SAR and Structural Analysis of Siderophore-Conjugated Monocarbam Inhibitors of Pseudomonas aeruginosa PBP3

Abstract

A main challenge in the development of new agents for the treatment of Pseudomonas aeruginosa infections is the identification of chemotypes that efficiently penetrate the cell envelope and are not susceptible to established resistance mechanisms. Siderophore-conjugated monocarbams are attractive because of their ability to hijack the bacteria's iron uptake machinery for transport into the periplasm and their inherent stability to metallo-β-lactamases. Through development of the SAR we identified a number of modifications to the scaffold that afforded active anti-P. aeruginosa agents with good physicochemical properties. Through crystallographic efforts we gained a better understanding into how these compounds bind to the target penicillin binding protein PBP3 and factors to consider for future design. KEYWORDS: Pseudomonas aeruginosa, β-lactam, penicillin binding protein, siderophore, monocarbam, structure-guided design O ne of the largest challenges in the discovery of new Gram-negative antibacterial agents is the identification of chemotypes that can penetrate the cell envelope. 1 The pathogens, such as Pseudomonas aeruginosa (P. aeruginosa), have evolved complex cell architectures including an outer membrane composed of charged lipopolysaccharides, a thin peptidogylcan layer, and an inner membrane made up of phospholipids. 2 Identifying molecules with the necessary features to enable permeation has been a challenge.β-Lactams are one chemotype that have been successful in the treatment of P. aeruginosa. 3 Since the discovery of penicillin, β-lactams have been used in the clinic and are still widely prescribed. One of the most effective classes of β-lactams for the treatment of P. aeruginosa infections are the carbapenems (e.g., meropenem, 1, Figure 1). 4 Their effectiveness stems from their ability to acylate their penicillin-binding protein (PBP) targets, aided by high permeability into P. aeruginosa through the outer membrane porins. 5 However, they are currently being challenged in the clinic by the increasing emergence of broadspectrum serine β-lactamases and metallo-β-lactamases which hydrolyze most β-lactams and render them ineffective. 6 There is one class of β-lactams that is stable to the metallo-β-lactamases: the monocyclic β-lactams represented by aztreonam (2). Aztreonam however has limited effectiveness against P. aeruginosa presumably due to its poor permeation of the outer membrane, β-lactamase susceptibility, and high propensity for efflux (P. aeruginosa MIC 90 ≥ 1024 μg/mL, n = 20 panel). 3,7 To address the poor activity of 2, we focused on improving permeation by introducing siderophore mimics to promote uptake. 8−10 Siderophores are small Fe-chelating molecules synthesized and secreted by bacteria to scavenge iron from the host. 9,11 The iron-complexed siderophores are then brought into the cell via the iron uptake machinery, enabling the bacteria to access the much needed nutrient. It has been shown that introduction of iron-chelating groups to a monocyclic β-lactam scaffold ca...

Targeting Antibiotic Resistance

“…Indeed, compared to aztreonam ( 49 ; Figures 33 and 34 A),160 another similar monobactam, the molecule misses some favorable interactions, such as a salt bridge with Arg489 and a hydrophobic pocket interaction with the gem ‐dimethyl group of the antibiotic (Figure 34 B) 161. Based on these structure‐based findings, medicinal chemists tried to install the siderophore moiety at a more beneficial position 161, 162, 163. Compound 50 (Figure 33, discovered at AstraZeneca) represents a most recent successful example of such a structure‐based approach that allows the design of siderophore‐conjugated monocarbams with optimized binding interactions to P. aeruginosa PBP3 (Figure 34 C) 163.…”

“…Based on these structure‐based findings, medicinal chemists tried to install the siderophore moiety at a more beneficial position 161, 162, 163. Compound 50 (Figure 33, discovered at AstraZeneca) represents a most recent successful example of such a structure‐based approach that allows the design of siderophore‐conjugated monocarbams with optimized binding interactions to P. aeruginosa PBP3 (Figure 34 C) 163. Besides reinstalling the strong interaction of the drug molecule with Arg489, it positions the polar siderophore in a more hydrophilic environment and allows the drug to make additional interactions with the target protein PBP3 (Figure 34 C).…”

Antibiotikaresistenzen gezielt überwinden

“…B. die Salzbrücke mit Arg489 und die hydrophobe Wechselwirkung mit den zwei geminalen Methylgruppen des Antibiotikums (Abbildung B) . Auf Grundlage dieser strukturbasierten Erkenntnisse haben Medizinalchemiker versucht, die Siderophorgruppe an einer geeigneteren Stelle zu platzieren …”

“…Verbindung 50 (Abbildung , entwickelt von AstraZeneca) stellt das neueste erfolgreiche Beispiel eines solchen strukturbasierten Vorgehens dar, das es ermöglichte, ein Siderophor‐Monocarbam‐Konjugat mit verbesserten Wechselwirkungen mit PBP3 von P. aeruginosa zu entwerfen (Abbildung C) . Neben der Wiederherstellung der starken Wechselwirkung des Wirkstoffs mit Arg489 positioniert es das polare Siderophor in einer hydrophileren Umgebung, sodass der Wirkstoff zusätzliche Wechselwirkungen mit dem Zielprotein PBP3 eingehen kann (Abbildung C).…”

“…Neben der Wiederherstellung der starken Wechselwirkung des Wirkstoffs mit Arg489 positioniert es das polare Siderophor in einer hydrophileren Umgebung, sodass der Wirkstoff zusätzliche Wechselwirkungen mit dem Zielprotein PBP3 eingehen kann (Abbildung C). Verbindung 50 hat exzellente pharmakokinetische Eigenschaften und starke zelluläre Wirksamkeit gegen P. aeruginosa ( P. aeruginosa ARC545; MHK=0.5 μg mL −1 ) …”