Structure-Guided Synthesis of Next-Generation Group B Streptogramins to Overcome Resistances via Synergistic Effects with Their Group A Counterparts

• Applicant: Dr. Manuel Einsiedler
• Subject Area: Organic Molecular Chemistry - Synthesis and Characterisation ; Pharmacy
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 558816711

In recent decades, dangerous pathogens like methicillin-resistant S. aureus (MRSA) or vancomycin-resistant Enterococci (VRE) spread mainly across hospitals. VREs exhibit intrinsic resistance against a wide range of known antibiotics and were notoriously known for their high mortality rates of up to 40% in hospitals in the 1990s. The first drug applicable to VRE infections was Synercid(R), which contains a 70/30 mixture of streptogramins (SGs) A and B (dalfopristin/quinupristin), which are semisynthetic analogs of the natural products virginiamycin M2 and pristinamycin IA. These unique, paired antibiotics exhibit highly synergistic activity by sequentially binding to their target, the bacterial ribosome. While the Seiple Group have optimized group A SGs to overcome several resistance mechanisms using chemical synthesis, the group B components have not yet been the subject of such an optimization. The present proposal aims to synthesize next-generation group B SGs with enhanced activity, the ability to overcome resistances, and improved water solubility. These analogs will also be designed to synergize with group A SGs that have already been synthesized by the Seiple Group. To achieve this, the project is subdivided into three tasks:1) A set of fully synthetic group B SGs will be synthesized using an established solid-phase peptide synthesis (SPPS) route. The amino acid building blocks will be inspired by recent high-resolution structural data of SGs bound to the bacterial ribosome, which was obtained by cryo-electron microscopy (cryo-EM), as well as related SG natural products. For a streamlined derivatization, selective modifications will be introduced on a late stage. 2) A recently described resistance mechanism of S. aureus against group B SGs is based on virginiamycin lyase (Vgb), which cleaves the backbone ester between the threonine and phenylglycine portion. This aim will focus on synthesizing backbone-modified analogs, such as derivatives that replace the ester bond in the macrocycle with more stable isosteres. An initial goal will be replacement with an amide by the stereoselective synthesis of amino-threonine and integration of this compound into the SPPS route. The activity of these compounds against Vgb-harboring strains will be evaluated. 3) Most promising candidates of aims 1) and 2) will be optimized concerning their solubility. This will be achieved by sophisticated exchange/modification of amino acid building blocks to increase polarity. All novel analogs will be assessed for their minimal inhibitory concentrations against a variety of bacterial pathogens and their synergy with group A SGs. Through collaboration with the Fraser lab, the binding of promising candidates will be evaluated by cryo-EM. These data can then inform the next round of synthesis, hence forming an efficient pipeline for the generation of first-in-class, fully synthetic group B SG antibiotics that will overcome clinically urgent antimicrobial resistance.

• DFG Programme: WBP Fellowship
• International Connection: USA
• Host: Professor Dr. Ian Seiple