Biological and Medicinal Chemistry

Spherical Neutralizing Aptamer Inhibits SARS-CoV-2 Infection

Abstract

New neutralizing agents against SARS-CoV-2 and the associated mutant strains are urgently needed for the treatment and prophylaxis of COVID-19. Herein, we develop a spherical cocktail neutralizing aptamer-gold nanoparticle (SNAP) to synergistically block the interaction of SARS-CoV-2 receptor-binding domain (RBD) and angiotensin-converting enzyme-2 (ACE2). Taking advantage of the simultaneous recognition of multi-homologous and multi-heterogenous neutralizing aptamers and dimensionally matched nano-scaffolds, the SNAP exhibits increased affinity to the RBD with a dissociation constant value of 5.46 pM and potent neutralization against authentic SARS-CoV-2 with a half-maximal inhibitory concentration of 142.80 aM. Additional benefits include the multi-epitope blocking capability of the aptamer cocktail and the steric hindrance of the nano-scaffold, which further covers the ACE2 binding interfaces and affects the conformational transition of the spike protein. As a result, the SNAP strategy exhibits broad neutralizing activity, almost completely blocking the infection of N501Y and D614G mutant strains. Overall, the SNAP strategy provides a new direction for development of anti-virus infection mechanisms, both to fight the COVID-19 pandemic and serve as a powerful technical reserve for future unknown pandemics.

Content

Thumbnail image of Manuscript.pdf

Supplementary material

Thumbnail image of SI.pdf
SI