Classifications

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  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
  • C07K16/08—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from viruses
  • C07K16/10—RNA viruses
  • C07K16/102—Coronaviridae (F)
  • C07K16/104—Severe acute respiratory syndrome coronavirus 2 [SARS‐CoV‐2]
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  • A61K31/21—Esters, e.g. nitroglycerine, selenocyanates
  • A61K31/215—Esters, e.g. nitroglycerine, selenocyanates of carboxylic acids
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  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
  • A61K31/445—Non condensed piperidines, e.g. piperocaine
  • A61K31/45—Non condensed piperidines, e.g. piperocaine having oxo groups directly attached to the heterocyclic ring, e.g. cycloheximide
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  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
  • A61K31/47—Quinolines; Isoquinolines
  • A61K31/4706—4-Aminoquinolines; 8-Aminoquinolines, e.g. chloroquine, primaquine
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  • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
  • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
  • A61K31/4965—Non-condensed pyrazines
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  • A61K31/66—Phosphorus compounds
  • A61K31/675—Phosphorus compounds having nitrogen as a ring hetero atom, e.g. pyridoxal phosphate
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  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
  • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
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  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
  • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
  • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
  • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
  • A61K31/7068—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
• • A—HUMAN NECESSITIES
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  • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
  • A61K31/7088—Compounds having three or more nucleosides or nucleotides
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K39/12—Viral antigens
  • A61K39/215—Coronaviridae, e.g. avian infectious bronchitis virus
• • A—HUMAN NECESSITIES
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  • A61K39/395—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum
  • A61K39/42—Antibodies; Immunoglobulins; Immune serum, e.g. antilymphocytic serum viral
• • A—HUMAN NECESSITIES
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  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
  • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• • A—HUMAN NECESSITIES
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  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
  • A61P31/12—Antivirals
  • A61P31/14—Antivirals for RNA viruses
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
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  • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
  • A61K2039/507—Comprising a combination of two or more separate antibodies
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K38/00—Medicinal preparations containing peptides
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
  • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
  • C07K2317/33—Crossreactivity, e.g. for species or epitope, or lack of said crossreactivity
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
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  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/30—Immunoglobulins specific features characterized by aspects of specificity or valency
  • C07K2317/34—Identification of a linear epitope shorter than 20 amino acid residues or of a conformational epitope defined by amino acid residues
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  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/55—Fab or Fab'
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  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
  • C07K2317/567—Framework region [FR]
• • C—CHEMISTRY; METALLURGY
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  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding
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  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
  • C07K2317/92—Affinity (KD), association rate (Ka), dissociation rate (Kd) or EC50 value
• • C—CHEMISTRY; METALLURGY
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  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/90—Immunoglobulins specific features characterized by (pharmaco)kinetic aspects or by stability of the immunoglobulin
  • C07K2317/94—Stability, e.g. half-life, pH, temperature or enzyme-resistance
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
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  • C07K2319/00—Fusion polypeptide
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  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/30—Non-immunoglobulin-derived peptide or protein having an immunoglobulin constant or Fc region, or a fragment thereof, attached thereto
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2319/00—Fusion polypeptide
  • C07K2319/31—Fusion polypeptide fusions, other than Fc, for prolonged plasma life, e.g. albumin

Definitions

• a polypeptide has a broadly neutralizing activity against a plurality of known and predicted betacoronaviruses, and a binding affinity for an S2 domain epitope that is highly conserved across a plurality of betacoronaviruses.
• the disclosure provides, among other things, polypeptides that specifically bind SARS-CoV-2-Spike, wherein the polypeptide comprises a paratope that is substantially similar to a paratope of an antibody comprising a V H /V L pair selected from: any combination of the foregoing.
• a polypeptide specifically binds the S2 domain of a sarbecovirus (e.g., a SARS-CoV-1 virus, a SARS-CoV-2 virus) Spike protein. In some embodiments, a polypeptide specifically binds the S2 domain of a SARS-CoV-1 virus (e.g., a plurality of SARS-CoV-1 variants) Spike protein. In some embodiments, a polypeptide specifically binds S2 domain of a SARS-CoV-2 virus (e.g., a plurality of SARS-CoV-2 variants) Spike protein.
• a mutant, engineered and/or modified form of SARS-CoV- 2-Spike comprises, relative to SEQ ID NO:1, one or more mutations selected from: L5F, S13I, T19R, A67V, del69, del70, del69-70, D80G, T95I, G142D, del142-144, del144, Y145D, W152C, E154K, F157S, del211, L212I, ins214EPE, A222V, D253G, G261D, G339D, V367F, S371L, S371L, S373P, S375F, K417N, N439K, N440K, G446S, L452R, Y453F, S477N, T478K, E484A, E484K, E484Q, F486L, S494P, Q493R, G496S, Q498R,
• a mutant, engineered and/or modified form of SARS-CoV- 2-Spike comprises, relative to SEQ ID NO:1, one or more mutations selected from: T19R, G142D, 156del, 157del, R158G, L452R, T478K, D614G, P681R or D950N, or a combination thereof.
• a mutant, engineered and/or modified form of SARS-CoV-2-Spike comprises T19R, 156del, 157del, R158G, L452R, T478K, D614G, P681R, and D950N.
• a mutant, engineered and/or modified form of SARS-CoV- 2-Spike comprises, relative to SEQ ID NO:1, one or more mutations selected from: E484K, N501Y or D614G, or a combination thereof.
• a mutant, engineered and/or modified form of SARS-CoV- 2 Spike protein comprises, relative to SEQ ID NO:1, one or more mutations selected from: F817P, A892P, A899P, A942P, K986P or V987P, or a combination thereof.
• sequence identity is expressed as the percentage of positions across the entire length of the reference sequence where the reference and test sequences share the same nucleotide or amino acid upon alignment of the reference and test sequences to achieve a maximal level of identity.
• two sequences are considered to have 70% sequence identity when, upon alignment to achieve a maximal level of identity, the test sequence has the same nucleotide or amino acid residue at 70% of the same positions over the entire length of the reference sequence.
• Alignment of sequences for comparison to achieve maximal levels of identity can be readily performed by a person of ordinary skill in the art using an appropriate alignment method or algorithm. In some instances, the alignment can include introduced gaps to provide for the maximal level of identity. Examples include the local homology algorithm of Smith & Waterman, Adv. Appl.
• a protein, peptide or polypeptide can comprise any suitable L-and/or D-amino acid, for example, common ⁇ -amino acids (e.g., alanine, glycine, valine), non- ⁇ -amino acids (e.g., ⁇ -alanine, 4-aminobutyric acid, 6- aminocaproic acid, sarcosine, statine), and unusual amino acids (e.g., citrulline, homocitruline, homoserine, norleucine, norvaline, ornithine).
• the amino, carboxyl and/or other functional groups on a peptide can be free (e.g., unmodified) or protected with a suitable protecting group.
• Suitable protecting groups for amino and carboxyl groups, and methods for adding or removing protecting groups are known in the art and are disclosed in, for example, Green and Wuts, “Protecting Groups in Organic Synthesis,” John Wiley and Sons, 1991.
• the functional groups of a protein, peptide or polypeptide can also be derivatized (e.g., alkylated) or labeled (e.g., with a detectable label, such as a fluorogen or a hapten) using methods known in the art.
• An interaction can be a hydrogen bond, a salt bridge, a van der Waals interaction, an electrostatic interaction, a hydrophobic interaction, pi-interaction effects, an ionic bond, and/or any combination thereof.
• An interaction can be direct, or indirect, e.g., via a coordinated intermediate molecule, such as an ion or water.
• the residues of a paratope in some embodiments, comprise only residues that are part of a defined CDR. In some embodiments, the residues of a paratope further comprise one or more residues that are not part of a defined CDR (e.g., residues within a defined framework region).
• a polypeptide disclosed herein comprises a V L that has at least about 70% sequence identity to the amino acid sequence of SEQ ID NO:51.
• the V L can has at least about: 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% sequence identity to the amino acid sequence of SEQ ID NO:51.
• the V L has at least about 85% or at least about 90% sequence identity to the amino acid sequence of SEQ ID NO:51.
• a polypeptide disclosed herein comprises a V H that comprises at least 1 amino acid substitution (e.g., at least 1 conservative substitution such as highly conservative amino acid substitution) relative to the amino acid sequence of SEQ ID NO:3.
• the number of amino acid substitutions can be at least about: 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20, or about: 1-20, 1-19, 2-19, 2-18, 2-17, 3- 17, 3-16, 4-16, 4-15, 5-15, 5-14, 6-14, 6-13, 7-13, 7-12, 8-12, 8-11 or 9-11.
• the at least 1 amino acid substitution replaces only a non-CDR residue (e.g., within a framework region), of SEQ ID NO:50.
• the amino acid substitutions are conservative substitutions.
• the term “conservative amino acid substitution(s)” or “conservative substitution(s)” refers to an amino acid substitution having a value of 0 or greater in BLOSUM62.
• the amino acid substitutions are highly conservative substitutions.
• the term “highly conservative amino acid substitution(s)” or “highly conservative substitution(s)” refers to an amino acid substitution having a value of at least 1 (e.g., at least 2) in BLOSUM62.
• a polypeptide comprises: a) a HCDR2 comprising at least 1 amino acid substitution relative to at least one amino acid sequence set forth in SEQ ID NOs:79-88 (e.g., at least one amino acid sequence set forth in SEQ ID NOs:80-88); b) a HCDR3 comprising at least 1 amino acid substitution relative to at least one amino acid sequence set forth in SEQ ID NOs:90-131 (e.g., at least one amino acid sequence set forth in SEQ ID NOs:91-131); c) a LCDR1 comprising at least 1 amino acid substitution relative to the amino acid sequence set forth in SEQ ID NOs:133-140 (e.g., at least one amino acid sequence set forth in SEQ ID NOs:134-140); or d) a LCDR3 comprising at least 1 amino acid substitution relative to at least one amino acid sequence set forth in SEQ ID NOs:143-162 (e.g., at least one amino acid sequence set forth in SEQ ID NOs:
• Camelid antibodies are antibodies from the Camelidae family of mammals that include llamas, camels, and alpacas.
• a polypeptide disclosed herein is an antibody comprising two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds or multimers thereof (for example, IgM).
• Each heavy chain comprises a heavy chain variable domain (V H ) and a heavy chain constant domain (comprising domains CH1, hinge CH2 and CH3).
• Each light chain comprises a light chain variable domain (V L ) and a light chain constant domain (CL).
• V H and the V L regions may be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed within framework regions (FR).
• CDR complementarity determining regions
• FR framework regions
• V H and V L each comprises three CDRs and four FR segments, arranged from the amino-terminus to the carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4.
• the antibody can be of any species, such as a murine antibody, a human antibody or a humanized antibody.
• the extent of the framework region and the CDRs of an antibody can be identified using one of several suitable methodologies that are well known in the art, for example, by the Kabat definition, the Chothia definition, the AbM definition, and/or the contact definition.
• a polypeptide binds SARS-CoV-1-Spike (e.g., of CoV-1 and/or WIV1) and/or SARS-CoV-2-Spike (e.g.
• a polypeptide reduces betacoronavirus (e.g., SARS-CoV-2) infectivity of human cells by at least about 30%.
• a polypeptide reduces betacoronavirus (such as SARS- CoV-2 (e.g.
• a polypeptide reduces SARS-CoV-1 (e.g., CoV-1 and/or WIV1) infectivity of host cells (e.g., human host cells).
• a polypeptide reduces SARS-CoV-1 (e.g., CoV-1 and/or WIV1) infectivity of host cells (e.g., human host cells) by at least about 10%, e.g., by at least about: 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99%.
• the polynucleotide comprises a nucleotide sequence that is codon-optimized for a chosen host cell.
• the disclosure provides a vector (e.g., an expression vector, including a viral-delivery vector) comprising any one or more of the polynucleotides described herein.
• expression vector refers to a replicable nucleic acid from which one or more proteins can be expressed when the expression vector is transformed into a suitable expression host cell.
• the subject has (e.g., confirmed by testing, such as by PCR or rapid test), or is suspected of having, COVID-19. In some embodiments, the subject has COVID-19. In some embodiments, the subject has been diagnosed with COVID-19. In some embodiments, the subject is at risk of developing COVID-19. [00307] In some embodiments, the subject is a mammal.
• suitable dosages can be from about 0.001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.01 mg/kg to about 1 mg/kg body weight per treatment. Determining the dosage for a particular agent, subject and disease is well within the abilities of one of skill in the art. Preferably, the dosage does not cause or produces minimal adverse side effects.
• Desired response or desired results include effects at the cellular level, tissue level, or clinical results. As such, “a therapeutically effective amount” or synonym thereto depends upon the context in which it is being applied.
• the reduction in viral load is about 10-99%, e.g., about: 10-98%, 15-98%, 15-97%, 20-97%, 20- 96%, 25-96%, 25-95%, 30-95%, 30-94%, 35-94%, 35-93%, 40-93%, 40-92%, 45-92%, 45- 91%, 50-91%, 50-90%, 55-90%, 55-85%, 60-85%, 60-80%, 65-80%, 65-75%, or 70-75%.
• the effective dosage is sufficient to inhibit binding of the virus to its target proteins, target cells, or both.
• the disclosure provides methods of inhibiting virus mediated fusion with a target cell, comprising contacting the target cell an effective amount of any polypeptide or fusion protein described herein.
• all terms of art, notations and other scientific terms or terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this disclosure pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a substantial difference over what is generally understood in the art.
• the polypeptide of any one of embodiments 1-20 wherein: a) the V H comprises the amino acid sequence of SEQ ID NO:14; and b) the V L comprises the amino acid sequence of SEQ ID NO:60 (AB-11). 33. The polypeptide of any one of embodiments 1-20, wherein: a) the V H comprises the amino acid sequence of SEQ ID NO:15; and b) the V L comprises the amino acid sequence of SEQ ID NO:56 (AB-12). 34. The polypeptide of any one of embodiments 1-20, wherein: a) the V H comprises the amino acid sequence of SEQ ID NO:16; and b) the V L comprises the amino acid sequence of SEQ ID NO:51 (AB-13). 35.
• the polypeptide of any one of embodiments 1-20 wherein: a) the V H comprises the amino acid sequence of SEQ ID NO:20; and b) the V L comprises the amino acid sequence of SEQ ID NO:61 (AB-20). 42. The polypeptide of any one of embodiments 1-20, wherein: a) the V H comprises the amino acid sequence of SEQ ID NO:21; and b) the V L comprises the amino acid sequence of SEQ ID NO:65 (AB-21). 43. The polypeptide of any one of embodiments 1-20, wherein: a) the V H comprises the amino acid sequence of SEQ ID NO:22; and b) the V L comprises the amino acid sequence of SEQ ID NO:66 (AB-22). 44.
• a polynucleotide (e.g., DNA or RNA; linear or circular; optionally containing one or more modified nucleotides) comprising a sequence encoding the polypeptide of any one of embodiments 1-80 or the fusion protein of embodiment 92. 94.
• a vector (e.g., an expression vector, including a viral-delivery vector) comprising the polynucleotide of embodiment 93.
• a host cell comprising the polynucleotide of embodiment 93 or the vector of embodiment 94.
• a composition comprising the polypeptide of any one of embodiments 1-91 or the fusion protein of embodiment 92 or the polynucleotide of embodiment 93. 97.
• the method of any one of embodiments 98-122 comprising administering an effective amount of a combination of AB-1 and Evusheld to the subject. 126.
• the method of any one of embodiments 98-122 comprising administering an effective amount of a combination of AB-1 and AZD-1061 to the subject.
• the method of any one of embodiments 98-122 comprising administering an effective amount of a combination of AB-1 and P2G3 to the subject. 128.
• the method of any one of embodiments 98-122 comprising administering an effective amount of a combination of AB-1 and RBD Class 4 mAb-1a to the subject.
• Serial dilutions (1:4) of the antibodies were made in PBS/bovine serum albumin (BSA) starting from 4.5 ⁇ g/ml. After one wash with TBS-T, the serially diluted antibodies were transferred to the pre- coated plates and incubated for 1 hour at room temperature. Next, the plates were washed 3 times with TBS-T, and a Europium-labeled secondary antibody (PerkinElmer, Waltham, MA, Cat #1244-330) was added for 30 minutes at room temperature. Following the incubation, the plates were washed 3 times in TBS-T, and an enhancement solution (PerkinElmer, Waltham, MA, Cat #4001-0010) was applied.
• BSA PBS/bovine serum albumin
• the three lead molecules exhibited comparable neutralization profiles across all pseudoviruses and overall improved neutralization potencies (as measured by IC 50 ) and/or efficacies (maximum neutralization) compared to the Reference Antibody.
• the three lead molecules showed improved neutralization potencies and efficacies against BA.2 sublineages (BA.2, BA.2.12.1, BA.4/5) compared to Sotrovimab, and BA.4/5 neutralization profiles comparable to AZD1061 (FIGs.10A-10B, Tables 5 and 6).
• Preliminary experiments with live viruses also confirmed neutralization of SARS-CoV-2 Delta and Omicron BA.1 by the three lead molecules (FIG.11, Table 7).
• FIGs.17A-17D, 18A-18C, and 19 show that AB-1 demonstrated significant neutralization potency and efficacy against multiple variants, such as Omicron BQ.1.1, Omicron BA.5, and Delta, either alone or in combined with another antibody (e.g., a class 4 anti-RBD antibody).
• AB-1 has robust neutralizing activity against SARS-CoV-2 variants in vitro and in vivo.
• Recently many SARS-CoV-2 variants have emerged with marked escape from clinical-stage antibodies. Some of these variants show signs of convergent evolution sich as mutations at position K444.
• the antibodies were 4-fold serially diluted in PBS/0.2% BSA/1x Penicillin-Streptomycin (Pen-Strep) buffer, starting from 72 ⁇ g/ml (4x final concentration), in round bottom 96-well plates (ThermoFisher, Waltham, MA, Cat #268200).
• the antibodies were mixed with equal volumes of diluted SARS-CoV-2 pseudoviruses (VSV-dG pseudotyped with SARS-CoV-2 BQ.1.1 Spike).
• Antibody-virus mixtures were incubated at 37C, 5% CO 2 for 30-60 minutes.
• the pseudotyping system will be used to assess neutralizing activity of a polypeptide disclosed herein (e.g., AB-1) against current and novel SARS-CoV-2 variants that may arise. These results will be confirmed with live viruses. Pseudoviruses bearing mutations in Spike epitopes that may lead to impaired neutralization activity of the polypeptide (e.g., AB-1) will be developed and evaluated. These mutations will be selected based on structural and/or biochemical assessment of binding epitope, analysis of mutations in selected sequences reported in public databases and escape experiments with replication-competent VSV, or a combination of the foregoing.
• Dilution plates 96 well plate round bottom, non-treated, polypropylene (Corning, Corning, NY, catalog #3365; Greiner, Kremsmünster, Austria, catalog #650201).
• DELFIA plates 384 well plate white, MaxiSorp, polystyrene (Thermo Fisher Scientific, catalog #460372).
• TBS-T 20X TBS Tween-20 (Thermo Fisher Scientific, catalog #28360) diluted 1:20 in ddH 2 O.
• Blocking solution ELISA Assay Diluent B (5X) (BioLegend, San Diego, CA, catalog #421205) diluted 1:5 in PBS.
• the Eu ion is dissociated from the labeled immunocomponent bound to the solid phase by adding Enhancement solution. Then Eu fluorescence is measured by TRF.
• 384 well plates were coated with neutravidin (2 ⁇ g/mL) overnight at room temperature. The plates were washed and coated with biotinylated peptides (50 nM) for 1 hour at room temperature. The plates were then washed and incubated with blocking solution for 2 hours at room temperature, washed again and incubated with antibodies (AB-1, the Reference Antibody, and isotype control) for 1 hour at room temperature.
• AB-1 Fab binds to the SARS-CoV-2 spike S2 peptide representative of the C-terminal end of the stem helix (aa 1149-1167) with higher affinity as compared to the Reference Antibody (K D values: AB-1, 0.9 nM; the Reference Antibody, 5.4 nM (Table 14, FIGs.23A-23D)).
• the four regions of interest of the SARS-CoV-2 spike protein are: the AB-1 epitope (referred to as “Epitope”), residues adjacent to the epitope (referred to as “Epitope Adjacent”), HR1, and HR2.
• Epitope residues referred to as “Epitope”
• Epitope Adjacent residues adjacent to the epitope
• HR1 and HR2 residues adjacent to the epitope
• HR1 and HR2 a publicly available structure of the SARS-CoV-2 spike protein
• AB-1 shows similar binding affinities to the spike trimers with polymorphisms in the AB-1 epitope as compared to the spike trimer derived from the parent SARS-CoV-2 BA.2 variant, with overall higher affinities than the Reference Antibody (FIGs.32-33, Tables 18-20).
• AB-1 consistently binds to multiple spike trimers representative of SARS-CoV-2 variants and non-SARS-CoV-2 sarbecoviruses.
• SARS-CoV-2 pre-Omicron variants D614G (ancestral
• the pseudovirus panel for combination experiments included: a) SARS-CoV-2 pre-Omicron variants (D614G (ancestral strain with D614G mutation), and Delta (B.1.617.2)); and b) SARS-CoV-2 Omicron variants (BQ.1.1, and XBB.1.5).
• Vero E6 or TMPRSS2-Vero E6 recombinant cells were seeded in 384-well tissue culture plates at a density of 3,500 cells per well in 20 ⁇ l of stimulation medium and incubated at 37 o C, 5% CO 2 for 2-4 hours.
• the antibodies were serially diluted and incubated with the diluted pseudovirus at a desired multiplicity of infection (0.25 for SARS- CoV-2 pre-Omicron variants, and non-SARS-CoV-2 Sarbecoviruses; 0.5 for SARS-CoV-2 Omicron variants).
• SARS-CoV-2 pseudoviruses are non-replicating lentiviruses or deltaG-VSVs expressing a spike protein of interest.
• a reporter system e.g., luciferase
• permissive cell lines e.g., Vero E6, with or without TMPRSS2 expression.
• This experimental system enables evaluation of therapeutics that affect SARS-CoV-2 cell entry in a BSL-2 environment.
• DeltaG-VSVs expressing luciferase and pseudotyped with spike proteins representative of SARS-CoV-2 D614G (ancestral strain with D614G mutation) and BA.2 strain were employed to assess neutralization profiles of monoclonal antibodies in hamster challenge models.
• Antibodies AB-1 (Lonza, lot #1100-130922-01), AB-1 VH/VL - huIgG1 (GenScript USA, Inc., lot #U507ZHF090-3, AB-1 variable regions expressed as human IgG1 without LS mutation in the Fc region), AB-1 VH/VL - hamIgG2a (GenScript USA, Inc., lot #U9330HG280-3, AB-1 variable regions expressed as hamster IgG2a), sotrovimab VH/VL - huIgG1-LS (in-house production, sotrovimab variable regions expressed as human IgG1 with LS mutation in the Fc region), sotrovimab VH/VL - huIgG1 (GenScript USA, Inc., lot #U069FHA200-14, sotrovimab variable regions expressed as human IgG1 without LS mutation in the Fc region), sotrovimab VH/VL
• Stimulation medium MEM (#SH30024.02, lot #AH29890509) with 2.5% FBS (#A38403-01, lot #262908SRP), 0.1 mM nonessential amino acids (#11140-050, lot #2390759), 1 mM sodium pyruvate (#11360-070, lot #2323639), 1% Penicillin/Streptomycin (#15140-122, lot #2441835).
• Luciferase detection buffer ONE-StepTM Luciferase Assay System, mix components A and B at 100:1 ratio respectively (BPS Bioscience, #60690-3, lot #221221).
• TMPRSS2-Vero E6 cells were used as positive control for SARS-CoV-2 pseudovirus infection.
• Pseudovirus spike (SARS-CoV-2, D614G) pseudotyped deltaG-VSV (Luciferase Reporter) (BPS Bioscience, #78642, lot #220512).
• Antibodies AB-1 (Lonza, lot #1100-130922-01), AB-1 VH/VL - huIgG1 (GenScript USA, Inc., lot #U507ZHF090-3, AB-1 variable regions expressed as human IgG1 without LS mutation in the Fc region but identical variable domain), bebtelovimab (GenScript USA, Inc., lot #U819KHL150), isotype (GenScript USA, Inc., lot #U799WHJ270-3, palivizumab variable regions targeting RSV F protein and expressed as human IgG1 with LS mutation in the Fc region).
• TMPRSS2-Vero E6 Cell culture medium: MEM/EBSS (Thermo Fisher Scientific #SH30024.02, lot #AH29890509) 10% FBS (#A38403-01, lot #262908SRP), 0.1 mM nonessential amino acids (#11140-050, lot #2390759), 1 mM sodium pyruvate (#11360- 070, lot #2323639), 1% Penicillin/Streptomycin (#15140-122, lot #2441835).
• Stimulation medium for THP-1, U-937, PBMCs: RPMI-1640 (Thermo Fisher Scientific #61870036, lot #2522773).
• Hurlburt et al. Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit, Commun Biol.5(1):342 (2022).
• Ingraham et al. Generative models for graph-based protein design, 33rd Conference on Neural Information Processing Systems (NeurIPS 2019), Vancouver, Canada.
• Jennewein et al. Isolation and characterization of cross-neutralizing coronavirus antibodies from COVID-19+ subjects, Cell Rep.36(2):109353 (2021).

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