Design of a chimeric ACE-2/Fc-silent fusion protein with ultrahigh affinity and neutralizing capacity for SARS-CoV-2 variants

Abstract

Background: As SARS-CoV-2 continues to mutate into Variants of Concern (VOC), there is growing and urgent need to develop effective antivirals to combat COVID-19. Monoclonal antibodies developed earlier are no longer capable of effectively neutralizing currently active VOCs. This report describes the design of variant-agnostic chimeric molecules consisting of an Angiotensin Converting Enzyme-2 (ACE-2) domain mutated to retain ultrahigh affinity binding to a wide variety of SARS-CoV-2 variants, coupled to an Fc-silent immunoglobulin domain that eliminates antibody-dependent enhancement (ADE) and extends biological half-life. Methods: Molecular modeling, Surrogate Viral Neutralization tests (sVNT) and infection studies of human airway organoid cultures were performed with synthetic chimeras, SARS-CoV-2 spike protein mimics and SARS-CoV-2 Omicron variants B.1.1.214, BA.1, BA.2 and BA.5. Results: ACE-2 mutations L27, V34 and E90 resulted in ultrahigh affinity binding of the LVE-ACE-2 domain to the widest variety of VOCs, with KDs of 93 pM and 73 pM for binding to the Alpha B1.1.7 and Omicron B.1.1.529 variants, and notably, 78fM, 133fM and 1.81pM affinities to the Omicron BA.2, BA2.75 and BQ.1.1 subvariants, respectively. sVNT assays revealed titers of ≥4.9 ng/ml, for neutralization of recombinant viral proteins corresponding to the Alpha, Delta and Omicron variants. The values above were obtained with LVE-ACE-2/mAB chimeras containing the FcRn-binding Y-T-E sequence which extends biological half-life 3–4-fold. Conclusions: The ACE-2-mutant/Fc silent fusion proteins described have ultrahigh affinity to a wide variety of SARS-CoV-2 variants including Omicron. It is proposed that these chimeric ACE-2/mABs will constitute variant-agnostic and cost-effective prophylactics against SARS-CoV-2, particularly when administered nasally. Statement of Significance. A new class of ACE-2/Fc-silent IgG fusion proteins was designed to have ultrahigh affinity and superior neutralizing capacity against a variety of SARS-CoV-2 VOCs. The highest binding affinity (femtomolar) was observed against Omicron variant BA.2. Inclusion of the Y-T-E sequence in the IgG domain is expected to triple biological halflife.

Feasibility and Effective Binding Inhibitors against COVID-19 BA.2.86

“…Pros and Cons results have been reported for Ivermectin because the saccharides adsorb glycoproteins and damage their activity [23,24]. Effectiveness of several compounds such as Ursodeoxycholic acid [25], a combination of Nirmatrelvir and Ritonavir [26], fungal metabolites [27], Bruceine A [28], Gamabufotalin [28], VITAMIC BIOSEN [29], prophylactics [30], and Azvudine [31] was reported and Sotrovimab remained weakly reactive and broadly neutralizing antibody SA55 was still highly effective [32]. However, Nirmatrelvir, Ritonavir, Bruceine A and D, Gamabufotalin, and Azvudine were adsorbed on the ACE-2 in the above experiment.…”