Structural Design and Synthesis of Cyclosenegalin A Analogue

Abstract

Computational approaches have become increasingly popular in peptide synthesis. In this study, we report the computationally assisted design and synthesis of a cyclosenegalin A analogue. The original cyclosenegalin A was previously synthesized with low yield and exhibited no antimicrobial activity. To address these limitations, computational tools such as PEP-FOLD4, iAMPpred, and AI4AMP were employed to design the analogue, aiming to facilitate cyclization and enhance antimicrobial properties. The computational analysis of cyclosenegalin A and its analogs identified c-AVKPGLK as the most promising candidate for further development. It demonstrated strong antimicrobial potential with the highest antibacterial and antifungal activity, along with a compact structure favorable for cyclization. The linear precursor of c-AVKPGLK also formed a stable β-turn structure, making it well-suited for synthesis. The synthesis was conducted using a combination of solid-phase and liquid-phase peptide synthesis. The linear precursor was synthesized using the Fmoc strategy with HATU as the coupling agent and 2-chlorotrityl chloride resin. Head-to-tail cyclization was performed in dilute concentration using a dropwise method with HATU as the coupling agent. The linear precursor synthesis achieved a yield of 97.76%, while the cyclization process yielded 23.38%. The final compound, c-AVKPGLK, was characterized using HR-ToFMS, ¹H NMR, ¹³C NMR, HMQC, HMBC, TOCSY, and ROESY.