The signal recognition particle (SRP) is an essential ribonucleoprotein complex responsible for the co-translational delivery of membrane and secretory proteins to the plasma membrane in bacteria and to the endoplasmic reticulum in eukaryotes . The SRP cycle involves recognition of the signal peptide on the translating ribosome (RNC) by the SRP followed by complex formation with SRP Receptor upon GTP binding and finally the delivery of the RNC to the translocon and GTP hydrolysis . In Eubacteria, the SRP system consists of one SRP protein (Ffh), a 4.5S RNA and a receptor (FtsY). Truncations or mutations on any of the bacterial components of the SRP system have proven to be either lethal or severely impact cell viability, indicating that disruption of this system is a suitable target for antibiotic development .
Here, we propose the bacterial SRP and its interactions with the cognate SRP receptor, FtsY, as an ideal target for the development of novel antibiotics. Using a Fragment-Based Drug Design (FBDD) approach coupled with NMR we have identified two fragments from a commercial library that bind to FtsY. Overlay of 15N-1H-TROSY-HSQC spectra of 15N-2H-FtsY in the presence and absence of the fragments revealed shifts in several peak positions, indicating a protein:fragment interaction. Interestingly, the observed shifts were different from those caused by the addition of GTP analogues, indicating that the fragments are not contacting the GTP-binding pocket. We have crystallized FtsY in an Apo form and soaked GTP analogues as well as the two fragments and determined their X-ray crystal structures at resolution ranging from 1.3-1.8 Å. Despite the low affinity of the compounds, we were able to identify unambiguously their binding site and show that soaking of fragments or lead compounds for drug discovery even at low affinity is possible to aid in our drug discovery project.