Patent Grant
11779629
A computer readable form of the Sequence Listing “7685-P53259US04_RevisedSequenceListing.txt” (111,429 bytes), submitted via EFS-WEB and created on Mar. 4, 2021, is herein incorporated by reference.
The present disclosure relates to methods for treating or inhibiting amyloid-beta oligomer related diseases and particularly to methods exploiting the use of conformational A-beta epitopes that were predicted and shown to be selectively accessible in A-beta oligomers.
Amyloid-beta (A-beta), which exists as a 36-43 amino acid peptide, is a product released from amyloid precursor protein (APP) by the enzymes β and γ secretase. In AD patients, A-beta can be present in soluble monomers, insoluble fibrils and soluble oligomers. In monomer form, A-beta exists as a predominantly unstructured polypeptide chain. In fibril form, A-beta can aggregate into distinct morphologies, often referred to as strains. Several of these structures have been determined by solid-state NMR.
For, example, structures for several strains of fibrils are available in the Protein Data Bank (PDB), a crystallographic database of atomic resolution three dimensional structural data, including a 3-fold symmetric Aβ structure (PDB entry, 2M4J); a two-fold symmetric structure of Aβ-40 monomers (PDB entry 2LMN), and a single-chain, parallel in-register structure of Aβ-42 monomers (PDB entry 2MXU).
The structure of 2M4J is reported in Lu et al [8], and the structure of 2MXU is reported in Xiao et al [9]. The structure of 2LMN is reported in Petkova et al [10].
A-beta oligomers have been shown to kill cell lines and neurons in culture and block a critical synaptic activity that subserves memory, referred to as long term potentiation (LTP), in slice cultures and living animals.
The structure of the oligomer has not been determined to date. Moreover, NMR and other evidence indicates that the oligomer exists not in a single well-defined structure, but in a conformationally-plastic, malleable structural ensemble with limited regularity. Moreover, the concentration of toxic oligomer species is far below either that of the monomer or fibril (estimates vary but are on the order of 1000-fold below or more), making this target elusive.
Antibodies that bind A-beta have been described.
WO2009048538A2 titled USE OF ANTI-AMYLOID ANTIBODY IN OCULAR DISEASES discloses chimeric antibodies that recognize one or more binding sites on A-beta and are useful for the treatment for ocular diseases.
U.S. Pat. No. 9,221,812B2 titled COMPOUNDS FOR THE TREATMENT OF DISEASES ASSOCIATED WITH AMYLOID OR AMYLOID-LIKE PROTEINS describes pharmaceutical compositions and discontinuous antibodies that bind A-beta including an epitope between amino acid residues 12 to 24 for the treatment of amyloid-related diseases.
WO2003070760A2 titled ANTI-AMYLOID BETA ANTIBODIES AND THEIR USE discloses antibodies that recognize an A-beta discontinuous epitope, wherein the first region comprises the amino acid sequence AEFRHDSGY (SEQ ID NO: 203) or a fragment thereof and wherein the second region comprises the amino acid sequence VHHQKLVFFAEDVG (SEQ ID NO: 204) or a fragment thereof.
US20110171243A1 titled COMPOUNDS TREATING AMYLOIDOSES discloses a peptide mimotope capable of inducing the in vivo formation of antibodies that bind HQKLVF (SEQ ID NO: 17) and/or HQKLVFFAED (SEQ ID NO: 13), and its use.
WO2008088983A1 and WO2001062801A2 disclose a pegylated antibody fragment that binds A-beta amino acids 13-28 (HHQKLVFFAEDVGSNK) (SEQ ID NO: 14) and its use in treating A-beta related diseases.
WO2009149487A2 titled COMPOUNDS FOR TREATING SYMPTOMS ASSOCIATED WITH PARKINSON'S DISEASE describes compounds comprising a peptide having binding capacity for an antibody specific for an A-beta epitope such as EVHHQKL (SEQ ID NO: 205), HQKLVF (SEQ ID NO: 17) and HQKLVFFAED (SEQ ID NO: 13).
The HHQK (SEQ ID NO: 1) domain is described as involved in plaque induction of neurotoxicity in human microglia, as described in Giulian D et al. [11] and Winkler et al. [12]. Non-antibody therapeutic agents that bind HHQK (SEQ ID NO: 1) have been disclosed for the treatment of protein folding diseases (US20150105344A1, WO2006125324A1).
WO2010128139A1 titled BIOMARKERS AND METHODS FOR DIAGNOSING ALZHEIMER'S DISEASE AND/OR MILD COGNITIVE IMPAIRMENT discloses a diagnostic method for Alzheimer's disease through assessing levels of antibodies capable of binding pGlu A-Beta in a given subject's body fluid.
WO2011033046A1 titled NOVEL ASSAY FOR THE DETECTION OF AMYLOID BETA PEPTIDES discloses a method for detection of A-beta (1-40).
WO2014161875A1 titled METHOD FOR DETECTING Aβ-SPECIFIC ANTIBODIES IN A BIOLOGICAL SAMPLE discloses a method for detecting A-beta-specific antibodies using A-beta variants for the diagnosis of Alzheimer's disease.
U.S. Pat. Nos. 5,766,846; 5,837,672; and 5,593,846 (which are incorporated herein by reference) describe the production of murine monoclonal antibodies to the central domain of the Aβ peptide. WO 01/62801 describes antibodies that bind A-beta between amino acids 13-28. WO2004071408 discloses humanized antibodies. WO2008088983A1 describes an antibody fragment that binds amyloid beta (A-beta) peptide and is covalently attached to one or more molecules of polyethylene glycol (PEG), the antibody fragment specifically binding human A-beta peptide between amino acid positions 13-28. Solanezumab and Crenezumab bind amino acids 16-26 on A-beta. Crenezumab interacts with the monomer, oligomer and fibril. Midregion antibodies, including solanezumab (picomolar affinity) and crenezumab (nanomolar affinity), appear to preferentially bind monomeric A-beta [16].
Antibodies that preferentially or selectively bind A-beta oligomers and inhibit A-beta oligomerization are desirable for therapeutic intervention.
Described herein and in International Application WO2017/079833 filed Nov. 9, 2016 and International Application PCT/CA2017/050866 filed Jul. 18, 2017 each of which are incorporated herein by reference are conformational epitopes in A-beta comprising and/or consisting of residues HHQK (SEQ ID NO: 1) or a part thereof, and antibodies thereto. Also described herein and in International application WO2017/079835 filed Nov. 9, 2016, incorporated herein by reference, are conformational epitopes in A-beta comprising and/or consisting of residues QKLV (SEQ ID NO: 5) or a part thereof, and antibodies thereto. Further described herein and in International application WO2017/079831 filed Nov. 9, 2016 incorporated herein by reference, are conformational epitopes in A-beta comprising and/or consisting of residues HDSG (SEQ ID NO: 9) or a part thereof, and antibodies thereto.
Unlike some other A-beta antibodies, antibodies raised to immunogenic cyclic conformations of the epitopes HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9) specifically bound oligomeric A-beta in preference to monomeric or fibril forms (see for example
Injection of oligomer forms of A-beta into the brains of mice causes a neurological deficit that can be assessed in a memory-behavior test called novel object recognition as described further below. Normal mice exposed to an object remember the familiar object when re-exposed to it and spend more time exploring a newly introduced object. In contrast, A-beta oligomer-injected mice lose the ability to discriminate between known and novel objects and spend equivalent amounts of time exploring both. Results obtained in this assay showed that administration to mice of an antibody that selectively binds cyclo(CGHHQKG) (SEQ ID NO: 2), cyclo(CGQKLVG) (SEQ ID NO: 6) or cyclo(CGHDSGG) (SEQ ID NO:10) inhibited the loss of short-term memory formation caused by injection of soluble A-beta oligomers.
Accordingly, provided herein are methods for treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer comprising administering to a subject in need thereof a compound, immunogen, composition, antibody, nucleic acid or cell described herein.
In an embodiment, the method of treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer comprises administering to a subject in need thereof: an isolated conformation specific and/or selective antibody or binding fragment thereof that specifically and/or selectively binds to a cyclic compound comprising an A-beta peptide having a sequence of QKL, HQK, KLV, HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9), they cyclic compound optionally having a sequence of SEQ ID NO: 2, 3, 4, 6, 7, 8, 10, 11 or 12; an immunogen comprising a cyclic compound comprising an A-beta peptide having a sequence of QKL, HQK, KLV, HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9); a cell expressing said antibody or binding fragment thereof; or a nucleic acid encoding said antibody or binding fragment thereof.
In an embodiment, the disease or condition associated with and/or induced by soluble A-beta oligomer is cognitive deficits, optionally loss of short term memory formation.
In an embodiment, the disease or condition associated with and/or induced by soluble soluble A-beta oligomer A-beta is Alzheimer's disease (AD).
In an embodiment, the treatment is prophylactic treatment. For example in an embodiment, the antibody is administered to a subject with a predisposition to developing a disease or condition associated with and/or induced by soluble A-beta oligomer or showing an early sign of AD pathology. For example, AD pathology develops first in the perirhinal and enthorinal cortex before the hippocampus.
In an embodiment, the disease or condition is perirhinal cortex dysfunction or pathology. In another embodiment, the disease or condition is enthorinal cortex dysfunction or pathology.
In an embodiment, the disease or condition is associated with and/or induced by soluble A-beta 1-42 oligomer.
In an aspect, an immunogen described herein is administered for treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer.
In an aspect the immunogen comprises a cyclic compound which comprises: an A-beta peptide the peptide comprising HQK and up to 6 A-beta contiguous residues, and a linker, wherein the linker is covalently coupled to the A-beta peptide N-terminus residue and the A-beta C-terminus residue.
In another aspect, the cyclic compound comprises: an A-beta peptide, the A-beta peptide comprising QKL and up to 8, 7 or 6 A-beta residues, and a linker, wherein the linker is covalently coupled to the A-beta peptide N-terminus residue and the A-beta C-terminus residue.
In yet another aspect, the cyclic compound comprises: an A-beta peptide, the A-beta peptide comprising HDSG (SEQ ID NO: 9) and up to 8, 7 or 6 A-beta residues, and a linker, wherein the linker is covalently coupled to the A-beta peptide N-terminus residue and the A-beta C-terminus residue.
In an embodiment, the A-beta peptide is selected from a peptide having a sequence of any one of SEQ ID NOS: 1, 5, 10, 202 or a part thereof.
In another embodiment, the cyclic compound is cyclic peptide.
In another embodiment, the linker comprises or consists of 1-8 amino acids, optionally, 3, 4 or 5, and/or equivalently functioning molecules and/or one or more functionalizable moieties.
In another embodiment, the linker amino acids are selected from A and G, and/or wherein the functionalizable moiety is C. In another embodiment, the linker comprises or consists of amino acids GCG or CGC.
In another embodiment, the linker comprises a PEG molecule.
In another embodiment, the cyclic compound is selected from the structures in
An aspect includes an immunogen comprising the cyclic compound optionally for treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer. In an embodiment, the compound is coupled to a carrier protein or immunogenicity enhancing agent.
In another embodiment, the carrier protein is bovine serum albumin (BSA) or the immunogenicity-enhancing agent is keyhole Keyhole Limpet Haemocyanin (KLH).
In another aspect a composition comprising the immunogen described herein is administered.
In an embodiment, the composition described herein, further comprises an adjuvant.
In another embodiment, the adjuvant is aluminum phosphate or aluminum hydroxide.
In another aspect an isolated conformation specific and/or selective antibody that specifically and/or selectively binds to an A-beta peptide having a sequence of HQK, HHQK (SEQ ID NO: 1), HQKL (SEQ ID NO: 202), QKL, QKLV (SEQ ID NO: 5), HDSG (SEQ ID NO: 9) or a related epitope sequence presented in a cyclic compound described herein, is provided. In embodiments said antibody is administered in a method described herein.
In another embodiment, the antibody selectively binds to a cyclic compound comprising HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5), HDSG (SEQ ID NO: 9) over a corresponding linear peptide, optionally wherein the antibody is at least 2 fold, 3 fold, at least 5 fold, at least 10 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 100 fold, at least 500 fold, at least 1000 fold more selective for the cyclic compound over the corresponding linear compound.
In another embodiment, the antibody selectively binds A-beta oligomer over A-beta monomer and/or A-beta fibril.
In another embodiment, the selectivity is at least 2 fold, at least 3 fold, at least 5 fold, at least 10 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 100 fold, at least 500 fold, at least 1000 fold more selective for A-beta oligomer over A-beta monomer and/or A-beta fibril.
In another embodiment, the antibody does not specifically and/or selectively bind a linear peptide comprising sequence HHQK (SEQ ID NO: 1) or a related epitope, optionally wherein the sequence of the linear peptide is a linear version of a cyclic compound used to raise the antibody, optionally a linear peptide having a sequence as set forth in SEQ ID NO: 2.
In another embodiment, the antibody does not specifically and/or selectively bind a linear peptide comprising sequence QKLV (SEQ ID NO: 5) or a related epitope, optionally wherein the sequence of the linear peptide is a linear version of a cyclic compound used to raise the antibody, optionally a linear peptide having a sequence CGQKLVG (SEQ ID NO: 6).
In another embodiment, the antibody does not specifically and/or selectively bind a linear peptide comprising sequence HDSG (SEQ ID NO: 9) or a related epitope, optionally wherein the sequence of the linear peptide is a linear version of a cyclic compound used to raise the antibody, optionally a linear peptide having a sequence SEQ ID NO: 10.
In another embodiment, the antibody lacks or has negligible binding to A-beta monomer and/or A-beta fibril plaques in situ.
In another embodiment, the antibody is a monoclonal antibody or a polyclonal antibody.
In another embodiment, the antibody is a humanized antibody, optionally comprising a variable domain described in Table 12 or 13.
In another embodiment, the antibody is an antibody binding fragment selected from Fab, Fab′, F(ab′)2, scFv, dsFv, ds-scFv, dimers, nanobodies, minibodies, diabodies, and multimers thereof.
In an embodiment, the antibody comprises a light chain variable region and a heavy chain variable region, optionally fused, the heavy chain variable region comprising complementarity determining regions CDR-H1, CDR-H2 and CDR-H3, the light chain variable region comprising complementarity determining region CDR-L1, CDR-L2 and CDR-L3 and with the amino acid sequences of said CDRs comprising the sequences in Table 9 A to I or Table 15.
For example, in an embodiment, the antibody comprises a light chain variable region and a heavy chain variable region, optionally fused, the heavy chain variable region comprising complementarity determining regions CDR-H1, CDR-H2 and CDR-H3, the light chain variable region comprising complementarity determining region CDR-L1, CDR-L2 and CDR-L3 and with the amino acid sequences of said CDRs comprising the sequences: SEQ ID NOs: 20-25, SEQ ID NOs: 26-31, SEQ ID NOs:32-37, SEQ ID NOs:32-34 and 38-40; SEQ ID NOs:41-46; SEQ ID NOs:47-52, SEQ ID NOs:53-58, SEQ ID NOs:59-64, SEQ ID NOs:59-61 and 65-67; SEQ ID NOs:59-61 and 68-70; SEQ ID NOs:71-76, SEQ ID NOs:71-73 and 77-79; SEQ ID NOs:71-73 and 80-82 and SEQ ID NOs: 185-190.
In an embodiment, the antibody or binding fragment comprises a heavy chain variable region comprising: i) an amino acid sequence of a heavy chain variable sequence as set forth in Table 10; ii) an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80% or at least 90% sequence identity to said heavy chain variable sequence set out in Table 10, 12 or 13, wherein the CDR sequences are the corresponding CDRs as set forth in Table 9, or iii) a conservatively substituted amino acid sequence i) wherein the CDR sequences are the corresponding CDRs as set forth in Table 9; and a light chain variable region comprising i) an amino acid sequence of a light chain variable sequence as set forth in Table 10, ii) an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 90% sequence identity to said light chain variable sequence as set out in Table 10, 12 or 13, wherein the CDR sequences are the corresponding CDRs as set forth in Table 9, or iii) a conservatively substituted amino acid sequence i) wherein the CDR sequences a are the corresponding CDRs as set forth in Table 9.
In an embodiment a combination of antibodies and/or binding fragments thereof described herein are administered.
In another embodiment, the antibody of binding fragment competes for binding to human A-beta with an antibody comprising the CDR sequence set (e.g. CDR H1-3 and CDR L1-3) as recited herein, for example in Table 9, the variable sequence set (e.g. Heavy chain and light chain variable regions, for example in Table 10, 12 or 13) and/or antibody produced by the hybridoma cell line deposited under the provisions of the Budapest Treaty with the American Type Culture Collection (ATCC®) 10801 University Blvd., Manassas, Va., 20110-2209, USA on Jul. 19, 2017 and given the Accession number PTA-124318.
In yet another aspect an immunoconjugate comprising the antibody or binding fragment described herein and a detectable label or cytotoxic agent. In embodiments, said immunoconjugate is administered in methods provided herein.
An aspect includes a composition comprising the antibody or binding fragment described herein, or the immunoconjugate described herein as well as combinations of two or more antibodies or binding fragments thereof described herein, optionally with a diluent. In embodiments, the composition is administered in methods provided herein
In yet a further aspect a nucleic acid molecule encoding a proteinaceous portion of the compound or immunogen described herein, the antibody described herein or proteinaceous immunoconjugates described herein. In some embodiments the nucleic acid molecule is administered in methods provided herein.
In another aspect a vector comprising the nucleic acid described herein is provided and optionally administered in methods provided herein.
In another aspect a cell expressing an antibody or binding fragment described herein is provided. In embodiments, said cell is administered in methods provided herein.
Also provided is a hybridoma cell line deposited under the provisions of the Budapest Treaty with the American Type Culture Collection (ATCC®) 10801 University Blvd., Manassas, Va., 20110-2209, USA on Jul. 19, 2017 and given the Accession number PTA-124318.
An aspect includes a kit comprising the compound described herein, the immunogen described herein, an antibody described herein, the immunoconjugate described herein, the composition described herein, the nucleic acid molecule described herein, the vector described herein or the cell described herein optionally for use in treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer.
An aspect includes a method of making the antibody described herein, comprising administering the compound or immunogen described herein or a composition comprising said compound or immunogen to a subject and isolating antibody and/or cells expressing antibody specific or selective for the compound or immunogen administered and/or A-beta oligomers, optionally lacking or having negligible binding to a linear peptide comprising the A-beta peptide and/or lacking or having negligible plaque binding for use in treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer.
An aspect includes a method of determining if a biological sample comprises A-beta, the method comprising:
In another embodiment, the method comprises:
In another embodiment, the amount of complex is measured.
In another embodiment, the sample comprises brain tissue or an extract thereof, whole blood, plasma, serum and/or CSF.
In another embodiment, the sample is a human sample.
In another embodiment, the sample is compared to a control, optionally a previous sample.
In another embodiment, the level of A-beta is detected by SPR.
An aspect includes a method of measuring a level of A-beta oligomers in a subject, the method comprising administering to a subject at risk or suspected of having or having AD, an immunoconjugate comprising an antibody described herein wherein the antibody is conjugated to a detectable label; and detecting the label, optionally quantitatively detecting the label.
In an embodiment, the label is a positron emitting radionuclide.
An aspect includes a method of inducing an immune response for treating or preventing a disease or condition related with and/or induced by soluble A-beta oligomer in a subject, comprising administering to the subject a compound or combination of compounds described herein, optionally a cyclic compound comprising HQK or HHQK (SEQ ID NO: 1), QKL, QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9) or a related epitope peptide sequence, an immunogen and/or composition comprising said compound or said immunogen; and optionally isolating cells and/or antibodies that specifically or selectively bind the A-beta peptide in the compound or immunogen administered.
An aspect includes a method of inhibiting A-beta oligomer propagation for treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer, the method comprising contacting a cell or tissue expressing A-beta with or administering to a subject in need thereof an effective amount of an A-beta oligomer specific or selective antibody, binding fragment or immunoconjugate described herein.
Another aspect includes a method of treating AD and/or other A-beta amyloid associated and/or induced diseases and conditions, the method comprising administering to a subject in need thereof i) an effective amount of an antibody or immunoconjugate described herein, optionally an A-beta oligomer specific or selective antibody, or a pharmaceutical composition comprising said antibody; 2) administering an isolated cyclic compound comprising HQK, HHQK (SEQ ID NO: 1), QKL, QKLV (SEQ ID NO: 5) or HDSG (SE ID NO: 9) or a related epitope sequence or immunogen or pharmaceutical composition comprising said cyclic compound, or 3) a nucleic acid or vector comprising a nucleic acid encoding the antibody of 1 or the immunogen of 2, to a subject in need thereof.
In an embodiment, a biological sample from the subject to be treated is assessed for the presence or levels of A-beta using an antibody described herein.
In another embodiment, more than one antibody or immunogen is administered.
In another embodiment, the antibody, immunoconjugate, immunogen, composition or nucleic acid or vector is administered directly to the brain or other portion of the CNS.
In another embodiment, the composition is a pharmaceutical composition comprising the compound or immunogen in admixture with a pharmaceutically acceptable, diluent or carrier.
Other features and advantages of the present disclosure will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples while indicating preferred embodiments of the disclosure are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those skilled in the art from this detailed description.
An embodiment of the present disclosure will now be described in relation to the drawings in which:
Provided herein are methods for using antibodies, immunotherapeutic compositions and methods which target epitopes preferentially accessible in toxic oligomeric species of A-beta, including oligomeric species associated with Alzheimer's disease. A region in A-beta has been identified that may be specifically and/or selectively accessible to antibody binding in oligomeric species of A-beta.
Generation of oligomer-specific or oligomer selective antibodies was accomplished through the identification of targets on A-beta peptide that are not present, or present to a lesser degree, on either the monomer and/or fibril. Oligomer-specific epitopes need not differ in primary sequence from the corresponding segment in the monomer or fibril, however they would be conformationally distinct in the context of the oligomer. That is, they would present a distinct conformation in terms of backbone and/or side-chain orientation in the oligomer that would not be present (or would be unfavourable) in the monomer and/or fibril.
Antibodies raised to linear peptide regions tend not to be selective for oligomer, and thus bind to monomer as well.
As described herein, to develop antibodies that may be selective for oligomeric forms of A-beta, the inventors sought to identify regions of A-beta sequence that are prone to disruption in the context of the fibril, and that may be exposed as well on the surface of the oligomer.
The inventors have identified region predicted to be prone to disruption in the context of the fibril. The inventors designed cyclic compounds comprising the identified target region to satisfy criteria of an alternate conformation such as a different curvature profile vs residue index, higher exposed surface area, and/or did not readily align by root mean squared deviation (RMSD) to either the linear or fibril ensembles. HQK, HHQK (SEQ ID NO: 1), HQKL (SEQ ID NO: 202), QKLV (SEQ ID NO: 5) and HDSG (SEQ ID NO: 9) were identified as regions prone to disruption and cyclic compounds were designed comprising the identified target regions.
As shown in the Examples, an immunogen comprising the cyclic compounds SEQ ID Nos: 2, 6 and 10 were used to produce monoclonal antibodies. Antibodies could be raised using a cyclic peptide comprising the target region, that selectively bound the cyclic peptide compared to a linear peptide of the same sequence (e.g. corresponding linear sequence). Experimental results are described and identify epitope-specific and conformationally selective antibodies that bind synthetic oligomer selectively compared to synthetic monomers. Further staining of AD brain tissue identified antibodies that show no or negligible plaque binding and in vitro studies found that the antibodies inhibited Aβ oligomer propagation and aggregation. Furthermore, antibody that selectively binds SEQ ID Nos: 2, 6 or 10 inhibits and/or prevents neurotoxicity and loss of memory formation induced by soluble A-beta oligomers in a mouse model.
As used herein, the term ‘A-beta’ may alternately be referred to as ‘amyloid beta’, ‘amyloid D’, A-beta, A-beta or ‘Aβ’. Amyloid beta is a peptide of 36-43 amino acids and includes all wild-type and mutant forms of all species, particularly human A-beta. A-beta40 refers to the 40 amino acid form; A-beta42 refers to the 42 amino acid form, etc. The amino acid sequence of human wildtype A-beta42 is shown in SEQ ID NO: 19.
As used herein, the term “A-beta monomer” herein refers to any of the individual subunit forms of the A-beta (e.g. 1-40, 1-42, 1-43) peptide.
As used herein, the term “A-beta oligomer” herein refers to a plurality of any of the A-beta subunits wherein several (e.g. at least two) A-beta monomers are non-covalently aggregated in a conformationally-flexible, partially-ordered, three-dimensional globule of less than about 100, or more typically less than about 50 monomers. For example, an oligomer may contain 3 or 4 or 5 or more monomers. The term “A-beta oligomer” as used herein includes both synthetic A-beta oligomer and/or native A-beta oligomer. “Native A-beta oligomer” refers to A-beta oligomer formed in vivo, for example in the brain and CSF of a subject with AD.
As used herein, the term “A-beta fibril” refers to a molecular structure that comprises assemblies of non-covalently associated, individual A-beta peptides which show fibrillary structure under an electron microscope. The fibrillary structure is typically a “cross beta” structure; there is no theoretical upper limit on the size of multimers, and fibrils may comprise thousands or many thousands of monomers. Fibrils can aggregate by the thousands to form senile plaques, one of the primary pathological morphologies diagnostic of AD.
The term “HHQK (SEQ ID NO: 1)” means the amino acid sequence histidine, histidine, glutamine, lysine, as shown in SEQ ID NO: 1. Similarly HQK, HHQ, HHQKLV (SEQ ID NO: 8) HQKL (SEQ ID NO: 202) refers to the amino acid sequence identified by the 1-letter amino acid code. The term “QKLV (SEQ ID NO: 5)” means the amino acid sequence glutamine, lysine, leucine, and valine, as shown in SEQ ID NO: 5 and “HDSG (SEQ ID NO: 9)” means the amino acid sequence of histidine, aspartic acid, serine and glycine as shown in SEQ ID NO: 9. Depending on the context, the reference of the amino acid sequence can refer to a sequence in A-beta or an isolated peptide, such as the amino acid sequence of a cyclic compound.
The term “amino acid” includes all of the naturally occurring amino acids as well as modified L-amino acids. The atoms of the amino acid can include different isotopes. For example, the amino acids can comprise deuterium substituted for hydrogen nitrogen-15 substituted for nitrogen-14, and carbon-13 substituted for carbon-12 and other similar changes.
The term “antibody” as used herein is intended to include, monoclonal antibodies, polyclonal antibodies, single chain, veneered, humanized and other chimeric antibodies and binding fragments thereof, including for example a single chain Fab fragment, Fab′2 fragment or single chain Fv fragment. The antibody may be from recombinant sources and/or produced in animals such as rabbits, llamas, sharks etc. Also included are human antibodies that can be produced in transgenic animals or using biochemical techniques or can be isolated from a library such as a phage library. Humanized or other chimeric antibodies may include sequences from one or more than one isotype or class or species.
The phrase “isolated antibody” refers to antibody produced in vivo or in vitro that has been removed from the source that produced the antibody, for example, an animal, hybridoma or other cell line (such as recombinant insect, yeast or bacteria cells that produce antibody). The isolated antibody is optionally “purified”, which means at least: 80%, 85%, 90%, 95%, 98% or 99% purity.
The term “binding fragment” as used herein to a part or portion of an antibody or antibody chain comprising fewer amino acid residues than an intact or complete antibody or antibody chain and which binds the antigen or competes with intact antibody. Exemplary binding fragments include without limitations Fab, Fab′, F(ab′)2, scFv, dsFv, ds-scFv, dimers, nanobodies, minibodies, diabodies, and multimers thereof. Fragments can be obtained via chemical or enzymatic treatment of an intact or complete antibody or antibody chain. Fragments can also be obtained by recombinant means. For example, F(ab′)2 fragments can be generated by treating the antibody with pepsin. The resulting F(ab′)2 fragment can be treated to reduce disulfide bridges to produce Fab′ fragments. Papain digestion can lead to the formation of Fab fragments. Fab, Fab′ and F(ab′)2, scFv, dsFv, ds-scFv, dimers, minibodies, diabodies, bispecific antibody fragments and other fragments can also be constructed by recombinant expression techniques.
The terms “IMGT numbering” or “ImMunoGeneTics database numbering”, which are recognized in the art, refer to a system of numbering amino acid residues which are more variable (i.e. hypervariable) than other amino acid residues in the heavy and light chain variable regions of an antibody, or antigen binding portion thereof.
When an antibody is said to bind to an epitope within specified residues, such as HHQK (SEQ ID NO: 1), what is meant is that the antibody specifically binds to a peptide or polypeptide containing the specified residues or a part thereof for example at least 1 residue or at least 2 residues, with a minimum affinity, and does not bind an unrelated sequence or unrelated sequence spatial orientation greater than for example an isotype control antibody. Such an antibody does not necessarily contact each residue of HHQK (SEQ ID NO: 1) (or a related epitope), and every single amino acid substitution or deletion within said epitope does not necessarily significantly affect and/or equally affect binding affinity.
When an antibody is said to selectively bind an epitope such as a conformational epitope, such as HHQK (SEQ ID NO: 1), what is meant is that the antibody preferentially binds one or more particular conformations containing the specified residues or a part thereof with greater affinity than it binds said residues in another conformation. For example, when an antibody is said to selectively bind a cyclopeptide comprising SEQ ID NO: 1, 5 or 9 or related epitope relative to a corresponding linear peptide, the antibody binds the cyclopeptide with at least a 2 fold greater affinity than it binds the linear peptide.
As used herein, the term “conformational epitope” refers to an epitope where the epitope amino acid sequence has a particular three-dimensional structure wherein at least an aspect of the three-dimensional structure not present or less likely to be present in a corresponding linear peptide is specifically and/or selectively recognized by the cognate antibody. The epitope e.g. HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9) may be partially or completely exposed on the molecular surface of oligomeric A-beta and partially or completely obscured from antibody recognition in monomeric or fibrillar plaque A-beta. Antibodies which specifically bind a conformation-specific epitope recognize the spatial arrangement of one or more of the amino acids of that conformation-specific epitope. For example, an HHQK (SEQ ID NO: 1) conformational epitope refers to an epitope of HHQK (SEQ ID NO: 1) that is recognized by antibodies selectively, for example at least 2 fold, 3 fold, 5 fold, 10 fold, 50 fold, 100 fold, 250 fold, 500 fold or 1000 fold or greater more selectivity as compared to antibodies raised using linear HHQK (SEQ ID NO: 1).
The term “related epitope” as used herein means at least two residues of HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9) that are antigenic when for example conjugated to KLH, optionally with respect to HHQK (SEQ ID NO: 1) sequences comprising HQK, and/or sequences comprising 1 2 or 3 amino acid residues in a A-beta N-terminal and/or 1 residue C-terminal to at least two residues of HHQK (SEQ ID NO: 1), for HDSG (SEQ ID NO: 9) 1 2 or 3 amino acid residues in a A-beta N-terminal and/or 1 2 or 3 amino acid residues in a A-beta C-terminal to HDSG (SEQ ID NO: 9) or for QKLV (SEQ ID NO: 5), comprising 1 2 or 3 amino acid residues in a A-beta C-terminal and/or 1 residue N-terminal to QKLV (SEQ ID NO: 5). For example HHQK (SEQ ID NO: 1) and HQKL (SEQ ID NO: 202) which share the subregion HQK were identified as regions prone to disorder in an A-beta fibril. HQK and HQKL (SEQ ID NO: 202) are accordingly related epitopes. Exemplary related epitopes can include epitopes whose sequences are shown in Table 8 (1). The related epitope is for example up to 6 A-beta residues.
The term “no or negligible plaque binding” or “lacks or has negligible plaque binding” as used herein with respect to an antibody means that the antibody does not show typical plaque morphology staining on immunohistochemistry (e.g. in situ) and the level of staining is comparable to or no more than 2 fold the level seen with an IgG negative (e.g. irrelevant) isotype control.
The term “Isolated peptide” refers to peptide that has been produced, for example, by recombinant or synthetic techniques, and removed from the source that produced the peptide, such as recombinant cells or residual peptide synthesis reactants. The isolated peptide is optionally “purified”, which means at least: 80%, 85%, 90%, 95%, 98% or 99% purity and optionally pharmaceutical grade purity.
The term “detectable label” as used herein refers to moieties such as peptide sequences (such a myc tag, HA-tag, V5-tag or NE-tag), fluorescent proteins that can be appended or introduced into a peptide or compound described herein and which is capable of producing, either directly or indirectly, a detectable signal. For example, the label may be radio-opaque, positron-emitting radionuclide (for example for use in PET imaging), or a radioisotope, such as 3H, 13N, 14C, 18F, 32P, 35S, 123I, 125I, 131I; a fluorescent (fluorophore) or chemiluminescent (chromophore) compound, such as fluorescein isothiocyanate, rhodamine or luciferin; an enzyme, such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase; an imaging agent; or a metal ion. The detectable label may be also detectable indirectly for example using secondary antibody.
The term “epitope” as commonly used means an antibody binding site, typically a polypeptide segment, in an antigen that is specifically recognized by the antibody. As used herein “epitope” can also refer to the amino acid sequences or part thereof identified on A-beta using the collective coordinates method described. For example an antibody generated against an isolated peptide corresponding to a cyclic compound comprising the identified target region HHQK SEQ ID NO: 1), recognizes part or all of said epitope sequence. An epitope is “accessible” in the context of the present specification when it is accessible to binding by an antibody.
The term “greater affinity” as used herein refers to a relative degree of antibody binding where an antibody X binds to target Y more strongly (Kon) and/or with a smaller dissociation constant (Koff) than to target Z, and in this context antibody X has a greater affinity for target Y than for Z. Likewise, the term “lesser affinity” herein refers to a degree of antibody binding where an antibody X binds to target Y less strongly and/or with a larger dissociation constant than to target Z, and in this context antibody X has a lesser affinity for target Y than for Z. The affinity of binding between an antibody and its target antigen, can be expressed as KA equal to 1/KD where KD is equal to kon/koff. The kon and koff values can be measured using surface plasmon resonance technology, for example using a Molecular Affinity Screening System (MASS-1) (Sierra Sensors GmbH, Hamburg, Germany). An antibody that is selective for a conformation presented in a cyclic compound optional a cyclic peptide for example has a greater affinity for the cyclic compound (e.g. cyclic peptide) compared to a corresponding sequence in linear form (e.g. the sequence non-cyclized).
Also as used herein, the term “immunogenic” refers to substances that elicit the production of antibodies, activate T-cells and other reactive immune cells directed against an antigenic portion of the immunogen.
The term “corresponding linear compound” with regard to a cyclic compound refers to a compound, optionally a peptide, comprising or consisting of the same sequence or chemical moieties as the cyclic compound but in linear (i.e. non-cyclized) form, for example having properties as would be present in solution of a linear peptide. For example, the corresponding linear compound can be the synthesized peptide that is not cyclized.
As used herein “specifically binds” in reference to an antibody means that the antibody recognizes an epitope sequence and binds to its target antigen with a minimum affinity. For example a multivalent antibody binds its target with a KD of at least 1e-6, at least 1e-7, at least 1e-8, at least 1e-9, or at least 1e-10. Affinities greater than at least 1e-8 may be preferred. An antigen binding fragment such as Fab fragment comprising one variable domain, may bind its target with a 10 fold or 100 fold less affinity than a multivalent interaction with a non-fragmented antibody.
The term “selectively binds” as used herein with respect to an antibody that selectively binds a form of A-beta (e.g. fibril, monomer or oligomer) or a cyclic compound means that the antibody binds the form with at least 2 fold, at least 3 fold, or at least 5 fold, at least 10 fold, at least 100 fold, at least 250 fold, at least 500 fold or at least 1000 fold or more greater affinity. Accordingly an antibody that is more selective for a particular conformation (e.g. oligomer) preferentially binds the particular form of A-beta with at least 2 fold etc. greater affinity compared to another form and/or a linear peptide.
The term “linker” as used herein means a chemical moiety that can be covalently linked to the peptide comprising HHQK (SEQ ID NO: 1), optionally linked to HHQK (SEQ ID NO: 1) peptide N- and C-termini to produce a cyclic compound. The linker can comprise a spacer and/or one or more functionalizable moieties. The linker can be linked via the functionalizable moieties to a carrier protein or an immunogen enhancing agent such as keyhole limpet hemocyanin (KLH).
The term “spacer” as used herein means any preferably non-immunogenic or poorly immunogenic chemical moiety that can be covalently-linked directly or indirectly to a peptide N- and C-termini to produce a cyclic compound of longer length than the peptide itself, for example the spacer can be linked to the N- and C-termini of a peptide consisting of HHQK (SEQ ID NO: 1) to produce a cyclic compound of longer backbone length than the HHQK (SEQ ID NO: 1) sequence itself. That is, when cyclized the peptide with a spacer (for example of 3 amino acid residues) makes a larger closed circle than the peptide without a spacer. The spacer may include, but is not limited to, non-immunogenic moieties such as G, A, or PEG repeats. The spacer may comprise or be coupled to one or more functionalizing moieties, such as one or more cysteine (C) residues, which can be interspersed within the spacer or covalently linked to one or both ends of the spacer. Where a functionalizable moiety such as a C residue is covalently linked to one or more termini of the spacer, the spacer is indirectly covalently linked to the peptide. The spacer can also comprise the functionalizable moiety in a spacer residue as in the case where a biotin molecule is introduced into an amino acid residue.
The term “functionalizable moiety” as used herein refers to a chemical entity with a “functional group” which as used herein refers to a group of atoms or a single atom that will react with another group of atoms or a single atom (so called “complementary functional group”) to form a chemical interaction between the two groups or atoms. In the case of cysteine, the functional group can be —SH which can be reacted to form a disulfide bond. Accordingly the linker can for example be CCC. The reaction with another group of atoms can be covalent or a strong non-covalent bond, for example as in the case as biotin-streptavidin bonds, which can have Kd˜1e-14. A strong non-covalent bond as used herein means an interaction with a Kd of at least 1e-9, at least 1e-10, at least 1e-11, at least 1e-12, at least 1e-13 or at least 1e-14.
Proteins and/or other agents may be functionalized (e.g. coupled) to the cyclic compound, either to aid in immunogenicity, or to act as a probe in in vitro studies. For this purpose, any functionalizable moiety capable of reacting (e.g. making a covalent or non-covalent but strong bond) may be used. In one specific embodiment, the functionalizable moiety is a cysteine residue which is reacted to form a disulfide bond with an unpaired cysteine on a protein of interest, which can be, for example, an immunogenicity enhancing agent such as Keyhole limpet hemocyanin (KLH), or a carrier protein such as Bovine serum albumin (BSA) used for in vitro immunoblots or immunohistochemical assays.
The term “reacts with” as used herein generally means that there is a flow of electrons or a transfer of electrostatic charge resulting in the formation of a chemical interaction.
The term “animal” or “subject” as used herein includes all members of the animal kingdom including mammals, optionally including or excluding humans.
A “conservative amino acid substitution” as used herein, is one in which one amino acid residue is replaced with another amino acid residue without abolishing the protein's desired properties. Suitable conservative amino acid substitutions can be made by substituting amino acids with similar hydrophobicity, polarity, and R-chain length for one another. Examples of conservative amino acid substitution include:
The term “sequence identity” as used herein refers to the percentage of sequence identity between two polypeptide sequences or two nucleic acid sequences. To determine the percent identity of two amino acid sequences or of two nucleic acid sequences, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of a first amino acid or nucleic acid sequence for optimal alignment with a second amino acid or nucleic acid sequence). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in the first sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % identity=number of identical overlapping positions/total number of positions·times·100%). In one embodiment, the two sequences are the same length. The determination of percent identity between two sequences can also be accomplished using a mathematical algorithm. A preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul, 1990, Proc. Natl. Acad. Sci. U.S.A. 87:2264-2268, modified as in Karlin and Altschul, 1993, Proc. Natl. Acad. Sci. U.S.A. 90:5873-5877. Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al., 1990, J. Mol. Biol. 215:403. BLAST nucleotide searches can be performed with the NBLAST nucleotide program parameters set, e.g., for score=100, word length=12 to obtain nucleotide sequences homologous to a nucleic acid molecules of the present application. BLAST protein searches can be performed with the XBLAST program parameters set, e.g., to score-50, word length=3 to obtain amino acid sequences homologous to a protein molecule described herein. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al., 1997, Nucleic Acids Res. 25:3389-3402. Alternatively, PSI-BLAST can be used to perform an iterated search which detects distant relationships between molecules (Id.). When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., of XBLAST and NBLAST) can be used (see, e.g., the NCBI website). Another preferred non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller, 1988, CABIOS 4:11-17. Such an algorithm is incorporated in the ALIGN program (version 2.0) which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. The percent identity between two sequences can be determined using techniques similar to those described above, with or without allowing gaps. In calculating percent identity, typically only exact matches are counted.
For antibodies, percentage sequence identities can be determined when antibody sequences maximally aligned by IMGT or other (e.g. Kabat numbering convention). After alignment, if a subject antibody region (e.g., the entire mature variable region of a heavy or light chain) is being compared with the same region of a reference antibody, the percentage sequence identity between the subject and reference antibody regions is the number of positions occupied by the same amino acid in both the subject and reference antibody region divided by the total number of aligned positions of the two regions, with gaps not counted, multiplied by 100 to convert to percentage.
The term “nucleic acid sequence” as used herein refers to a sequence of nucleoside or nucleotide monomers consisting of naturally occurring bases, sugars and intersugar (backbone) linkages. The term also includes modified or substituted sequences comprising non-naturally occurring monomers or portions thereof. The nucleic acid sequences of the present application may be deoxyribonucleic acid sequences (DNA) or ribonucleic acid sequences (RNA) and may include naturally occurring bases including adenine, guanine, cytosine, thymidine and uracil. The sequences may also contain modified bases. Examples of such modified bases include aza and deaza adenine, guanine, cytosine, thymidine and uracil; and xanthine and hypoxanthine. The nucleic acid can be either double stranded or single stranded, and represents the sense or antisense strand. Further, the term “nucleic acid” includes the complementary nucleic acid sequences as well as codon optimized or synonymous codon equivalents. The term “isolated nucleic acid sequences” as used herein refers to a nucleic acid substantially free of cellular material or culture medium when produced by recombinant DNA techniques, or chemical precursors, or other chemicals when chemically synthesized. An isolated nucleic acid is also substantially free of sequences which naturally flank the nucleic acid (i.e. sequences located at the 5′ and 3′ ends of the nucleic acid) from which the nucleic acid is derived.
“Operatively linked” is intended to mean that the nucleic acid is linked to regulatory sequences in a manner which allows expression of the nucleic acid. Suitable regulatory sequences may be derived from a variety of sources, including bacterial, fungal, viral, mammalian, or insect genes. Selection of appropriate regulatory sequences is dependent on the host cell chosen and may be readily accomplished by one of ordinary skill in the art. Examples of such regulatory sequences include: a transcriptional promoter and enhancer or RNA polymerase binding sequence, a ribosomal binding sequence, including a translation initiation signal. Additionally, depending on the host cell chosen and the vector employed, other sequences, such as an origin of replication, additional DNA restriction sites, enhancers, and sequences conferring inducibility of transcription may be incorporated into the expression vector.
The term “vector” as used herein comprises any intermediary vehicle for a nucleic acid molecule which enables said nucleic acid molecule, for example, to be introduced into prokaryotic and/or eukaryotic cells and/or integrated into a genome, and include plasmids, phagemids, bacteriophages or viral vectors such as retroviral based vectors, Adeno Associated viral vectors and the like. The term “plasmid” as used herein generally refers to a construct of extrachromosomal genetic material, usually a circular DNA duplex, which can replicate independently of chromosomal DNA.
By “at least moderately stringent hybridization conditions” it is meant that conditions are selected which promote selective hybridization between two complementary nucleic acid molecules in solution. Hybridization may occur to all or a portion of a nucleic acid sequence molecule. The hybridizing portion is typically at least 15 (e.g. 20, 25, 30, 40 or 50) nucleotides in length. Those skilled in the art will recognize that the stability of a nucleic acid duplex, or hybrids, is determined by the Tm, which in sodium containing buffers is a function of the sodium ion concentration and temperature (Tm=81.5° C.−16.6 (Log 10 [Na+])+0.41(%(G+C)−600/1), or similar equation). Accordingly, the parameters in the wash conditions that determine hybrid stability are sodium ion concentration and temperature. In order to identify molecules that are similar, but not identical, to a known nucleic acid molecule a 1% mismatch may be assumed to result in about a 1° C. decrease in Tm, for example if nucleic acid molecules are sought that have a >95% identity, the final wash temperature will be reduced by about 5° C. Based on these considerations those skilled in the art will be able to readily select appropriate hybridization conditions. In preferred embodiments, stringent hybridization conditions are selected. By way of example the following conditions may be employed to achieve stringent hybridization: hybridization at 5× sodium chloride/sodium citrate (SSC)/5×Denhardt's solution/1.0% SDS at Tm−5° C. based on the above equation, followed by a wash of 0.2×SSC/0.1% SDS at 60° C. Moderately stringent hybridization conditions include a washing step in 3×SSC at 42° C. It is understood, however, that equivalent stringencies may be achieved using alternative buffers, salts and temperatures. Additional guidance regarding hybridization conditions may be found in: Current Protocols in Molecular Biology, John Wiley & Sons, N.Y., 2002, and in: Sambrook et al., Molecular Cloning: a Laboratory Manual, Cold Spring Harbor Laboratory Press, 2001.
The term “treating” or “treatment” as used herein and as is well understood in the art, means an approach for obtaining beneficial or desired results, including clinical results. Beneficial or desired clinical results can include, but are not limited to, alleviation or amelioration of one or more symptoms or conditions, diminishment of extent of disease, stabilized (i.e. not worsening) state of disease, preventing spread of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, diminishment of the reoccurrence of disease, and remission (whether partial or total), whether detectable or undetectable. “Treating” and “Treatment” can also mean prolonging survival as compared to expected survival if not receiving treatment. “Treating” and “treatment” as used herein also include prophylactic treatment. For example, a subject with early stage AD can be treated to prevent progression can be treated with a compound, antibody, immunogen, nucleic acid or composition described herein to prevent progression.
The term “administered” as used herein means administration of a therapeutically effective dose of a compound or composition of the disclosure to a cell or subject.
As used herein, the phrase “effective amount” means an amount effective, at dosages and for periods of time necessary to achieve a desired result. Effective amounts when administered to a subject may vary according to factors such as the disease state, age, sex, weight of the subject. Dosage regime may be adjusted to provide the optimum therapeutic response.
The term “pharmaceutically acceptable” means that the carrier, diluent, or excipient is compatible with the other components of the formulation and not substantially deleterious to the recipient thereof.
Compositions or methods “comprising” or “including” one or more recited elements may include other elements not specifically recited. For example, a composition that “comprises” or “includes” an antibody may contain the antibody alone or in combination with other ingredients.
In understanding the scope of the present disclosure, the term “consisting” and its derivatives, as used herein, are intended to be close ended terms that specify the presence of stated features, elements, components, groups, integers, and/or steps, and also exclude the presence of other unstated features, elements, components, groups, integers and/or steps.
The recitation of numerical ranges by endpoints herein includes all numbers and fractions subsumed within that range (e.g. 1 to 5 includes 1, 1.5, 2, 2.75, 3, 3.90, 4, and 5). It is also to be understood that all numbers and fractions thereof are presumed to be modified by the term “about.” Further, it is to be understood that “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise. The term “about” means plus or minus 0.1 to 50%, 5-50%, or 10-40%, preferably 10-20%, more preferably 10% or 15%, of the number to which reference is being made.
Further, the definitions and embodiments described in particular sections are intended to be applicable to other embodiments herein described for which they are suitable as would be understood by a person skilled in the art. For example, in the following passages, different aspects of the invention are defined in more detail. Each aspect so defined may be combined with any other aspect or aspects unless clearly indicated to the contrary. In particular, any feature indicated as being preferred or advantageous may be combined with any other feature or features indicated as being preferred or advantageous.
The singular forms of the articles “a,” “an,” and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a compound” or “at least one compound” can include a plurality of compounds, including mixtures thereof.
Conformation selective antibodies were raised to A-beta epitope sequences presented in a cyclic format as described herein. Said antibodies selectively bound synthetic and/or native oligomeric A-beta species compared to monomeric A-beta and A-beta fibril plaques. Further said antibodies were able to inhibit in vitro propagation of A-beta aggregation. In addition, as demonstrated in toxicity assays, said antibodies inhibited A-beta oligomer in vitro neural cell toxicity and prevented neurotoxicity and loss of memory formation induced by soluble A-beta oligomers in an in vivo mouse model. Several of the specific antibody sequences are described in PCT/CA2016/051300, filed Nov. 9, 2016; PCT/CA2016/051305, filed Nov. 9, 2016; PCT/CA2016/051303, filed Nov. 9, 2016; and PCT/CA2017/050866, filed Jul. 18, 2017. Additional antibodies are described herein. Uses of said antibodies are also provided.
Accordingly, the present disclosure provides for treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer comprising administering to a subject in need thereof a compound, immunogen, composition, antibody, nucleic acid or cell described herein described herein.
In an embodiment, the compound, immunogen or antibody is directed to a conformational epitope in A-beta consisting of amino acids HHQK (SEQ ID NO: 1), HQKL (SEQ ID NO: 202) or a part thereof such as HQK, HHQK (SEQ ID NO: 1) corresponding to amino acids residues 13-16 on A-beta and HQKL (SEQ ID NO: 202) corresponding to amino acids 14-17. HHQK (SEQ ID NO: 1) and HQKL (SEQ ID NO: 202) were identified as regions prone to disorder in an A-beta fibril. The residues HHQK (SEQ ID NO: 1) and HQKL (SEQ ID NO: 202) emerged in predictions.
The residues QKLV (SEQ ID NO: 5) were identified as a region prone to disorder in an A-beta fibril. In an embodiment, the compound, immunogen or antibody is directed to a conformational epitope in A-beta consisting of amino acids QKLV (SEQ ID NO: 5), a part thereof such as QKL or a related epitope.
Also, the residues HDSG (SEQ ID NO: 9) were identified as a region prone to disorder in an A-beta fibril. In another embodiment, the compound, immunogen or antibody is directed to a conformational epitope in A-beta consisting of amino acids HDSG (SEQ ID NO: 9), a part thereof such as HDS or a related epitope.
In another aspect the subject is administered a compound comprising an A-beta peptide comprising or consisting of QKLV (SEQ ID NO: 5), HDSG (SEQ ID NO:9), a part thereof or a related epitope sequence and or combinations thereof.
In an aspect the subject is administered a compound comprising an A-beta peptide comprising or consisting of HHQK (SEQ ID NO: 1), a related epitope sequence including a part of any of the foregoing, wherein if the peptide is HHQK (SEQ ID NO: 1), the peptide is in a conformation that is distinct in at least one feature from linear HHQK (SEQ ID NO: 1). In an embodiment, the A-beta peptide is selected from HHQK (SEQ ID NO: 1). HQKL (SEQ ID NO: 202) and is comprised in a cyclic compound. The epitopes are included in the epitopes collectively referred to herein as HHQK (SEQ ID NO: 1) and related epitopes (and their sequences are collectively referred to as related epitope sequences). In an embodiment, the related epitope comprises or consists of HQKL (SEQ ID NO: 202), HQK and epitopes that comprise 1, 2 or 3 amino acids in A-beta either N-terminal and/or 1 amino acid C-terminal to HQK.
In an embodiment, the A-beta peptide comprises HQK or HHQK (SEQ ID NO: 1) or a related epitope, can include 1, 2 or 3 additional residues in A-beta N terminus of and/or 1, 2 or 3 amino acid C-terminus of HHQK (SEQ ID NO: 1). For example, the 3 amino acids N-terminal to HHQK (SEQ ID NO: 1) in A-beta are YEV and the 3 amino acids C-terminal to HHQK (SEQ ID NO: 1) are LVF. In an embodiment, the A-beta peptide is a maximum of 7 or 6 A-beta residues. In an embodiment, the A-beta peptide is a maximum of 5 A-beta residues. In yet another embodiment A-beta peptide (e.g. in the compound such as a cyclic compound) is 4 A-beta residues, optionally HHQK (SEQ ID NO: 1).
In an embodiment, the A-beta peptide comprising QKLV (SEQ ID NO: 5) can include 1, 2 or 3 additional residues in A-beta C-terminus and/or 1, 2 or 3 additional residue in A-beta N-terminus of QKLV (SEQ ID NO: 5). The 3 amino acids N-terminal to QKLV (SEQ ID NO: 5) in A-beta are VHH and the 3 amino acids C-terminal to QKLV (SEQ ID NO: 5) are FFA. In an embodiment the A-beta peptide is a maximum of 7 amino acids, 6 amino acids or 5 amino acids.
In an embodiment, the A-beta peptide comprising HDSG (SEQ ID NO: 9) can include 1, 2 or 3 additional residues in A-beta C-terminus and/or 1, 2 or 3 additional residue in A-beta N-terminus of HDSG (SEQ ID NO: 9). The 3 amino acids N-terminal to HDSG (SEQ ID NO: 9) in A-beta are EFR and the 3 amino acids C-terminal to HDSG (SEQ ID NO: 9) are YEV. In an embodiment the A-beta peptide is a maximum of 7 amino acids, 6 amino acids or 5 amino acids.
In an embodiment, the compound further includes a linker. The linker comprises a spacer and/or one or more functionalizable moieties. The linker can for example comprise 1, 2, 3, 4, 5, 6, 7 or 8 amino acids and/or equivalently functioning molecules such as polyethylene glycol (PEG) moieties, and/or a combination thereof. In an embodiment, the spacer amino acids are selected from non-immunogenic or poorly immunogenic amino acid residues such as G and A, for example the spacer can be GGG, GAG, G(PEG)G, PEG-PEG (also referred to as PEG2)-GG and the like. One or more functionalizable moieties e.g. amino acids with a functional group may be included for example for coupling the compound to an agent or detectable tag or a carrier such as BSA or an immunogenicity enhancing agent such as KLH.
In an embodiment the linker comprises GC-PEG, PEG-GC, GCG or PEG2-CG.
In an embodiment, the linker comprises 1, 2, 3, 4, 5, 6, 7 or 8 amino acids.
In certain embodiments, the cyclic compound has a maximum of 12, 11, 10, 9, 8, or 7 residues, optionally amino acids and/or equivalent units such as PEG units or other similar sized chemical moieties.
In embodiments wherein the A-beta peptide comprising for example HQK or HHQK (SEQ ID NO: 1), HDSG (SEQ ID NOL9) or QKLV (SEQ ID NO: 5), includes 1, 2 or 3 additional residues found in A-beta that are N- and/or C-terminal to the epitope sequence the linker in the cyclized compound is covalently linked to the N- and/or C-termini of the A-beta residues. Where the A-beta peptide is HHQK (SEQ ID NO: 1), the linker is covalently linked to residues H and K.
In an embodiment, the compound is a cyclic compound, such as a cyclopeptide, optionally a cyclopeptide described herein.
Proteinaceous portions of compounds (or the compound wherein the linker is also proteinaceous) may be prepared by chemical synthesis using techniques well known in the chemistry of proteins such as solid phase synthesis or synthesis in homogenous solution.
Reference to the “cyclic peptide” or “cyclopeptide” herein can refer to a fully proteinaceous compound (e.g. wherein the linker is for example 1, 2, 3, 4, 5, 6, 7 or 8 amino acids). It is understood that properties described for the cyclic peptide determined in the examples can be incorporated in other compounds (e.g. other cyclic compounds) comprising non-amino acid linker molecules.
The linear peptide comprising the A-beta sequence can be comprised in a linear compound. The linear compound or the linear peptide comprising HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9) is in an embodiment, a corresponding linear peptide. In another embodiment, the linear peptide is any length of A-beta peptide comprising the epitope sequence), including for example a linear peptide comprising A-beta residues 1-35, or smaller portions thereof such as A-beta residues 10-20, 11-20, 12-20, 13-20, 10-19, 10-18 and the like etc. The linear peptide can in some embodiments also be a full length A-beta peptide.
The cyclic compound can be synthesized as a linear molecule with the linker covalently attached to the N-terminus or C-terminus of the peptide comprising the A-beta peptide, prior to cyclization. Alternatively part of the linker is covalently attached to the N-terminus and part is covalently attached to the C-terminus prior to cyclization. In either case, the linear compound is cyclized for example in a head to tail cyclization (e.g. amide bond cyclization).
In some embodiments, the linker is indirectly coupled to the N- and C-terminus residues of the A-beta peptide.
In an embodiment, the cyclic compound is a compound in
Methods for making cyclized peptides are known in the art and include SS-cyclization or amide cyclization (head-to-tail, or backbone cyclization). Methods are further described in the Examples. For example, a peptide with “C” residues at its N- and C-termini, can be reacted by SS-cyclization to produce a cyclic peptide.
In an embodiment an immunogen comprising a compound, optionally a cyclic compound described herein is administered for treating or preventing an oligomeric A-beta disease. In an embodiment, the immunogen is prepared with sterile reagents and/or distilled water.
In an embodiment, the immunogen is a cyclic peptide comprising A-beta peptide described herein.
In an embodiment, the immunogen comprises immunogenicity enhancing agent such as Keyhole Limpet Hemocyanin (KLH). The immunogenicity enhancing agent can be coupled to the compound either directly, such as through an amide bound, or indirectly through a chemical linker.
The immunogen can be produced by conjugating the cyclic compound containing the A-beta peptide to an immunogenicity enhancing agent such as Keyhole Limpet Hemocyanin (KLH) or a carrier such bovine serum albumin (BSA) using for example the method described in Lateef et al 2007, herein incorporated by reference. In an embodiment, the method described in Example 1 is used.
An immunogen is suitably prepared or formulated for administration to a subject, for example, the immunogen may be sterile, or purified.
A further aspect is administration of an isolated nucleic acid encoding the proteinaceous portion of a compound or immunogen described herein.
In embodiment, the nucleic acid molecule encodes any one of the amino acid sequences sent forth herein, such as antibody or fragment thereof, optionally a binding fragment.
A further aspect is administration of a vector comprising said nucleic acid. Suitable vectors are described elsewhere herein.
Also provided is an antibody or binding fragment described herein, cells expressing such antibody or binding fragment, such as hybridoma cell lines as well as nucleic acids encoding said antibodies. Also provided are uses thereof for inhibiting A-beta propagation, and treating or preventing A-beta oligomer associated and/or induced conditions and diseases including memory loss, and Alzheimer's disease.
Accordingly, in an aspect, antibodies raised using the compounds and immunogens, including compounds and immunogens comprising the cyclic peptides described above can be used for treating AD and/or other A-beta amyloid associated and/or induced diseases and conditions.
Accordingly, an aspect includes an antibody or binding fragment thereof described herein. In an embodiment the antibody or binding fragment thereof comprises a light chain variable region and a heavy chain variable region, optionally fused, the heavy chain variable region comprising complementarity determining regions CDR-H1, CDR-H2 and CDR-H3, the light chain variable region comprising complementarity determining region CDR-L1, CDR-L2 and CDR-L3 and with the amino acid sequences of said CDRs comprising the sequences in Table 9, optionally Table 9B, 9C, 9G, 9H or 91.
Also provided in another aspect is an immunoconjugate comprising an antibody or binding fragment described herein, optionally with the amino acid sequences of said CDRs comprising the sequences in Table 9B, 9C, 9G, 9H or 91 and a detectable label or cytotoxic agent, optionally, wherein the detectable label comprises a positron emitting radionuclide, optionally for use in subject imaging such as PET imaging.
A further aspect includes a hybrdioma cell line deposited under the provisions of the Budapest Treaty with the American Type Culture Collection (ATCC®) 10801 University Blvd., Manassas, Va., 20110-2209, USA on Jul. 19, 2017 and given the Accession number PTA-124318.
Also provided in another aspect is an antibody produced by the hybrdioma cell line deposited under the provisions of the Budapest Treaty with the American Type Culture Collection (ATCC®) 10801 University Blvd., Manassas, Va., 20110-2209, USA on Jul. 19, 2017 and given the Accession number PTA-124318.
Antibodies described herein and immunoconjugates comprising a cytotoxic agent can be used to inhibit A-beta oligomer associated and/or induced conditions and diseases and/or to inhibit A-beta oligomer propagation.
Accordingly, an aspect includes a method of treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer comprising administering to a subject in need thereof: an isolated conformation specific and/or selective antibody or binding fragment thereof that specifically and/or selectively binds to a cyclic compound comprising an A-beta peptide having a sequence of QKL, HQK, KLV, HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9), they cyclic compound optionally having a sequence of SEQ ID NO: 2, 3, 4, 6, 7, 8, 10, 11 or 12; an immunogen comprising a cyclic compound comprising an A-beta peptide having a sequence of QKL, HQK, KLV, HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9); a cell expressing said antibody or binding fragment thereof; or a nucleic acid encoding said antibody or binding fragment thereof.
Also provided in an embodiment, is a method of inhibiting A-beta oligomer propagation, the method comprising contacting a cell or tissue expressing A-beta with or administering to a subject in need thereof an effective amount of an isolated A-beta oligomer specific or selective antibody or binding fragment thereof that specifically and/or selectively binds to a cyclic compound comprising an A-beta peptide having a sequence of QKL, HQK, KLV, HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9), they cyclic compound optionally having a sequence of SEQ ID NO: 2, 3, 4, 6, 7, 8, 10, 11 or 12; an immunogen comprising a cyclic compound comprising an A-beta peptide having a sequence of QKL, HQK, KLV, HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9); a cell expressing said antibody or binding fragment thereof; or a nucleic acid encoding said antibody or binding fragment therefore immunoconjugate thereof, to inhibit A-beta aggregation and/or oligomer propagation.
In an embodiment, the method includes administration of an antibody (including a binding fragment thereof) that specifically binds to an A-beta peptide having a sequence HQK, HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5), HDSG (SEQ ID NO: 9) or a related epitope sequence described herein.
In an embodiment the antibody is specific and/or selective for A-beta peptide presented in the cyclic compound.
In an embodiment, the cyclic compound is a cyclic peptide optionally one described herein. The terms cyclopeptide and cyclic peptide are used interchangeably herein.
In an embodiment, the antibody specifically and/or selectively binds the A-beta peptide presented in the cyclic compound relative to a corresponding linear compound comprising the A-beta peptide.
In an embodiment, the antibody does not bind a linear peptide comprising the sequence HHQK (SEQ ID NO: 1), QKLV (SEQ ID NO: 5), or HDSG (SEQ ID NO: 9) optionally wherein the sequence of the linear peptide is a linear version of a cyclic sequence used to raise the antibody, optionally as set forth in SEQ ID NOs: 2, 6 or 10.
In an embodiment the antibody is isolated. In an embodiment, the antibody is an exogenous antibody.
In an embodiment, the antibody does not specifically bind and/or is not selective for linear HQKLVF (SEQ ID NO: 17), linear HQKLVFF (SEQ ID NO: 18), linear HQKLVFFAED (SEQ ID NO: 13), or linear HHQKLVFFAEDVGSNK (SEQ ID NO: 14) relative to cyclic compound comprising an A-beta peptide consisting of HHQK (SEQ ID NO: 1), HQK or HQKL (SEQ ID NO: 202). In an embodiment, the antibody does not specifically bind and/or is not selective for linear peptides consisting of HHQK (SEQ ID NO: 1). Selective binding can be measured using an ELISA or surface plasmon resonance measurement, as described herein.
In an embodiment, the antibody does not bind a linear peptide comprising the sequence QKLV (SEQ ID NO: 5) or HDSG (SEQ ID NO: 9), optionally wherein the sequence of the linear peptide is a linear version of a cyclic sequence used to raise the antibody as described herein.
In an embodiment, the antibody does not specifically or appreciably bind monomeric A-beta. In an embodiment, the antibody does not specifically or appreciably bind A-beta senile plaques, for example, in situ in AD brain tissue.
In another embodiment, the antibody does not selectively bind monomeric A-beta compared to native- or synthetic oligomeric A-beta.
In an embodiment, the antibody selectively binds a cyclic compound comprising SEQ ID NO: 1 or a part thereof, SEQ ID NO: 5 or a part thereof, or SEQ ID NO: 9 or a part thereof or a related epitope optionally in the context of cyclo(CGHHQKG) (SEQ ID NO: 2), cyclo(CGQKLVG) (SEQ ID NO: 6) or cyclo (CGHDSGG) (SEQ ID NO: 10), respectively relative to the corresponding linear peptide. For example, in an embodiment the antibody selectively binds HHQK (SEQ ID NO: 1) QKLV (SEQ ID NO: 5), HDSG (SEQ ID NO: 9) or a related epitope sequence in a cyclic conformation and has at least 2 fold, at least 5 fold, at least 10 fold at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 100 fold, at least 500 fold, at least 1000 fold more selectivity for the epitope in the cyclic conformation compared to a linear compound such as a corresponding linear compound, for example as measured by ELISA or surface plasmon resonance, optionally using a method described herein.
In an embodiment, the antibody selectively binds a cyclic compound comprising the epitope sequence relative to linear peptide or a species of A-beta such as A-beta oligomer relative to monomer. In an embodiment, the selectivity is at least 2 fold, at least 3 fold, at least 5 fold, at least 10 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 100 fold, at least 500 fold, at least 1000 fold more selective for the cyclic compound and/or A-beta oligomer over a species of A-beta selected from A-beta monomer and/or A-beta fibril
In an embodiment, the A-beta oligomer comprises A-beta 1-42 subunits.
In an embodiment, the antibody lacks A-beta fibril plaque (also referred to as senile plaque) staining. Absence of plaque staining can be assessed by comparing to a positive control such as A-beta-specific antibodies 6E10 and 4G8 (Biolegend, San Diego, CA), or 2C8 (Enzo Life Sciences Inc., Farmingdale, NY) and an isotype control. An antibody described herein lacks or has negligible A-beta fibril plaque staining if the antibody does not show typical plaque morphology staining and the level of staining is comparable to or no more than 2 fold the level seen with an IgG negative isotype control. The scale can for example set the level of staining with isotype control at 1 and with 6E10 at 10. An antibody lacks A-beta fibril plaque staining if the level of staining on such a scale is 2 or less. In embodiment, the antibody shows minimal A-beta fibril plaque staining, for example on the foregoing scale, levels scored at less about or less than 3.
In an embodiment, the antibody is produced using a cyclic compound or immunogen described herein, optionally using a method described herein.
In an embodiment, the antibody is a monoclonal antibody. In an embodiment, the antibody is a chimeric antibody such as a humanized antibody comprising the CDR sequences as recited in Table 9.
To produce monoclonal antibodies, antibody producing cells (lymphocytes) can be harvested from a subject immunized with an immunogen described herein, and fused with myeloma cells by standard somatic cell fusion procedures thus immortalizing these cells and yielding hybridoma cells. Such techniques are well known in the art, (e.g. the hybridoma technique originally developed by Kohler and Milstein (Nature 256:495-497 (1975)) as well as other techniques such as the human B-cell hybridoma technique (Kozbor et al., Immunol. Today 4:72 (1983)), the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., Methods Enzymol, 121: 140-67 (1986)), and screening of combinatorial antibody libraries (Huse et al., Science 246:1275 (1989)). Hybridoma cells can be screened immunochemically for production of antibodies specifically reactive with the desired epitopes and the monoclonal antibodies can be isolated.
Specific antibodies, or antibody fragments, reactive against particular antigens or molecules, may also be generated by screening expression libraries encoding immunoglobulin genes, or portions thereof, expressed in bacteria with cell surface components. For example, complete Fab fragments, VH regions and FV regions can be expressed in bacteria using phage expression libraries (see for example Ward et al., Nature 41:544-546 (1989); Huse et al., Science 246:1275-1281 (1989); and McCafferty et al., Nature 348:552-554 (1990).
In an embodiment, the antibody is a humanized antibody.
The humanization of antibodies from non-human species has been well described in the literature. See for example EP-B1 0 239400 and Carter & Merchant 1997 (Curr Opin Biotechnol 8, 449-454, 1997 incorporated by reference in their entirety herein). Humanized antibodies are also readily obtained commercially (e.g. Scotgen Limited, 2 Holly Road, Twickenham, Middlesex, Great Britain.).
Humanized forms of rodent antibodies are readily generated by CDR grafting (Riechmann et al. Nature, 332:323-327, 1988). In this approach the six CDR loops comprising the antigen binding site of the rodent monoclonal antibody are linked to corresponding human framework regions. CDR grafting often yields antibodies with reduced affinity as the amino acids of the framework regions may influence antigen recognition (Foote & Winter. J Mol Biol, 224: 487-499, 1992). To maintain the affinity of the antibody, it is often necessary to replace certain framework residues by site directed mutagenesis or other recombinant techniques and may be aided by computer modeling of the antigen binding site (Co et al. J Immunol, 152: 2968-2976, 1994).
Humanized forms of antibodies are optionally obtained by resurfacing (Pedersen et al. J Mol Biol, 235: 959-973, 1994). In this approach only the surface residues of a rodent antibody are humanized.
Humanized antibodies can be produced as antigen binding fragments such as Fab, Fab′ F(ab′)2, Fd, Fv and single domain antibody fragments, or as single chain antibodies in which the heavy and light chains are linked by a spacer. Also, the human or humanized antibodies may exist in monomeric or polymeric form. The humanized antibody optionally comprises one non-human chain and one humanized chain (i.e. one humanized heavy or light chain).
In an embodiment, the humanized antibody comprises a heavy chain variable domain and/or light chain variable domain listed in Table 12 or 13 or a sequence with at least 50% or more sequence identity thereto wherein the CDR sequences are maintained.
Human antibodies specific to a particular antigen may be identified by a phage display strategy (Jespers et al. Bio/Technology, 12: 899-903, 1994). In one approach, the heavy chain of a rodent antibody directed against a specific antigen is cloned and paired with a repertoire of human light chains for display as Fab fragments on filamentous phage. The phage is selected by binding to antigen. The selected human light chain is subsequently paired with a repertoire of human heavy chains for display on phage, and the phage is again selected by binding to antigen. The result is a human antibody Fab fragment specific to a particular antigen. In another approach, libraries of phage are produced where members display different human antibody fragments (Fab or Fv) on their outer surfaces (Dower et al., WO 91/17271 and McCafferty et al., WO 92/01047). Phage displaying antibodies with a desired specificity are selected by affinity enrichment to a specific antigen. The human Fab or Fv fragment identified from either approach may be recloned for expression as a human antibody in mammalian cells.
Human antibodies are optionally obtained from transgenic animals (U.S. Pat. Nos. 6,150,584; 6,114,598; and 5,770,429). In this approach the heavy chain joining region (JH) gene in a chimeric or germ-line mutant mouse is deleted. Human germ-line immunoglobulin gene array is subsequently transferred to such mutant mice. The resulting transgenic mouse is then capable of generating a full repertoire of human antibodies upon antigen challenge.
Antibodies including humanized or human antibodies are selected from any class of immunoglobulins including: IgM, IgG, IgD, IgA or IgE; and any isotype, including: IgG1, IgG2, IgG3 and IgG4. The humanized or human antibody may include sequences from one or more than one isotype or class.
Additionally, antibodies specific for the epitopes described herein are readily isolated by screening antibody phage display libraries. For example, an antibody phage library is optionally screened by using a disease specific epitope of the current invention to identify antibody fragments specific for the disease specific epitope. Antibody fragments identified are optionally used to produce a variety of recombinant antibodies that are useful with different embodiments of the present invention. Antibody phage display libraries are commercially available, for example, through Xoma (Berkeley, California) Methods for screening antibody phage libraries are well known in the art.
A further aspect is administration of an antibody and/or binding fragment thereof comprising a light chain variable region and a heavy chain variable region, the heavy chain variable region comprising complementarity determining regions CDR-H1, CDR-H2 and CDR-H3, the light chain variable region comprising complementarity determining region CDR-L1, CDR-L2 and CDR-L3 and with the amino acid sequences of said CDRs comprising the sequences set forth in Table 9.
In an embodiment, the antibody is a humanized antibody comprising the CDR sequences as recited in Table 9.
Also provided in another embodiment, is an antibody or binding fragment thereof or administration of an antibody or binding fragment thereof comprising the CDRs in Table 9 or Table 15 and a light chain variable region and a heavy chain variable region, optionally in the context of a single chain antibody.
For example, the antibody and/or binding fragment thereof administered comprises a light chain variable region and a heavy chain variable region, the heavy chain variable region comprising complementarity determining regions CDR-H1, CDR-H2 and CDR-H3, the light chain variable region comprising complementarity determining region CDR-L1, CDR-L2 and CDR-L3 and with the amino acid sequences of said CDRs comprising the sequences set forth in Table 9.
In an embodiment, the antibody or binding fragment comprises a heavy chain variable region comprising: i) an amino acid sequence of a heavy chain variable sequence as set forth in Table 10; ii) an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80% or at least 90% sequence identity to said heavy chain variable sequence set out in Table 10, 12 or 13, wherein the CDR sequences are the corresponding CDRs as set forth in Table 9, or iii) a conservatively substituted amino acid sequence i) wherein the CDR sequences are the corresponding CDRs as set forth in Table 9; and wherein the antibody or binding fragment thereof comprises a light chain variable region comprising i) an amino acid sequence of a light chain variable sequence as set forth in Table 10, 12 or 13, ii) an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 90% sequence identity to said light chain variable sequence as set out in Table 10, 12 or 13, wherein the CDR sequences are the corresponding CDRs as set forth in Table 9, or iii) a conservatively substituted amino acid sequence i) wherein the CDR sequences a are the corresponding CDRs as set forth in Table 9.
For example, in an embodiment the antibody administered comprises a heavy chain variable region comprises: i) an amino acid sequence as set forth in SEQ ID NO: 84; ii) an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80% or at least 90% sequence identity to SEQ ID NO: 84, wherein the CDR sequences are as set forth in SEQ ID NO: 20, 21 and 22, or iii) a conservatively substituted amino acid sequence i). In another aspect the antibody administered comprises a light chain variable region comprising i) an amino acid sequence as set forth in SEQ ID NO: 86, ii) an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80% or at least 90% sequence identity to SEQ ID NO: 86, wherein the CDR sequences are as set forth in SEQ ID NO: 23, 24 and 25 or iii) a conservatively substituted amino acid sequence of i), wherein the CDR sequences are as set forth in SEQ ID NO: 23, 24 and 25. In another embodiment, the heavy chain variable region amino acid sequence is encoded by a nucleotide sequence as set out in SEQ ID NO: 83 or a codon degenerate optimized version thereof. In another embodiment, the antibody comprises a light chain variable region amino acid sequence encoded by a nucleotide sequence as set out in SEQ ID NO: 85 or a codon degenerate or optimized version thereof. In an embodiment, the heavy chain variable region comprises an amino acid sequence as set forth in SEQ ID NO: 84. In an embodiment, the light chain variable region comprises an amino acid sequence as set forth in SEQ ID NO: 86.
As another example, the antibody comprises a heavy chain variable region comprises: i) an amino acid sequence as set forth in SEQ ID NO: 98 or 102; ii) an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80% sequence identity to SEQ ID NO: 98 or 102, wherein the CDR sequences are as set forth in SEQ ID NO: 41, 42, 43, 47, 48, and/or 49, or iii) a conservatively substituted amino acid sequence i) wherein the CDR sequences are as set forth in SEQ ID NO:41, 42, 43, 47, 48, and/or 49. In another aspect the antibody comprises a light chain variable region comprising i) an amino acid sequence as set forth in SEQ ID NO: 100 or 104, ii) an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80% 70% sequence identity to SEQ ID NO:100 or 104, wherein the CDR sequences are as set forth in SEQ ID NO: 44, 45, 46, 50, 51, and/or 52, or iii) a conservatively substituted amino acid sequence of i) wherein the CDR sequences are as set forth in SEQ ID NO: 41, 42, 43, 47, 48, and/or 49. In another embodiment, the heavy chain variable region amino acid sequence is encoded by a nucleotide sequence as set out in SEQ ID NO: 97 or 101 or a codon degenerate optimized version thereof. In another embodiment, the antibody comprises a light chain variable region amino acid sequence encoded by a nucleotide sequence as set out in SEQ ID NO: 99 or 103 or a codon degenerate or optimized version thereof. In an embodiment, the heavy chain variable region comprises an amino acid sequence as set forth in SEQ ID NO: 98 or 102. In an embodiment, the light chain variable region comprises an amino acid sequence as set forth in SEQ ID NO: 100 or 104.
Other similar examples there the variable region of the heavy and/or light chain have at least 50%, at least 60%, at least 70%, at least 80% 70% sequence identity and where the CDRs are maintained can be determined on the basis of the Tables 9 and 10, 12 and 14.
In another aspect the antibody that is administered is an antibody that specifically binds a same epitope as the antibody with CDR sequences as recited in Table 9, with variable regions as recited in Table 10, 12 or 13 or produced by the hybrdioma cell line deposited under the provisions of the Budapest Treaty with the American Type Culture Collection (ATCC®) 10801 University Blvd., Manassas, Va., 20110-2209, USA on Jul. 19, 2017 and given the Accession number PTA-124318.
Another aspect is an antibody that specifically binds A-beta or SEQ ID NO: 2, 6 or 10 (e.g. the same epitope as the antibody with CDR sequences as recited in Table 9).
Another aspect includes an antibody or binding fragment or administration of an antibody that competes for binding to human A-beta with an antibody comprising the CDR sequences as recited in Table 9 or 15, or the variable domain sequences in Tables 10, 12 or 13.
In an embodiment, the antibody or binding fragment thereof competes for binding with an antibody comprising a light chain variable region and a heavy chain variable region the heavy chain variable region comprising complementarity determining regions CDR-H1, CDR-H2 and CDR-H3, the light chain variable region comprising complementarity determining region CDR-L1, CDR-L2 and CDR-L3 and with the amino acid sequences of said CDRs comprising the sequences in Tables 9B, 9C, 9G, 9H or 91.
Competition between antibodies can be determined for example using an assay in which an antibody under test is assessed for its ability to inhibit specific binding of a reference antibody to the common antigen. A test antibody competes with a reference antibody if an excess of a test antibody (e.g., at least a 2 fold, 5, fold, 10 fold or 20 fold) inhibits binding of the reference antibody by at least 50%, at least 75%, at least 80%, at least 90% or at least 95% as measured in a competitive binding assay.
In a further aspect the antibody administered is an antibody conjugated to a therapeutic, detectable label or cytotoxic agent.
A further aspect relates to an antibody complex comprising an antibody described herein and/or a binding fragment thereof and oligomeric A-beta.
In a further aspect an isolated nucleic acid encoding an antibody or part thereof described herein is administered.
Nucleic acids encoding a heavy chain or a light chain can also be administered, for example encoding a heavy chain comprising CDR-H1, CDR-H2 and/or CDR-H3 regions described herein or encoding a light chain comprising CDR-L1, CDR-L2 and/or CDR-L3 regions described herein.
The present disclosure also includes administration of variants of the nucleic acid sequences that encode for the antibody and/or binding fragment thereof disclosed herein. For example, the variants include nucleotide sequences that hybridize to the nucleic acid sequences encoding the antibody and/or binding fragment thereof disclosed herein under at least moderately stringent hybridization conditions or codon degenerate or optimized sequences. In another embodiment, the variant nucleic acid sequences have at least 50%, at least 60%, at least 70%, most preferably at least 80%, even more preferably at least 90% and even most preferably at least 95% sequence identity to nucleic acid sequences encoding in Table 10, 12 or 13.
A further aspect is an isolated nucleic acid encoding an antibody described herein. In embodiments said isolated nucleic acid is administered to a subject in need thereof.
Another aspect is an expression cassette or vector comprising the nucleic acid herein disclosed. In an embodiment, the vector is an isolated vector, optionally for administration to a subject in need thereof.
The vector can be any vector, including vectors suitable for producing an antibody and/or binding fragment thereof or expressing a peptide sequence described herein.
The nucleic acid molecules may be incorporated in a known manner into an appropriate expression vector which ensures expression of the protein. Possible expression vectors include but are not limited to cosmids, plasmids, or modified viruses (e.g. replication defective retroviruses, adenoviruses and adeno-associated viruses). The vector should be compatible with the host cell used. The expression vectors are “suitable for transformation of a host cell”, which means that the expression vectors contain a nucleic acid molecule encoding the peptides corresponding to epitopes or antibodies described herein.
In an embodiment, the vector is suitable for expressing for example single chain antibodies by gene therapy. The vector can be adapted for specific expression in neural tissue, for example using neural specific promoters and the like. In an embodiment, the vector comprises an IRES and allows for expression of a light chain variable region and a heavy chain variable region. Such vectors can be used to deliver antibody in vivo.
Suitable regulatory sequences may be derived from a variety of sources, including bacterial, fungal, viral, mammalian, or insect genes.
Examples of such regulatory sequences include: a transcriptional promoter and enhancer or RNA polymerase binding sequence, a ribosomal binding sequence, including a translation initiation signal. Additionally, depending on the host cell chosen and the vector employed, other sequences, such as an origin of replication, additional DNA restriction sites, enhancers, and sequences conferring inducibility of transcription may be incorporated into the expression vector.
In an embodiment, the regulatory sequences direct or increase expression in neural tissue and/or cells.
In an embodiment, the vector is a viral vector.
The recombinant expression vectors may also contain a marker gene which facilitates the selection of host cells transformed, infected or transfected with a vector for expressing an antibody or epitope peptide described herein.
The recombinant expression vectors may also contain expression cassettes which encode a fusion moiety (i.e. a “fusion protein”) which provides increased expression or stability of the recombinant peptide; increased solubility of the recombinant peptide; and aid in the purification of the target recombinant peptide by acting as a ligand in affinity purification, including for example tags and labels described herein. Further, a proteolytic cleavage site may be added to the target recombinant protein to allow separation of the recombinant protein from the fusion moiety subsequent to purification of the fusion protein. Typical fusion expression vectors include pGEX (Amrad Corp., Melbourne, Australia), pMAL (New England Biolabs, Beverly, MA) and pRIT5 (Pharmacia, Piscataway, NJ) which fuse glutathione S-transferase (GST), maltose E binding protein, or protein A, respectively, to the recombinant protein.
Systems for the transfer of genes for example into neurons and neural tissue both in vitro and in vivo include vectors based on viruses, most notably Herpes Simplex Virus, Adenovirus, Adeno-associated virus (AAV) and retroviruses including lentiviruses. Alternative approaches for gene delivery include the use of naked, plasmid DNA as well as liposome-DNA complexes. Another approach is the use of AAV plasmids in which the DNA is polycation-condensed and lipid entrapped and introduced into the brain by intracerebral gene delivery (Leone et al. US Application No. 2002076394).
Accordingly, in another aspect, the compounds, immunogens, nucleic acids, vectors and antibodies described herein for administration may be formulated in vesicles such as liposomes, nanoparticles, and viral protein particles, for example for delivery of antibodies, compounds, immunogens and nucleic acids described herein. In particular synthetic polymer vesicles, including polymersomes, can be used to administer antibodies.
Also provided in another aspect is administration of a cell, optionally an isolated and/or recombinant cell, expressing an antibody described herein or comprising a vector herein disclosed.
The recombinant cell can be generated using any cell suitable for producing a polypeptide, for example suitable for producing an antibody and/or binding fragment thereof. For example to introduce a nucleic acid (e.g. a vector) into a cell, the cell may be transfected, transformed or infected, depending upon the vector employed.
Suitable host cells include a wide variety of prokaryotic and eukaryotic host cells. For example, the proteins described herein may be expressed in bacterial cells such as E. coli, insect cells (using baculovirus), yeast cells or mammalian cells.
In an embodiment, the cell is a eukaryotic cell selected from a yeast, plant, worm, insect, avian, fish, reptile and mammalian cell.
In an embodiment, the cell is a neural cell.
Yeast and fungi host cells suitable for expressing an antibody or peptide include, but are not limited to Saccharomyces cerevisiae, Schizosaccharomyces pombe, the genera Pichia or Kluyveromyces and various species of the genus Aspergillus. Examples of vectors for expression in yeast S. cerivisiae include pYepSec1, pMFa, pJRY88, and pYES2 (Invitrogen Corporation, San Diego, CA). Protocols for the transformation of yeast and fungi are well known to those of ordinary skill in the art.
Mammalian cells that may be suitable include, among others: COS (e.g., ATCC No. CRL 1650 or 1651), BHK (e.g. ATCC No. CRL 6281), CHO (ATCC No. CCL 61), HeLa (e.g., ATCC No. CCL 2), 293 (ATCC No. 1573) and NS-1 cells. Suitable expression vectors for directing expression in mammalian cells generally include a promoter (e.g., derived from viral material such as polyoma, Adenovirus 2, cytomegalovirus and Simian Virus 40), as well as other transcriptional and translational control sequences. Examples of mammalian expression vectors include pCDM8 and pMT2PC.
In an embodiment, the cell is a fused cell producing an antibody specific and/or selective for an epitope or epitope sequence described herein, including for example that selectively binds A-beta oligomers over A-beta monomers, selectively binds an epitope sequence presented in a cyclic compound relative to a linear compound or lacks or has negligible plaque binding.
A further aspect is a composition comprising a compound, immunogen, nucleic acid, vector or antibody or binding fragment described herein. In embodiments, said composition is administered in a method described herein.
The composition can for example include 1, 2, 3 or more antibodies or binding fragments thereof, immunoconjugates, compounds, cells or nucleic acids described herein.
In an embodiment, the composition comprises a diluent.
Suitable diluents for nucleic acids include but are not limited to water, saline solutions and ethanol.
Suitable diluents for polypeptides, including antibodies or fragments thereof and/or cells include but are not limited to saline solutions, pH buffered solutions and glycerol solutions or other solutions suitable for freezing polypeptides and/or cells.
In an embodiment, the composition is a pharmaceutical composition comprising any of the peptides, immunogens, antibodies, nucleic acids or vectors disclosed herein, and optionally comprising a pharmaceutically acceptable carrier.
The compositions described herein can be prepared by per se known methods for the preparation of pharmaceutically acceptable compositions that can be administered to subjects, optionally as a vaccine, such that an effective quantity of the active substance is combined in a mixture with a pharmaceutically acceptable vehicle.
Pharmaceutical compositions include, without limitation, lyophilized powders or aqueous or non-aqueous sterile injectable solutions or suspensions, which may further contain antioxidants, buffers, bacteriostats and solutes that render the compositions substantially compatible with the tissues or the blood of an intended recipient. Other components that may be present in such compositions include water, surfactants (such as Tween), alcohols, polyols, glycerin and vegetable oils, for example. Extemporaneous injection solutions and suspensions may be prepared from sterile powders, granules, tablets, or concentrated solutions or suspensions. The composition may be supplied, for example but not by way of limitation, as a lyophilized powder which is reconstituted with sterile water or saline prior to administration to the patient.
Pharmaceutical compositions may comprise a pharmaceutically acceptable carrier. Suitable pharmaceutically acceptable carriers include essentially chemically inert and nontoxic compositions that do not interfere with the effectiveness of the biological activity of the pharmaceutical composition. Examples of suitable pharmaceutical carriers include, but are not limited to, water, saline solutions, glycerol solutions, ethanol, N-(1(2,3-dioleyloxy)propyl)N,N,N-trimethylammonium chloride (DOTMA), diolesylphosphotidyl-ethanolamine (DOPE), and liposomes. Such compositions should contain a therapeutically effective amount of the compound, together with a suitable amount of carrier so as to provide the form for direct administration to the patient.
The composition may be in the form of a pharmaceutically acceptable salt which includes, without limitation, those formed with free amino groups such as those derived from hydrochloric, phosphoric, acetic, oxalic, tartaric acids, etc., and those formed with free carboxyl groups such as those derived from sodium, potassium, ammonium, calcium, ferric hydroxides, isopropylamine, triethylamine, 2-ethylamino ethanol, histidine, procaine, etc.
In an embodiment comprising a compound or immunogen described herein, the composition comprises an adjuvant.
Adjuvants that can be used for example, include Intrinsic adjuvants (such as lipopolysaccharides) normally are the components of killed or attenuated bacteria used as vaccines. Extrinsic adjuvants are immunomodulators which are typically non-covalently linked to antigens and are formulated to enhance the host immune responses. Aluminum hydroxide, aluminum sulfate and aluminum phosphate (collectively commonly referred to as alum) are routinely used as adjuvants. A wide range of extrinsic adjuvants can provoke potent immune responses to immunogens. These include saponins such as Stimulons (QS21, Aquila, Worcester, Mass.) or particles generated therefrom such as ISCOMs and (immunostimulating complexes) and ISCOMATRIX, complexed to membrane protein antigens (immune stimulating complexes), pluronic polymers with mineral oil, killed mycobacteria and mineral oil, Freund's complete adjuvant, bacterial products such as muramyl dipeptide (MDP) and lipopolysaccharide (LPS), as well as lipid A, and liposomes.
In an embodiment, the adjuvant is aluminum hydroxide. In another embodiment, the adjuvant is aluminum phosphate. Oil in water emulsions include squalene; peanut oil; MF59 (WO 90/14387); SAF (Syntex Laboratories, Palo Alto, Calif.); and Ribi™ (Ribi Immunochem, Hamilton, Mont.). Oil in water emulsions may be used with immunostimulating agents such as muramyl peptides (for example, N-acetylmuramyl-L-threonyl-D-isoglutamine (thr-MDP), -acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutamyl-L-alanine-2-(1′-2′dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (MTP-PE), N-acetylglucsaminyl-N-acetylmuramyl-L-AI-D-isoglu-L-Ala-dipalmitoxy propylamide (DTP-DPP) theramide (TM)), or other bacterial cell wall components.
The adjuvant may be administered with an immunogen as a single composition. Alternatively, an adjuvant may be administered before, concurrent and/or after administration of the immunogen.
Commonly, adjuvants are used as a 0.05 to 1.0 percent solution in phosphate−buffered saline. Adjuvants enhance the immunogenicity of an immunogen but are not necessarily immunogenic themselves. Adjuvants may act by retaining the immunogen locally near the site of administration to produce a depot effect facilitating a slow, sustained release of immunogen to cells of the immune system. Adjuvants can also attract cells of the immune system to an immunogen depot and stimulate such cells to elicit immune responses. As such, embodiments may encompass compositions further comprising adjuvants.
Adjuvants for parenteral immunization include aluminum compounds (such as aluminum hydroxide, aluminum phosphate, and aluminum hydroxy phosphate). The antigen can be precipitated with, or adsorbed onto, the aluminum compound according to standard protocols. Other adjuvants such as RIBI (ImmunoChem, Hamilton, MT) can also be used in parenteral administration.
Adjuvants for mucosal immunization include bacterial toxins (e.g., the cholera toxin (CT), the E. coli heat-labile toxin (LT), the Clostridium difficile toxin A and the pertussis toxin (PT), or combinations, subunits, toxoids, or mutants thereof). For example, a purified preparation of native cholera toxin subunit B (CTB) can be of use. Fragments, homologs, derivatives, and fusion to any of these toxins are also suitable, provided that they retain adjuvant activity. Preferably, a mutant having reduced toxicity is used. Suitable mutants have been described (e.g., in WO 95/17211 (Arg-7-Lys CT mutant), WO 96/6627 (Arg-192-Gly LT mutant), and WO 95/34323 (Arg-9-Lys and Glu-129-Gly PT mutant)). Additional LT mutants that can be used in the methods and compositions include, for example Ser-63-Lys, Ala-69-Gly, Glu-110-Asp, and Glu-112-Asp mutants. Other adjuvants (such as a bacterial monophosphoryl lipid A (MPLA) of various sources (e.g., E. coli, Salmonella minnesota, Salmonella typhimurium, or Shigella flexneri, saponins, or polylactide glycolide (PLGA) microspheres) can also be used in mucosal administration.
Other adjuvants include cytokines such as interleukins for example IL-1, IL-2 and IL-12, chemokines, for example CXCL10 and CCL5, macrophage stimulating factor, and/or tumor necrosis factor. Other adjuvants that may be used include CpG oligonucleotides (Davis. Curr Top Microbiol Immunol., 247:171-183, 2000).
Oil in water emulsions include squalene; peanut oil; MF59 (WO 90/14387); SAF (Syntex Laboratories, Palo Alto, Calif.); and Ribi™ (Ribi Immunochem, Hamilton, Mont.). Oil in water emulsions may be used with immunostimulating agents such as muramyl peptides (for example, N-acetylmuramyl-L-threonyl-D-isoglutamine (thr-MDP), -acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), N-acetylmuramyl-L-alanyl-D-isoglutamyl-L-alanine-2-(1′-2′dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine (MTP-PE), N-acetylglucsaminyl-N-acetylmuramyl-L-AI-D-isoglu-L-Ala-dipalmitoxy propylamide (DTP-DPP) theramide (TM), or other bacterial cell wall components.
Adjuvants useful for both mucosal and parenteral immunization include polyphosphazene (for example, WO 95/2415), DC-chol (3 b-(N—(N′,N′-dimethyl aminomethane)-carbamoyl) cholesterol (for example, U.S. Pat. No. 5,283,185 and WO 96/14831) and QS-21 (for example, WO 88/9336).
An adjuvant may be coupled to an immunogen for administration. For example, a lipid such as palmitic acid, may be coupled directly to one or more peptides such that the change in conformation of the peptides comprising the immunogen does not affect the nature of the immune response to the immunogen.
In an embodiment, the composition comprises an antibody described herein. In another embodiment, the composition comprises an antibody described herein and a diluent. In an embodiment, the composition is a sterile composition.
A further aspect provides prior to administering the compound, immunogen, composition, antibody, nucleic acid or cell described herein detecting whether a biological sample comprises A-beta oligomers the method comprising contacting the biological sample with an antibody described herein and/or detecting the presence of any antibody complex. In an embodiment the method is for detecting whether the biologic sample comprises oligomeric A-beta.
In an embodiment, if A-beta oligomer is detected the subject is administered a compound, immunogen, antibody or compositions described herein.
In an embodiment, the method comprises:
In an embodiment, the level of complex formed is compared to a test antibody such as a suitable Ig control or irrelevant antibody.
In an embodiment, the detection is quantitated and the amount of complex produced is measured. The measurement can for example be relative to a standard.
In an embodiment, the measured amount is compared to a control.
In another embodiment, the method comprises:
The control can be a sample control (e.g. from a subject without AD, or from a subject with a particular form of AD, mild, moderate or advanced), or be a previous sample from the same subject for monitoring changes in A-beta oligomer levels in the subject.
In an embodiment, an antibody described herein is used.
In an embodiment, the sample is a biological sample. In an embodiment, the sample comprises brain tissue or an extract thereof and/or CSF. In an embodiment, the sample comprises whole blood, plasma or serum. In an embodiment, the sample is obtained from a human subject. In an embodiment, the subject is suspected of, at a risk of or has AD.
A number of methods can be used to detect an A-beta: antibody complex and thereby determine if the sample comprises A-beta oligomers are present in a sample using the antibodies described herein, including immunoassays such as flow cytometry, Western blots, ELISA, and immunoprecipitation followed by SDS-PAGE immunocytochemistry.
As described in the Examples surface plasmon resonance technology can be used to assess conformation specific binding. If the antibody is labeled or a detectably labeled secondary antibody specific for the complex antibody is used, the label can be detected. Commonly used reagents include fluorescent emitting and HRP labeled antibodies. In quantitative methods, the amount of signal produced can be measured by comparison to a standard or control. The measurement can also be relative.
A further aspect includes a method of measuring a level of or imaging A-beta in a subject or tissue, optionally where the A-beta to be measured or imaged is oligomeric A-beta prior to administering, a compound, immunogen, composition, antibody, nucleic acid or cell described herein. In an embodiment, the method comprises administering to a subject at risk or suspected of having or having AD, an antibody conjugated to a detectable label; and detecting the label, optionally quantitatively detecting the label. The label in an embodiment is a positron emitting radionuclide which can for example be used in PET imaging.
A further aspect includes a method of inducing an immune response in a subject to treat or prevent a disease associated with and/or induced by soluble A-beta, comprising administering to the subject a compound, immunogen and/or composition comprising a compound described herein.
In an embodiment, the immunogen administered comprises a compound of
In an embodiment, the subject is a non-human subject such as a rodent. Antibody producing cells generated can also be used in an embodiment to produce a hybridoma cell line.
It is demonstrated herein that the antibodies raised against immunogens comprising SEQ ID NO: 2, 6 and 10, can specifically and/or selectively bind A-beta oligomers and lack A-beta plaque staining. Oligomeric A-beta species are believed to be the toxic propagating species in AD. Further as shown herein, said antibodies inhibited A-beta aggregation and A-beta oligomer propagation. Accordingly, also provided are methods of inhibiting A-beta oligomer propagation, the method comprising contacting a cell or tissue expressing A-beta with or administering to a subject in need thereof an effective amount of an A-beta oligomer specific or selective antibody described herein to inhibit A-beta aggregation and/or oligomer propagation. In vitro the assay can be monitored as described in the Examples.
The antibodies can be used for example for treating AD and/or other A-beta amyloid associated and/or induced diseases and conditions. For example, variants of Lewy body dementia and in inclusion body myositis (a muscle disease) exhibit similar plaques as AD and A-beta can also form aggregates implicated in cerebral amyloid angiopathy.
In an embodiment the method is for treating or preventing AD and/or other A-beta amyloid associated and/or induced diseases or conditions, the method comprising administering to a subject in need thereof i) an effective amount of an antibody described herein, optionally an A-beta oligomer specific or selective or a pharmaceutical composition comprising said antibody; or 2) administering an isolated cyclic compound comprising SEQ ID NO: 1 5 or 9 or a related epitope sequence or immunogen or pharmaceutical composition comprising said cyclic compound, to a subject in need thereof. In other embodiments, nucleic acids encoding the antibodies or immunogens described herein can also be administered to the subject, optionally using vectors suitable for delivering nucleic acids in a subject.
In an embodiment, a biological sample from the subject to be treated is assessed for the presence or levels of A-beta using an antibody described herein. In an embodiment, a subject with detectable A-beta levels (e.g. A-beta antibody complexes measured in vitro or measured by imaging) is treated with the antibody.
The antibody and immunogens can for example be comprised in a pharmaceutical composition as described herein, and formulated for example in vesicles for improving delivery.
One or more antibodies targeting HHQK (SEQ ID NO: 1), HDSG (SEQ ID NO: 9) or QKLV (SEQ ID NO: 5) and/or related antibodies can be administered in combination. In addition the antibodies disclosed herein can be administered with one or more other treatments such as a beta-secretase inhibitor or a cholinesterase inhibitor.
In an embodiment, the antibody is a conformation specific/selective antibody, optionally that specifically or selectively binds A-beta oligomer.
Also provided are uses of the compositions, antibodies, isolated peptides, immunogens and nucleic acids for treating or preventing AD and/or other A-beta associated and/or induced diseases or conditions.
In an embodiment, the disease or condition associated with and/or induced by soluble A-beta oligomer is cognitive deficits, optionally loss of short term memory formation.
In an embodiment, the disease or condition associated with and/or induced by soluble soluble A-beta oligomer A-beta is Alzheimer's disease (AD).
In an embodiment, the treatment is prophylactic treatment. For example in an embodiment, the antibody is administered to a subject with a predisposition to developing a disease or condition associated with and/or induced by soluble A-beta oligomer.
In an embodiment, the disease or condition is perirhinal cortex dysfunction or pathology. In another embodiment, the disease or condition is enthorinal cortex dysfunction or pathology.
In an embodiment, the disease or condition is associated with and/or induced by soluble A-beta 1-42 oligomer.
The compositions, compounds, antibodies, isolated peptides, immunogens and nucleic acids, vectors etc. described herein can be administered for example, by parenteral, intravenous, subcutaneous, intramuscular, intracranial, intraventricular, intrathecal, intraorbital, ophthalmic, intraspinal, intracisternal, intraperitoneal, intranasal, aerosol or oral administration.
In certain embodiments, the pharmaceutical composition is administered systemically.
In other embodiments, the pharmaceutical composition is administered directly to the brain or other portion of the CNS. For example such methods include the use of an implantable catheter and a pump, which would serve to discharge a pre-determined dose through the catheter to the infusion site. A person skilled in the art would further recognize that the catheter may be implanted by surgical techniques that permit visualization of the catheter so as to position the catheter adjacent to the desired site of administration or infusion in the brain. Such techniques are described in Elsberry et al. U.S. Pat. No. 5,814,014 “Techniques of Treating Neurodegenerative Disorders by Brain Infusion”, which is herein incorporated by reference. Also contemplated are methods such as those described in US patent application 20060129126 (Kaplitt and During “Infusion device and method for infusing material into the brain of a patient”. Devices for delivering drugs to the brain and other parts of the CNS are commercially available (e.g. SynchroMed© EL Infusion System; Medtronic, Minneapolis, Minnesota)
In another embodiment, the pharmaceutical composition is administered to the brain using methods such as modifying the compounds to be administered to allow receptor-mediated transport across the blood brain barrier.
Other embodiments contemplate the co-administration of the compositions, compounds, antibodies, isolated peptides, immunogens and nucleic acids described herein with biologically active molecules known to facilitate the transport across the blood brain barrier.
Also contemplated in certain embodiments, are methods for administering the compositions, compounds, antibodies, isolated peptides, immunogens and nucleic acids described herein across the blood brain barrier such as those directed at transiently increasing the permeability of the blood brain barrier as described in U.S. Pat. No. 7,012,061 “Method for increasing the permeability of the blood brain barrier”, herein incorporated by reference.
A further aspect relates to a kit comprising i) an antibody and/or binding fragment thereof, ii) a nucleic acid, iii) peptide or immunogen, iv) composition or v) recombinant cell described herein, comprised in a vial such as a sterile vial or other housing and optionally a reference agent and/or instructions for use thereof for use in treating or preventing a disease or condition associated with and/or induced by soluble A-beta oligomer.
In an embodiment, the kit further comprises one or more of a collection vial, standard buffer and detection reagent.
The above disclosure generally describes the present application. A more complete understanding can be obtained by reference to the following specific examples. These examples are described solely for the purpose of illustration and are not intended to limit the scope of the application. Changes in form and substitution of equivalents are contemplated as circumstances might suggest or render expedient. Although specific terms have been employed herein, such terms are intended in a descriptive sense and not for purposes of limitation.
The following non-limiting examples are illustrative of the present disclosure:
Immunogens
Cyclic peptides cyclo(CGHHQKG) (SEQ ID NO: 2) cyclo(CGQKLVG) (SEQ ID NO: 6), and cyclo(CGHDSGG) (SEQ ID NO: 10) and corresponding linear peptides were prepared (CPC Scientific, Sunnyvale, CA, USA)
Peptides were generated at CPC Scientific, Sunnyvale, CA, USA (both cyclic and linear). Peptides were conjugated to KLH (for immunizing) and BSA (for screening) using a trifluoroacetate counter ion protocol. Peptides were desalted and checked by MS and HPLC and deemed 95% pure. Peptides were shipped to IPA for use in production of monoclonal antibodies in mouse.
Antibody Generation
Hybridomas and monoclonal antibodies were generated to cyclo(CGHHQKG) (SEQ ID NO: 2), cyclo(CGQKLVG) (SEQ ID NO: 6) and cyclo (CGHDSGG) (SEQ ID NO: 10) each linked to Keyhole Limpet Hemocyanin (KLH).
The cyclopeptides linked to KLH were sent for mouse monoclonal antibody production (ImmunoPrecise Antibodies LTD (Victoria BC, Canada), following protocols approved by the Canadian Council on Animal Care. Mouse sera were screened using the conformational peptide used for producing the antibodies linked to BSA and the linear peptides.
Fifty day old female BALB/c mice (Charles River Laboratories, Quebec) were immunized. A series of subcutaneous aqueous injections containing antigen but no adjuvant were given over a period of 19 days. Mice were immunized with 100 μg per mouse per injection of a 0.5 mg/mL cyclic peptide-KLH solution in sterile saline. All 4 mice were euthanized on Day 19 and lymphocytes were harvested for hybridoma cell line generation.
Fusion/Hybridoma Development
Lymphocytes were isolated and fused with murine SP2/0 myeloma cells in the presence of poly-ethylene glycol (PEG 1500). Fused cells were cultured using HAT selection. This method uses a semi-solid methylcellulose-based HAT selective medium to combine the hybridoma selection and cloning into one step. Single cell-derived hybridomas grow to form monoclonal colonies on the semi-solid media. 10 days after the fusion event, resulting hybridoma clones were transferred to 96-well tissue culture plates and grown in HT containing medium until mid-log growth was reached (5 days).
Hybridoma Analysis
Tissue culture supernatants from the hybridomas were tested by indirect ELISA on screening antigen (cyclic peptide-BSA) and probed for both IgG and IgM antibodies using a Goat anti-IgG/IgM(H&L)-HRP secondary and developed with TMB substrate. Clones >0.2 OD in this assay were taken to the next round of testing. Positive cultures were retested on screening antigen to confirm secretion and on an irrelevant antigen (Human Transferrin) to eliminate non-specific mAbs and rule out false positives. Selected clones were isotyped by antibody trapping ELISA to determine if they are IgG or IgM isotype. Selected clones were also tested by indirect ELISA on other cyclic peptide-BSA conjugates as well as linear peptide-BSA conjugates to evaluate cross-reactivity and linker reactivity. Antibodies were also screened by SPR analysis.
ELISA Antibody Screening
ELISA plates were coated with 1) 0.1 ug/well cyclopeptide-conjugated-BSA at 100 uL/well in carbonate coating buffer (pH 9.6) O/N at 4 C; 2) 0.1 ug/well linear-peptide-conjugated-BSA at 100 uL/well in carbonate coating buffer (pH 9.6) O/N at 4 C; or 3) 0.1 ug/well Negative-Peptide at 100 uL/well in carbonate coating buffer (pH 9.6) O/N at 4 C. Primary Antibody: Hybridoma supernatant at 100 uL/well incubated for 1 hour at 37 C with shaking. Secondary Antibody 1:10,000 Goat anti-mouse IgG/IgM(H+L)-HRP at 100 uL/well in PBS-Tween for 1 hour at 37 C with shaking. All washing steps were performed for 30 mins with PBS-Tween. The substrate TMB was added at 50 uL/well, developed in the dark and stopped with equal volume 1 M HCl.
SPR Binding Assays
SPR Analysis of Antibody Binding to Cyclic Peptides, A-Beta Monomers and Oligomers
A-beta Monomer and Oligomer Preparation: Recombinant A-beta40 and 42 peptides (California Peptide, Salt Lake City UT, USA) were dissolved in ice-cold hexafluoroisopropanol (HFIP). The HFIP was removed by evaporation overnight and dried in a SpeedVac centrifuge. To prepare monomers, the peptide film was reconstituted in DMSO to 5 mM, diluted further to 100 μM in dH2O and used immediately. Oligomers were prepared by diluting the 5 mM DMSO peptide solution in phenol red-free F12 medium (Life Technologies Inc., Burlington ON, Canada) to a final concentration of 100 μM and incubated for 24 hours to 7 days at 4° C.
SPR Analysis of Cyclic Peptide, A-beta Monomer and Oligomer binding: All SPR measurements were performed using a Molecular Affinity Screening System (MASS-1) (Sierra Sensors GmbH, Hamburg, Germany), an analytical biosensor that employs high intensity laser light and high speed optical scanning to monitor binding interactions in real time. The primary screening of tissue culture supernatants was performed using an SPR direct binding assay, whereby BSA-conjugated peptides, A-beta42 Monomer and A-beta42 Oligomer are covalently immobilized on individual flow cells of a High Amine Capacity (HAC) sensorchip (Sierra Sensors GmbH, Hamburg, Germany) and antibodies flowed over the surface. Each sample was diluted and injected in duplicate over the immobilized peptide and BSA reference surfaces, followed by injection of running buffer only for the dissociation phase. After every analytical cycle, the sensor chip surfaces were regenerated. Sensorgrams were double-referenced by subtracting out binding from the BSA reference surfaces and blank running buffer injections, and binding response report points collected in the dissociation phase.
Protein G purified mAbs were analyzed in a secondary screen using an SPR indirect (capture) binding assay, whereby the antibodies were immobilized on a protein A-derivatized sensorchip (XanTec Bioanalytics GmbH, Duesseldorf, Germany) and A-beta40 Monomer, A-beta42 Oligomer, pooled soluble brain extracts flowed over the surface. The specificity of the antibodies was verified in an SPR direct binding assay by covalently immobilizing A-beta42 Monomer and A-beta42 Oligomer on individual flow cells of a HAC sensorchip and flowing purified mAbs over the surface.
To further verify and validate A-beta42 Oligomer binding, antibodies were covalently immobilized, followed by the injection over the surface of commercially-prepared stable A-beta42 Oligomers (SynAging SAS, Vandœuvre-lès-Nancy, France),
Isotyping
The hybridoma antibodies were isotyped using antibody trap experiments. Trap plates were coated with 1:10,000 Goat anti-mouse IgG/IgM(H&L) antibody at 100 uL/well carbonate coating buffer pH9.6 overnight at 4 C. No blocking step was used. Primary antibody (hybridoma supernatants) was added (100 ug/mL). Secondary Antibody 1:5,000 Goat anti-mouse IgGγ-HRP or 1:10,000 Goat anti-mouse IgMμ-HRP at 100 uL/well in PBS-Tween for 1 hour at 37 C with shaking. All washing steps were performed for 30 mins with PBS-Tween. The substrate TMB was added at 50 uL/well, developed in the dark and stopped with equal volume 1 M HCl.
Antibody Sequencing
The CDR and variable regions of the heavy and light chains were sequenced. Immunoglobulin gene transcripts expressed by the hybridomas were amplified from cDNA generated from the hybridoma cells using standard RT-PCR and sequenced using a standard dye-terminator capillary sequencing method.
Biological Deposit
The 301-17 hybridoma was deposited under the provisions of the Budapest Treaty with the American Type Culture Collection (ATCC®) 10801 University Blvd., Manassas, Va., 20110-2209, USA on Jul. 19, 2017 and given the Accession number PTA-124318.
HHQK (SEQ ID NO: 1)
Antibodies to Cyclo(CGHHQKG) (SEQ ID NO: 2)
The Antibodies were Tested as Described in Example 2.
ELISA and SPR testing found that hybridoma clones bound the cyclopeptide preferentially over the linear peptide.
Clones 301-3, 301-11 and 301-17 raised against cyclo(CGHHQKG) (SEQ ID NO: 2) were selected for further analysis.
Isotyping revealed 301-3, 301-11 and 301-17 were IgG3 subtypes.
Antibodies were tested in one or more assays for their ability to bind cyclic peptide, linear peptide, A-beta 1-42 monomer and A-beta 1-42 oligomers prepared as described above.
ELISA and SPR assays confirmed that the antibodies preferentially bound the cylopeptide relative to the linear peptide (and were not cross reactive to unrelated cyclic peptides) and/or preferentially bound Ab oligomers relative to monomers.
Antibody Sequence
Clones 301-3, 301-11 and 301-17 antibodies were sequenced as further provided below. The CDR sequences of 301-3 and 301-11 are provided in Table 9(C and B). The CDRs for 301-17 are provided in SEQ ID NOs: 20-25. The consensus DNA sequence and polypeptide sequences of the variable portion of the heavy and light chain of the antibodies are provided in Table 10A.
As shown, the heavy chain CDRs for 301-3 and 301-11 were identical for CDRs 1 and 2 and CDR3 varied at one position. Two light chains were sequenced for 301-3. One light chain was near identical to the light chain for 301-11.
Antibodies to cyclo(CGQKLVG) (SEQ ID NO: 6)
The antibodies were tested as described in Example 2.
ELISA and SPR testing found that hybridoma clones bound the cyclopeptide preferentially over the linear peptide.
Clones 305-59, 305-61, 350-62 raised against cyclo(CGQKLVG) (SEQ ID NO: 6) were selected for further analysis.
Isotyping revealed 305-59, 305-61, 350-62 were IgG1, IgG3 and IgG1 subtypes respectively.
Antibodies were tested in one or more assays for their ability to bind cyclic peptide, linear peptide, A-beta 1-42 monomer and A-beta 1-42 oligomers prepared as described above.
ELISA and SPR assays confirmed that the antibodies preferentially bound the cylopeptide relative to the linear peptide (and were not cross reactive to unrelated cyclic peptides) and/or preferentially bound Ab oligomers relative to monomers.
Antibody Sequence
Clones 305-59, 305-61, 350-62 antibodies were sequenced as further provided below. The CDR sequences of 305-61, 301-62 and 305-59, are provided in Table 9 (D, E and I). The consensus DNA sequence and polypeptide sequences of the variable portion of the heavy and light chain of the antibodies are provided in Table 10B.
Antibodies to cyclo(CGHDSGG) (SEQ ID NO: 10)
The antibodies were tested as described in Example 2.
ELISA and SPR testing found that hybridoma clones bound the cyclopeptide preferentially over the linear peptide.
Clones 303-25, 303-26 and 303-30 raised against cyclo(CGHDSGG) (SEQ ID NO: 10) were selected for further analysis.
Isotyping revealed 303-25, 303-26 and 303-30 were IgG2a, IgG1 and IgG1 subtypes respectively. Threes clones of antibody 303-26 and three clones of 303-30 which differed in their kappa chain were identified.
Antibodies were tested in one or more assays for their ability to bind cyclic peptide, linear peptide, A-beta 1-42 monomer and A-beta 1-42 oligomers prepared as described above.
ELISA and SPR assays confirmed that the antibodies preferentially bound the cylopeptide relative to the linear peptide (and were not cross reactive to unrelated cyclic peptides) and/or preferentially bound Ab oligomers relative to monomers.
Antibody Sequence
Clones 303-25, 303-26 and 303-30 antibodies were sequenced as further provided below. The CDR sequences are provided in Table 9 (F, G and H). The consensus DNA sequence and polypeptide sequences of the variable portion of the heavy and light chain of the antibodies are provided in Table 10C.
Methods:
Immunohistochemistry
Immunohistochemistry was performed on frozen human brain sections, with no fixation or antigen retrieval. In a humidified chamber, non-specific staining was blocked by incubation with serum-free protein blocking reagent (Dako Canada Inc., Mississauga, ON, Canada) for 1 h. The following primary antibodies were used for immunostaining: mouse monoclonal isotype controls IgG1, IgG2a, and IgG2b, and anti-amyloid β 6E10, all purchased from Biolegend, and purified antibodies 301-11, 301-17, 305-59, 305-61, 305-62, 303-25, 303-26 and 303-30 reactive to the corresponding cyclopeptide. All antibodies were used at 1 μg/mL. Sections were incubated at room temperature for 1 h, and washed 3×5 min in TBS-T. Anti-Mouse IgG Horseradish Peroxidase conjugated (1:1000, ECL) was applied to sections and incubated 45 min, then washed 3×5 min in TBS-T. DAB chromogen reagent (Vector Laboratories, Burlington ON, Canada) was applied and sections rinsed with distilled water when the desired level of target to background staining was achieved. Sections were counterstained with Mayer's haematoxylin, dehydrated and cover slips were applied. Slides were examined under a light microscope (Zeiss Axiovert 200M, Carl Zeiss Canada, Toronto ON, Canada) and representative images captured at 20 and 40× magnification using a Leica DC300 digital camera and software (Leica Microsystems Canada Inc., Richmond Hill, ON). Images were optimized in Adobe Photoshop using Levels Auto Correction.
CSF and Brain Extracts
Brain Extracts
Human brain tissues were obtained from the University of Maryland Brain and Tissue Bank upon approval from the UBC Clinical Research Ethics Board (C04-05 95). CSFs were obtained from patients assessed at the UBC Hospital Clinic for Alzheimer's and Related Disorders. The study was approved by the UBC Clinical Research Ethics Board, and written consent from the participant or legal next of kin was obtained prior to collection of CSF samples. Clinical diagnosis of probable AD was based on NINCDS-ADRDA criteria. CSFs were collected in polypropylene tubes, processed, aliquoted into 100 μL polypropylene vials, and stored at −80° C. within 1 hour after lumbar puncture.
Homogenization: Human brain tissue samples were weighed and subsequently submersed in a volume of fresh, ice cold TBS and EDTA-free protease inhibitor cocktail from Roche Diagnostics (Laval QC, Canada) such that the final concentration of brain tissue was 20% (w/v). Tissue was homogenized in this buffer using a mechanical probe homogenizer (3×30 sec pulses with 30 sec pauses in between, all performed on ice). TBS homogenized samples were then subjected to ultracentrifugation (70,000×g for 90 min). Supernatants were collected, aliquoted and stored at −80° C. The protein concentration of TBS homogenates was determined using a BCA protein assay (Pierce Biotechnology Inc, Rockford IL, USA).
CSF
CSF was pooled from 9 donors with AD and 9 donors without AD. Samples were analyzed by SPR using purified IgG at a concentration of 30 micrograms/ml for all antibodies. Mouse IgG was used as an antibody control, and all experiments were repeated at least 2 times.
Positive binding in CSF and brain extracts was confirmed using antibody 6E10.
SPR Analysis of Brain Extracts
4 brain extracts from AD patients and 4 brain extracts from age-matched controls were pooled and analyzed. Brain samples, homogenized in TBS, included frontal cortex Brodmann area 9. All experiments were performed using a Molecular Affinity Screening System (MASS-1) (Sierra Sensors GmbH, Hamburg, Germany), an analytical biosensor that employs high intensity laser light and high speed optical scanning to monitor binding interactions in real time as described in Example 6. Purified antibodies generated for cyclopeptides described herein were captured on separate flow cells of a protein A-derivatized sensor chip and diluted samples injected over the surfaces for 180 seconds, followed by 120 seconds of dissociation in buffer and surface regeneration. Binding responses were double-referenced by subtraction of mouse control IgG reference surface binding and assay buffer, and the different groups of samples compared.
SPR Analysis of Synthetic Oligomer Binding
Serial 2-fold dilutions (7.8 nM to 2000 nM) of commercially-prepared synthetic amyloid beta oligomers (SynAging SAS, Vandœuvre-lès-Nancy, were tested for binding to covalently immobilized antibodies by SPR. Antibody mAb6E10 and mouse control IgG were used as positive and negative controls respectively. Monomer binding was assessed in a separate assay as described in Example 2.
Results
CSF, Brain Extracts and Immunohistochemistry
Antibodies were tested for their ability to bind A-beta in CSF, soluble brain extracts and tissue samples of cavaderic AD brains. Strength of relative positivity in the tables is shown by the number plus signs.
IHC results are also summarized in Table 1, 3 and 5 where “+/−” denotes staining similar to or distinct from isotype control but without clear plaque morphology.
As shown in Tables 1-6 and
Each of the antibodies tested (301-17, 301-3, 301-11, 303-25, 303-26, 303-30 305-59, 305-61. 305-62) as well as the positive control antibody but not the control IgG antibody bound the commercial preparation of oligomeric A-beta.
Formalin fixed brain tissue of a confirmed AD patient was also tested. The results are shown in Table 7. The brain tissues were fixed in 10% buffered formalin for several days and paraffin processed in the Sakura VIP tissue processors. Tissue sections were probed with 1 μg/ml of antibody with and without microwave antigen retrieval (AR). The pan-amyloid beta reactive antibody 6E10 was included along with selected antibody clones as a positive control. Antibodies were diluted in Antibody Diluent (Ventana), color was developed with OptiView DAB (Ventana). The staining was performed on the Ventana Benchmark XT IHC stainer. Images were obtained with an Olympus BX45 microscope. Images were analyzed blind by a professional pathologist with expertise in neuropathology.
Inhibition of Oligomer Propagation
The biological functionality of antibodies was tested in vitro by examining their effects on Amyloid Beta (Aβ) aggregation using the Thioflavin T (ThT) binding assay. Aβ aggregation is induced by and propagated through nuclei of preformed small Aβ oligomers, and the complete process from monomeric Aβ to soluble oligomers to insoluble fibrils is accompanied by concomitantly increasing beta sheet formation. This can be monitored by ThT, a benzothiazole salt, whose excitation and emission maxima shifts from 385 to 450 nm and from 445 to 482 nm respectively when bound to beta sheet-rich structures and resulting in increased fluorescence. Briefly, Aβ 1-42 (Bachem Americas Inc., Torrance, CA) was solubilized, sonicated, diluted in Tris-EDTA buffer (pH7.4) and added to wells of a black 96-well microtitre plate (Greiner Bio-One, Monroe, NC) to which equal volumes of cyclopeptide raised antibody or irrelevant mouse IgG antibody isotype controls were added, resulting in a 1:5 molar ratio of Aβ31-42 peptide to antibody. ThT was added and plates incubated at room temperature for 24 hours, with ThT fluorescence measurements (excitation at 440 nm, emission at 486 nm) recorded every hour using a Wallac Victor3v 1420 Multilabel Counter (PerkinElmer, Waltham, MA). Fluorescent readings from background buffer were subtracted from all wells, and readings from antibody only wells were further subtracted from the corresponding wells.
As shown in
Results obtained with antibody 301-17 (IgG3 isotype) are shown in
Results were also obtained with antibody 303-25 which is shown in
As the ThT aggregation assay mimics the in vivo biophysical/biochemical stages of Aβ propagation and aggregation from monomers, oligomers, protofibrils and fibrils that is pivotal in AD pathogenesis, the antibodies raised to cyclo(CGHHQKG) (SEQ ID NO: 2), cyclo CGQKLVG (SEQ ID NO: 6) or cyclo(CGHDSGG) (SEQ ID NO: 10), demonstrate the potential to completely abrogate this process. Isotype control performed using mouse IgG control showed no inhibition.
Toxicity Inhibition Assay
The inhibition of toxicity of A-beta42 oligomers by antibodies raised to the cyclopeptides were tested in a rat primary cortical neuron assay.
Antibody and control IgG are each adjusted to a concentration such as 2 mg/mL. Various molar ratios of A-beta oligomer and antibody are tested along with a vehicle control, A-beta oligomer alone and a positive control such as the neuroprotective peptide humanin HNG.
An exemplary set up is shown in Table 8.
Following preincubation for 10 minutes at room temperature, the volume is adjusted to 840 microlitres with culture medium. The solution is incubated for 5 min at 37 C. The solution is then added directly to the primary cortical neurons and cells are incubated for 24 h. Cell viability can be determined using the MTT assay.
In a first assay, the antibody 301-17 alone showed some toxicity at the highest concentration (½ oligomer/antibody ratio), likely due to endotoxin contamination of the antibody preparation, but demonstrated inhibition of A-beta oligomer toxicity when added at lower concentrations (1/1 and 5/1 oligomer/antibody ratios) (
The assay was repeated using an antibody preparation generated under low endotoxin conditions. This time, in the absence of A-beta oligomers, the antibody alone had no effect on neuronal cell viability. When incubated in the presence of A-beta oligomers, the antibody inhibited A-beta oligomer-induced neuronal death at all molar ratios tested (
Antibody 301-3 was also tested in the assay. Like 301-17, antibody alone showed no toxicity to neuronal cell viability whereas when antibody when incubated in the presence of A-beta oligomers, the antibody inhibited A-beta oligomer-induced neuronal death at all molar ratios tested (
This test was also conducted using antibody 305-62. The antibody alone showed no toxicity (
The test was also conducted using antibody 303-25. The antibody alone showed no toxicity (
Controls are shown in
RT-PCR was carried out using 5′ RACE and gene specific reverse primers which amplify the appropriate mouse immunoglobulin heavy chain (IgG1/IgG3/IgG2A) and light chain (kappa) variable region sequences.
The specific bands were excised and cloned into pCR-Blunt II-TOPO vector for sequencing, and the constructs were transformed into E. coli
At least 8 colonies of each chain were picked & PCR screened for the presence of amplified regions prior to sequencing. Selected PCR positive clones were sequenced. The complementarity determining regions (CDRs) are identified according to IMGT/LIGM-DB.
CDR Sequencing-cyclo(CGHHQKG) (SEQ ID NO: 2) Antibodies
The CDR sequences of 301-17 which was determined to have an IgG3 heavy chain and a kappa light chain are in Table 9A. The consensus DNA sequence and protein sequences of the variable portion of the heavy and light chain are provided in Table 10A.
The CDR sequences of 301-11 are in Table 9B. The consensus DNA sequence and protein sequences of the variable portion of the heavy and light chain are provided in Table 10A.
The CDR sequences of antibody 301-03 (1 and 2) raised against cyclo(CGHHQKG) are provided in Table 9C. The consensus DNA sequence and protein sequences of the variable portion of the heavy and light chain are provided in Table 10A.
CDR Sequencing-cyclo(CGQKLVG) (SEQ ID NO: 6) Antibodies
The CDR sequences of 305-61 (7E9.1) which was determined to have an IgG3 heavy chain and a kappa light chain are in Table 9D. The consensus DNA sequence and protein sequences of the variable portion of the heavy and light chain are provided in Table 10B.
The CDR sequences of 305-62 (8H10) which was determined to have an IgG1 heavy chain and a kappa light chain are in Table 9E. The consensus DNA sequence and protein sequences of the variable portion of the heavy and light chain are provided in Table 10B.
The CDR sequences of 305-59 which was determined to have an IgG1 heavy chain and a kappa light chain are in Table 91. The consensus DNA sequence and protein sequences of the variable portion of the heavy and light chain are provided in Table 10B.
CDR Sequencing-cyclo(CGHDSGG) (SEQ ID NO: 10) Antibodies
The CDR sequences of 303-25 which was determined to have an IgG heavy chain and a kappa light chain are in Table 9F. The consensus DNA sequence and protein sequences of the variable portion of the heavy and light chain are provided in Table 10C.
The CDR sequences of 303-26 (3 kappa chains) and 303-30 are in Table 9G and 9H respectively. The consensus DNA sequence and protein sequences of the variable portion of the heavy and light chain are provided in Table 10C.
TGTTTCTACC
TACAATGCGAAGTTCAAGAGCAAGGCCACACTGACTCTAGACACGT
NTYWFFDV
WGAGTTVTVSSA
TTCC
AACCGATTTTCTGGGGTCCCAGACAGGTTCAGTGGCAGTGGATCAGGGACAG
TTTCAAGGTTCACATGTTCCATTCACG
TTCGGCTCGGGGACAAAGTTGGAAATAAA
T
FGSGTKLEIKRADA
TTACACC
TCCTATCCAGACAGTGTGAAGGGACGATTCACCATCTCCAGAGACAATG
GSSSYTSGFAY
WGQGTLVTV
C
TGGGGCCAAGGGACTCTGGTCACTGTCTCTGCA
AACTAC
TTGGCTTGGTACCAGCAGAAACCAGGGCAGTCTCCTAAACTGCTGATCTA
YT
EGGGTKLEIK
TTACACC
TCCTATCCAGACAGTGTGAAGGGGCGATTCACCATCTCCAGAGACAGTG
GSNSYTSGFAY
WGQGTLVTV
C
TGGGGCCAAGGGACTCTGGTCACTGTCTCTGCA
AACTAC
TTGGCTTGGTACCAGCAGAAACCAGGGCAGTCTCCTAAACTGCTGATCTA
YT
FGGGTKLEIK
TTCC
AACCGATTTTCTGGGGTCCCAGACAGGTTCAGTGGCAGTGGATCAGGGACAG
TTTCAAGGTTCACATGTTCCTCTCACG
TTCGGTGCTGGGACCAAGCTGGAGCTGAA
T
FGAGTKLELK
TACACATTTACTGACTAT
GAAATGCACTGGGTGAAGCAGACACCT
TDYE
MHWVKQTPVHGL
GATACT
GCCTACAATCAGGAGTTCAAGGGCAAGGCCACACTGACT
TATGATTACGACTGGTTTGCTTAC
TGGGGCCACGGGACTCTGGTC
LLNNRTRKNY
LAWYQQ
TGGGCATCC
ACTAGGGAATCTGGGGTCCCTGATCGCTTCACAGGC
CGGACG
TTCGGTGGAGGCACCAAGCTGGAAATCAAACGGGCTGAT
TTTTCACTGAGCACTTCTG
GTATGGGTGTAGGCTGGATTCGTCAG
STSGMG
VGWIRQPSGK
GATGATAAG
TACTATAACCCATCCCTGAAGAGCCAGCTCACAATC
ACTACGGTAGTAGCTACGCCCTTTGACTAC
TGGGGCCAAGGCACC
DY
WGQGTTLTVSSAKT
TCC
AACCGGCACACTGGAGTCCCTGATCGCTTCACAGGCAGTGGA
LQHWNSPFT
FGGGTKL
ACG
TTCGGAGGGGGGACCAAGCTGGAAATAAAACGGGCTGATGCT
TTCAACATTAAAGACACCTAT
GTGCACTGGGTGAAGCAGAGGCCT
KDTY
VHWVKQRPEQGL
AATACT
AAATATGCCCCGAATTTCCAGGACAAGGCCACTATAACA
VSND
VVWYQQKPGQSP
ISPYT
FGGGTKLEIK
TACACCTTCACCAGCTACTGG
ATGAACTGGGTGAAGCAGAGGCCT
TSYW
MNWVKQRPGQGL
CAAACT
CACTACAATCAAATGTTCAAGGACAAGGCCACATTGACT
INNY
IAWYQHKPGKGP
NLWT
FGGGTKLEIK
tacaccttcaccagctactgg
ATGAACTGGGTGAAGCAGAGGCCT
TSYW
MNWVKQRPGQGL
gaaact
CACTACAATCAAATGTTCAAGGACAAGGCCACATTGACT
VSTSSYSY
MHWYQQKP
tcc
AACCTAGAATCTGGGGTCCCTGCCAGGTTCAGTGGCAGTGGG
QHSLEIPWT
FGGGTKL
acg
TTCGGTGGAGGCACCAAGCTGGAAATCAAA
SSVSSAY
LHWYQQKPG
QYHRSPFT
FGAGTKLE
agccaagacattaacaagtatatagcttggtac
CAACACAAGCCT
INKYIAWY
QHKPGKGP
NLWT
FGGGTKLEIK
tacaccttcaccagctactgg
ATGAACTGGGTGAAGCAGAGGCCT
TSYW
MNWVKQRPGQGL
gaaact
CACTACAATCAAATGTTCAAGGACAAGGCCACATTGACT
VSTSSYSY
MHWYQQKP
tcc
AACCTAGAATCTGGGGTCCCTGCCAGGTTCAGTGGCAGTGGG
QHSLEIPWT
FGGGTKL
acg
TTCGGTGGAGGCACCAAGCTGGAAATCAAA
SSVSSAY
LHWYQQKPG
QYHRSPFT
FGAGTKLE
agccaagacattaacaagtatatagcttggtac
CAACACAAGCCT
INKYIAWY
QHKPGKGP
NLWT
FGGGTKLEIK
Mouse Novel Recognition Assay
The Novel Object Recognition (NOR) model utilizes the normal behavior of rodents to investigate novel objects for a significantly longer time than known objects. This test assesses recognition memory for items and its human equivalent is the visual pairwise-comparison (VPC). Recognition of objects is mediated by the perirhinal cortex in rodents, primates and humans. AD pathology develops first in the perirhinal and enthorinal cortex before the hippocampus. The VPC task detects memory deficit in mild cognitive impairment (MCI) and conversion from MCI to AD is predicted by this task.
The assay was performed by (SynAging SAS, Vandœuvre-lès-Nancy, France). Twelve C57BL6J mice per group (11-12 weeks old) were ICV-injected with vehicle (buffer used for Aβ oligomerization) or AβO (50 pmoles) in the presence of vehicle (PBS) or antibody (e.g. 301-17, 303-25 or 305-61) on day 0. The cognitive performance of all mice was determined by a Novel Object Recognition (NOR) test performed at days +7 and +8.
The study, done in blind to the operators, involved a total of 48 mice divided in four experimental groups with 12 mice per experimental group. All animals received a single (and unilateral) ICV injection of vehicle OR AβO in the absence or presence of antibody in a total volume of 5 μL. The experimental groups were defined as follow:
Because a maximum of 24 mice can be ICV injected per day, the injections were performed in two independent runs. Six mice from all groups were included in each run.
Before ICV injection, 4 μL of antibody 1 (e.g. 112 pmoles) were incubated for 30 minutes at room temperature with 1 μL vehicle (i.e. buffer for Aβ oligomerization) or 1 μL ADO (50 pmoles) corresponding to an antibody/AβO molar ratio of 2.24 mouse monoclonal 301-17 antibody. Other ratios as noted were used in other experiments with other antibodies.
At day 0, mice received a single 5 μL ICV injection of vehicle or AβO in the presence of vehicle or antibody. The stereotactic coordinates were: from the Bregma (in mm): AP −0.22, L −1.0 and D 2.5. Under anesthesia (ip injection of a mixture of ketamine/xylasine at a dose of 110 and 15 mg/kg, respectively), 5 μL were injected into the right lateral ventricle. Injections are made using 10 μL Hamilton micro syringes fitted with a 26-gauge needle. The procedure is terminated by a subcutaneous injection of metacam (analgesia) at a dose of 5 mg/kg. Animals are then placed individually in their home cage and the cage is placed in a heated cabinet until the animal has fully recovered. Animals are carefully monitored to control recovery after anesthesia.
The NOR test was conducted in one trial with all 48 mice at days +7 and +8. One day before the cognitive test (i.e. at Day +7), mice are habituated during a 10 min trial during which they are placed in an empty open field. The day of the cognitive test (i.e. Day +8), animals are placed in the same open field and are allowed to explore freely two identical objects for a trial of five minutes (acquisition trial). Then the animals are returned to their home cage for an inter-trial time of five minutes. During the retention trial, animals are allowed to explore two different objects: the same familiar object and one novel object. During this time, the experimenter, blind to the treatment, records the time the mouse is actively exploring each object. All trials are video recorded (Smart v3.0 software, Bioseb). A discrimination index (DI) is then generated: (DI)=(time exploring novel object−time exploring familiar object)/total exploration time. If the total exploration time is <5 s, animals are excluded from the calculation of the discrimination index and statistical analysis.
Data analysis: Graphpad/Prism computer software is used for the statistical analyses. A non-parametric analysis of variance (Kruskal Wallis test) is carried out followed by non-parametric Mann-Whitney U tests in order to compare between groups. Values of p<0.05 are considered statistically significant. Data are presented as mean DI±SEM.
The novel recognition test described in Example 10 was used to test an antibody raised using cyclo(CGHHQKG) (301-17) (SEQ ID NO:2). As mentioned above, before ICV injection, 4 μL of antibody 1 (112 pmoles) were incubated for 30 minutes at room temperature with 1 μL vehicle (i.e. buffer for Aβ oligomerization) or 1 μL AβO (50 pmoles) corresponding to an antibody/AβO molar ratio of 2.24.
Results:
Mice from the vehicle control group (Group A) exhibited normal behavior with a mean discrimination index of 0.443±0.053 (
Mice dosed with antibody in the presence of vehicle (Group C) were found to exhibit normal cognitive performances with a mean discrimination index of 0.439±0.049 (
When co-injected with AβO, the antibody fully prevented AβO-induced cognitive deficits in the NOR test. Indeed, mice from Group D exhibited a mean discrimination index of 0.481-0.055, not different from control mice (p=0.6126) but different from AβO-injected mice (p=0.0002) (
The NOR assay was repeated with the recombinant 301-17 comprising a mouse IgG1 backbone. The concentration of antibody used was however was less than the previously described experiment with the oligomer: antibody ratio being only 1.62. As shown in
The novel object recognition test described in Example 10 was used to test a recombinant 305-61 antibody (mouse IgG1) (parent monoclonal raised using cyclo(CGQKLVG) (SEQ ID NO:6)). The following treatment schedule was used.
As described in Example 10, 24 animals were injected per day. In the present assay, before ICV injection, 4 μL of antibody 1 were incubated for 30 minutes at room temperature with 1 μL vehicle (i.e. buffer for Aβ oligomerization) or 1 μL ADO (50 pmoles) corresponding to an antibody/AβO molar ratio of 5:1.
Results
Mice from the vehicle control group (Group A) exhibited normal behavior with a mean discrimination index of 0.39±0.05 (
Mice dosed with antibody in the presence of vehicle (Group C) were found to exhibit normal cognitive performances with a mean discrimination index of 0.36±0.05 (
When co-injected with AβO, antibody 305-61 fully prevented AβO-induced cognitive deficits in the NOR test. Indeed, mice from Group D exhibited a mean discrimination index of 0.38±0.06, not different from control mice but different from AβO-injected mice (p=0.0135) (
The novel object recognition test described in Example 10 was used to test an recombinant antibody (303-25, IgG1). The following treatment schedule was used.
An antibody:oligomer ratio of 5:1 was used. As described in Example 10, 24 animals were injected per day, ICV injection took place on day 0, the behavioural assay was conducted on day 7 or 8, and brains collected on day 10 for ELISA on hippocampal markers.
Results
Mice from the vehicle control group (Group A) exhibited normal behavior with a mean discrimination index of 0.29±0.03 (
Mice dosed with the recombinant 303-25 antibody in the presence of vehicle (Group C) were found to exhibit normal cognitive performances with a mean discrimination index of 0.35±0.06 (
Similarly, mice dosed with antibody 2 (isotype control) in the presence of vehicle (Group E) were found to exhibit normal cognitive performances with a mean discrimination index of 0.29±0.05 (
When co-injected with AβO, test antibody prevented AβO-induced cognitive deficits in the NOR test. Indeed, mice from Group D exhibited a mean discrimination index of 0.30±0.08, not different from control mice (p=0.6715) but different from AβO-injected mice (p=0.0120) (
When co-injected with AβO, antibody 2 (isotype control) failed to prevent AβO-induced cognitive deficits in the NOR test. Indeed, mice from Group F exhibited a mean discrimination index of 0.080±0.079, not different from AβO-injected mice (p=0.1962), and lower but not statistically different from control mice (p=0.1176) (
Brains were collected from the same mice that underwent the behavioral testing in Examples 11-13. The hippocampus (relevant structure for memory formation) was dissected and homogenized in RIPA buffer containing an anti-protease cocktail. The tissue was lysed by 3 freeze thaw cycles carried out in liquid nitrogen and a water bath at 37 C and the supernatants were recovered after centrifuging.
The lysate was analyzed for levels of TNF-alpha (increases with inflammation) and levels of the synaptic markers PSD-95 and SNAP-25 (which go down when there is synaptic damage) using commercial ELISA assays. Data are represented as mean±SEM. Data are expressed as pg protein per pg total protein. Statistical significance between groups are evaluated and considered statistically different to another group when p<0.05 (*: different from vehicle control mice, and #: different from AβO-injected mice).
303-25
As expected, mice ICV injected with AβO oligomers exhibited a decreased level of hippocampal PSD-95 (4.01±0.14 μg/pg total protein) statistically different from control mice (p<0.0001) (
Mice dosed with antibody 301-25 (antibody 1) or isotype control (antibody 2) in the presence of vehicle exhibited a normal level, not different from control mice, of hippocampal PSD-95 of 5.02±0.14 and 4.98±0.08 μg/pg total protein for antibody 1 and 2, respectively (
When co-injected with AβO, antibody 1 significantly improved PSD-95 level. Mice from Group D exhibited a level of hippocampal PSD-95 of 4.79±0.09 μg/pg total protein, different from control mice (p=0.0016) but also different from AβO-injected mice (p=0.0003) (
When co-injected with AβO, antibody 2 failed to improve hippocampal PSD-95 level. Mice from Group F exhibited a PSD-95 concentration of 4.34±0.11 μg/pg total protein, significantly lower than control mice (p<0.0001) and not different from AβO-injected mice (p=0.1189) (
As expected, mice ICV injected with AβO oligomers exhibited a decreased level of hippocampal SNAP25 (9.36±0.34 μg/pg total protein) different from control mice (p<0.0001) (
Mice dosed with antibody 1 or antibody 2 in the presence of vehicle exhibited a normal level of hippocampal SNAP25 of 13.93±0.57 and 12.94±0.26 μg/pg total protein for antibody 1 and antibody 2, respectively (
As expected, mice ICV injected with AβO oligomers exhibited an increased level of hippocampal TNFα (2.39±0.14 μg/pg total protein) different from control mice (p<0.0001) (
Mice dosed with antibody 1 in the presence of vehicle exhibited a normal level of hippocampal TNFα of 0.95±0.1 μg/pg total protein (
The presence antibody 1 resulted in a decreased level of TNFα in mice co-injected with AβO (
305-61
Similar results were seen with 305-61. The 305-61 antibody showed complete protection in the behavioral assay and also showed statistically significant improvement in both AbO induced SNAP25 (
301-17
Both NOR experiments using 301-17 antibodies (e.g. monoclonal and IgG1 recombinant) showed complete protection in the behavioral assay. The brain of the animals treated with or without recombinant 301-17 were tested PSD-95, SNAP25 and TNF-alpha levels. The antibody also significantly improved both SNAP25 (
Recombinant Antibodies (HHQK)
Recombinant IgG1 and IgG2a 301-17 constructs were made by grafting the variable region of hybridoma-derived 301-17 onto a murine IgG1 or IgG2a backbone (WuXi, Biologics).
The 301-17 IgG1 and IgG2a antibodies were tested and compared to the parent hybridoma-purified IgG3 antibody for binding characteristics as described below.
301-17 IgG2a ProteOn Biosensor (BioRad) Binding to AbO: Recombinant 301-17 IgG2a and hybridoma-purified 301-17 IgG3 were captured with anti-mouse IgG or amine coupling on Proteon GLM Sensor chips and tested for AbO binding (SynAging AbO). AbO 3 fold-dilutions were used: 1 uM, 0.33 uM, 0.11 uM, 37 nM, 12.3 nM. Assay buffer was PBS-E+Tween 20+2 mg/ml BSA.
Results:
Approximate kinetic values were:
Hybridoma: KD=26.9 nM
IgG2a-301-17 antibody: KD=16.2-19.5 nM
No binding was detected with control mouse IgG.
Recombinant 301-17 IgG1 had a similar KD to the IgG2a recombinant.
301-17 IgG2a ProteOn Biosensor (BioRad) Binding to cyclic peptide epitope: Recombinant 301-17 IgG2a was amine-coupled to Proteon GLH biosensor chip and tested for binding to cyclopeptide of SEQ ID NO: 2 coupled to BSA. Cyclo-BSA 3-fold dilutions were used from 9 nM to 111 μM. Assay buffer was PBS-E+0.05% Tween+10 mg/ml BSA. Antibody 301-17 IgG2a was found to bind cyclic peptide (SEQ ID NO: 2) conjugated to BSA with an approximate KD of 17 μM (average of 3 tests). No or negligible binding was detected for other commercial A-beta antibodies tested (pan-Abeta 6E10, Biolegend) and rabbit anti-A-beta antibodies (D54D2, Cell Signaling; ab201060, (abcam; NBP1-78007, Novus).
301-17 IgG1 MAAS-2 binding to AbO: Recombinant 301-17 IgG1 and hybridoma-purified 301-17 IgG3 were immobilized on MAAS-2 sensor chips and tested for binding to AbO (SynAging) at 1 uM. Under the conditions tested, the recombinant IgG1 301-17 antibody gave a greater signal than the hybridoma-purified antibody in 2 tests (40-55 BRU vs 15-25 BRU, respectively). Little or no binding was detected with control mouse IgG.
301-17IgG1 MAAS-2 binding to cyclic peptide epitope: Recombinant 301-17 IgG1 was immobilized on MAAS-2 sensor chip and tested for binding to cyclopeptide of SEQ ID NO: 2 coupled to BSA at pH 6.5, 7.5 or 8.0. Equivalently high levels of binding were observed for 301-17 IgG1 under all 3 pH conditions (˜400 BRUs). Little or no binding was detected under any of the pH conditions for control mouse IgG or the pan-Abeta 6E10 antibody (Biolegend)
Humanized Antibodies (HHQK)
Humanized IgG4 antibody constructs were prepared for 301-17 and sequenced (Abzena Cambridge UK).
Briefly RNA was extracted from the hybridoma 301-17 cell pellet using an RNeasy Mini Kit (Qiagen, Hilden, Germany). V-regions were amplified by RT-PCR using degenerate primer pools for murine antibody signal sequences together with constant region primers for each of IgG and Igκ. Heavy chain V region mRNA was amplified using a set of six degenerate primer pools (A to F) specific for VH signal sequences together with IgG-specific constant region primers. The light chain V region mRNA was amplified using a set of eight signal sequence-specific degenerate primer pools, seven for the kappa cluster (Igκ-A to Igκ-G) and one for the lambda cluster (IgA), together with κ or λ constant region primers. The PCR products obtained were purified, cloned into a ‘TA’ cloning vector (pGEM-T Easy, Promega, Madison, USA), transformed into E. coli and individual colonies sequenced.
Chimeric constructs (V0H0 and V0k0) were prepared using the variable regions from the hybridoma which were cloned into a human IgG4 framework. The chimeric constructs were then humanized to create 6 humanized heavy chains (VH1-6) and 6 light chains (Vk1-6). VH1-6 and Vk4-6 constructs were mixed to create different humanized antibodies e.g. VH2Vk4.
The fully humanized antibodies were prepared using Composite Human Antibody™ technology. The designed variable region genes were cloned into vectors encoding a human IgG4 (S241P) heavy chain constant domain and a human kappa light chain constant domain. Chimeric and humanized antibodies were transiently expressed in CHO cells and Protein A purified and tested. All 301-17 humanized antibodies selectively bound SEQ ID NO: 2 BSA with binding affinities within 2-fold of the reference chimeric antibody. Binding was determined using single cycle Biacore analysis. Antibodies were analysed in two separate experiments.
Humanized antibody sequences are provided in Table 13 and 14 (301-17). The CDR sequences of each antibody sequences are bolded and underlined. The CDRs of 301-11 or any other antibody described herein can be used to replace the CDRs in the humanized constructs as shown for example in Table 12.
GACTATTAC
ATAAACTGGGTGAAGCAGAGGCCTGGACAAGGCCTT
Y
INWVKQRPGQGLEWI
RDYYGSSSYTSGFAY
W
ACCTCGGGCTTTGCTTAC
TGGGGCGCAGGCACCACGGTCACCGTC
GACTATTAC
ATAAACTGGGTGAAGCAGAGGCCTGGACAAGGCCTT
Y
INWVKQRPGQGLEWI
RDYYGSSSYTSGFAY
W
ACCTCGGGCTTTGCTTAC
TGGGGCCAAGGCACCACGGTCACCGTC
GACTATTAC
ATAAACTGGGTGAAGCAGAGGCCTGGACAAGGCCTT
Y
INWVKQRPGQGLEWI
RDYYGSSSYTSGFAY
W
ACCTCGGGCTTTGCTTAC
TGGGGCCAAGGCACCACGGTCACCGTC
GACTATTAC
ATAAACTGGGTGCGACAGAGGCCTGGACAAGGCCTT
Y
INWVRQRPGQGLEWI
RDYYGSSSYTSGFAY
W
ACCTCGGGCTTTGCTTAC
TGGGGCCAAGGCACCACGGTCACCGTC
GACTATTAC
ATAAACTGGGTGCGACAGAGGCCTGGACAAGGCCTT
Y
INWVRQRPGQGLEWI
RDYYGSSSYTSGFAY
W
ACCTCGGGCTTTGCTTAC
TGGGGCCAAGGCACCACGGTCACCGTC
GACTATTAC
ATAAACTGGGTGCGACAGAGGCCTGGACAAGGCCTT
Y
INWVRQRPGQGLEWM
RDYYGSSSYTSGFAY
W
ACCTCGGGCTTTGCTTAC
TGGGGCCAAGGCACCACGGTCACCGTC
GACTATTAC
ATAAACTGGGTGCGACAGAGGCCTGGACAAGGCCTT
Y
INWVRQRPGQGLEWM
RDYYGSSSYTSGFAY
W
ACCTCGGGCTTTGCTTAC
TGGGGCCAAGGCACCACGGTCACCGTC
AACAGTAGAACCCGAAAGAACTAC
TTAGAATGGTACCTGCAGAAA
RTRKNY
LEWYLQKPGQ
SYNLYT
FGSGTKLEIK
AACAGTAGAACCCGAAAGAACTAC
TTAGAATGGTTTCAGCAGAAA
RTRKNY
LEWFQQKPGQ
SYNLYT
FGQGTKLEIK
AACAGTAGAACCCGAAAGAACTAC
TTAGAATGGTTTCAGCAGAAA
RTRKNY
LEWFQQKPGQ
SYNLYT
FGQGTKLEIK
AACAGTAGAACCCGAAAGAACTAC
TTAGAATGGTTTCAGCAGAGG
RTRKNY
LEWFQQRPGQ
SYNLYT
FGQGTKLEIK
AACAGTAGAACCCGAAAGAACTAC
TTAGAATGGTACCTGCAGAGG
RTRKNY
LEWYLQRPGQ
SYNLYT
FGQGTKLEIK
AACAGTAGAACCCGAAAGAACTAC
TTAGAATGGTACCAGCAGAGG
RTRKNY
LEWYQQRPGQ
SYNLYT
FGQGTKLEIK
AACAGTAGAACCCGAAAGAACTAC
TTAGAATGGTACCAGCAGAGG
RTRKNY
LEWYQQRPGQ
SYNLYT
FGQGTKLEIK
AGCTACTGG
ATAAACTGGGTGAAGCAGAGGCCTGGACAAGGCCTT
W
INWVKQRPGQGLEWI
SRSHGNTYWFFDV
WGA
TTTTTTGACGTC
TGGGGCGCAGGCACCACGGTCACCGTCTCCTCA
AGCTACTGG
ATAAACTGGGTGAAGCAGAGGCCTGGACAAGGCCTT
W
INWVKQRPGQGLEWI
SRSHGNTYWFFDV
WGQ
TTTTTTGACGTC
TGGGGCCAAGGCACCACGGTCACCGTCTCCTCA
AGCTACTGG
ATAAACTGGGTGAAGCAGAGGCCTGGACAAGGCCTT
W
INWVKQRPGQGLEWI
SRSHGNTYWFFDV
WGQ
TTTTTTGACGTC
TGGGGCCAAGGCACCACGGTCACCGTCTCCTCA
AGCTACTGG
ATAAACTGGGTGCGACAGAGGCCTGGACAAGGCCTT
W
INWVRQRPGQGLEWI
SRSHGNTYWFFDV
WGQ
TTTTTTGACGTC
TGGGGCCAAGGCACCACGGTCACCGTCTCCTCA
AGCTACTGG
ATAAACTGGGTGCGACAGAGGCCTGGACAAGGCCTT
W
INWVRQRPGQGLEWI
SRSHGNTYWFFDV
WGQ
TTTTTTGACGTC
TGGGGCCAAGGCACCACGGTCACCGTCTCCTCA
AGCTACTGG
ATAAACTGGGTGCGACAGAGGCCTGGACAAGGCCTT
W
INWVRQRPGQGLEWM
SRSHGNTYWFFDV
WGQ
TTTTTTGACGTC
TGGGGCCAAGGCACCACGGTCACCGTCTCCTCA
AGCTACTGG
ATAAACTGGGTGCGACAGAGGCCTGGACAAGGCCTT
W
INWVRQRPGQGLEWM
SRSHGNTYWFFDV
WGQ
TTTTTTGACGTC
TGGGGCCAAGGCACCACGGTCACCGTCTCCTCA
CATAGTAATGGAAACACCTAT
TTAGAATGGTACCTGCAGAAACCA
NGNTY
LEWYLQKPGQS
SHVPFT
FGSGTKLEIK
CATAGTAATGGAAACACCTAT
TTAGAATGGTTTCAGCAGAAACCA
NGNTY
LEWFQQKPGQS
SHVPFT
FGQGTKLEIK
CATAGTAATGGAAACACCTAT
TTAGAATGGTTTCAGCAGAAACCA
NGNTY
LEWFQQKPGQS
SHVPFT
FGQGTKLEIK
CATAGTAATGGAAACACCTAT
TTAGAATGGTTTCAGCAGAGGCCA
NGNTY
LEWFQQRPGQS
SHVPFT
FGQGTKLEIK
CATAGTAATGGAAACACCTAT
TTAGAATGGTACCTGCAGAGGCCA
NGNTY
LEWYLQRPGQS
SHVPFT
FGQGTKLEIK
CATAGTAATGGAAACACCTAT
TTAGAATGGTACCAGCAGAGGCCA
NGNTY
LEWYQQRPGQS
SHVPFT
FGQGTKLEIK
CATAGTAATGGAAACACCTAT
TTAGAATGGTACCAGCAGAGGCCA
NGNTY
LEWYQQRPGQS
SHVPFT
FGQGTKLEIK
A dot blot assay was used to detect antibody binding of antibodies to monomeric, oligomeric and fibrillary A-beta. 10 ng of monomeric and fibril and 100 ng oligomeric A-beta was spotted on a PVDF membrane. The membrane was blotted with antibodies 301-17, 303-25 and 305-62 as well as prior art antibodies aducanumab, solanezumab and bapinezumab (Creative Biolabs). Antibodies 301-17 (
CDRs can also be identified using the Kabat numbering scheme. For example the CDRs for the humanized 301-17 constructs using the Kabat numbering system are:
While the present application has been described with reference to what are presently considered to be the preferred examples, it is to be understood that the application is not limited to the disclosed examples. To the contrary, the application is intended to cover various modifications and equivalent arrangements included within the spirit and scope of the appended claims.
All publications, patents and patent applications are herein incorporated by reference in their entirety to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference in its entirety. Specifically, the sequences associated with each accession numbers provided herein including for example accession numbers and/or biomarker sequences (e.g. protein and/or nucleic acid) provided in the Tables or elsewhere, are incorporated by reference in its entirely.
The scope of the claims should not be limited by the preferred embodiments and examples, but should be given the broadest interpretation consistent with the description as a whole.
This application is a continuation of U.S. patent application Ser. No. 16/148,601 (now issued as U.S. Pat. No. 10,751,382B2), filed Oct. 1, 2018, which is a continuation of U.S. patent application Ser. No. 15/808,842 (now abandoned), filed Nov. 9, 2017; which is a continuation in part of PCT/CA2016/051300, filed Nov. 9, 2016; PCT/CA2016/051305, filed Nov. 9, 2016; PCT/CA2016/051303, filed Nov. 9, 2016; and PCT/CA2017/050866, filed Jul. 18, 2017; and which also claims priority to U.S. provisional applications Ser. No. 62/443,766, filed Jan. 8, 2017; 62/507,633, filed May 17, 2017; and 62/507,587, filed May 17, 2017. All of these applications are incorporated herein by reference in their entirety.
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| Number | Date | Country | |
|---|---|---|---|
| 20210038678 A1 | Feb 2021 | US |
| Number | Date | Country | |
|---|---|---|---|
| 62507587 | May 2017 | US | |
| 62507633 | May 2017 | US | |
| 62443766 | Jan 2017 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16148601 | Oct 2018 | US |
| Child | 16999849 | US | |
| Parent | 15808842 | Nov 2017 | US |
| Child | 16148601 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/CA2017/050866 | Jul 2017 | US |
| Child | 15808842 | US | |
| Parent | PCT/CA2016/051300 | Nov 2016 | US |
| Child | PCT/CA2017/050866 | US | |
| Parent | PCT/CA2016/051303 | Nov 2016 | US |
| Child | PCT/CA2016/051300 | US | |
| Parent | PCT/CA2016/051305 | Nov 2016 | US |
| Child | PCT/CA2016/051303 | US |
