SARS-CoV-2 Mpro and its inhibitory peptides from Spirulina platensis: Preparation, identification, in vitro and in silico characterization of activity and binding

Inhibition of the biological activity of SARS-CoV-2 main protease (Mpro) effectively prevents viral replication, thereby presenting a promising therapeutic target for Corona Virus Disease 2019 (COVID-19) intervention. This study aims to screen the Mpro inhibitory peptides from the natural nutritional supplement Spirulina platensis (S. platensis). Firstly, Mpro was successfully prepared by heterologous expression in E. coli and Mpro's activity was detected. Meanwhile, four distinct peptides derived from S. platensis were obtained through enzymatic hydrolysis of protein. Subsequently, highly active peptides were synthesized and their inhibition effects on Mpro were verified by in vitro experiment and computer simulations. Results showed that the extraction rate of the protein from S. platensis was 96.11 %, the activity of Mpro was 845.90 U mg⁻¹, the peptide MQGPNY could inhibit the activity of Mpro at the inhibition rate of 20.21 % ± 3.8 % at the concentration of 2 mmol L⁻¹. Furthermore, results from computer Simulation showed that the peptide MQGPNY forms four pairs of hydrogen bonds with Mpro, which are Gln189, Ser46, Thr26 and Glu166. In addition, there were ten free residues involved in hydrophobic contacts, including His164, His41, Thr24, Met49, Thr45, Thr25, Gly143, Asn142, Cys145 and Met165. The foundings could provide theoretical support for the use of protein and its hydrolysates from S. platensis in functional food and supplement formulations in the post-epidemic era.