Chemoenzymatic synthesis of daptomycin analogs active against daptomycin-resistant strains

• Published in: Applied microbiology and biotechnology 2020-09, Vol.104 (18), p.7853-7865
• Main Authors: Scull, Erin M., Bandari, Chandrasekhar, Johnson, Bryce P., Gardner, Eric D., Tonelli, Marco, You, Jianlan, Cichewicz, Robert H., Singh, Shanteri
• Format: Article
• Language: English
• Subjects: Alkylation; Analogs; Anti-Bacterial Agents - pharmacology; Anti-Bacterial Agents - therapeutic use; Antibacterial activity; Antibiotic resistance; Antibiotics; Biomedical and Life Sciences; Biotechnologically Relevant Enzymes and Proteins; Biotechnology; Care and treatment; Complexity; Daptomycin; Daptomycin - pharmacology; Drug resistance; Drug resistance in microorganisms; Enterococcus; Enzymes; Health aspects; Indoles; Life Sciences; Methicillin; Methicillin-Resistant Staphylococcus aureus; Microbial Genetics and Genomics; Microbial Sensitivity Tests; Microbiology; Prenyltransferases; Protein engineering; Pyrophosphates; Residues; Selectivity; Staphylococcus aureus; Staphylococcus aureus infections; Staphylococcus infections; Strains (organisms); Substrates; Synthesis; Tryptophan; Vancomycin
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-020-10790-x

Daptomycin is a last resort antibiotic for the treatment of infections caused by many Gram-positive bacterial strains, including vancomycin-resistant Enterococcus (VRE) and methicillin- and vancomycin-resistant Staphylococcus aureus (MRSA and VRSA). However, the emergence of daptomycin-resistant strains of S. aureus and Enterococcus in recent years has renewed interest in synthesizing daptomycin analogs to overcome resistance mechanisms. Within this context, three aromatic prenyltransferases have been shown to accept daptomycin as a substrate, and the resulting prenylated analog was shown to be more potent against Gram-positive strains than the parent compound. Consequently, utilizing prenyltransferases to derivatize daptomycin offered an attractive alternative to traditional synthetic approaches, especially given the molecule’s structural complexity. Herein, we report exploiting the ability of prenyltransferase CdpNPT to synthesize alkyl-diversified daptomycin analogs in combination with a library of synthetic non-native alkyl-pyrophosphates. The results revealed that CdpNPT can transfer a variety of alkyl groups onto daptomycin’s tryptophan residue using the corresponding alkyl-pyrophosphates, while subsequent scaled-up reactions suggested that the enzyme can alkylate the N1, C2, C5, and C6 positions of the indole ring. In vitro antibacterial activity assays using 16 daptomycin analogs revealed that some of the analogs displayed 2–80-fold improvements in potency against MRSA, VRE, and daptomycin-resistant strains of S. aureus and Enterococcus faecalis . Thus, along with the new potent analogs, these findings have established that the regio-chemistry of alkyl substitution on the tryptophan residue can modulate daptomycin’s potency. With additional protein engineering to improve the regio-selectivity, the described method has the potential to become a powerful tool for diversifying complex indole-containing molecules. Key points • CdpNPT displays impressive donor promiscuity with daptomycin as the acceptor. • CdpNPT catalyzes N1-, C2-, C5-, and C6-alkylation on daptomycin’s tryptophan residue. • Differential alkylation of daptomycin’s tryptophan residue modulates its activity.