Nanobody-peptide-conjugate (NPC) for passive immunotherapy against SARS-CoV-2 variants of concern (VoC): a prospective pan-coronavirus therapeutics

Abstract

The COVID-19 crisis, incited by the zoonotic SARS-CoV-2 virus, has quickly escalated into a catastrophic public health issue and a grave threat to humankind owing to the advent of mutant viruses. Multiple pharmaceutical therapies or biologics envision stopping the virus from spreading further; however, WHO has voiced concerns about the variants of concern (VoCs) inability to respond. Nanobodies are a new class of antibody mimics with binding affinity and specificity similar to classical mAbs, as well as the privileges of a small molecular weight, ease of entry into solid tissues, and binding cryptic epitopes of the antigen. Herein, we investigated multiple putative anti-SARS-CoV-2 nanobodies targeting the Receptor binding domain of the WHO-listed SARS-CoV-2 variants of concern using a comprehensive computational immunoinformatics methodology. With affinity maturation via alanine scanning mutagenesis, we remodeled an ultrapotent nanobody with substantial breadth and potency, exhibiting pico-molar binding affinities against all the VoCs. An antiviral peptide with specificity for ACE-2 receptors was affixed to make it multispecific and discourage viral entry. Collectively, we constructed a broad-spectrum therapeutic biparatopic nanobody-peptide conjugate (NPC) extending coverage to SARS-CoV-2 VoCs RBDs. We PEGylated the biparatopic construct with 20kD maleimide-terminated PEG (MAL-(PEG)n-OMe) to improve its clinical efficacy limiting rapid renal clearance, and performed in silico cloning to facilitate future experimental studies. Our findings suggest that combining biparatopic nanobody conjugate with standard treatment may be a promising bivariate tool for combating viral entry during COVID-19 illness. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s11030-022-10570-x.

SARS-CoV-2 Specific Nanobodies Neutralize Different Variants of Concern and Reduce Virus Load in the Brain of h-ACE2 Transgenic Mice

“…So far, several Nbs have been developed with promising diagnostic and therapeutic applications [ 20 , 50 , 51 , 52 , 53 , 54 ]. Both monomeric Nbs and engineered molecules showed strong neutralizing activity to the different VOCs that have emerged, including the Omicron subvariants [ 52 , 55 , 56 , 57 , 58 , 59 , 60 , 61 ]. The intense production of new recombinant Nbs highlights the relevance of this technological platform, which is expected to reach clinical use for SARS-CoV-2 and other viral diseases in the near future [ 62 ].…”

Nanobodies against SARS-CoV-2 reduced virus load in the brain of challenged mice and neutralized Wuhan, Delta and Omicron Variants

“…So far, several Nbs have been developed with promising diagnostic and therapeutic applications [20,38]. Both monomeric Nbs and engineered molecules showed strong neutralizing activity to the different VOCs that have emerged, including the Omicron variants [39][40][41][42][43][44][45][46]. The intense production of new recombinant Nbs highlights the relevance of this technological platform, which is expected to reach clinical use for SARS-CoV-2 and other viral diseases in the near future [47].…”

Revolutionizing antiviral therapy with nanobodies: Generation and prospects

“…PEGylation : PEGylation involves covalently attaching polyethylene glycol (PEG) chains to Nbs. This modification increases their hydrodynamic size and reduces renal clearance, resulting in a longer half-life [23] .…”

“…While Nbs are highly stable and can be produced at large scale using recombinant DNA technology, they can be rapidly cleared from circulation by the kidneys. Strategies such as PEGylation (attaching polyethylene glycol molecules) or fusing Nbs with other proteins can improve their half-life and tissue distribution [23] .…”