Tying the Knot: In Silico Design of Foldable Lasso Peptides

Area of Science:

• Natural Product Synthesis
• Peptide Chemistry
• Computational Biology

Background:

• Lasso peptides possess unique threaded structures offering exceptional stability.
• Chemical synthesis of lasso peptides is challenging, yielding non-threaded isomers due to entropic folding difficulties.
• Understanding and enhancing pre-lasso conformations is crucial for successful synthesis.

Purpose of the Study:

• To investigate strategies for enhancing the stability of pre-lasso conformations.
• To explore sequence optimization, chemical modification, and disulfide incorporation for improved lasso peptide formation.

Main Methods:

• Utilized Rosetta fixed backbone design to identify optimal sequences for class II lasso peptides.
• Employed enhanced sampling with well-tempered metadynamics to assess pre-lasso stability.
• Investigated chemical modifications and disulfide cross-linking effects on pre-lasso conformation stability.

Main Results:

• Designed sequences showed improved pre-lasso stability compared to non-threaded conformations.
• Chemical modifications, particularly with non-canonical amino acids, increased pre-lasso formation probability.
• Disulfide cross-linking alone decreased stability, but combined with modifications, enhanced pre-lasso stabilization.

Conclusions:

• Sequence design, non-canonical amino acids, and guided cross-linking can augment lasso peptide stability.
• These strategies increase the accessibility of the lasso motif for de novo formation.
• The study provides foundational strategies for designing synthetically accessible lasso peptides.