Cyclic-di-AMP is an essential second messenger metabolite which occurs mostly in gram positive bacteria. It regulates various cell processes like the bacterial osmolyte and potassium ion homeostasis. c-di-AMP is produced by enzymes that possess a diadenylate cyclase domain (DAC) and have been identified in several human-pathogen bacteria. In several of them CdaA is the sole and therefor essential enzyme responsible for production of c-di-AMP (1). This renders CdaA a promising target for the development of new antibiotics. As method to identify potential CdaA inhibitors we employed the fragment-based drug design approach relying on crystal structures.
Crystallization of N-terminal truncated CdaAs from different organisms like E. faecium, S. pneumoniae, L. monocytogenes and B. subtilis in various catalytic states allow us to gain a deep knowledge about the underlying mechanism of the enzymatic function (2). Furthermore, we were able to obtain structural details at true atomic resolution, enabling the execution of a fragment screening campaign. This approach delivered structural snapshots of multiple compounds bound not only to the active centre of CdaA but also at other regions. These fragments can serve as starting points for the design of follow-up compounds, which can finally lead to a highly specific inhibitor of CdaA.