Versatile synthesis of pathogen specific bacterial cell wall building blocks

Abstract

Full details on the design, strategies and tactics for development of a novel synthetic sequence to farnesyl lipid I and II analogs is reported. The modular route was based on a three coupling strategy involving an efficient solid phase synthesis of the elaborate peptide fragment, which proceeded with excellent yield and stereoselectivity and was efficiently applied for the convergent synthesis of 3-lipid I and II. Furthermore, the generality of this route was demonstrated by synthesis of 3-lipid I congeners that are characteristic for S. aureus and E. faecalis. All 3-lipid I and II building blocks were obtained in high purity revealing high spectroscopic resolution.

Fig. 1. Natural lipid I (1) and biosynthetically derived lipid II (2), key building blocks of bacterial cell wall biosynthesis: its farnesyl derivatives 3, 4 as improved agents for functional studies and interpeptidic analogs 5 and 6, bearing interpeptidic sequences characteristic for S. aureus as well as E. faecalis and S. pneumoniae.

Scheme 1. Modular three fragment retrosynthetic approach towards 3-lipid I analogs 3 and 4: novel solid phase based synthesis of pentapeptide.

Scheme 2. Improved synthesis of protected saccharide building block 7.

Scheme 3. Efficient synthesis of required amino acid building blocks 17 (part a), 26 (part b), 31, 33 and 35 (part c).

Scheme 4. Solid phase synthesis of pentapeptide 39 and epimerization during TMSE protection of terminal d-Ala. Reagents and conditions: (a) HO–d-Ala–Fmoc (41), DIPEA (b) Ac₂O, N-methylimidazole, DMF (c), 20% piperidine/DMF (d) HBTU, HOBt, amino acid, DIPEA, DMF (e) 20% HFIP/DCM.

Scheme 5. Stereoselective preparation of protected pentapeptide 40 by solid phase synthesis of tetrapeptide 43 and attachment of the final d-Ala residue in solution. Reagents and conditions: (a) HO–d-Ala–Fmoc (41), DIPEA (b) Ac₂O, N-methylimidazole, DMF (c), 20% piperidine/DMF (d) HBTU, HOBt, amino acid, DIPEA, DMF (e) 20% HFIP/DCM.

Scheme 6. Unsuccessful direct protection of pentaglycine 46.

Scheme 7. Solid phase synthesis of decapeptide 45 characteristic for S. aureus. Reagents and conditions: (a) HO–d-Ala–Fmoc (41), DIPEA (b) Ac₂O, N-methylimidazole, DMF (c), 20% piperidine/DMF (d) HBTU, HOBt, amino acid, DIPEA, DMF (e) 20% HFIP/DCM.

Scheme 8. Solid phase synthesis of heptapeptide 55 characteristic for E. faecalis and S. pneumoniae. Reagents and conditions: (b) 20% piperidine/DMF, (c) HBTU, HOBt, amino acid, DIPEA, DMF, (d) 20% HFIP/DCM.

Scheme 9. Completion of the total synthesis of 3-lipid I.

Scheme 10. Completion of the total synthesis of 3-lipid I (S. aureus).

Scheme 11. Completion of the total synthesis of 3-lipid I (E. faecalis, S. pneumoniae).

Scheme 12. Chemoenzymatic conversion of 3-lipid I (3) to 3-lipid II (4) using UDP–GlcNAc (66).