Drug Resistance Predictions Based on a Directed Flag Transformer

The continuous evolution of the SARS-CoV-2 virus poses a significant challenge to global public health. Of particular concern is the potential resistance to the widely prescribed drug PAXLOVID, of which the main ingredient nirmatrelvir inhibits the viral main protease (Mpro). Here, we developed CAPTURE (direCted flAg laPlacian Transformer for drUg Resistance prEdictions) to analyze the effects of Mpro mutations on nirmatrelvir-Mpro binding affinities and identify potential drug-resistant mutations. CAPTURE combines a comprehensive mutation analysis with a resistance prediction module based on DFFormer-seq, which is a novel ensemble model that leverages a new Directed Flag Transformer and sequence embeddings from the protein and small-molecule-large-language models. Our analysis of the evolution of Mpro mutations revealed a progressive increase in mutation frequencies for residues near the binding site between May and December 2022, suggesting that the widespread use of PAXLOVID created a selective pressure that accelerated the evolution of drug-resistant variants. Applied to mutations at the nirmatrelvir-Mpro binding site, CAPTURE identified several potential resistance mutations, including H172Y and F140L, which have been experimentally confirmed, as well as five other mutations that await experimental verification. CAPTURE evaluation in a limited experimental data set on Mpro mutants gives a recall of 57\% and a precision of 71\% for predicting potential drug-resistant mutations. Our work establishes a powerful new framework for predicting drug-resistant mutations and real-time viral surveillance. The insights also guide the rational design of more resilient next-generation therapeutics.