Covalently Engineered Protein Minibinders with Enhanced Neutralization Efficacy against Escaping SARS-CoV-2 Variants

Abstract

The rapid emergence and spread of escaping mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has significantly challenged our efforts in fighting against the COVID-19 pandemic. A broadly neutralizing reagent against these concerning variants is thus highly desirable for the prophylactic and therapeutic treatments of SARS-CoV-2 infection. We herein report a covalent engineering strategy on protein minibinders for potent neutralization of the escaping variants such as B.1.617.2 (Delta), B.1.617.1 (Kappa), and B.1.1.529 (Omicron) through in situ cross-linking with the spike receptor binding domain (RBD). The resulting covalent minibinder (GlueBinder) exhibited enhanced blockage of RBD-human angiotensin-converting enzyme 2 (huACE2) interaction and more potent neutralization effect against the Delta variant than its noncovalent counterpart as demonstrated on authentic virus. By leveraging the covalent chemistry against escaping mutations, our strategy may be generally applicable for restoring and enhancing the potency of neutralizing antibodies to SARS-CoV-2 and other rapidly evolving viral targets.

Accelerating PERx Reaction Enables Covalent Nanobodies for Potent Neutralization of SARS-Cov-2 and Variants

“…By introducing electron withdrawing fluorine substitution we designed and genetically encoded a novel latent bioreactive Uaa FFY, which afforded a marked 2.4-fold increase in reaction rate in the cross-linking of mNb6 with the Spike RBD over the original FSY. In a recent communication, 47 Han et al . exploited the FSY and PERx mechanism developed by us 19,24 and incorporated FSY into the Spike-specific minibinders de novo designed by the Baker group.…”

“…By introducing electron withdrawing fluorine substitution we designed and genetically encoded a novel latent bioreactive Uaa FFY, which afforded a marked 2.4-fold increase in reaction rate in the cross-linking of mNb6 with the Spike RBD over the original FSY. In a recent communication, 47 Han et al exploited the FSY and PERx mechanism developed by us 19,24 and incorporated FSY into the Spike-specific minibinders de novo designed by the Baker group. 8 The resultant FSY-minibinder required 2 h incubation to crosslink with the Spike RBD in vitro, and 2 h incubation with virus to show a moderate 6-fold increase in potency in neutralizing a single SARS-CoV-2 variant.…”

Accelerating PERx reaction enables covalent nanobodies for potent neutralization of SARS-CoV-2 and variants

“…By introducing electron-withdrawing fluorine substitution, we designed and genetically encoded a unique latent bioreactive Uaa (FFY), which afforded a marked 2.4-fold increase in reaction rate in the cross-linking of mNb6 with the spike RBD over the original FSY. In a recent communication, 49 Han and co-workers exploited the FSY and PERx mechanism developed by us 20,25 and incorporated FSY into the spike-specific minibinders de novo designed by the Baker group. 8 The resultant FSY-minibinder required 2 h incubation to cross-link with the spike RBD in vitro and 2 h incubation with the virus to show a moderate 6-fold increase in potency in neutralizing a single SARS-CoV-2 variant.…”

Human ACE2 Peptide-Attached Plasmonic-Magnetic Heterostructure for Magnetic Separation, Surface Enhanced Raman Spectroscopy Identification, and Inhibition of Different Variants of SARS-CoV-2 Infections

“…Because of the emergence of mutations on the spike (S) protein gene in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the death toll for the coronavirus disease-19 (COVID-19) pandemic reached more than 6.2 million as of June 2022. − As per Centers for Disease Control and Prevention (CDC), due to the mutations in the spike gene, different SARS-CoV-2 lineages such as B.1.1.7 (Alpha variant), B.1.351 (Beta variant), B.1.1.28.1 (Gamma variant), B.1.617.2 (Delta variant), and B.1.1.529 (Omicron variant) have emerged. − It is also reported that Omicron and Delta variants spread more easily than earlier variants. − Recent clinical studies indicate that due to 15 mutations in the receptor-binding domain (RBD), the delta and omicron strains have the capability to escape the immune response, which has been acquired by people in our society via COVID-19 infection or through several vaccines which have been administered in last two years. − All of the above data clearly indicate that designing a new bioconjugated material-based strategy to separate, detect, and block the omicron variant interactions are very important for our society. Driven by the need, here we report the development of magnetic-plasmonic heterostructures which synergistically exhibit magnetic and plasmonic characteristics for magnetic separation, plasmonic-based SERS identification, and prevention of the different variants virus to enter into the host cells via blocking spike the protein RBD binding with the host cells’ angiotensin converting enzyme 2 (ACE2).…”