Zero-shot design of drug-binding proteins via neural selection-expansion
Benjamin N. Fry, Kaia Slaw, Nicholas F. Polizzi · bioRxiv (Cold Spring Harbor Laboratory) · 2025
Abstract Computational design of molecular recognition remains challenging despite advances in deep learning 1–3 . The design of proteins that bind to small molecules has been particularly difficult because it requires simultaneous optimization of protein sequence, protein structure, and ligand conformation 1–7 . Despite their promise, current deep-learning algorithms have struggled to navigate this landscape, precluding the zero- or few-shot design of binders. Here we show that the combination of two neural networks in an iterative design algorithm can create small-molecule binding proteins from scratch with high accuracy. To optimize a design in the joint distribution of sequence, structure, and ligand conformation, we use a pair of neural networks that were trained on reciprocal tasks. We train and use a graph neural network, LASErMPNN, to design protein sequence given protein−ligand co-structure, and we use RoseTTAFold-All Atom 8 (RFAA) to predict protein−ligand co-structure given protein sequence. We iteratively apply these two networks to design proteins that bind the drug, exatecan, a topoisomerase I inhibitor that is prone to inactivation by hydrolysis 9 . Each of four experimentally tested designs bound the drug, with the lowest dissociation constant ( K d ) near 100 nM. The hit rate and highest affinity design each surpassed the current state-of-the-art method by 5- and 70-fold, respectively. We further show that LASErMPNN can improve upon its own designs in a manner resembling chain-of-thought reasoning. Without experimental input, LASErMPNN suggested two mutations that increased affinity by over two orders of magnitude ( K d = 1.2 ± 0.2 nM). Designs were selective, structurally accurate, and achieved their intended purpose to protect the drug from hydrolysis. Our work describes a recipe for using neural networks to automate the design of high affinity small-molecule binding proteins, which should have wide application in the creation of novel drug-delivery vehicles, antidotes, sensors, and enzymes.