Binding Mode Characterization and Early in Vivo Evaluation of Fragment-Like Thiols as Inhibitors of the Virulence Factor LasB from Pseudomonas aeruginosa

Abstract

The increasing emergence of antibiotic resistance necessitates the development of anti-infectives with novel modes of action. Targeting bacterial virulence is considered a promising approach to develop novel antibiotics with reduced selection pressure. The extracellular collagenase elastase (LasB) plays a pivotal role in the infection process of Pseudomonas aeruginosa and therefore represents an attractive antivirulence target. Mercaptoacetamide-based thiols have been reported to inhibit LasB as well as collagenases from clostridia and bacillus species. The present work provides an insight into the structure-activity relationship (SAR) of these fragment-like LasB inhibitors, demonstrating an inverse activity profile compared to similar inhibitors of clostridial collagenase H (ColH). An X-ray cocrystal structure is presented, revealing distinct binding of two compounds to the active site of LasB, which unexpectedly maintains an open conformation. We further demonstrate in vivo efficacy in a Galleria mellonella infection model and high selectivity of the LasB inhibitors toward human matrix metalloproteinases (MMPs).

N-Aryl-3-mercaptosuccinimides as Antivirulence Agents Targeting Pseudomonas aeruginosa Elastase and Clostridium Collagenases

“…Overall, since the inhibitors presented in this work have a similar structure and SAR we described for N -aryl mercaptoacetamides, we expect the interactions with LasB and ColH to be similar as those in our previously published co-crystal structures. 29 , 30 …”

“…Previously, we described N -aryl mercaptoacetamides with high selectivity for the bacterial over a broad range of human MMPs. 29 , 30 MMPs are calcium-dependent zinc metalloproteases that play a pivotal role in numerous biochemical processes in humans. 39 , 40 Based on the depth of their S1′ binding pocket, MMPs can be divided into three classes: deep ( e.g ., MMP-3 and -14), intermediate ( e.g ., MMP-2 and -8), and shallow ( e.g ., MMP-1 and -7).…”

The therapeutic potential of the insect metalloproteinase inhibitor against infections caused by Pseudomonas aeruginosa

“…IMPI is more specific and more potent than other PE‐inhibitors such as those based on hydroxamate, metal‐chelating dipeptides, or small molecules . Kany et al . analyzed the structure‐activity relationship of several PE‐inhibitors in detail.…”

Structural Requirements of N-alpha-Mercaptoacetyl Dipeptide (NAMdP) Inhibitors of Pseudomonas Aeruginosa Virulence Factor LasB: 3D-QSAR, Molecular Docking, and Interaction Fingerprint Studies

“…To support these tasks, theoretical studies oriented to characterize inhibitor interactions with the LasB crystal enzyme [16] could help with the development of new specific drugs to avoid antibiotic resistance in P. aeruginosa. Despite the widespread use of computational methods for drug design, there are a few studies related to the LasB inhibitors [17][18][19]. Fortunately, LasB-ligand complexes have been reported by X-ray crystallography [19].…”

“…Despite the widespread use of computational methods for drug design, there are a few studies related to the LasB inhibitors [17][18][19]. Fortunately, LasB-ligand complexes have been reported by X-ray crystallography [19]. Notwithstanding of several biological evaluations of sets of LasB inhibitors [13][14][15]17,18,20,21], a quantitative structure-activity relationship (QSAR) to predict and correlate the efficiency of the molecules reported is not present in the literature; neither is a deep description of the LasB binding site.…”