Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initiates viral infection by binding its surface spike protein to the human angiotensin-converting enzyme 2 (hACE2) receptor. Precise delineation of spike–hACE2 engagement is essential for viral entry and a prime target for therapeutic intervention. However, the current antiviral strategies provided only endpoint readouts and delayed the prioritization against emerging variants. Here, this study introduced novel antiviral compounds designed via a NanoLuc Binary Technology-based pseudovirus [NanoBiT; a structural complementation reporter composed of a Large BiT (LgBiT) and a Small BiT (SmBiT)]. Upon Omicron BA.2-SmBiT spike pseudoviruses infecting LgBiT–hACE2 cells, reconstituted NanoLuc generated quantifiable bioluminescence for real-time spike–hACE2 interaction during viral infection. Within this framework, dual-functional theranostic Anti-spike peptide (S7; ACTPHVSPTHCS) and the Anti-hACE2 peptide (A6; WSTDPGAHLRDY) were identified that not only inhibit SARS-CoV-2 entry by targeting spike and hACE2 proteins, but also serve as diagnostic probes for real-time monitoring. Under optimized conditions, significant inhibition of virus infection was validated in both Anti-spike peptide-treated pseudovirus and Anti-hACE2 peptide-treated hACE2 cells, with a synergistic score of 17.092. Cross-variant efficacy extended to the Omicron JN.1 lineage using a newly constructed JN.1-SmBiT pseudovirus, with molecular docking supporting binding at conserved residues. LgBiT–hACE2 transgenic mice and noninvasive bioluminescence imaging verified in vivo suppression and demonstrated enhanced inhibition with combined treatment. This programmable peptide–NanoBiT framework provided multifunctional compounds that integrate therapeutic efficacy with diagnostic capability. Importantly, the modular design highlights its adaptability to other virus–receptor interactions to underscore its potential in pandemic preparedness.
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