Lasso peptides are a type of natural product made by bacteria that have a unique lasso shape, making them extremely stable and resistant to extreme conditions. These peptides have shown potential as therapeutics due to their antibacterial, antiviral, and anti-cancer properties. The peptides are ribosomally synthesized and post-translationally modified, with two enzymes working together to convert a linear precursor peptide into the distinctive lasso structure. However, the process of how the cyclase folds the lasso peptide has been a challenge due to the difficulty in working with the enzymes.
In a recent study published in Nature Chemical Biology, researchers used the artificial intelligence program AlphaFold to predict the structure of the FusC protein, a cyclase involved in the lasso peptide folding process. This prediction allowed the researchers to identify which cyclase active site residues were crucial for interacting with the lasso peptide substrate. Molecular dynamics simulations were also used to computationally understand how the lasso is folded by the cyclase. The researchers found that the backwall region of the active site, specifically helix 11 in FusC, played a significant role in the folding process.
Through cell-free biosynthesis experiments, the researchers identified a version of FusC with a mutation on helix 11 that could fold lasso peptides which were previously unable to be folded by the original cyclase. This data confirmed the model for lasso peptide folding developed by the researchers using their computational approaches. The researchers also showed that similar molecular interactions are present in different cyclases across different phyla, suggesting a generalizable model for lasso peptide folding. Collaborating with the company Lassogen, the researchers demonstrated how these insights can guide cyclase engineering to produce lasso peptides that were previously difficult to make.
The researchers engineered a different cyclase, McjC, to efficiently produce a potent inhibitor of a cancer-promoting integrin as a proof-of-concept. This ability to generate lasso peptide diversity through cyclase engineering is crucial for optimizing drugs and expanding the therapeutic potential of these molecules. The study highlights how interdisciplinary collaborations, powerful computing, and advances in artificial intelligence and cell-free biosynthetic methods have contributed to solving the complex problem of lasso peptide folding. The research was made possible through partnerships with external colleagues at Lassogen and within the Carl R. Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign.