Discovery of Highly Active Derivatives of Daptomycin by Assessing the Effect of Amino Acid Substitutions at Positions 8 and 11 on a Daptomycin Analogue.

Daptomycin is an important antibiotic used for treating serious infections caused by Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci. Establishing structure-activity relationships of daptomycin is important for developing new daptomycin-based antibiotics with expanded clinical applications and for tackling the ever-increasing problem of antimicrobial resistance. Toward this end, Dap-K6-E12-W13, an active analogue of daptomycin in which the uncommon amino acids in daptomycin are replaced with their common counterparts, was used as a model system for studying the effect of amino acid variation at positions 8 and 11 on in vitro biological activity against a model organism, Bacillus subtilis, and calcium-dependent insertion into model membranes. None of the new peptides were more active than Dap-K6-E12-W13; however, substitution at positions 8 and/or 11 with cationic residues resulted in little or no loss of activity, and some of these analogues were able to insert into model membranes at lower calcium ion concentrations than the parent peptide. Incorporation of these cationic residues into positions 8 and/or 11 of daptomycin itself yielded some derivatives that exhibited lower minimum inhibitory concentrations than daptomycin against B. subtilis 1046 as well as comparable and sometimes superior activity against clinical isolates of MRSA.

The effect of replacing the ester bond with an amide bond and of overall stereochemistry on the activity of daptomycin.

Daptomycin, a cyclic lipodepsipeptide antibiotic, has been used clinically since 2003 to treat serious infections caused by Gram-positive bacteria. Although 37 years have passed since daptomycin's discovery, its mechanism of action is still debated. In this report, the effect of replacing the ester bond with an amide bond, and overall stereochemistry, on daptomycin's biological activity was examined. Two peptides were prepared in which the threonine4 residue in the active daptomycin analog, Dap-K6-E12-W13, was replaced with (2S,3R)-diaminobutyric acid ((2S,3R)-DABA) or its epimer (2S,3S-DABA) converting the ring-closing ester bond to an amide bond. Both of these peptides were found to be considerably less active than Dap-K6-E12-W13. These results, along with our previous studies on other daptomycin analogs, enabled us to conclude that the ester bond is crucial to daptomycin's activity. ent-Dap-K6-E12-W13 was found to be at least 133-fold less active than Dap-K6-E12-W13, indicating that a chiral interaction with a chiral target is essential to daptomycin's activity. Studies examining the binding of Dap-K6-E12-W13 and ent-Dap-K6-E12-W13 to model liposomes consisting of phosphatidylglycerol (PG) and phosphatidylcholine suggest that the stereochemistry of PG plays a crucial role in daptomycin-membrane interactions.

An entirely fmoc solid phase approach to the synthesis of daptomycin analogs.

Daptomycin is an important Ca2+ -dependent cyclic lipodepsipeptide antibiotic used to treat serious gram-positive infections. The search for daptomycin analogs with improved activity and their application as tools for studying its mechanism of action has prompted us to develop an entirely Fmoc solid phase approach to the synthesis of daptomycin analogs. Key to the success of this approach was the development of conditions that allowed for the formation of the ester bond on resin-bound peptides consisting of residues 1-10 and the decanoyl lipid tail. The esterification reaction proceeded more efficiently on Tentagel resin as opposed to standard polystyrene resin. This approach was used to synthesize a series of analogs in which each position of Dap-E12-W13, a relatively active daptomycin analog, was individually substituted by alanine. Only positions 2, 6, and 11 were found to be amenable to substitution by alanine in that the corresponding alanine analogs were only 1.5- to 4-fold less active than Dap-E12-W13. We also found that the daptomycin analog, Dap-K6-E12-W13, exhibits in vitro activity approaching that of daptomycin at physiological Ca2+ concentration. Studies with Dap-K6-E12-W13 and model liposomes indicate that this analog interacts with membranes by the same mechanism as daptomycin. This analog is currently being used as a lead for the development daptomycin analogs with improved activity.