Flexible Fragment Growing Boosts Potency of Quorum‐Sensing Inhibitors against Pseudomonas aeruginosa Virulence

Abstract

Hit‐to‐lead optimization is a critical phase in drug discovery. Herein, we report on the fragment‐based discovery and optimization of 2‐aminopyridine derivatives as a novel lead‐like structure for the treatment of the dangerous opportunistic pathogen Pseudomonas aeruginosa. We pursue an innovative treatment strategy by interfering with the Pseudomonas quinolone signal (PQS) quorum sensing (QS) system leading to an abolishment of bacterial pathogenicity. Our compounds act on the PQS receptor (PqsR), a key transcription factor controlling the expression of various pathogenicity determinants. In this target‐driven approach, we made use of biophysical screening via surface plasmon resonance (SPR) followed by isothermal titration calorimetry (ITC)‐enabled enthalpic efficiency (EE) evaluation. Hit optimization then involved growth vector identification and exploitation. Astonishingly, the latter was successfully achieved by introducing flexible linkers rather than rigid motifs leading to a boost in activity on the target receptor and anti‐virulence potency.

A New PqsR Inverse Agonist Potentiates Tobramycin Efficacy to Eradicate Pseudomonas aeruginosa Biofilms

“…The following section describes the steps of medicinal chemistry‐driven optimization starting from the previously identified PqsR inverse agonist 2 (Figure 1B). [ 15 ] Our efforts arrived at lead QSI 4 (Figure 1B), which was then subject to in‐depth biological profiling in the subsequent sections.…”

“…A first consideration regarding the optimization of hit compound 2 involved the replacement of the amide bond, as it is inherently prone to enzymatic hydrolysis and might lead to undesirable aniline metabolites. [ 15,19 ] Our strategy aimed at installing a bioisosteric replacement followed by a fragment‐growing approach. Triazoles have been described as amide mimics [ 20 ] and were, hence, selected for our rational design approach.…”

“…We previously introduced a novel class of QSI originating from a fragment‐based screening hit 1 (Figure 1B). [ 15 ] Initial optimization yielded a small‐molecule, which was very efficient in attenuating PA virulence and displayed a promising starting point for a hit‐to‐lead campaign, ultimately resulting in an improved hit 2 with potential for further medicinal chemistry‐driven optimization (Figure 1B). [ 15 ] Herein, we report the successful generation of a lead QSI including in‐depth ADMET profiling.…”

“…[ 15 ] Initial optimization yielded a small‐molecule, which was very efficient in attenuating PA virulence and displayed a promising starting point for a hit‐to‐lead campaign, ultimately resulting in an improved hit 2 with potential for further medicinal chemistry‐driven optimization (Figure 1B). [ 15 ] Herein, we report the successful generation of a lead QSI including in‐depth ADMET profiling. We show that the new chemical matter not only provides potent anti‐virulence efficacy but also has favorable characteristics regarding in vitro and in vivo PK that are suitable for the applications in the lungs, while showing no overt findings in in vitro safety pharmacology assays.…”

Novel quinazolinone inhibitors of the Pseudomonas aeruginosa quorum sensing transcriptional regulator PqsR

“…Compounds 6 , 12 , 18 and 19 were successfully soaked into a truncated form of PqsR (PqsR 94-309 ) containing the ligand-binding domain of the protein (see S3-6 for additional data including electron density plots and crystallographic table of data collection and refinement). All four ligands occupied a similar space to that exhibited by a previously described quinazolinone-based inhibitor 45 and two endogenous ligands (HHQ, 3 , and NHQ, 46 ) bearing quinolone scaffolds [ 32 , 44 ]. In each case, the quinazolinone core occupies the previously defined B pocket of the LBD [ 32 ], and the alkyl chain extends into the open A pocket ( Fig.…”