Target‐directed Dynamic Combinatorial Chemistry: A Study on Potentials and Pitfalls as Exemplified on a Bacterial Target

Abstract

Target-directed dynamic combinatorial chemistry (DCC) is an emerging technique for the efficient identification of inhibitors of pharmacologically relevant targets. In this contribution, we present an application for a bacterial target, the lectin FimH, a crucial virulence factor of uropathogenic E. coli being the main cause of urinary tract infections. A small dynamic library of acylhydrazones was formed from aldehydes and hydrazides and equilibrated at neutral pH in presence of aniline as nucleophilic catalyst. The major success factors turned out to be an accordingly adjusted ratio of scaffolds and fragments, an adequate sample preparation prior to HPLC analysis, and the data processing. Only then did the ranking of the dynamic library constituents correlate well with affinity data. Furthermore, as a support of DCC applications especially to larger libraries, a new protocol for improved hit identification was established.

Protein‐Templated Dynamic Combinatorial Chemistry: Brief Overview and Experimental Protocol

“…Buffer described in literature Acylhydrazone formation [6,24,37] Ammonium-and Sodium acetate, Phosphate, Tris* Hydrazone formation [45,46] Phosphate, Tris* Disulfide [47,48] Phosphate, Borate Thioether [49] Water/DMSO Imine [13] Water Boronate ester [50,51] Ammonium acetate, Water For many protein targets, the stability at room temperature and the optimal buffer conditions are not known. We therefore recommend determining these conditions prior to performing DCC experiments.…”

“…As an illustrative example of the comparative approach, we drew HPLC chromatograms of a blank library and a target library (Figure 5). [37] (1) The total amount of building blocks stays the same, only the equilibrium can be shifted towards one or more products.…”

Dynamic Combinatorial Chemistry: A New Methodology Comes of Age

“…In the comparative approach, the composition of a library generated in the presence of a target (template library) is compared to a library generated in its absence (blank library) ,–. This approach is often combined with analysis by high‐performance liquid chromatography (HPLC),,––,,,– and generally includes dissociation of the ligand–target complex by either denaturation of the target or displacement of the ligand by a competitor ,,,,,. Subsequently, amplification of compounds can be deduced by comparing template and blank libraries.…”

“…Subsequently, amplification of compounds can be deduced by comparing template and blank libraries. Additionally, the approach can include a preliminary separation of target‐bound and unbound ligand fractions (not shown in Figure ), which improves the sensitivity of the method ,,…”

Current Screening Methodologies in Drug Discovery for Selected Human Diseases

“…The main advantage of DCC is that several potential ligands for a protein can be screened simultaneously, avoiding the individual synthesis of every compound. This emerging technology has been used for bacterial targets [180] and cancer targets such as VEGFR [181]. Another strategy is the use of drug repositioning, which is a process of discovering a new therapeutic use for existing drugs, allowing the prediction of novel targets and therapeutic indications [182].…”