E(3)-invariant diffusion model for pocket-aware peptide generation

TL;DR

This paper introduces an E(3)-invariant diffusion model for generating peptide structures and sequences tailored to specific pockets, advancing computer-assisted drug discovery with a novel end-to-end approach.

Contribution

It presents a new de novo pocket-aware peptide generation network using two sequential diffusion models with E(3)-invariant structure representation.

Findings

Achieves performance comparable to state-of-the-art models

Demonstrates potential for receptor-specific peptide design

Provides a new tool for precise drug discovery

Abstract

Biologists frequently desire protein inhibitors for a variety of reasons, including use as research tools for understanding biological processes and application to societal problems in agriculture, healthcare, etc. Immunotherapy, for instance, relies on immune checkpoint inhibitors to block checkpoint proteins, preventing their binding with partner proteins and boosting immune cell function against abnormal cells. Inhibitor discovery has long been a tedious process, which in recent years has been accelerated by computational approaches. Advances in artificial intelligence now provide an opportunity to make inhibitor discovery smarter than ever before. While extensive research has been conducted on computer-aided inhibitor discovery, it has mainly focused on either sequence-to-structure mapping, reverse mapping, or bio-activity prediction, making it unrealistic for biologists to utilize such tools. Instead, our work proposes a new method of computer-assisted inhibitor discovery: de novo pocket-aware peptide structure and sequence generation network. Our approach consists of two sequential diffusion models for end-to-end structure generation and sequence prediction. By leveraging angle and dihedral relationships between backbone atoms, we ensure an E(3)-invariant representation of peptide structures. Our results demonstrate that our method achieves comparable performance to state-of-the-art models, highlighting its potential in pocket-aware peptide design. This work offers a new approach for precise drug discovery using receptor-specific peptide generation.