Single Atom Editing of the Glycosylated Natural Product Fidaxomicin Improves Acid Stability and Retains Antibiotic Activity

22 February 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Fidaxomicin (Fdx) constitutes a glycosylated natural product with excellent antibacterial activity against various Gram-positive bacteria but is only approved for Clostridioides difficile infections. Poor water solubility and acid lability preclude its use for other infections. Herein, we describe our strategy to overcome the acid lability by introducing acid stable S-linked glycosides. We describe the direct, diastereoselective modification of unprotected Fdx without the need to avoid air or moisture. Using our newly established approach, Fdx was converted to the single atom exchanged analogue S-Fdx, in which the acid labile O-glycosidic bond to the noviose sugar is replaced by the acid stable S-glycosidic bond. Studies of the antibacterial activity of a structurally diverse set of thioglycoside derivatives revealed high potency of acyl derivatives of S-Fdx against Clostridioides difficile (MIC range: 0.12–4 μg/mL) and excellent potency against Clostridium perfringens (MIC range: 0.06–0.5 μg/mL).


Semi synthesis
natural products
single atom exchange

Supplementary materials

Supporting Information
Supplementary figures and tables, experimental procedures, compound characterization, crystallographic data, and NMR spectra of new compounds are provided in the Supplementary information file.
Detailed procedures and results of DP4+ calculations are provided in the Supplementary information DP4+ file (SI_DP4+).

Supplementary weblinks


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