Variant nucleic acid libraries for coronavirus
Inventors
Sato, Aaron • Liu, Qiang • YUAN, Tom
Assignees
Interested in licensing this patent?
MTEC can help explore whether this patent might be available for licensing for your application.
Publication Number
US-12304965-B2
Publication Date
2025-05-20
Expiration Date
Abstract
Provided herein are methods and compositions relating to libraries of optimized antibodies having nucleic acids encoding for an antibody comprising modified sequences. Libraries described herein comprise nucleic acids encoding SARS-CoV-2 or ACE2 antibodies. Further described herein are protein libraries generated when the nucleic acid libraries are translated. Further described herein are cell libraries expressing variegated nucleic acid libraries described herein.
Core Innovation
The invention provides a VHH antibody that binds to an ACE2 protein. The VHH comprises a variable domain and a heavy chain region (VH) with complementarity determining regions CDRH1, CDRH2, and CDRH3, and the amino acid sequences of CDRH1, CDRH2, and CDRH3 are defined by specific SEQ ID NOs, including multiple alternative specified sets.
The invention is directed to coronavirus antibody optimization using variant nucleic acid libraries that focus on CDR regions. The described libraries provide large CDR-focused variant sets with defined numbers of CDR variants relative to an input antibody sequence, enabling translation to protein and cell libraries, and selection and enrichment approaches are used to obtain antibody or antibody fragment variants with greatly improved binding.
The invention includes downstream use of the ACE2-binding VHH antibody for treating or preventing SARS-CoV-2 infection. The described implementations include administration timing windows relative to exposure and, in certain embodiments, an assay-gated treatment approach based on an expression level assay that determines expression levels of SARS-CoV-2 antibodies before administering the VHH antibody.
Claims Coverage
1 independent claim is present. The claim defines a VHH antibody that binds to the ACE2 protein, where the variable domain VH includes specified complementarity determining regions CDRH1, CDRH2, and CDRH3 with amino-acid sequences defined by specific SEQ ID NOs. Dependent claims further refine treatment by specifying administration timing relative to exposure and gating administration based on an expression level assay.
Ace2-binding VHH antibody with specified CDRH1/CDRH2/CDRH3 sequences
A VHH antibody that binds to the ACE2 protein, comprising a variable domain with a heavy chain region (VH) wherein VH comprises complementarity determining regions CDRH1, CDRH2, and CDRH3, and wherein the amino acid sequences of CDRH1, CDRH2, and CDRH3 are set forth in specified SEQ ID NOs, including multiple alternative specified sequence sets.
Assay-gated administration based on expression level of SARS-CoV-2 antibodies
A method for treating an individual infected with SARS-CoV-2 by obtaining a sample, running an expression level assay to determine expression levels of SARS-CoV-2 antibodies, and administering the VHH antibody when the assay shows the SARS-CoV-2 antibodies expression level.
Post-exposure administration timing no later than 24 hours
A method wherein administering the antibody no later than about 24 hours after exposure to SARS-CoV-2.
Post-exposure administration timing no more than one month
A method wherein administering the antibody no more than about 1 month after exposure to SARS-CoV-2.
Pre-exposure prophylactic timing at least one week
A method wherein administering the antibody at least about one week before exposure to SARS-CoV-2.
The claim coverage centers on an ACE2-binding VHH defined by specific CDRH1/CDRH2/CDRH3 amino-acid sequences, with additional claimed refinements that define when administration occurs relative to exposure and, in some embodiments, gate administration based on an expression level assay.
Stated Advantages
The described selection and enrichment approaches yield antibody or antibody fragments with greatly improved binding.
Administration may be configured using specified timing windows relative to exposure.
In certain embodiments, administration can be gated by an expression level assay determining expression levels of SARS-CoV-2 antibodies.
Provides experimental support for ACE2-binding VHH/nanobody variants and SARS-CoV-2 neutralization efficacy.
Flow cytometry affinity and binding improvements are indicated by MFI ratios.
Demonstrates VSV-pseudotype neutralization efficacy against SARS-CoV-2 strains and variants with IC50 and NT50 values.
Describes timing-dependent protection against weight loss and infectious virus in lungs in Syrian hamsters using a VHH and monoclonal antibody cocktail under cyclophosphamide immunosuppression.
Documented Applications
Treating an individual infected with SARS-CoV-2 by administering the ACE2-binding VHH antibody.
Preventing SARS-CoV-2 infection by administering the ACE2-binding VHH antibody with specified pre-exposure timing windows.
Neutralization testing of ACE2-binding VHH/nanobody variants against SARS-CoV-2 strains and variants using VSV-pseudotype neutralization analysis, including South African B.135 and D614G.
In vivo efficacy evaluation in Syrian hamsters for protection against weight loss and infectious virus in lungs using a cocktail of VHH and monoclonal antibody (6-63 + 1-20) under cyclophosphamide immunosuppression with timing-dependent outcomes.
Interested in licensing this patent?