Peptide mediated colorimetric detection of SARS-CoV-2 using gold nanoparticles: a molecular dynamics simulation study

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has necessitated the development of a rapid, simple yet selective naked-eye detection methodology that does not require any advanced instrumental techniques. In this study, we report our computational findings on the detection of SARS-CoV-2 using peptide- functionalized gold nanoparticles (GNPs). The peptide has been screened from angiotensin-converting enzyme 2 (ACE2) receptor situated on the surface of the host cell membrane which interacts with the spike protein of SARS-CoV-2, resulting entry of the virus into the host cell. As a result, the peptide-functionalized GNPs possess excellent affinity towards the spikes of SARS-CoV-2 and readily get aggregated once exposed to SARS-CoV-2 antigen or virus. The stability of the peptides on the surface of GNPs and their interaction with the spike protein of the virus have been investigated using coarse-grained molecular dynamic simulations. The potential of mean force calculation of spike protein confirmed strong binding between peptide and receptor-binding domain (RBD) of spike protein. Our in silico results demonstrate the potential of the peptide-functionalized GNPs in the development of simple and rapid colorimetric biosensors for clinical diagnosis. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00894-022-05184-x.