Natural product synthesis and optimization
Despite not having activity against wild type E. coli, two crystal structures of arylomycin A2 bound to a soluble fragment of E. coli SPase have been reported (Paetzel et al. 2004 and Luo et al. 2009). The arylomycin binds in an extended β-sheet conformation that likely mimics the binding of membrane bound pre-protein substrates. The C-terminal macrocycle of the arylomycin binds in a deep hydrophobic cleft and makes multiple H-bonds and hydrophobic interactions with the protein, while the C-terminal carboxyl group forms a critical salt bridge with the catalytic residues. The peptide tail extends down a shallow cleft in the surface of SPase and forms two H-bonds with backbone residues of the protein. The critical resistance-conferring residue, Pro84, interacts with the N-terminal end of the peptidic tail and appears to preclude the formation of a H-bond to a carbonyl oxygen of the arylomycin and possibly to alter the trajectory of the lipid moiety as it enters the membrane. While the crystal structures are likely to reveal little information about the biologically relevant structure of the lipid tail due to the use of a soluble truncated fragment of SPase and the absence of a membrane bilayer, it most likely adopts an extended conformation to maximize packing within the outer leaflet of the cytoplasmic membrane. Using this structural information as a guide, we are currently conducting structure-activity relationship studies of synthetic arylomycins.
In related work, we are also investigating the development of penem-based SPase inhibitors. In vitro SPase inhibition has been demonstrated for penem derivatives, but these compounds all lack antibacterial activity in vivo. We reported the first synthesis of a 5S penem SPase inhibitor, and we are doing SAR to investigate the determinants of SPase binding and antibiotic activity (examples of derivatives are shown below).
Our long-term goal is to use biological and genetic techniques to identify additional latent antibiotics that while currently narrow-spectrum, have the potential to be optimized by synthetic and medicinal chemistry into broad-spectrum therapeutics.