Multiplexed detection of viral proteases through dual response peptide-assisted nanopore sensing

Abstract

Owing to their central roles in viral replication, main protease (Mpro) and papain-like protease (PLpro) are promising biomarkers for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Hence, the simultaneous sensing of Mpro and PLpro activities is a valuable approach for SARS-CoV-2 detection. Herein, we developed a dual response peptide probe for simultaneously monitoring the protease activities of Mpro and PLpro using a single aerolysin nanopore. The target proteases can specifically digest the probe at the corresponding cleavage sites, releasing the output peptide fragments composed of different amino acids. These fragments generated clearly distinguishable blocking currents in nanopore recording that can be assigned to each analyte, allowing accurate differentiation among multiple proteases. The approach enabled the sensitive detection of Mpro and PLpro activity without the need for any amplification or labeling. Furthermore, with excellent discrimination ability, the method can be applied to evaluate the activity of the two model proteases against a background of exhaled breath condensate. Importantly, since peptides with specific sequences serve as catalytic substrates of multiple enzymes, the proposed strategy would be applicable for accurate and multiplex quantification of different types of enzymes, which is critical for non-invasive early disease diagnosis.