Synthesis and Mechanism of Action of Group a Streptogramin Antibiotics That Overcome Resistance

Natural products serve as chemical blueprints for the majority of classes of antibiotics in our clinical arsenal. The evolutionary process by which these molecules arise is inherently accompanied by the co-evolution of resistance mechanisms that shorten the clinical lifetime of any given class. Virginiamycin acetyltransferases (Vats) are resistance proteins that provide protection against streptogramins, potent Gram-positive antibiotics that inhibit the bacterial ribosome. Due to the challenge of selectively modifying the chemically complex, 23-membered macrocyclic scaffold of group A streptogramins, analogs that overcome Vat resistance have not been previously accessible. Here we report the design, synthesis, and antibacterial evaluation of group A streptogramin antibiotics with unprecedented structural variability. Using cryo-electron microscopy and forcefield-based refinement, we characterize the binding of eight analogs to the bacterial ribosome at high resolution (2.4-2.8 Å), revealing new binding interactions that extend into the peptidyl tRNA binding site and towards synergistic binders that occupy the nascent peptide exit tunnel. Two of these analogs have excellent activity against a streptogramin-resistant strain of S. aureus expressing VatA and exhibit decreased acetylation rates in vitro. Our results demonstrate that the combination of rational design and modular chemical synthesis can revitalize classes of antibiotics that are limited by naturally arising resistance mechanisms.