Rapid clearance of achiral small-molecule drugs using de novo-designed proteins and their cyclic and mirror-image variants

Small-molecule-binding proteins can neutralize toxins and cytotoxic drugs, but their development is hindered by unpredictable in vivo behaviour and the poor immunogenicity of small molecules, which limits antibody-based approaches. Here we present a strategy to engineer de novo-designed proteins for the effective clearance of Food and Drug Administration-approved drugs in healthy mice. As a proof of concept, we designed proteins that bind to the anticoagulant apixaban. Since apixaban lacks chirality, we used mirror-image synthesis and cyclization to enhance the designed protein’s in vivo stability. Both protein variants demonstrated effective activity, facilitating the rapid clearance of apixaban within 30 min. To assess the broader applicability of this approach, we extended our analysis to a de novo-designed protein targeting the anticancer drug rucaparib, further confirming its potential for small-molecule clearance. Our study shows that de novo-designed small-molecule-binding proteins can be used as antidotes in vivo, and that computational tools can be integrated with medicinal chemistry strategies for precise pharmacological interventions.