PepINVENT: generative peptide design beyond natural amino acids

Journal article, 2025

Peptides play a crucial role in drug design and discovery whether as a therapeutic modality or a delivery agent. Non-natural amino acids (NNAAs) have been used to enhance the peptide properties such as binding affinity, plasma stability and permeability. Incorporating novel NNAAs facilitates the design of more effective peptides with improved properties. The generative models used in the field have focused on navigating the peptide sequence space. The sequence space is formed by combinations of a predefined set of amino acids. However, there is still a need for a tool to explore the peptide landscape beyond this enumerated space to unlock and effectively incorporate the de novo design of new amino acids. To thoroughly explore the theoretical chemical space of peptides, we present PepINVENT, a novel generative AI-based tool as an extension to the small molecule molecular design platform, REINVENT. PepINVENT navigates the vast space of natural and non-natural amino acids to propose valid, novel, and diverse peptide designs. The generative model can serve as a central tool for peptide-related tasks, as it was not trained on peptides with specific properties or topologies. The prior was trained to understand the granularity of peptides and to design amino acids for filling the masked positions within a peptide. PepINVENT coupled with reinforcement learning enables the goal-oriented design of peptides using its chemistry-informed generative capabilities. This study demonstrates PepINVENT's ability to explore the peptide space with unique and novel designs and its capacity for property optimization in the context of therapeutically relevant peptides. Our tool can be employed for multi-parameter learning objectives, peptidomimetics, lead optimization, and a variety of other tasks within the peptide domain.