MeDCycFold: A Rosetta Distillation Model to Accelerate Structure Prediction of Cyclic Peptides with Backbone N-methylation and D-amino Acids

Cao, Z.; Shang, T.; Cao, S.; Wang, L.; Wang, Z.; Qingyi, M.; Guo, J.; Duan, H.

doi:10.1101/2025.04.10.648099

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bioRxiv · 10.1101/2025.04.10.648099

MeDCycFold: A Rosetta Distillation Model to Accelerate Structure Prediction of Cyclic Peptides with Backbone N-methylation and D-amino Acids

Cao, Z.·Shang, T.·Cao, S.·Wang, L.·Wang, Z.·Qingyi, M.·Guo, J.·Duan, H.

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Abstract

Cyclic peptides with backbone N-methylated amino acids(BNMeAAs) and D-amino acids(D-AAs) have gained attention for their stability, membrane permeability, and other therapeutic potentials. Currently, Rosetta can predict their structures using energy calculations, but this method is heavily time-consuming. Moreover, structural data for cyclic peptides containing BNMeAAs and D-AAs are extremely insufficient to build a data-driven structure prediction model. To address these problems, we propose MeDCycFold, a deep learning-based Rosetta distillation model by fine-tuning the AlphaFold model. First, a cyclic peptide structure dataset is constructed using Rosetta by sampling massive conformations for cyclic peptides with BNMeAAs and D-AAs and evaluating their energy scores. Then, the AlphaFold model is fine-tuned with the extended 56 BNMeAAs and D-AAs. Besides, a relative position cyclic matrix is introduced for head-to-tail cyclization in the cyclic peptides. Finally, a force field is employed to reduce clashes in the predicted structures. Empirical experiments show that our proposed MeDCycFold speeds up structure prediction by 49 times while maintaining the prediction accuracy comparable to Rosetta, which can greatly accelerate the development of cyclic peptide drugs.

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Cao, Z., Shang, T., Cao, S., Wang, L., Wang, Z., Qingyi, M., Guo, J., Duan, H.. 2025-04-16. MeDCycFold: A Rosetta Distillation Model to Accelerate Structure Prediction of Cyclic Peptides with Backbone N-methylation and D-amino Acids. https://doi.org/10.1101/2025.04.10.648099

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