Target-specific design of drug-like PPI inhibitors via hotspot-guided generative deep learning

Protein–protein interactions (PPIs) are vital therapeutic targets. However, the large and flat PPI interfaces pose challenges for the development of small-molecule inhibitors. Traditional computer-aided drug design approaches typically rely on pre-existing libraries or expert knowledge, limiting the exploration of novel chemical spaces needed for effective PPI inhibition. To overcome these limitations, we introduce Hot2Mol, a deep learning framework for the de novo design of drug-like, target-specific PPI inhibitors. Hot2Mol generates small molecules by mimicking the pharmacophoric features of hot-spot residues, enabling precise targeting of PPI interfaces without the need for bioactive ligands. The framework integrates three key components: a conditional transformer for pharmacophore-guided, drug-likeness-constrained molecular generation; an E(n)-equivariant graph neural network for accurate alignment with PPI hot-spot pharmacophores; and a variational autoencoder for generating novel and diverse molecular structures. Experimental evaluations demonstrate that Hot2Mol outperforms baseline models across multiple metrics, including docking affinities, drug-likenesses, synthetic accessibility, validity, uniqueness, and novelty. Furthermore, molecular dynamics simulations confirm the good binding stability of the generated molecules. Case studies underscore Hot2Mol’s ability to design high-affinity and selective PPI inhibitors, demonstrating its potential to accelerate rational PPI drug discovery.