moreover, they also display the ability to live in extreme pHs [9]. These attributes make biofilm infections extremely difficult to eradicate and nearly impossible to eliminate if they are not accessible to physical means of disruption [3; 4; 5; 10; 11]. The activation of the ribosomally-associated RelA enzyme via amino acid starvation triggers the bacterial stringent response that leads to the phenotypic changes that underlie the extreme recalcitrance that biofilms exhibit towards antibiotics [12]. Thus, this ancient bacterial stress response produces an active metabolic state that results in the inability to treat chronic infections resulting from biofilms.  
It has been known for more than half a century that the \"magic spot\" alarmones, guanine tetrapphosphate and guanine pentaphosphate, collectively known as (p)ppGpp, produced by RelA, play an integral role in cell signaling for induction of the stringent response [13; 14; 15; 16; 17]. In _Escherichia coli_, the production of (p)ppGpp is carried out by the enzyme RelA [18]. RelA, which is a highly conserved 84-kD pyrophosphokinase protein among all eubacterial phyla [19], displays a well-choreographed dance with stalled ribosomes to detect amino acid starvation by means of deacetylated tRNAs [20]. Upon detection of this uncharged tRNA, RelA subsequently binds to the ribosomal complex and structurally changes to its active synthase conformation. While in this \"open\" conformation, RelA continually produces (p)ppGpp [21; 22; 23]. During this time, the intracellular concentrations of (p)ppGpp increase dramatically. The increased concentration of (p)ppGpp modulates multiple downstream cellular signaling pathways, including interacting with the RNA polymerase's promoter binding region, thereby interfering with the cell's ability to produce additional ribosomes [24].  
Currently, there are only a very limited number of inhibitors known for RelA and (p)ppGpp that have been identified principally through traditional drug discovery methods, such as substrate analog design and high-throughput compound screening, none of which are candidates for clinical trials for the control of biofilm infections. The first of these inhibitors were analogs to ppGpp itself, such as Relacin and its derivatives [25]. These compounds, while mildly effective, suffer from off-target effects and low binding affinities [25; 26; 27; 28; 29].  
The next compound discovered to reduce the intracellular concentrations of ppGpp was the cationic peptide known as IDR1018. This peptide is an analog to bactenecin [30; 31; 32; 33] and it was reported to directly sequester and break down (p)ppGpp, thus lowering its intracellular concentration [30]. It is now thought that IDR1018 does not specifically target (p)ppGpp, but simply acts as an antimicrobial agent by means of its cationic nature [34]. Moreover, IDR1018 is a moderately sized peptide incapable of being an orally administered \"druggable\" compound.  
Recently, a trend toward the use of _in silico_ chemistry and molecular modeling for computer-aided drug design has gained significant momentum [35]. Previously, this was impossible to do with the RelA/RSH (RelA-SpoT homolog) family of enzymes, as there were no adequate high-resolution molecular structures available. However, several RelA and related enzyme structures have been recently characterized and published: RelA (_E. coli_) [36], RelP (_Staphylococcus aureus_) [37], RelQ (_S. aureus_) [38], Rel\({}_{\text{seq}}\) (_Streptococcus equisimilis_) [39], and Rel (_Mycobacterium tuberculosis_) [40]. Thus, it has become possible through alignment and homology studies to determine the active residues within the catalytic center of these enzymes and to specifically target this region to predict and understand the ligand binding events for the rational identification of inhibitors.