Structure-activity relationships in lipopolysaccharide neutralizers: Design, synthesis, and biological evaluation of a 540-membered amphipathic bisamide library

Lipopolysaccharides (LPS), also called "endotoxins", are outer-membrane constituents of Gram-negative bacteria. Lipopolysaccharides play a key role in the pathogenesis of "septic shock", a major cause of mortality in the critically ill patient. We had earlier shown that small molecules bind and neutralize LPS if they contain (i) two protonatable cationic groups separated by a distance of ∼14 Å to facilitate interactions with the phosphate moieties on the lipid A component of LPS and (ii) a long-chain aliphatic hydrocarbon to promote hydrophobic interactions. In an effort to identify optimal scaffolds possessing the above structural requirements, we now present an evaluation of a rationally designed combinatorial library in which the elements of the scaffold are systematically varied to maximize sampling of chemical space. Leads obtained via molecular analyses of the screening results were resynthesized and evaluated in greater detail with regard to the affinity of the interaction with LPS, as well as neutralization of endotoxicity in in vitro assays. The examination of a moderately sized 6 × 6 × 15 (540-membered) focused library allowed the assessment of the structural contributions to binding by the long-chain aliphatic tails, distance between charged amino groups, and potential aromatic CH-π or OH-π interactions. These findings are of value in further iterations of design and development of specific and potent endotoxin sequestrants.