl ring at P3 and related derivatives also exhibit a high affinity for hCatL.…”

Investigating the Lack of Translation from Cruzain Inhibition to Trypanosoma cruzi Activity with Machine Learning and Chemical Space Analyses

“…[4] The extensive research around K777 has provided a status of "validated target" for cruzain, which has led several research groups to explore cruzain inhibitors as potential new treatments for Chagas disease. [16][17][18][19][20] However, despite the essentiality of cruzain for the T. cruzi life cycle, it has been observed in several cases a lack of translation from in vitro cruzain activity to T. cruzi biological activity (both in vitro and in vivo). [19,[21][22][23][24] Some studies have suggested that reversible cruzain inhibitors would be less likely to present trypanocidal activity.…”

Structure-Based Optimization of Quinazolines as Cruzain and TbrCATL Inhibitors

“…Moreover, it is recognized by the host as an antigen and modulates the host macrophage response. , Tbr CATL is important for penetration through the blood–brain barrier and is essential for parasite survival. ,, Efforts to develop inhibitors have led to the discovery of many potent chemotypes against both proteases (reviewed in refs , , and ). Recently reported inhibitors include peptidomimetics − and nonpeptidic small molecules that inhibit the enzymes irreversibly or reversibly. − In addition to their efficacy in in vitro assays against trypanosomes, ,,, cysteine protease inhibitors have shown efficacy in mice − and dog models of Chagas disease, and to reduce parasitemia and/or increase survival ,, in mouse models of T. brucei infection.…”