Target-Specific De Novo Peptide Binder Design with DiffPepBuilder

TL;DR

This paper introduces DiffPepBuilder, a novel diffusion-based method for de novo design of target-specific peptide binders that effectively recalls native structures, generates novel binders, and enhances stability through disulfide bonds.

Contribution

The study presents DiffPepBuilder, a new SE(3)-equivariant diffusion model trained on a large synthetic dataset for peptide binder design, outperforming existing methods in structure and sequence recall.

Findings

DiffPepBuilder accurately recalls native peptide structures and sequences.

It generates novel peptide binders with improved binding free energy.

Disulfide bonds increase peptide stability and binding performance.

Abstract

Despite the exciting progress in target-specific de novo protein binder design, peptide binder design remains challenging due to the flexibility of peptide structures and the scarcity of protein-peptide complex structure data. In this study, we curated a large synthetic dataset, referred to as PepPC-F, from the abundant protein-protein interface data and developed DiffPepBuilder, a de novo target-specific peptide binder generation method that utilizes an SE(3)-equivariant diffusion model trained on PepPC-F to co-design peptide sequences and structures. DiffPepBuilder also introduces disulfide bonds to stabilize the generated peptide structures. We tested DiffPepBuilder on 30 experimentally verified strong peptide binders with available protein-peptide complex structures. DiffPepBuilder was able to effectively recall the native structures and sequences of the peptide ligands and to generate novel peptide binders with improved binding free energy. We subsequently conducted de novo generation case studies on three targets. In both the regeneration test and case studies, DiffPepBuilder outperformed AfDesign and RFdiffusion coupled with ProteinMPNN, in terms of sequence and structure recall, interface quality, and structural diversity. Molecular dynamics simulations confirmed that the introduction of disulfide bonds enhanced the structural rigidity and binding performance of the generated peptides. As a general peptide binder de novo design tool, DiffPepBuilder can be used to design peptide binders for given protein targets with three dimensional and binding site information.