Towards total synthesis and medicinal chemistry of calcium-dependent antibacterial cyclic peptides

Abstract

Calcium-dependent antibacterial cyclic peptides (CDAs) are compounds that require calcium ions to exhibit antibacterial activities. They are active against Gram-positive bacteria, including multidrug-resistant strains such as methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococci (VRE). Currently, there are seven classes of CDAs which have been discovered by employing culture-dependent method and genome-mining method. The most recognized member of CDAs is daptomycin, which has been approved by the U.S. Food and Drug Administration in 2003 for the treatment of complicated skin-structure infections and in 2006 for the treatment of bacteremia. Since the launching of daptomycin in 2003, daptomycin remains the only CDA in clinical use to-date. The development of other CDAs and daptomycin derivatives as new systematic antibiotics for clinical use has been unsuccessful. In addition, the mechanism of action of daptomycin has yet to be fully elucidated, despite its clinical use since 2003. One of the reasons that impeded the development of next-generation daptomycin antibiotics was the lack of efficient synthetic routes to access structurally diverse analogues, which are crucial for systematic structure-activity relationship (SAR) studies. In this study, we have prepared a library of 80 daptomycin analogues with modifications spanning different parts of the molecule based on the total synthesis of daptomycin that our group developed in 2013. These structurally diverse daptomycin analogues allowed us to establish a systematic SAR. Among them, analogues with higher antibacterial activities compared to daptomycin were identified. One of these analogues, termed kynomycin, was further examined by a series of in vitro and in vivo assays to demonstrate its superior antibacterial activities compared to daptomycin against daptomycin-susceptible and resistant pathogens. Based on the results, kynomycin exhibits the potential to be developed as the next-generation daptomycin antibiotic. A54145 is a CDA which shares remarkable structural similarity to daptomycin. These two CDAs are believed to possess very similar mechanism of actions, except that A54145 is less inhibited by pulmonary surfactant. To produce daptomycin analogues that retain high potency in the presence of the surfactant, development of hybrid analogues of A54145 and daptomycin was proposed and attempted previously. However, being limited by the biosynthetic or chemoenzymatic methods employed, the studies on hybrid analogues had little success. To overcome the limitation, we established the first total synthesis of A54145 in this study. To establish the total synthesis, we first developed efficient synthetic routes to access the nonproteinogenic amino acids building blocks of 3-hydroxyasparagine (3-HO-Asn), 3-methoxyaspatic acid (3-MeO-Asp) and 3-methylglutamic acid (3-mGlu). Importantly, the total synthesis of A54145 has allowed for unambiguous stereochemical determination of the absolute configurations at the  carbon of 3-HO-Asn and 3-MeOAsp, consisting of 3S-HO-Asn and 3R-MeOAsp. The findings reported in this study, which include a systematic SAR study of daptomycin, identification of a daptomycin analogue as the potential drug candidate, and the establishment of total synthesis of A54145, will facilitate the search of daptomycin-based compounds with improved pharmacological properties, and the development of CDAs other than daptomycin as antibiotics in clinical use in the future.