Synthesis of Triazole-Linked Analogues of c‑di-GMP and Their Interactions with Diguanylate Cyclase

Cyclic di-GMP (c-di-GMP) is a widespread
second messenger that
plays a key role in bacterial biofilm formation. The compound’s
ability to assume multiple conformations allows it to interact with
a diverse set of target macromolecules. Here, we analyzed the binding
mode of c-di-GMP to the allosteric inhibitory site (I-site) of diguanylate
cyclases (DGCs) and compared it to the conformation adopted in the
catalytic site of the EAL phosphodiesterases (PDEs). An array of novel
molecules has been designed and synthesized by simplifying the native
c-di-GMP structure and replacing the charged phosphodiester backbone
with an isosteric nonhydrolyzable 1,2,3-triazole moiety. We developed
the first neutral small molecule able to selectively target DGCs discriminating
between the I-site of DGCs and the active site of PDEs; this molecule
represents a novel tool for mechanistic studies, particularly on those
proteins bearing both DGC and PDE modules, and for future optimization
studies to target DGCs in vivo.