Structural optimization and photopharmacological studies of the cystobactamids class of natural products

Abstract

There is an urgent need to discover novel antibiotics, particularly with activity against Gram-negative bacteria that are the most threatening for public health. In the past, nature has been the main source of antibiotic scaffolds and can still provide novel chemical architectures. Cystobactamids are novel natural products isolated from Myxobacteria that possess an intriguing oligomeric scaffold composed of para-aminobenzoic acid derived moieties and show remarkable activity against clinically relevant Gram-negative bacteria. This thesis details a medicinal chemistry investigation of this novel natural product class based around cystobactamid 861-2. Multiple synthetic routes to the cystobactamids were established in order to prepare analogues with variations at different sites of the molecular scaffold. In sum more than 50 derivatives were synthesized and extensive structure-activity relationships were established. Cystobactamids with clearly improved antibacterial properties were identified from this study. Notably, the spectrum coverage of the class was extended to highly relevant Gram-negative bacteria such as K. pneumoniae and E. cloacae. Furthermore, several analogs active against P. aeruginosa were synthesized and the antimicrobial potency was enhanced against selected pathogens such as A. baumannii. Additionally, two possible bacterial resistance mechanisms were investigated. It was demonstrated that the protein Tsx does not affect the uptake of the cystobactamids and that the hydrolytic instability determined by the endopeptidase AlbD can potentially be overcome with a structural innovation, replacing the critical amide bond with a triazole. Finally, photoswitchable cystobactamids were synthesized with either the N- or C-terminal side of the molecule modified. These photoresponsive antibiotics suggested intriguing information regarding the binding mode of the cystobactamids with their target enzyme. To sum up, the chemical scaffold of the cystobactamids natural product was optimized and the activity against Gram-negative bacteria was enhanced. Essential structure activity relationships have been defined. This confirmed and highlighted the great potential of this class of natural products to yield novel antibiotics for the future.