[PMC free article] [PubMed] [Google Scholar] 34. using pre-tRNA and the pre-tRNA-like substrate, which ultimately verified four compounds as inhibitors. Biolayer interferometry-based binding assays and molecular dynamics simulations were then used to characterize the interactions between each validated inhibitor and the P protein, P RNA and pre-tRNA. X-ray crystallographic studies subsequently elucidated the structure of the P protein bound to the most promising hit, purpurin, and revealed how this inhibitor adversely affects tRNA 5 leader binding. This integrated platform affords improved structure-function studies of RNA processing enzymes and facilitates the discovery of novel regulators or inhibitors. INTRODUCTION Regulatory RNAs, ribozymes, and RNA-protein complexes are appealing antibiotic targets due to their essential functions in microbial metabolism (1C3). This clinical importance is exemplified by the ribosome, which is currently the target of roughly 50% of known antibiotics (4). The focus of this work is Ribonuclease P (RNase P), the only ribozyme other than the ribosome that is present in all three domains of life (see (5C8) for some reviews). This CY-09 essential ribonucleoprotein complex remains to be exploited as a target for much-needed CY-09 novel antibacterial agents (9). The composition of RNase P varies across the three domains of life (10) and therefore may afford high selectivity in drug targeting (11,12). While in archaea and eukaryotes, RNase P is comprised of one RNA subunit and four to ten proteins (13), in bacteria, this complex is formed by an RNA subunit (P RNA, 350C400 nucleotides, 110C125 kDa) and a single protein HS3ST1 (P protein, 110 amino acids, 13 kDa) (14). In all species, the P RNA serves as the primary biocatalyst (15) for the cleavage of the 5-leader sequence of pre-tRNAs during tRNA maturation (16). The P protein, on the other hand, binds the distal 5-leader region of the pre-tRNA substrate, enhances the affinity of metal ions, and assists in product release (17C20). RNase P is dependent on divalent metal ions (Mg2+ is needed for proper folding and activity (21C23)) and and through X-ray crystallography, on the binding of potential inhibitors to the P protein. In this work, we present an RNase P activity assay that exploits a previously reported minimal model substrate (pMini3bpUG, herein referred to as Minihelix or Mh) (32,33). This substrate utilizes a FRET mechanism in which the RNase P substrate couples both a 3 fluorophore and a 5 non-fluorescent quencher. Cleavage and release of the quencher molecule by RNase P enables the detection of enzymatic activity by measuring fluorescence emission over time, which is amenable for monitoring steady-state kinetics and for high-throughput screening assays. CY-09 We then implemented this method to assess a compound library of 2560 small molecules and found four compounds that inhibit RNase P activity. These inhibitors were effective in the presence of both a canonical pre-tRNA substrate and a novel pre-tRNA-like substrate (herein referred to as bipartite pre-tRNA) that is composed of two RNA oligonucleotides and monitors the reaction in an analogous way to the Mh substrate. To avoid the sensitivity of RNase P processing to organic solvents using the bipartite pre-tRNA substrate, we dissolved the hits in PEG 200 rather than DMSO. This procedure allowed us to validate the inhibitory properties of these molecules under varied conditions. Positive hits were then verified and characterized using biolayer interferometry (34), which allowed us to perform the following tasks: (i) define the affinity parameters of the RNase P holoenzyme, P RNA and P protein to the RNA substrates, (ii) discriminate between the interactions of a given compound with the holoenzyme, P RNA, P protein or the substrate and (iii) determine if a given compound hinders the binding of the holoenzyme to pre-tRNA or the P protein to the 5-leader. Once validated, we performed docking and molecular dynamics simulations with each hit and identified putative binding sites for two inhibitors on the P protein. Furthermore, purpurin, a competitive inhibitor which behaved as the most consistent hit across our assays, was shown to bind the P protein by X-ray crystallography, with its binding site corresponding to part of the 5-leader binding site. MATERIALS AND METHODS Selection of bacterial RNase P We chose to work with RNase P from the thermophilic bacterium for several reasons. First, it represents the ancestral and most common type A ribozyme, the same that is present in (35). Second, the crystal structure of the RNase P holoenzyme from in complex with tRNA (19) as well as the apo-structure of the RNA subunit (36) are known, thus facilitating structure-function studies. Third, the folding protocol of the RNase P holoenzyme from (described below) leads to crystals that present a functional and homogeneous molecular complex.