Exploring Latent Space for Generating Peptide Analogs Using Protein Language Models

TL;DR

A novel method was proposed that utilized autoencoder shaped models to explore the protein embedding space, and generate novel peptide analogs by leveraging protein language models, and shows significant improvements over baseline models in similarity indicators of peptide structures, descriptors and bioactivities.

Abstract

Generating peptides with desired properties is crucial for drug discovery and biotechnology. Traditional sequence-based and structure-based methods often require extensive datasets, which limits their effectiveness. In this study, we proposed a novel method that utilized autoencoder shaped models to explore the protein embedding space, and generate novel peptide analogs by leveraging protein language models. The proposed method requires only a single sequence of interest, avoiding the need for large datasets. Our results show significant improvements over baseline models in similarity indicators of peptide structures, descriptors and bioactivities. The proposed method validated through Molecular Dynamics simulations on TIGIT inhibitors, demonstrates that our method produces peptide analogs with similar yet distinct properties, highlighting its potential to enhance peptide screening processes.

Figures (9)

• Figure 1: Method Flow Chart
• Figure 2: Morgan Fingerprint Similarities
• Figure 3: Sequences QSAR Similarities
• Figure 4: RDkit Descriptor Similarities
• Figure 5: Similarities & Alignment Score Difference