RBD-based high affinity ACE2 antagonist limits SARS-CoV-2 replication in upper and lower airways

SARS-CoV-2 has the capacity to evolve mutations to escape vaccine-and infection-acquired immunity and antiviral drugs. A variant-agnostic therapeutic agent that protects against severe disease without putting selective pressure on the virus would thus be a valuable biomedical tool. Here, we challenged rhesus macaques with SARS-CoV-2 Delta and simultaneously treated them with aerosolized RBD-62, a protein developed through multiple rounds of in vitro evolution of SARS-CoV-2 RBD to acquire 1000-fold enhanced ACE2 binding affinity. RBD-62 treatment gave equivalent protection in upper and lower airways, a phenomenon not previously observed with clinically approved vaccines. Importantly, RBD-62 did not block the development of memory responses to Delta and did not elicit anti-drug immunity. These data provide proof-of-concept that RBD-62 can prevent severe disease from a highly virulent variant.

[1]  P. Bieniasz,et al.  Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies , 2023, Nature Microbiology.

[2]  E. Pariani,et al.  Nirmatrelvir treatment of SARS‐CoV‐2‐infected mice blunts antiviral adaptive immune responses , 2023, EMBO molecular medicine.

[3]  N. Landau,et al.  Prophylaxis and treatment of SARS-CoV-2 infection by an ACE2 receptor decoy in a preclinical animal model , 2023, iScience.

[4]  Ashutosh Kumar Singh,et al.  Optimizing variant-specific therapeutic SARS-CoV-2 decoys using deep-learning-guided molecular dynamics simulations , 2023, Scientific Reports.

[5]  J. Zahradník,et al.  Enhanced transmissibility, infectivity, and immune resistance of the SARS-CoV-2 omicron XBB.1.5 variant , 2023, bioRxiv.

[6]  F. Agou,et al.  Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 omicron sub-lineages , 2022, bioRxiv.

[7]  D. Douek,et al.  Neutralization against BA.2.75.2, BQ.1.1, and XBB from mRNA Bivalent Booster , 2022, The New England journal of medicine.

[8]  M. Kiso,et al.  Efficacy of Antiviral Agents against Omicron Subvariants BQ.1.1 and XBB , 2022, The New England journal of medicine.

[9]  G. Freeman,et al.  Optimized ACE2 decoys neutralize antibody-resistant SARS-CoV-2 variants through functional receptor mimicry and treat infection in vivo , 2022, Science advances.

[10]  J. Bukh,et al.  Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system , 2022, Science advances.

[11]  R. Sanjuán,et al.  Resistance of Omicron subvariants BA.2.75.2, BA.4.6 and BQ.1.1 to neutralizing antibodies , 2022, bioRxiv.

[12]  Jin Ju Park,et al.  Nirmatrelvir/Ritonavir Prescription Rate and Outcomes in Coronavirus Disease 2019: A Single Center Study , 2022, Infection & chemotherapy.

[13]  H. Jäck,et al.  Omicron sublineage BQ.1.1 resistance to monoclonal antibodies , 2022, The Lancet Infectious Diseases.

[14]  Hao Tan,et al.  Naturally occurring mutations of SARS-CoV-2 main protease confer drug resistance to nirmatrelvir , 2022, bioRxiv.

[15]  Seo Jung Hong,et al.  Multiple pathways for SARS-CoV-2 resistance to nirmatrelvir , 2022, bioRxiv.

[16]  S. Jonjić,et al.  Anti-human ACE2 antibody neutralizes and inhibits virus production of SARS-CoV-2 variants of concern , 2022, iScience.

[17]  S. Benenson,et al.  Association of Receiving a Fourth Dose of the BNT162b Vaccine With SARS-CoV-2 Infection Among Health Care Workers in Israel , 2022, JAMA network open.

[18]  T. Tripathi,et al.  Hotspot residues and resistance mutations in the nirmatrelvir-binding site of SARS-CoV-2 main protease: Design, identification, and correlation with globally circulating viral genomes , 2022, bioRxiv.

[19]  A. Sette,et al.  Immunological memory to SARS‐CoV‐2 infection and COVID‐19 vaccines , 2022, Immunological reviews.

[20]  Lauren M. Hickling,et al.  Immune boosting by B.1.1.529 (Omicron) depends on previous SARS-CoV-2 exposure , 2022, Science.

[21]  S. Hoehl,et al.  Omicron BA.1 breakthrough infection drives cross-variant neutralization and memory B cell formation against conserved epitopes , 2022, Science Immunology.

[22]  P. Maes,et al.  Imprinted antibody responses against SARS-CoV-2 Omicron sublineages , 2022, bioRxiv.

[23]  Y. Rudich,et al.  Gelatin Stabilizes Nebulized Proteins in Pulmonary Drug Delivery against COVID-19 , 2022, ACS biomaterials science & engineering.

[24]  K. Katoh,et al.  An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo , 2022, Science Translational Medicine.

[25]  Gheyath K Nasrallah,et al.  Duration of mRNA vaccine protection against SARS-CoV-2 Omicron BA.1 and BA.2 subvariants in Qatar , 2022, Nature Communications.

[26]  M. Exline,et al.  Clinical severity of, and effectiveness of mRNA vaccines against, covid-19 from omicron, delta, and alpha SARS-CoV-2 variants in the United States: prospective observational study , 2022, BMJ.

[27]  J. Mascola,et al.  mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits similar B cell expansion, neutralizing responses, and protection from Omicron , 2022, Cell.

[28]  M. Baniecki,et al.  Oral Nirmatrelvir for High-Risk, Nonhospitalized Adults with Covid-19 , 2022, The New England journal of medicine.

[29]  Liyuan Liu,et al.  Antibody evasion properties of SARS-CoV-2 Omicron sublineages , 2022, Nature.

[30]  Troy C. Hinkley,et al.  Replicating RNA platform enables rapid response to the SARS-CoV-2 Omicron variant and elicits enhanced protection in naïve hamsters compared to ancestral vaccine , 2022, bioRxiv.

[31]  Xiangxi Wang,et al.  Close relatives of MERS-CoV in bats use ACE2 as their functional receptors , 2022, bioRxiv.

[32]  K. Swanson,et al.  Neutralization of SARS-CoV-2 Omicron by BNT162b2 mRNA vaccine–elicited human sera , 2022, Science.

[33]  E. Shin,et al.  T cell epitopes in SARS-CoV-2 proteins are substantially conserved in the Omicron variant , 2022, Cellular & Molecular Immunology.

[34]  S. Madhi,et al.  SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses , 2022, Cell.

[35]  Mark M. Davis,et al.  Immune imprinting, breadth of variant recognition, and germinal center response in human SARS-CoV-2 infection and vaccination , 2022, Cell.

[36]  G. Gao,et al.  Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2 , 2022, Cell.

[37]  M. Nussenzweig,et al.  Plasma Neutralization of the SARS-CoV-2 Omicron Variant , 2021, The New England journal of medicine.

[38]  L. Bekker,et al.  Effectiveness of BNT162b2 Vaccine against Omicron Variant in South Africa , 2021, The New England journal of medicine.

[39]  D. Douek,et al.  mRNA-1273 and BNT162b2 mRNA vaccines have reduced neutralizing activity against the SARS-CoV-2 Omicron variant , 2021, bioRxiv.

[40]  J. Butterton,et al.  Molnupiravir for Oral Treatment of Covid-19 in Nonhospitalized Patients , 2021, The New England journal of medicine.

[41]  J. Mascola,et al.  Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in rhesus macaques coincides with anamnestic antibody response in the lung , 2021, Cell.

[42]  H. Jäck,et al.  The Omicron variant is highly resistant against antibody-mediated neutralization: Implications for control of the COVID-19 pandemic , 2021, Cell.

[43]  Chaim A. Schramm,et al.  Protection against SARS-CoV-2 Beta variant in mRNA-1273 vaccine–boosted nonhuman primates , 2021, Science.

[44]  J. Mascola,et al.  Immune correlates of protection by mRNA-1273 vaccine against SARS-CoV-2 in nonhuman primates , 2021, Science.

[45]  K. Zatloukal,et al.  Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor , 2021, bioRxiv.

[46]  O. Dym,et al.  SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution , 2021, Nature Microbiology.

[47]  S. Elbashir,et al.  mRNA-1273 Protects against SARS-CoV-2 Beta Infection in Nonhuman Primates , 2021, Nature Immunology.

[48]  Christopher Allen,et al.  Characterization of a Novel ACE2-Based Therapeutic with Enhanced Rather than Reduced Activity against SARS-CoV-2 Variants , 2021, Journal of virology.

[49]  F. Rey,et al.  Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization , 2021, Nature.

[50]  Shiho Tanaka,et al.  An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants , 2021, Scientific Reports.

[51]  Linqi Zhang,et al.  Analysis of SARS-CoV-2 variant mutations reveals neutralization escape mechanisms and the ability to use ACE2 receptors from additional species , 2021, Immunity.

[52]  G. Barton,et al.  Effects of common mutations in the SARS-CoV-2 Spike RBD domain and its ligand the human ACE2 receptor on binding affinity and kinetics , 2021, bioRxiv.

[53]  Aaron M. Rosenfeld,et al.  Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination , 2021, Science Immunology.

[54]  A. Mirazimi,et al.  A super-potent tetramerized ACE2 protein displays enhanced neutralization of SARS-CoV-2 virus infection , 2021, Scientific Reports.

[55]  J. Mascola,et al.  Efficacy and Safety of the mRNA-1273 SARS-CoV-2 Vaccine , 2020, The New England journal of medicine.

[56]  P. Dormitzer,et al.  Safety and Efficacy of the BNT162b2 mRNA Covid-19 Vaccine , 2020, The New England journal of medicine.

[57]  Steven Lin,et al.  Humanized COVID‐19 decoy antibody effectively blocks viral entry and prevents SARS‐CoV‐2 infection , 2020, EMBO molecular medicine.

[58]  D. Qu,et al.  Decoy nanoparticles protect against COVID-19 by concurrently adsorbing viruses and inflammatory cytokines , 2020, Proceedings of the National Academy of Sciences.

[59]  Jorgen W. Nelson,et al.  A Potent Anti-Malarial Human Monoclonal Antibody Targets Circumsporozoite Protein Minor Repeats and Neutralizes Sporozoites in the Liver. , 2020, Immunity.

[60]  J. Dye,et al.  Engineering human ACE2 to optimize binding to the spike protein of SARS coronavirus 2 , 2020, Science.

[61]  J. Mascola,et al.  Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates , 2020, The New England journal of medicine.

[62]  S. Pierce,et al.  B cell memory: building two walls of protection against pathogens , 2019, Nature Reviews Immunology.

[63]  Carole J Henry,et al.  Remembrance of Things Past: Long-Term B Cell Memory After Infection and Vaccination , 2019, Front. Immunol..

[64]  K. Foulds,et al.  OMIP‐052: An 18‐Color Panel for Measuring Th1, Th2, Th17, and Tfh Responses in Rhesus Macaques , 2019, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[65]  C. Andrews,et al.  Genetic immunization in the lung induces potent local and systemic immune responses , 2010, Proceedings of the National Academy of Sciences.