Structure‐Based Design of Inhibitors of the Aspartic Protease Endothiapepsin by Exploiting Dynamic Combinatorial Chemistry

Abstract

Structure-based design (SBD) can be used for the design and/or optimization of new inhibitors for a biological target. Whereas de novo SBD is rarely used, most reports on SBD are dealing with the optimization of an initial hit. Dynamic combinatorial chemistry (DCC) has emerged as a powerful strategy to identify bioactive ligands given that it enables the target to direct the synthesis of its strongest binder. We have designed a library of potential inhibitors (acylhydrazones) generated from five aldehydes and five hydrazides and used DCC to identify the best binder(s). After addition of the aspartic protease endothiapepsin, we characterized the protein-bound library member(s) by saturation-transfer difference NMR spectroscopy. Cocrystallization experiments validated the predicted binding mode of the two most potent inhibitors, thus demonstrating that the combination of de novo SBD and DCC constitutes an efficient starting point for hit identification and optimization.

Dynamic combinatorial chemistry: a tool to facilitate the identification of inhibitors for protein targets

“…In parallel, all possible six imines (10-11 im ) and their corresponding amines (10)(11) were synthesized separately and tested for their inhibition (K i ) against hCA I and hCA II. The biochemical results correlate with the DCL-screening results (Table 3).…”

“…Acylhydrazone formation, which was first introduced by Sanders as a powerful reversible system for abiological DCC, [42][43][44] was used for biological targets by the group of Lehn. 11,20,46 Nucleophilic catalysis of acylhydrazone equilibration was first demonstrated by the group of Greaney in 2010. 11,20,46 Nucleophilic catalysis of acylhydrazone equilibration was first demonstrated by the group of Greaney in 2010.…”

“…11 Whereas SBD is widely used for hit optimization, there are only a few reports of true de novo SBD. 11 Whereas SBD is widely used for hit optimization, there are only a few reports of true de novo SBD.…”

“…11 B-NMR spectroscopy was used to monitor the interaction of boronic acids 74a and 74b with the enzyme aCT in presence and absence of sugars. 11 B-NMR spectroscopy was used to monitor the interaction of boronic acids 74a and 74b with the enzyme aCT in presence and absence of sugars.…”

“…2 Ultimately, this leads to amplification of the best binders, which can be identified circumventing the need for synthesis, purification and characterization of every individual library member. [11][12][13][14][15][16][17][18] Most of these reversible reactions can be carried out in aqueous media, which makes them biocompatible. 5 Protein-templated DCC thus offers an efficient and powerful approach for the acceleration of the identification and optimization of novel ligands for biological targets, and therefore holds an enormous potential for drug discovery (Scheme 1).…”