Nucleophilic catalysis of acylhydrazone equilibration for protein-directed dynamic covalent chemistry

Abstract

Dynamic covalent chemistry uses reversible chemical reactions to set up an equilibrating network of molecules at thermodynamic equilibrium, which can adjust its composition in response to any agent capable of altering the free energy of the system. When the target is a biological macromolecule, such as a protein, the process corresponds to the protein directing the synthesis of its own best ligand. Here, we demonstrate that reversible acylhydrazone formation is an effective chemistry for biological dynamic combinatorial library formation. In the presence of aniline as a nucleophilic catalyst, dynamic combinatorial libraries equilibrate rapidly at pH 6.2, are fully reversible, and may be switched on or off by means of a change in pH. We have interfaced these hydrazone dynamic combinatorial libraries with two isozymes from the glutathione S-transferase class of enzyme, and observed divergent amplification effects, where each protein selects the best-fitting hydrazone for the hydrophobic region of its active site.

Localized Template‐Driven Functionalization of Nanoparticles by Dynamic Combinatorial Chemistry

“…[11a, 13] A promising approach to obtain a receptor complementary to its target is to synthesize it under thermodynamic control in the presence of the target that acts as a template. This approach has been successfully utilized in dynamic combinatorial chemistry (DCC) [14] to make receptors for small molecules, [15] ligands binding to pockets of biomacromolecules, [16] and multivalent polymers. [14n, 17] We reasoned that the same approach may be utilized to achieve the selective functionalization of nanoparticle surfaces.…”

Generation of Dynamic Combinatorial Libraries Using Hydrazone‐Functionalized Surface Mimetics

“…Nucleophilic catalysts have been used to promote hydrazone exchange reactions in biologically relevant media 40, 42, 43. Aniline 11 and anthranilic acid 12 were chosen, as they are cheap and relatively soluble.…”

“…Hydrazone exchange chemistry has been used in a range of DCC studies including host–guest systems,35 interlocked36 architectures, polymers37, 38 and nanoparticles:39 it is an attractive reversible covalent bond forming reaction for DCC in water because the resultant hydrazone bond is stable in water, but its use has been limited because the exchange reaction typically operates at acidic pH. Both Dawson and co‐workers and Greaney and co‐workers elaborated methods to render the use of hydrazone exchange more useful under biologically relevant conditions by introducing aniline as a nucleophilic catalyst, to facilitate the reaction at pH 6.2 40, 41. Several alternative catalysts have subsequently been introduced 42, 43.…”

Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial Chemistry

“…In addition to FBDD, DCC14, 15, 16, 17, 18 and dynamic ligation screening (DLS)19, 20, 21, 22 are powerful strategies for identifying/optimizing hit compounds for biological targets. In a dynamic combinatorial library (DCL), the bonds between the building blocks are reversible and are continuously being made and broken.…”