Patent Application
20230203158
The instant application contains a Sequence Listing which has been submitted electronically in XML file format and is hereby incorporated by reference in its entirety. Said XML copy, created on Aug. 25, 2022, is named 51666-002003_SL.xml and is 116,519 bytes in size.
Undesirable off-target effects are a problem for otherwise desirable therapeutic targets that are present in healthy as well as diseased tissues.
The present disclosure describes, in part, macromolecule compositions and related methods that effect targeted delivery of therapeutic agents to effector targets in a desired cell, tissue and/or organ of interest while minimizing or avoiding undesirable delivery to other cells, tissues or organs. Generally, compositions described herein comprise macromolecules, such as an ANDbody™, that include an effector target binding domain specific for an effector target, and an address binding domain specific for an address target. The address target is generally sufficiently restricted in the subject to target the macromolecule to the desired cell, tissue or organ. In some embodiments, the effector target binding domain does not influence an effector target in the absence of an address target binding domain. Moreover, the address target binding domain does not influence signaling upon binding the address target. However, localization of the effector target binding domain by the address target binding domain enables the effector target binding domain to bind the effector target sufficiently to elicit an influence on signaling by the effector target in the target cell or tissue. The compositions described herein can be used, e.g., to specifically deliver a therapeutic agent to a desired location, e.g., a cell, tissue or organ, in a subject, while avoiding undesirable off-target effects.
In one aspect, the present disclosure provides a method of localizing a macromolecule at a target tissue or cell of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in the subject, and (b) the second binding site is specific for an address target expressed in the target tissue or cell in the subject; wherein: (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and allowing the macromolecule to localize at the target tissue or cell of the subject.
In some embodiments, at least 25% of the macromolecule detectable in the subject is detected at the target tissue or cell at a time point between 1 and 7 days following administration of the macromolecule to the subject.
In some embodiments, the potency of the first binding site at the target tissue or cell is substantially increased relative to a reference macromolecule lacking the second binding site.
In some embodiments, the first binding site has a low affinity for the effector target.
In some embodiments, the first binding site has a low avidity for the effector target.
In some embodiments, the affinity of the first binding site for the effector target is lower than the affinity of the second binding site for the address target.
In some embodiments, the avidity of the first binding site for the effector target is lower than the avidity of the second binding site for the address target.
In some embodiments, effector target signaling by the macromolecule in a non-target tissue or cell of the subject is substantially decreased relative to a reference macromolecule lacking the second binding site.
In some embodiments, the address target is regionally expressed in the subject. In some embodiments, the address target is locally expressed in the subject. In some embodiments, the expression of the address target is restricted to a cell type in the subject.
In some embodiments, the address target is expressed only by a cell in the subject when in a specific cell state.
In some embodiments, the address target is expressed only by a cell in the subject in a disease state.
In some embodiments, the first binding site or the second binding site comprises a polypeptide.
In some embodiments, the polypeptide is an antibody or antigen-binding fragment thereof.
In some embodiments, the macromolecule is an antibody comprising a first binding site that is specific for the effector target in the subject and a second binding site that is specific for the address target.
In some embodiments, the polypeptide is a ligand of the effector target or a ligand of the address target.
In some embodiments, (a) the first binding site comprises an antibody or antigen-binding fragment thereof and the second binding site comprises a ligand of the address target; or (b) the first binding site comprises a ligand of the effector target and the second binding site comprises an antibody or antigen-binding fragment thereof.
In some embodiments, the target tissue is skin and the second binding site is specific for desmoglein-1 (DSG-1).
In some embodiments, the target tissue is lung tissue and the second binding site is specific for RAGE.
In some embodiments, the target tissue is kidney tissue and the second binding site is specific for cadherin 16 (CDH16).
In some embodiments, the target tissue is intestine tissue and the second binding site is specific for cadherin 17 (CDH17).
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein: (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein: (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and wherein localization of the macromolecule to a non-target tissue or cell is substantially reduced relative to localization of a reference macromolecule lacking the second binding site.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and wherein localization of the macromolecule to a target tissue or cell is substantially increased relative to localization of a reference macromolecule lacking the second binding site.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and wherein at least 25% of the macromolecule administered to a subject is detected at the target tissue or cell at a time point between 1 and 7 days following administration.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and wherein the affinity of the first binding site for the effector target is lower than the affinity of the second binding site for the address target.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and wherein the avidity of the first binding site for the effector target is lower than the avidity of the second binding site for the address target.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and wherein the potency of the first binding site at the target tissue or cell is substantially increased relative to a reference macromolecule lacking the second binding site.
In some embodiments, the first binding site has a low affinity for the effector target.
In some embodiments, the first binding site has a low avidity for the effector target.
In some embodiments, the affinity of the first binding site for the effector target is lower than the affinity of the second binding site for the address target.
In some embodiments, the avidity of the first binding site for the effector target is lower than the avidity of the second binding site for the address target.
In some embodiments, (a) the Kd of the first binding site for the effector target is higher than the Kd of the second binding site for the address target; (b) the EC50 of the first binding site for the effector target is higher than the EC50 of the second binding site for the address target; or (c) the IC50 of the first binding site for the effector target is higher than the IC50 of the second binding site for the address target.
In some embodiments, the first binding site has an affinity to the effector target of at least about 2 times, at least about 5 times, or at least about 10 times less than the affinity of the second binding site to the address target.
In some embodiments, the affinity of the second binding site to the address target has a Kd of greater than about 1 nM, greater than about 2 nM, or greater than about 50 nm.
In some embodiments, the effector target is a protein, lipid, or sugar.
In some embodiments, the effector target is a cell membrane-associated target.
In some embodiments, the effector target is a protein. In some embodiments, the effector target is a secreted protein.
In some embodiments, the effector target is encoded by a gene selected from the group consisting of the genes recited in Table 1.
In some embodiments, the macromolecule agonizes the effector target.
In some embodiments, the macromolecule antagonizes the effector target.
In some embodiments, the address target is a protein, lipid, or sugar.
In some embodiments, the address target is a protein.
In some embodiments, expression of the effector target or the address target is expression of an RNA sequence encoding the effector target or the address target.
In some embodiments, the expression level of the effector target or the address target is assessed by using a RNA sequence dataset.
In some embodiments, the RNA sequence dataset is a Genotype-Tissue Expression (GTEx) dataset or a Human Protein Atlas (HPA) dataset.
In some embodiments, expression of the effector target or the address target is protein expression.
In some embodiments, the effector target is systemically expressed in the subject.
In some embodiments, the effector target is regionally expressed in the subject.
In some embodiments, the effector target is locally expressed in the subject.
In some embodiments, the address target is regionally expressed in the subject.
In some embodiments, the address target is locally expressed in the subject.
In some embodiments, the expression of the address target is restricted to a cell type in the subject.
In some embodiments, the address target is a soluble protein or an extracellular matrix (ECM)-associated protein and is not present in detectable amounts on the cell surface.
In some embodiments, the address target is expressed in the ECM and is not present in detectable amounts elsewhere in the subject.
In some embodiments, the address target is expressed only by a cell in the subject when in a specific cell state.
In some embodiments, the address target is expressed only by a cell in the subject when in a disease state.
In some embodiments, the address target is not expressed in a tissue in which binding of the second binding site to the effector target is deleterious to the subject.
In some embodiments, the binding site for the address target does not bind in detectable amounts to the binding site of a natural ligand of the address target.
In some embodiments, expression of the effector target or address target includes expression in one or more of minor salivary gland, thyroid, lung, breast, mammary tissue, pancreas, adrenal gland, liver, kidney, kidney cortex, kidney medulla, adipose-visceral tissue, omentum, small intestine, terminal ileum, fallopian tube, ovary, uterus, skin, skin not sun exposed, suprapubic skin, cervix, endocervix, ectocervix, vagina, skin sun exposed, lower leg skin, eneanterior cingulate cortex, Brodmann area 24 (BA24), basal ganglia, caudate nucleus, putamen, nucleus acumbens, hypothalamus, amygdala, hippocampus, cerebellum, cerebellar hemisphere, substantia nigra, pituitary gland, spinal cord, cervical spinal cord, artery, aorta, heart, atrial appendage, coronary artery, left ventricle, esophagus, esophagus mucosa, esophagus muscularis, gastroesophageal junction, spleen, stomach, colon, transverse colon, sigmoid colon, testis, whole blood cells, EBV-transformed lymphocytes, artery-tibial, or nerve-tibial tissues.
In some embodiments, expression of the effector target or address target includes expression in skin tissue, lung tissue, kidney tissue, or intestine tissue. In some embodiments, expression of the address target is substantially higher in skin tissue, lung tissue, kidney tissue, or intestine tissue than in any other tissue.
In some embodiments, the effector target and/or the address target is expressed on a structural tissue in the subject.
In some embodiments, the effector target and address target are on the same cell.
In some embodiments, the effector target and address target are on different cells.
In some embodiments, the effector target and address target are on different cells of the same cell type.
In some embodiments, the effector target and address target are on different cells of different cell types.
In some embodiments, the effector target and address target are on different cells in the same tissue.
In some embodiments, (a) the effector target is on a circulating cell and the address target is on a tissue-restricted cell; or (b) the effector target is on a tissue-restricted cell and the address target is on a circulating cell.
In some embodiments, the effector target and address target are on different cells located within 100 nm of each other in the subject.
In some embodiments, either the effector target or the address target is present on a cell surface.
In some embodiments, the macromolecule is a DNA polynucleotide.
In some embodiments, the macromolecule comprises an RNA or RNA-polypeptide conjugate.
In some embodiments, the macromolecule comprises a polypeptide. In some embodiments, the macromolecule is a polypeptide.
In some embodiments, the polypeptide is an antibody or antigen-binding fragment thereof.
In some embodiments, the first binding site and the second binding site each comprise a VH and/or a VL.
In some embodiments, the macromolecule is an antibody comprising a first binding site that is specific for the effector target in the subject and a second binding site that is specific for the address target.
In some embodiments, the macromolecule is an asymmetric antibody or a symmetric antibody.
In some embodiments, the antibody or antigen-binding fragment thereof comprises an scFv, BsIgG, a BsAb fragment, a BiTE, a dual-affinity re-targeting protein (DART), a tandem diabody (TandAb), a diabody, an Fab2, a di-scFv, chemically linked F(ab′)2, an Ig molecule with 2, 3 or 4 different antigen binding sites, a DVI-IgG four-in-one, an ImmTac, an HSAbody, an IgG-IgG, a Cov-X-Body, an scFv1-PEG-scFv2, an appended IgG, an DVD-IgG, an affibody, an affilin, an affimer, an affitin, an alphabody, an anticalin, an avimer, a DARPin, a Fynomer, a monobody, a nanoCLAMP, a bis-Fab, an Fv, a Fab, a Fab′-SH, a linear antibody, an scFv, an antibody with only a heavy chain (Humabody), an ScFab, an IgG antibody fragment, a single-chain variable region antibody, a single-domain heavy chain antibody. a bispecific triplebody, a BiKE, a CrossMAb, a dsDb, an scDb, tandem a dAb/VHH, a triple dAb VHH, a tetravalent dAb/VHH, a Fab-scFv, a Fab-Fv, or a DART-Fc, an adnectin, a Kunitz-type inhibitor, or a receptor decoy.
In some embodiments, the polypeptide is a ligand of the effector target or a ligand of the address target.
In some embodiments, the ligand is a natural ligand, a modified ligand, or a synthetic ligand.
In some embodiments, the effector target or address target is a receptor and the polypeptide is a ligand thereof.
In some embodiments, the first binding site comprises an antibody or antigen-binding fragment thereof and the second binding site comprises a ligand of the address target.
In some embodiments, the first binding site comprises a ligand of the effector target and the second binding site comprises an antibody or antigen-binding fragment thereof.
In some embodiments, the amino acid sequences of the first and second binding sites are at least about 10% identical, at least about 20% identical, at least about 30% identical, at least about 40% identical, at least about 50% identical, at least about 60% identical, or at least about 70% identical.
In some embodiments, the address target has a Gini coefficient higher than about 0.4, about 0.5, about 0.57, about 0.65, about 0.7, about 0.85, about 0.90, or about 0.95.
In some embodiments, the address target has a Tau coefficient higher than about 0.67, about 0.75, about 0.8, about 0.85, about 0.90, or about 0.95.
In some embodiments, the effector target has a Gini coefficient lower than about 0.25, about 0.20, or about 0.15.
In some embodiments, the effector target has a Tau coefficient lower than about 0.25, about 0.20, or about 0.15.
In some embodiments, the macromolecule further comprises a third binding site. In some embodiments, the third binding site is the same as the first binding site. In some embodiments, the third binding site is the same as the second binding site.
In some embodiments, the first binding site and second binding site are directly joined to each other in the macromolecule.
In some embodiments, the first binding site and the second binding site in the macromolecule are joined by a stable domain.
In some embodiments, the effector target is Notch2 and the address target is RAGE.
In some embodiments, RAGE signaling is not influenced by the second site binding the RAGE address target.
In some embodiments, the effector target is Notch2 and the address target is uromodulin (UMOD).
In some embodiments, UMOD signaling is not influenced by the second site binding the UMOD address target.
In some embodiments, the effector target is Notch2 and the address target is meprin A subunit beta (MEP1B).
In some embodiments, MEP1B signaling is not influenced by the second site binding the MEP1B address target.
In some embodiments, the effector target is IL11Ra and the address target is RAGE. In some embodiments, RAGE signaling is not influenced by the second site binding the RAGE address target.
In some embodiments, the effector target is IL 11 Ra and the address target is UMOD. In some embodiments, UMOD signaling is not influenced by the second site binding the UMOD address target.
In some embodiments, the subject is a human.
In another aspect, the present disclosure provides a method of delivering a moiety to a target tissue or cell in a subject, comprising administering to the subject a macromolecule of any one of claims 1-86, wherein the target tissue comprises the address target.
In some embodiments, the moiety is a molecule.
In some embodiments, the moiety is not a toxin.
In some embodiments, the moiety is a cell.
In some embodiments, the moiety is not a T cell or an NK cell.
In some embodiments, the target tissue is not a tumor.
In another aspect, the present disclosure provides a method of modulating an effector target in a target tissue, comprising administering to the tissue a macromolecule of any one of claims 1-86, wherein the target tissue comprises the address target and the effector target.
In another aspect, the present disclosure provides a method of biasing a binding agent away from binding an effector target when the effector target is found in the heart or lungs, comprising administering the macromolecule of any one of claims 1-86, wherein the address target is not substantially expressed in the heart or lungs.
In another aspect, the present disclosure provides a method of modulating a target tissue in a subject, comprising administering to the subject a macromolecule of any one of claims 1-86, wherein the target tissue comprises the address target and the effector target.
In another aspect, the present disclosure provides a method of treating a subject having a disease or condition associated with an effector target, comprising administering to the subject a macromolecule of any one of claims 1-86, wherein the first binding site of the macromolecule binds the effector target.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell, wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site, and wherein the second binding site does not bind to the binding site of the natural ligand of the address target.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell, wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site, and wherein the first binding site and second binding site are directly joined to each other in the macromolecule.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell, wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site, and wherein the first binding site and second binding are joined to each other by a stable domain.
In another aspect, the present disclosure provides a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell, wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site, and wherein the effector target and/or the address target is expressed on a structural tissue in a host.
In another aspect, the present disclosure provides a pharmaceutical composition comprising the macromolecule of any one of the above embodiments.
In another aspect, the present disclosure provides a pharmaceutical composition comprising a macromolecule and one or more pharmaceutically acceptable excipients, wherein the macromolecule comprises a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell, and wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site.
In some embodiments, the pharmaceutical composition is an RNA pharmaceutical composition.
In some embodiments, the pharmaceutical composition further comprises a carrier.
In some embodiments, the carrier is a lipid nanoparticle.
In some embodiments, the carrier is a viral vector.
In some embodiments, the carrier is a membrane-based carrier.
In some embodiments, the membrane-based carrier is a cell.
In some embodiments, the membrane-based carrier is a vesicle.
In another aspect, the present disclosure provides a method for modulating activity of an effector target in the skin of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in the subject, and (b) the second binding site is specific for desmoglein-1 (DSG-1).
In another aspect, the present disclosure provides a method for modulating activity of an effector target in the lung of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in the subject, and (b) the second binding site is specific for RAGE.
In another aspect, the present disclosure provides a method for modulating activity of an effector target in the kidney of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in the subject, and (b) the second binding site is specific for cadherin 16 (CDH16).
In another aspect, the present disclosure provides a method for modulating activity of an effector target in the intestine of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in the subject, and (b) the second binding site is specific for cadherin 17 (CDH17).
In another aspect, the present disclosure provides a method of localizing a macromolecule at a target tissue or cell of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in the subject, and (b) the second binding site is specific for an address target expressed in the target tissue or cell in the subject; wherein: (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and allowing the macromolecule to localize at the target tissue or cell of the subject.
In another aspect, the present disclosure provides a method of concentrating a macromolecule in a target tissue or cell in a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein (a) the first binding site is specific for an effector target in a subject, and (b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein (i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell; (ii) the second binding site does not substantially influence signaling upon binding the address target; and (iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and allowing the macromolecule to concentrate at the target tissue or cell of the subject, wherein at least 25% of the macromolecule detectable in the subject is detected at the target tissue or cell at a time point between 1 and 7 days following administration of the macromolecule to the subject.
In some embodiments, the potency of the first binding site at the target tissue or cell is substantially increased relative to a reference macromolecule lacking the second binding site.
In some embodiments, effector target signaling by the macromolecule in a non-target tissue or cell of the subject is substantially decreased relative to a reference macromolecule lacking the second binding site.
In some embodiments, the macromolecule is a macromolecule of any one of the above embodiments.
The details of one or more embodiments of the invention are set forth in the description below. Other features or advantages of the present invention will be apparent from the following drawings and detailed description of several embodiments, and also from the appended claims.
Provided herein are ANDbody™ molecules that include a therapeutic effector target binding domain and an address target binding domain. The therapeutic effector target on the ANDbody molecule productively engages its therapeutic effector target only if the address target binding domain also engages an address target on a target tissue or cell to localize the effector target to the targeted cell or tissue, e.g., to form an AND-gate type of logic gate. For example, in some embodiments, an ANDbody is a macromolecule comprising at least (a) a first binding site specific for a therapeutic effector target that is expressed, e.g., broadly expressed, on a mammalian subject, e.g., on a cell surface; and (b) a second binding site specific for an address target. In embodiments, expression of the address target is restricted in vivo in a subject. In some embodiments, the binding of a first binding site to a therapeutic effector target is weaker than the binding of the second binding site to the address marker. The effector and address targets may be on the same cell, or in different cells or compartments within the same tissue.
In some embodiments, at least 25% of the macromolecule (e.g., ANDbody) detectable in the subject is detected at the target tissue or cell at a time point between 1 and 7 days (e.g., at 1 day, 2 days, 3 days, 4 days, 5, days, 6 days, and/or 7 days) following administration of the macromolecule (e.g., ANDbody) to the subject. For example, in some embodiments, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or 100% (e.g., 25-30%, 30-35%, 35-40%, 40-45%, 45-50%, 50-55%, 55-60%, 60-65%, 65-70%, 70-75%, 75-80%, 80-85%, 85-90%, 90-95%, or 95-100%) of the macromolecule detectable in the subject is detected at the target tissue or cell at a time point between 1 and 7 days following administration of the macromolecule the subject.
An ANDbody™ of the invention comprises an effector that modulates a therapeutic effector target in a subject, e.g., a mammalian subject such as a human, in need thereof. As used herein, an “effector target” is a discrete structure (e.g., a cell surface protein, a transmembrane protein, a receptor) of a cell or tissue of a subject, to which a therapeutic effector binding domain of an ANDbody can bind and exert a modulating effect, such as a therapeutic effect, on the subject. The ANDbody described herein has a binding site specific for an effector target. Upon binding of the effector binding domain to the effector target, the effector modulates the target cell or tissue to produce a biological response, such as a therapeutic effect, on the subject. However, in some embodiments, the effector target binding domain provided herein may not elicit a biological effect unless it is provided in conjunction with an address targeting domain to localize the effector to the desired target address in a targeted cell or tissue. In some embodiments, such therapeutic signaling may require the binding of multiple effector targets by multiple macromolecules according to the invention.
In some embodiments, an effector target binding domain may produce a small/weak biological effect when provided alone and provide a larger/stronger biological effect when provided in conjunction with an address targeting domain that localizes and concentrates/focuses the effector to the desired target address in a targeted cell or tissue. In some embodiments, an effector target binding domain may produce an acceptable biological effect when provided alone and provide an even larger/stronger biological effect when provided in conjunction with an address targeting domain to localize the effector target binding domain to a targeted cell or tissue. In some embodiments, an effector target binding domain may produce a strong biological effect when provided alone and provide a strong, or stronger, targeted effect when provided in conjunction with an address targeting domain to localize the effector target binding domain to a targeted cell or tissue. In some embodiments, an effector target binding domain may produce a biological effect with undesirable off target biological effects when provided alone, but can be targeted, concentrated, and focused to desired addresses in a targeted cell or tissue when provided in conjunction with an address targeting domain in order to decrease or eliminate undesirable off-target biological effects. Accordingly, effector target binding domains of the present technology provide superior therapeutic agents that provide stronger, targeted biological effects with less side effects, including less unintended off-target biological effects, when provided in conjunction with address target binding domains as described herein.
Examples of such therapeutic signaling effects include, but are not limited to:
In some embodiments, the therapeutic effector target is more broadly expressed than the address target in the subject. In some embodiments, the therapeutic effector target is expressed systemically, regionally, or locally in the organism. “Systemic expression” of a therapeutic effector target means that the therapeutic effector target is expressed at substantially the same levels in most parts of a subject organism body. Systemic expression involves a plurality of tissues “Regional expression” of a therapeutic effector target means that the therapeutic target is expressed in an area less than systemic expression but more than local expression. Regional expression is not limited to a single tissue but can occur in a plurality of different tissues. “Local expression” of a therapeutic effector target means that the therapeutic target is expressed in single or few tissue areas. Local expression is not limited to a single tissue but can occur in a plurality of different tissues.
In some embodiments, the effector target binding domain has a low affinity for the effector target. For example, a low affinity may be an affinity of greater than 10 nM (e.g., an affinity between 10 nM-1 μM, e.g., an affinity between 10 nM and 100 nM).
In some embodiments, the effector target binding domain has a low avidity for the effector target. Non-limiting examples of therapeutic effector targets that can be targeted with ANDbodies disclosed herein are listed in Table 1, along with the exemplary function for the effector targets.
An ANDbody of the invention also comprises an address target binder that binds to an address target to provide targeted delivery of the effector. As used herein, an “address target” is a structure on a cell or tissue whose expression is sufficiently restricted in an organism to allow it to identify an organ, tissue, cell, or cell state of interest in an organism. The address target can be, e.g., a cell surface protein, or a structure localizing to the extracellular matrix. As used herein, “restricted” expression of an address target means that the address target has a differential, e.g., less broad, in vivo expression, as opposed to systemic expression. In certain embodiments, the address target is expressed, for example, in a single cell type, tissue or cell state in a mammalian subject, such as a human subject.
In some embodiments, the currently provided address target binding domains do not substantially influence biological signaling upon binding to the address target, e.g., does not modulate a signal transduction pathway or other biological response in the target cell or tissue. For example, the address target binder can be inert or inactive, in which it lacks any additional activity (other than binding), including lacking catalytic activity, after binding to the address target. For example, the address target binder binds a non-signaling site or motif of the address target. “Signal” is used herein to indicate a conformational, enzymatic, and/or electrical consequence occurs as a result of target binding. Accordingly, as described herein, address target binding domains do not signal upon address target binding. A domain that does not “substantially” influence biological signaling, as used herein, is a domain that modulates a signal transduction pathway or other biological response in the target cell or tissue to which it binds by no more than 25% relative to a control condition, e.g., relative to signaling in the absence of the domain. For example, the domain may modulate (e.g., increase or decrease) the signal transduction pathway or other biological response by less than 20%, less than 15%, less than 10%, less than 5%, less than 2%, or less than 1% (e.g., 20-25%, 15-20%, 10-15%, 5-10%, 2-5%, or 1-2%).
Similarly, an effector target binding domain may not substantially signal, or may not signal at all, when it is not localized by an address target binding domain. In embodiments, an effector target binding domain signals with higher potency (e.g., has higher avidity) when it is localized by an address target binding domain compared to the signal when it is not localized by an address target binding domain. When an effector target binding domain is localized to a targeted cell or tissue by an address target binding domain as part of the same macromolecule, effector target signaling can be influenced as discussed above.
In some embodiments, the address target is used for organ-specific addressing, tissue-specific addressing, or cell-specific addressing.
The specificity of address target binding domains for a cell or tissue can be detected using methods known in the art. In one embodiment, a Gini coefficient (GC) score, which is a method for assessing the expression variation of a particular gene in a data set, is used. (See O'Hagan et al., GeneGini: assessment via the Gini coefficient of reference “housekeeping” genes and diverse human transporter expression profiles. Cell systems 6, 230-244, https://doi.org/10.1016/j.cels.2018.01.003 (2018); Wright Muelas et al., The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data. Sci Rep 9, 17960 (2019). https://doi.org/10.1038/s41598-019-54288-7). Address target binders can be identified using cell expression data generated for address target binders as described herein (Table 2A and 2B). In some embodiments, address target markers exhibit Gini scores of greater than 0.4, such as between 0.74 and 1.00. Conversely, non-address markers that are expressed more systemically exhibit Gini Scores of between 0.15 to 0.19.
In one embodiment, a Tau score, which represents the expression variation of a particular gene in a data set, is used. Calculating Tau uses the information of expression of a gene in each tissue and its maximal expression over all tissues while also taking into account the number of tissues where expression is measured (see Itai Yanai, et al., Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification, Bioinformatics, Volume 21, Issue 5, 1 Mar. 2005, Pages 650-659; Kryuchkova-Mostacci N, Robinson-Rechavi M. A benchmark of gene expression tissue-specificity metrics. Brief Bioinform. 2017 Mar. 1; 18(2):205-214. doi: 10.1093/bib/bbw008). In some embodiments, address target markers exhibit Tau scores of greater than 0.6, such as between 0.74 and 1.00. Conversely, non-address markers that are expressed more systemically exhibit Tau Scores of below 0.3, such as 0.15 to 0.19.
In some embodiments, specificity of address target binding domains for a particular cell or tissue, such as that indicated by an appropriate Gini and/or Tau score, is determined with a tissue based analysis that does not include tissues having a natural biological separation barrier (i.e., blood-brain barrier). For example, in some embodiments, Gini and/or Tau scores may be calculated without data from tissues such as (but not limited to): central nervous system, brain, eye, and/or testis tissues. In some embodiments, an address target as provided herein identifies a cell state. As used herein a “cell state” refers to a given physiological condition of a cell. A cell state may be, e.g., a disease state (relative to a non-disease state or normal state of a cell or tissue); or an activated state (relative to a non-activated state of a cell). Exemplary disease states include inflammation, infection (e.g., bacterial, viral, or fungal infection), and states relating to cancer (e.g., precancerous or cancerous cell states). In some aspects, cell state reflects the fact that cells of a particular type can exhibit variability with regard to one or more features and/or can exist in a variety of different conditions, while retaining the features of their particular cell type and not gain features that would cause them to be classified as a different cell type. The different states or conditions in which a cell can exist may be characteristic of a particular cell type (e.g., may involve properties or characteristics exhibited only by that cell type and/or involve functions performed only or primarily by that cell type) or may occur in multiple different cell types. In some embodiments, a cell state reflects the capability of a cell to respond to a particular stimulus or environmental condition (e.g., whether or not the cell will respond, or the type of response that will be elicited) or is a condition of the cell brought about by a stimulus or environmental condition. Cells in different cell states may be distinguished from one another in a variety of ways. For example, they may express, produce, or secrete one or more different genes, proteins, or other molecules (“markers”, such as the address targets provided herein), exhibit differences in protein modifications such as phosphorylation, acetylation, etc., or may exhibit differences in appearance. Thus a cell state may be a condition of the cell in which the cell expresses, produces, or secretes one or more markers, exhibits particular protein modification(s), has a particular appearance, and/or will or will not exhibit one or more biological response(s) to a stimulus or environmental condition. Exemplary address targets of the present technology are provided in Tables 2A (HPA database analysis) and 2B (Gtex database analysis), below.
Table 2B contains address targets based on a Gtex database analysis:
In general, an ANDbody can be any macromolecule, such as a polypeptide or protein that contains both an effector target binding site or binding domain, and an address target binding site or binding domain. The binding sites may be present on the same polypeptide chain or different polypeptide chains that are linked together, e.g., through disulfide bonds.
In some embodiments, the binding site for the effector target and the binding site for the address target of the ANDbody each comprise an antibody heavy chain and/or a light chain domain. In some embodiments the ANDbody comprises a first antibody variable domain which has binding specificity for the effector target and a second antibody variable domain that has binding specificity for the address target. In other embodiments the ANDbody comprises a first antigen binding site of an antibody, which first antigen binding site has binding specificity for the effector target, and a second antigen binding site of an antibody, which second antigen binding site has binding specificity for the address target.
In some embodiments, the ANDbody may have the structure of an antibody molecule. The term “antibody” as used herein includes full-length antibodies and antigen binding antibody fragments (e.g., scFvs). In some embodiments, an antibody molecule has specificity for more than one. e.g., 2, 3, 4 antigens, e.g., the antibody molecule comprises a plurality of variable domain sequences, wherein a first variable domain sequence of the plurality has binding specificity for a first epitope the effector target) and a second variable domain sequence of the plurality has binding specificity for a second epitope (e.g., the address target) In some embodiments, the ANDbody is an antibody molecule that has an arm or domain that binds the effector target and an arm or domain that binds the address target. In embodiments, the ANDbody is an antibody molecule that comprises light chains that bind one of the effector target and address target, and heavy chains that bind the other of the effector target and address target.
In some embodiments, the ANDbody has the structure of an scFv, BsIgG, a BsAb fragment, a BiTE, a dual-affinity re-targeting protein (DART), a tandem diabody (TandAb), a diabody, an Fab2, a di-scFv, chemically linked F(ab′)2, an Ig molecule with 2, 3 or 4 different antigen binding sites, a DVI-IgG four-in-one, an ImmTac, an HSAbody, an IgG-IgG, a Cov-X-Body, an scFv1-PEG-scFv2, an appended IgG, an DVD-IgG, an affibody, an affilin, an affimer, an affitin, an alphabody, an anticalin, an avimer, a DARPin, a Fynomer, a monobody, a nanoCLAMP, a bis-Fab, an Fv, a Fab, a Fab′-SH, a linear antibody, an scFv, an antibody with only a heavy chain (Humabody), an ScFab, an IgG antibody fragment, a single-chain variable region antibody, a single-domain heavy chain antibody. a bispecific triplebody, a BiKE, a CrossMAb, a dsDb, an scDb, tandem a dAb/VHH, a triple dAb VHH, a tetravalent dAb/VHH, a Fab-scFv, a Fab-Fv, or a DART-Fc, an adnectin, a Kunitz-type inhibitor, or a receptor decoy.
The affinity of the effector target binding site and address target binding site of an ANDbody for their respective binding partners may differ. In some embodiments the affinity of the first binding site to the therapeutic effector target it binds is weaker than the affinity of the second binding site to the address target. In some embodiments the affinity of the first binding site to the therapeutic effector target it binds is more than 2-fold, 3-fold, 4-fold, 5-fold, 10-fold, 15-fold, 20-fold, 50-fold, 100-fold, 200-fold, 500-fold, 1000-fold weaker than the affinity of the second binding site to the address target.
The terms “binding affinity” and “binding activity” refer to the tendency of a macromolecule, e.g., a polypeptide molecule, to bind or not to bind to a target. For purposes of the present invention, which combines two binding sites, the relative affinities of the two binding sites can be determined by, for example, measuring their respective affinities when each binding site is present on a common scaffold, such as in the form of a single chain antibody. Such a comparison allows a comparison of the affinities of two binding sites while eliminating any interference from other binding sites present on the macromolecule of the present invention.
Binding affinity may be quantified by determining the dissociation constant (Kd) for a polypeptide and its binder. A lower Kd is indicative of a higher affinity for a binding partner. Similarly, the specificity of binding of a polypeptide to its binding partner may be defined in terms of the comparative dissociation constants (Kd) of the polypeptide for its binding partner as compared to the dissociation constant with respect to the polypeptide and another, non-target molecule.
The value of this dissociation constant can be determined by known methods. For example, the Kd may be established using a double-filter nitrocellulose filter binding assay such as that disclosed by Wong & Lohman (Proc. Natl. Acad. Sci. USA 90, 5428-5432, 1993). Other standard assays to evaluate the binding ability of ligands such as antibodies towards targets are known in the art, including for example, ELISAs, Western blots, RIAs, and flow cytometry analysis. The binding kinetics (e.g., binding affinity) of the antibody also can be assessed by standard assays known in the art, such as by Biacore™ system analysis.
As an alternative to Kd, EC50 or IC50 may be used to determine relative affinities. In this context EC50 indicates the concentration at which a polypeptide achieves 50% of its maximum binding to a fixed quantity of binding partner. IC50 indicates the concentration at which a polypeptide inhibits 50% of the maximum binding of a fixed quantity of competitor to a fixed quantity of binding partner. In both cases, a lower level of EC50 or IC50 indicates a higher affinity for a target. The EC50 and IC50 values of an ANDbody binding site for its binding partner can both be determined by well-known methods, for example ELISA.
In some embodiments the Kd of therapeutic effector target binder might be higher than about 1 pM, about 10 pM, about 100 pM, about 1 nM, about 10 nM, about 100 nM, about 500 nM, or about 1 uM (e.g., may be between 1 pM and 10 pM, between 10 pM and 100 pM, between 100 pM and 1 nM, between 1 nM and 10 nM, between 10 nM and 100 nM, between 100 nM and 500 nM, or between 500 nM and 1 uM). In some embodiments the Kd of the address target binder might be less than about 1 uM, about 500 nM, about 100 nM, about 10 nM, about 1 nM, about 100 pM, about 10 pM, or about 1 pM (e.g., may be between 1 uM and 500 nM, between 500 nM and 100 nM, between 100 nM and 10 nM, between 10 nM and 1 nM, between 1 nM and 100 pM, between 100 pM and 10 pM, or between 10 pM and 1 pM). In some embodiments, the Kd for the therapeutic effector target binder may be about 6-fold, about 5-fold, about 4-fold, about 3-fold, or about 2-fold higher than the Kd for the address target binder.
In some embodiments the EC50 of therapeutic effector target binder might be higher than about 1 pM, about 10 pM, about 100 pM, about 1 nM, about 10 nM, about 100 nM, about 500 nM, or about 1 uM (e.g., may be between 1 pM and 10 pM, between 10 pM and 100 pM, between 100 pM and 1 nM, between 1 nM and 10 nM, between 10 nM and 100 nM, between 100 nM and 500 nM, or between 500 nM and 1 uM). In some embodiments the EC50 of the address target binder might be less than about 1 uM, about 500 nM, about 100 nM, about 10 nM, about 1 nM, about 100 pM, about 10 pM, or about 1 pM (e.g., may be between 1 uM and 500 nM, between 500 nM and 100 nM, between 100 nM and 10 nM, between 10 nM and 1 nM, between 1 nM and 100 pM, between 100 pM and 10 pM, or between 10 pM and 1 pM). In some embodiments, the EC50 for the therapeutic effector target binder may be about 6-fold, about 5-fold, about 4-fold, about 3-fold, or about 2-fold higher than the EC50 for the address target binder.
In some embodiments the IC50 of therapeutic effector target binder might be higher than about 1 pM, about 10 pM, about 100 pM, about 1 nM, about 10 nM, about 100 nM, about 500 nM, or about 1 uM (e.g., may be between 1 pM and 10 pM, between 10 pM and 100 pM, between 100 pM and 1 nM, between 1 nM and 10 nM, between 10 nM and 100 nM, between 100 nM and 500 nM, or between 500 nM and 1 uM). In some embodiments the IC50 of the address target binder might be less than about 1 uM, about 500 nM, about 100 nM, about 10 nM, about 1 nM, about 100 pM, about 10 pM, or about 1 pM (e.g., may be between 1 uM and 500 nM, between 500 nM and 100 nM, between 100 nM and 10 nM, between 10 nM and 1 nM, between 1 nM and 100 pM, between 100 pM and 10 pM, or between 10 pM and 1 pM). In some embodiments, the IC50 for the therapeutic effector target binder may be about 6-fold, about 5-fold, about 4-fold, about 3-fold, or about 2-fold higher than the IC50 for the address target binder.
The cellular or tissue density of the effector target and address target bound by an ANDbody may differ. In embodiments, the density of the therapeutic effector target on a cell bound by the effector target binding site of an ANDbody is more than about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 10-fold, about 15-fold, about 20-fold, about 50-fold, about 100-fold, about 200-fold, about 500-fold, about 1000-fold, about 10,000-fold, about 100,000-fold less than the density of the address target on a cell bound by the address target binding site.
In some embodiments, the affinity of the first binding site to the therapeutic effector target it binds is about one-half (½)×Kd less than the affinity of the second binding site to the address target it binds and the density of the therapeutic effector target on a cell bound by the first binding site is about one-half (½)×Kd less than the density of the address target on a cell bound by the second binding site.
In some embodiments, the ANDbody has both the affinity and density parameters as described hereinabove.
In some embodiments the first binding site and second binding site in the ANDbody are directly joined to each other. By directly joined is meant that the first binding site coding sequences abut the second binding site coding sequences and no sequences derived from other sequences (such as linkers) are present. In some embodiments the first binding site and second binding site in the ANDbody are not directly joined to each other.
An ANDbody, as disclosed herein, can be linked to an additional moiety or moieties, e.g., an extracellular component, an intracellular component, a soluble factor (e.g., an enzyme, hormone, cytokine, growth factor, toxin, venom, pollutant, etc.), or a transmembrane protein (e.g., a cell surface receptor).
Exemplary effector target and address target sequences for which ANDbodies of the present technology may have affinity are provided in Table 3 and in the Sequence Listing. In some instances, the sequences comprise full-length protein sequences and/or Fc fusion sequences with or without the signal peptide regions. In some embodiments, ANDbodies of the present technology include binding domains that bind address target or effector target proteins. In embodiments, binding domains of the present ANDbodies may bind protein sequences that include a signal peptide. In other embodiments, binding domains of the present ANDbodies may bind proteins that lack a signal protein. In some embodiments, binding domains of the present ANDbodies may bind full-length proteins. In other embodiments, binding domains of the present ANDbodies may bind protein fusions, such as full-length protein sequences, or peptide fragments thereof, with or without signal peptide regions, fused to other proteins, such as, for example, Fc sequences. In other embodiments, binding domains of the present ANDbodies may bind proteins that comprise less than the full-length protein sequence, such as a peptide fragment of the address target or effector target.
Production of ANDbody polypeptides
ANDbody polypeptides of the invention may be produced by any suitable means. For example, all or part of the ANDbody may be expressed by a host cell comprising a nucleotide which encodes the ANDbody. Such methods of making a therapeutic polypeptide are routine in the art. See, in general, Smales & James (Eds.), Therapeutic Proteins: Methods and Protocols (Methods in Molecular Biology), Humana Press (2005); and Crommelin, Sindelar & Meibohm (Eds.), Pharmaceutical Biotechnology: Fundamentals and Applications, Springer (2013).
Methods for producing an ANDbody may involve expression in mammalian cells, although recombinant proteins can also be produced using insect cells, yeast, bacteria, or other cells under the control of appropriate promoters. Mammalian expression vectors may comprise nontranscribed elements such as an origin of replication, a suitable promoter and enhancer, and other 5′ or 3′ flanking nontranscribed sequences, and 5′ or 3′ nontranslated sequences such as necessary ribosome binding sites, a polyadenylation site, splice donor and acceptor sites, and termination sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, enhancer, splice, and polyadenylation sites may be used to provide the other genetic elements required for expression of a heterologous DNA sequence. Appropriate cloning and expression vectors for use with bacterial, fungal, yeast, and mammalian cellular hosts are described in Green & Sambrook, Molecular Cloning: A Laboratory Manual (Fourth Edition), Cold Spring Harbor Laboratory Press (2012).
Various mammalian cell culture systems can be employed to express and manufacture an ANDbody described herein. Examples of mammalian expression systems include CHO cells, COS cells, HeLA and BHK cell lines. Processes of host cell culture for production of protein therapeutics are described in, e.g., Zhou and Kantardjieff (Eds.), Mammalian Cell Cultures for Biologics Manufacturing (Advances in Biochemical Engineering/Biotechnology), Springer (2014). Purification of protein therapeutics is described in Franks, Protein Biotechnology: Isolation, Characterization, and Stabilization, Humana Press (2013); and in Cutler, Protein Purification Protocols (Methods in Molecular Biology), Humana Press (2010). Formulation of protein therapeutics is described in Meyer (Ed.), Therapeutic Protein Drug Products: Practical Approaches to formulation in the Laboratory, Manufacturing, and the Clinic, Woodhead Publishing Series (2012).
Antibody production techniques are known. See, for example, Zhiqiang (Editor), Therapeutic Monoclonal Antibodies: From Bench to Clinic. 1st Edition. Wiley 2009; Greenfield (Ed.) Antibodies: A Laboratory Manual. (Second edition) Cold Spring Harbor Laboratory Press 2013; Ferrara et al. 2012. Using Phage and Yeast Display to Select Hundreds of Monoclonal Antibodies: Application to Antigen 85, a Tuberculosis Biomarker. PLoS ONE 7(11): e49535, for methods of making recombinant antibodies, including antibody engineering, use of degenerate oligonucleotides, 5′-RACE, phage display, and mutagenesis; antibody testing and characterization; antibody pharmacokinetics and pharmacodynamics; antibody purification and storage; and screening and labeling techniques.
Production of ANDbody RNAs
In some embodiments, ANDbodies RNAs may be produced, e.g., for delivery to a subject. Generally, therapeutic mRNAs are made by in vitro transcription. Modification such as incorporation of modified bases, 5′cap analogues, and polyA tails can optimize activity and function. For example, translation and stability of mRNA can be accomplished, by cap and poly A tail modifications. E.g., incorporation of cap analogs such as ARCA (anti-reverse cap analogs) and a poly(A) tail of 100-200 bp into in vitro transcribed (IVT) mRNAs improves expression and stability (Kaczmarek et al. Genome Medicine (2017) 9:60). New types of cap analogs, such as 1,2-dithiodiphosphate-modified caps, can further improve efficiency of translation (Strenkowska et al. Nucleic Acids Res. 2016; 44:9578-90). Codon optimization can also improve efficacy of protein synthesis and limit mRNA destabilization by rare codons (Presnyak et al. Cell. 2015; 160:1111-24.93; Thess et al. Mol Ther. 2015; 23: 1456-64). Modifying 3′ and 5′ untranslated regions (UTRs), which contain sequences responsible for recruiting RNA-binding proteins (RBPs) and miRNAs, can enhance the level of protein product (Kaczmarek). Further, UTRs can be modified to encode regulatory elements (e.g., K-turn motifs and miRNA binding sites), in order to control RNA expression in a cell-specific manner (Wroblewska et al. Nat Biotechnol. 2015; 33:839-41). RNA base modifications (e.g., pseudouridine incorporated mRNA, e.g., N1-methyl-pseudouridine) contribute to masking mRNA immune-stimulatory activity and increase mRNA translation by enhancing translation initiation (Andries et al. J Control Release. 2015; 217:337-44; Svitkin et al. Nucleic Acids Res. 2017; 45:6023-36). mRNA compositions and methods of their manufacture are known and are disclosed, e.g., in WO2016011306; WO2016014846; WO2016022914; WO2016077123; WO2016164762; WO2016201377; WO2017049275; U.S. Pat. Nos. 9,937,233; 8,710,200; U.S. Ser. No. 10/022,425; U.S. Pat. Nos. 9,878,056; 9,572,897; Jemielity et al. RNA. 2003; 9:1108-22. 90; Mockey et al. Biochem Biophys Res Commun. 2006; 340:1062-8. 91; Strenkowska et al. Nucleic Acids Res. 2016; 44:9578-90. 92; Presnyak et al. Cell. 2015; 160:1111-24. 93; Kaczmarek et al. Genome Medicine (2017) 9:60.
Production Of ANDbodies With Altered Affinities
ANDbodies with binding sites with altered affinities can be made using methods known in the art, e.g., an ANDbody can be engineered to have a target binding site that has decreased affinity for the effector target. See, e.g., U.S. Pat. No. 10,654,928. In general, an ANDBody may be modified to alter the affinity of an effector target binding site to its effector target or to alter the affinity of an address target binding site to its address target. The modification can increase or decrease affinity for the binding site's binding partner.
Expression of a therapeutic target can be assessed at either the RNA or protein level using methods known in the art. In embodiments, expression of the therapeutic target is assessed by measuring RNA expression, e.g., using an RNA sequence dataset as a proxy for protein expression levels. RNA datasets include those a genotype-Tissue Expression (GTEx) dataset (see, e.g., https://www.genome.gov/Funded-Programs-Projects/Genotype-Tissue-Expression-Project) or a Human Protein Atlas (HPA) dataset (https://www.proteinatlas.org/).
A non-limiting list of tissues in which expression of the therapeutic target can be assessed includes, e.g., the minor salivary gland, thyroid, lung, breast (mammary tissue), pancreas, adrenal gland, liver, kidney (cortex), kidney (medulla), adipose-viscaral (omentum), small intestine—terminal ileum, fallopian tube, ovary, uterus, skin not sun exposed (suprapubic); cervix—endocervix, cervix-ectocervix, vagina, skin sun exposed (lower leg), cells eneanterior cingulate cortex (BA24), caudate (basal ganglia), putamen (basal ganglia), nucleus acumbens (basal ganglia), hypothalamus, amygdala, hippocampus, cerebellum/cerebellar hemisphere, substantia nigra, pituitary, spinal cord (cervical), artery-aorta, heart-atrial appendage, artery-coronary-heart, left ventricle, esophagus-mucosa, esophagus-muscularis, esophagus-gastroesophageal junction, spleen, stomach, colon-transverse, colon—sigmoid, testis, whole blood, cells—(EBV-transformed lymphocytes, artery-tibial, or nerve-tibial tissues.
Address markers can be assessed using methods well known in the art, e.g., gene expression can be assessed at the mRNA level using Northern blots, cDNA or oligonucleotide microarrays, or sequencing (e.g., RNA-Seq), or at the level of protein expression using protein microarrays, Western blots, flow cytometry, immunohistochemistry, etc. Modifications can be assessed, e.g., using antibodies that are specific for a particular modified form of a protein, e.g., phospho-specific antibodies, or mass spectrometry.
ANDbodies and their pharmaceutical compositions provided herein are suitable for administration to a subject in need thereof, wherein the subject is a human or a non-human animal, for example, suitable for human therapeutic or veterinary use.
Veterinary use includes use for treatment of mammals, including commercially relevant mammals, e.g., pet and live-stock animals, such as cattle, pigs, horses, sheep, goats, cats, dogs, mice, and/or rats; and/or birds, including commercially relevant birds such as parrots, poultry, chickens, ducks, geese, hens or roosters and/or turkeys; zoo animals, e.g., a feline; non-mammal animals, e.g., reptiles, fish, amphibians, etc.
The invention is further directed to a subject or subject cell comprising the ANDbody composition described herein. In some embodiments, the subject or subject cell is a plant, insect, bacteria, fungus, vertebrate, mammal (e.g., human), or other organism or cell.
In some embodiments, a subject or a subject cell is contacted with (e.g., delivered to or administered to) the ANDbody composition. In some embodiments, the subject is a mammal, such as a human. The amount of the ANDbody composition, expression product, or both in the subject can be measured at any time after administration.
Polypeptide Pharmaceutical Compositions
The ANDbody compositions described herein (e.g., ANDbody polypeptide or RNA compositions) may be administered to a subject in need thereof. The invention includes pharmaceutical compositions that include an ANDbody composition in combination with one or more pharmaceutically acceptable excipients.
Formulation of protein therapeutics is routine. See, for example, Ribeiro et al., Insights on the Formulation of Recombinant Proteins. Adv Biochem Eng Biotechnol. 2020; 171:23-54. doi: 10.1007/10_2019_119. PMID: 31844925.
RNA Pharmaceutical Compositions
Nucleic acids (e.g., RNA) encoding an ANDBody can alternatively or additionally be administered to a subject. Generally, therapeutic mRNAs are made by in vitro transcription. Modification such as incorporation of modified bases, 5′cap analogues, and polyA tails can optimize activity and function. For example, translation and stability of mRNA can be accomplished, by cap and poly A tail modifications. E.g., incorporation of cap analogs such as ARCA (anti-reverse cap analogs) and a poly(A) tail of 100-200 bp into in vitro transcribed (IVT) mRNAs improves expression and stability (Kaczmarek et al. Genome Medicine (2017) 9:60). New types of cap analogs, such as 1,2-dithiodiphosphate-modified caps, can further improve efficiency of translation (Strenkowska et al. Nucleic Acids Res. 2016; 44:9578-90). Codon optimization can also improve efficacy of protein synthesis and limit mRNA destabilization by rare codons (Presnyak et al. Cell. 2015; 160:1111-24. 93; Thess et al. Mol Ther. 2015; 23: 1456-64). Modifying 3′ and 5′ untranslated regions (UTRs), which contain sequences responsible for recruiting RNA-binding proteins (RBPs) and miRNAs, can enhance the level of protein product (Kaczmarek). Further, UTRs can be modified to encode regulatory elements (e.g., K-turn motifs and miRNA binding sites), in order to control RNA expression in a cell-specific manner (Wroblewska et al. Nat Biotechnol. 2015; 33:839-41). RNA base modifications (e.g., pseudouridine incorporated mRNA, e.g., N1-methyl-pseudouridine) contribute to masking mRNA immune-stimulatory activity and increase mRNA translation by enhancing translation initiation (Andries et al. J Control Release. 2015; 217:337-44; Svitkin et al. Nucleic Acids Res. 2017; 45:6023-36). mRNA compositions and methods of their manufacture are known and are disclosed, e.g., in WO2016011306; WO2016014846; WO2016022914; WO2016077123; WO2016164762; WO2016201377; WO2017049275; U.S. Pat. Nos. 9,937,233; 8,710,200; U.S. Ser. No. 10/022,425; U.S. Pat. Nos. 9,878,056; 9,572,897; Jemielity et al. RNA. 2003; 9:1108-22. 90; Mockey et al. Biochem Biophys Res Commun. 2006; 340:1062-8. 91; Strenkowska et al. Nucleic Acids Res. 2016; 44:9578-90. 92; Presnyak et al. Cell. 2015; 160:1111-24. 93; Kaczmarek et al. Genome Medicine (2017) 9:60.
In embodiments, the RNA is a circular RNA. See, for example, WO2019118919, describing the expression of a therapeutic RNA, such as an antibody RNA, from a circular RNA. In some embodiments, the invention includes a circular polyribonucleotide that comprises (a) an internal ribosome entry site (IRES), (b) an expression sequence encoding a ANDbody described herein and lacking a poly-A sequence, and (c) a termination element. A circular RNA encoding an ANDbody described herein may be delivered naked (i.e., without formulation with a carrier) or with a carrier.
Carriers
Lipid Nanoparticles
Formulations of the compositions described herein (e.g., polypeptide or RNA ANDbody compositions) for in vivo delivery with a carrier include lipid nanoparticle (LNP) formulations. See, e.g., U.S. Pat. Nos. 9,764,036; 9,682,139; Kauffman et al. Nano Lett. 2015; 15: 7300-6. 37; Fenton et al. Adv Mater. 2016; 28:2939-43). LNPs, in some embodiments, comprise one or more ionic lipids, such as non-cationic lipids (e.g., neutral or anionic, or zwitterionic lipids); one or more conjugated lipids (such as PEG-conjugated lipids or lipids conjugated to polymers described in Table 5 of WO2019217941; incorporated herein by reference in its entirety); one or more sterols (e.g., cholesterol); and, optionally, one or more targeting molecules (e.g., conjugated receptors, receptor ligands, antibodies); or combinations of the foregoing.
Lipids that can be used in nanoparticle formations (e.g., lipid nanoparticles) include, for example those described in Table 4 of WO2019217941, which is incorporated herein by reference—e.g., a lipid-containing nanoparticle can comprise one or more of the lipids in Table 4 of WO2019217941. Lipid nanoparticles can include additional elements, such as polymers, such as the polymers described in Table 5 of WO2019217941, incorporated by reference.
In some embodiments, conjugated lipids, when present, can include one or more of PEG-diacylglycerol (DAG) (such as Kmonomethoxy-polyethyleneglycol)-2,3-dimyristoylglycerol (PEG-DMG)), PEG-dialkyloxypropyl (DAA), PEG-phospholipid, PEG-ceramide (Cer), a pegylated phosphatidylethanoloamine (PEG-PE), PEG succinate diacylglycerol (PEGS-DAG) (such as 4-0-(2′,3′-di(tetradecanoyloxy)propyl-I-0-(w-methoxy(polyethoxy)ethyl) butanedioate (PEG-S-DMG)), PEG dialkoxypropylcarbam, N-(carbonyl-methoxypoly ethylene glycol 2000)-1,2-distearoyl-sn-glycero phosphoethanolamine sodium salt, and those described in Table 2 of WO2019051289 (incorporated by reference), and combinations of the foregoing.
In some embodiments, sterols that can be incorporated into lipid nanoparticles include one or more of cholesterol or cholesterol derivatives, such as those in WO2009/127060 or US2010/0130588, which are incorporated by reference. Additional exemplary sterols include phytosterols, including those described in Eygeris et al (2020), dx.doi.org/10.1021/acs.nanolett.0c01386, incorporated herein by reference.
In some embodiments, the lipid particle comprises an ionizable lipid, a non-cationic lipid, a conjugated lipid that inhibits aggregation of particles, and a sterol. The amounts of these components can be varied independently and to achieve desired properties. For example, in some embodiments, the lipid nanoparticle comprises an ionizable lipid is in an amount from about 20 mol % to about 90 mol % of the total lipids (in other embodiments it may be 20-70% (mol), 30-60% (mol) or 40-50% (mol); about 50 mol % to about 90 mol % of the total lipid present in the lipid nanoparticle), a non-cationic lipid in an amount from about 5 mol % to about 30 mol % of the total lipids, a conjugated lipid in an amount from about 0.5 mol % to about 20 mol % of the total lipids, and a sterol in an amount from about 20 mol % to about 50 mol % of the total lipids. The ratio of total lipid to nucleic acid can be varied as desired. For example, the total lipid to nucleic acid (mass or weight) ratio can be from about 10:1 to about 30:1.
In some embodiments, the lipid to nucleic acid ratio (mass/mass ratio; w/w ratio) can be in the range of from about 1:1 to about 25:1, from about 10:1 to about 14:1, from about 3:1 to about 15:1, from about 4:1 to about 10:1, from about 5:1 to about 9:1, or about 6:1 to about 9:1. The amounts of lipids and nucleic acid can be adjusted to provide a desired N/P ratio, for example, N/P ratio of 3, 4, 5, 6, 7, 8, 9, 10 or higher. Generally, the lipid nanoparticle formulation's overall lipid content can range from about 5 mg/ml to about 30 mg/mL.
Some non-limiting example of lipid compounds that may be used (e.g., in combination with other lipid components) to form lipid nanoparticles for the delivery of compositions described herein, e.g., nucleic acid (e.g., RNA) described herein includes,
In some embodiments an LNP comprising Formula (i) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
In some embodiments an LNP comprising Formula (ii) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
In some embodiments an LNP comprising Formula (iii) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
In some embodiments an LNP comprising Formula (v) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
In some embodiments an LNP comprising Formula (vi) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
In some embodiments an LNP comprising Formula (viii) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
In some embodiments an LNP comprising Formula (ix) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
wherein
X1 is O, NR1, or a direct bond, X2 is C2-5 alkylene, X3 is C(═O) or a direct bond, R1 is H or Me, R3 is C1-3 alkyl, R2 is C1-3 alkyl, or R2 taken together with the nitrogen atom to which it is attached and 1-3 carbon atoms of X2 form a 4-, 5-, or 6-membered ring, or X1 is NR1, R1 and R2 taken together with the nitrogen atoms to which they are attached form a 5- or 6-membered ring, or R2 taken together with R3 and the nitrogen atom to which they are attached form a 5-, 6-, or 7-membered ring, Y1 is C2-12 alkylene, Y2 is selected from
(in either orientation),
(in either orientation),
(in either orientation),
n is 0 to 3, R4 is Ci-15 alkyl, Z1 is Ci-6 alkylene or a direct bond,
Z2 is
(in either orientation) or absent, provided that if Z1 is a direct bond, Z2 is absent;
R5 is C5-9 alkyl or C6-10 alkoxy, R6 is C5-9 alkyl or C6-10 alkoxy, W is methylene or a direct bond, and R7 is H or Me, or a salt thereof, provided that if R3 and R2 are C2 alkyls, X1 is O, X2 is linear C3 alkylene, X3 is C(═O), Y1 is linear Ce alkylene, (Y2)n-R4 is
R4 is linear C5 alkyl, Z1 is C2 alkylene, Z2 is absent, W is methylene, and R7 is H, then R5 and R6 are not Cx alkoxy.
In some embodiments an LNP comprising Formula (xii) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
In some embodiments an LNP comprising Formula (xi) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
In some embodiments an LNP comprises a compound of Formula (xiii) and a compound of Formula (xiv).
In some embodiments an LNP comprising Formula (xv) is used to deliver an ANDbody RNA composition described herein to the liver and/or hepatocyte cells.
In some embodiments an LNP comprising a formulation of Formula (xvi) is used to deliver an ANDbody RNA composition described herein to the lung endothelial cells.
In some embodiments, a lipid compound used to form lipid nanoparticles for the delivery of compositions described herein, e.g., nucleic acid (e.g., RNA) described herein is made by one of the following reactions:
In some embodiments, a composition described herein (e.g., a nucleic acid or a protein) is provided in an LNP that comprises an ionizable lipid. In some embodiments, the ionizable lipid is heptadecan-9-yl 8-((2-hydroxyethyl)(6-oxo-6-(undecyloxy)hexyl)amino)octanoate (SM-102); e.g., as described in Example 1 of U.S. Pat. No. 9,867,888 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is 9Z,12Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl)oxy)methyl)propyl octadeca-9,12-dienoate (LP01), e.g., as synthesized in Example 13 of WO2015/095340 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is Di((Z)-non-2-en-1-yl) 9-((4-dimethylamino)butanoyl)oxy)heptadecanedioate (L319), e.g. as synthesized in Example 7, 8, or 9 of US2012/0027803 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is 1,1′-((2-(4-(2-((2-(Bis(2-hydroxydodecyl)amino)ethyl)(2-hydroxydodecyl) amino)ethyl)piperazin-1-yl)ethyl)azanediyl)bis(dodecan-2-ol) (C12-200), e.g., as synthesized in Examples 14 and 16 of WO2010/053572 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is Imidazole cholesterol ester (ICE) lipid (3S, 10R, 13R, 17R)-10, 13-dimethyl-17-((R)-6-methylheptan-2-yl)-2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-yl 3-(1H-imidazol-4-yl)propanoate, e.g., Structure (I) from WO2020/106946 (incorporated by reference herein in its entirety).
In some embodiments, an ionizable lipid may be a cationic lipid, an ionizable cationic lipid, e.g., a cationic lipid that can exist in a positively charged or neutral form depending on pH, or an amine-containing lipid that can be readily protonated. In some embodiments, the cationic lipid is a lipid capable of being positively charged, e.g., under physiological conditions. Exemplary cationic lipids include one or more amine group(s) which bear the positive charge. In some embodiments, the lipid particle comprises a cationic lipid in formulation with one or more of neutral lipids, ionizable amine-containing lipids, biodegradable alkyne lipids, steroids, phospholipids including polyunsaturated lipids, structural lipids (e.g., sterols), PEG, cholesterol and polymer conjugated lipids. In some embodiments, the cationic lipid may be an ionizable cationic lipid. An exemplary cationic lipid as disclosed herein may have an effective pKa over 6.0. In embodiments, a lipid nanoparticle may comprise a second cationic lipid having a different effective pKa (e.g., greater than the first effective pKa), than the first cationic lipid. A lipid nanoparticle may comprise between 40 and 60 mol percent of a cationic lipid, a neutral lipid, a steroid, a polymer conjugated lipid, and a therapeutic agent, e.g., a nucleic acid (e.g., RNA) described herein, encapsulated within or associated with the lipid nanoparticle. In some embodiments, the nucleic acid is co-formulated with the cationic lipid. The nucleic acid may be adsorbed to the surface of an LNP, e.g., an LNP comprising a cationic lipid. In some embodiments, the nucleic acid may be encapsulated in an LNP, e.g., an LNP comprising a cationic lipid. In some embodiments, the lipid nanoparticle may comprise a targeting moiety, e.g., coated with a targeting agent. In embodiments, the LNP formulation is biodegradable. In some embodiments, a lipid nanoparticle comprising one or more lipid described herein, e.g., Formula (i), (ii), (ii), (vii) and/or (ix) encapsulates at least 1%, at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 92%, at least 95%, at least 97%, at least 98% or 100% of an RNA molecule.
Exemplary ionizable lipids that can be used in lipid nanoparticle formulations include, without limitation, those listed in Table 1 of WO2019051289, incorporated herein by reference. Additional exemplary lipids include, without limitation, one or more of the following formulae: X of US2016/0311759; I of US20150376115 or in US2016/0376224; I, II or III of US20160151284; I, IA, II, or IIA of US20170210967; I-c of US20150140070; A of US2013/0178541; I of US2013/0303587 or US2013/0123338; I of US2015/0141678; II, III, IV, or V of US2015/0239926; I of US2017/0119904; I or II of WO2017/117528; A of US2012/0149894; A of US2015/0057373; A of WO2013/116126; A of US2013/0090372; A of US2013/0274523; A of US2013/0274504; A of US2013/0053572; A of WO2013/016058; A of WO2012/162210; I of US2008/042973; I, II, III, or IV of US2012/01287670; I or II of US2014/0200257; I, II, or III of US2015/0203446; I or III of US2015/0005363; I, IA, IB, IC, ID, II, IIA, IIB, IIC, IID, or III-XXIV of US2014/0308304; of US2013/0338210; I, II, III, or IV of WO2009/132131; A of US2012/01011478; I or XXXV of US2012/0027796; XIV or XVII of US2012/0058144; of US2013/0323269; I of US2011/0117125; I, II, or III of US2011/0256175; I, II, III, IV, V, VI, VII, VIII, IX, X, XI, XII of US2012/0202871; I, II, III, IV, V, VI, VII, VIII, X, XII, XIII, XIV, XV, or XVI of US2011/0076335; I or II of US2006/008378; I of US2013/0123338; I or X-A-Y-Z of US2015/0064242; XVI, XVII, or XVIII of US2013/0022649; I, II, or III of US2013/0116307; I, II, or III of US2013/0116307; I or II of US2010/0062967; I-X of US2013/0189351; I of US2014/0039032; V of US2018/0028664; I of US2016/0317458; I of US2013/0195920; 5, 6, or 10 of U.S. Pat. No. 10,221,127; 111-3 of WO2018/081480;I-5 or I-8 of WO2020/081938; 18 or 25 of U.S. Pat. No. 9,867,888; A of US2019/0136231; II of WO2020/219876; 1 of US2012/0027803; OF-02 of US2019/0240349; 23 of U.S. Pat. No. 10,086,013; cKK-E12/A6 of Miao et al (2020); C12-200 of WO2010/053572; 7C1 of Dahlman et al (2017); 304-013 or 503-013 of Whitehead et al; TS-P4C2 of U.S. Pat. No. 9,708,628; I of WO2020/106946; I of WO2020/106946.
In some embodiments, the ionizable lipid is MC3 (6Z,9Z,28Z,3 IZ)-heptatriaconta-6,9,28,3 I-tetraen-19-yl-4-(dimethylamino) butanoate (DLin-MC3-DMA or MC3), e.g., as described in Example 9 of WO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is the lipid ATX-002, e.g., as described in Example 10 of WO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is (13Z,16Z)-A,A-dimethyl-3-nonyldocosa-13, 16-dien-1-amine (Compound 32), e.g., as described in Example 11 of WO2019051289A9 (incorporated by reference herein in its entirety). In some embodiments, the ionizable lipid is Compound 6 or Compound 22, e.g., as described in Example 12 of WO2019051289A9 (incorporated by reference herein in its entirety).
Exemplary non-cationic lipids include, but are not limited to, distearoyl-sn-glycero-phosphoethanolamine, distearoylphosphatidylcholine (DSPC), dioleoylphosphatidylcholine (DOPC), dipalmitoylphosphatidylcholine (DPPC), dioleoylphosphatidylglycerol (DOPG), dipalmitoylphosphatidylglycerol (DPPG), dioleoyl-phosphatidylethanolamine (DOPE), palmitoyloleoylphosphatidylcholine (POPC), palmitoyloleoylphosphatidylethanolamine (POPE), dioleoyl-phosphatidylethanolamine 4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (DOPE-mal), dipalmitoyl phosphatidyl ethanolamine (DPPE), dimyristoylphosphoethanolamine (DMPE), distearoyl-phosphatidyl-ethanolamine (DSPE), monomethyl-phosphatidylethanolamine (such as 16-O-monomethyl PE), dimethyl-phosphatidylethanolamine (such as 16-O-dimethyl PE), I8-I-trans PE, I-stearoyl-2-oleoyl-phosphatidyethanolamine (SOPE), hydrogenated soy phosphatidylcholine (HSPC), egg phosphatidylcholine (EPC), dioleoylphosphatidylserine (DOPS), sphingomyelin (SM), dimyristoyl phosphatidylcholine (DMPC), dimyristoyl phosphatidylglycerol (DMPG), distearoylphosphatidylglycerol (DSPG), dierucoylphosphatidylcholine (DEPC), palmitoyloleyolphosphatidylglycerol (POPG), dielaidoyl-phosphatidylethanolamine (DEPE), lecithin, phosphatidylethanolamine, lysolecithin, lysophosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, egg sphingomyelin (ESM), cephalin, cardiolipin, phosphatidicacid,cerebrosides, dicetylphosphate, lysophosphatidylcholine, dilinoleoylphosphatidylcholine, or mixtures thereof. It is understood that other diacylphosphatidylcholine and diacylphosphatidylethanolamine phospholipids can also be used. The acyl groups in these lipids are preferably acyl groups derived from fatty acids having C10-C24 carbon chains, e.g., lauroyl, myristoyl, paimitoyl, stearoyl, or oleoyl. Additional exemplary lipids, in certain embodiments, include, without limitation, those described in Kim et al. (2020) dx.doi.org/10.1021/acs.nanolett.0c01386, incorporated herein by reference. Such lipids include, in some embodiments, plant lipids found to improve liver transfection with mRNA (e.g., DGTS).
Other examples of non-cationic lipids suitable for use in the lipid nanoparticles include, without limitation, nonphosphorous lipids such as, e.g., stearylamine, dodeeylamine, hexadecylamine, acetyl palmitate, glycerol ricinoleate, hexadecyl stereate, isopropyl myristate, amphoteric acrylic polymers, triethanolamine-lauryl sulfate, alkyl-aryl sulfate polyethyloxylated fatty acid amides, dioctadecyl dimethyl ammonium bromide, ceramide, sphingomyelin, and the like. Other non-cationic lipids are described in WO2017/099823 or US patent publication US2018/0028664, the contents of which is incorporated herein by reference in their entirety.
In some embodiments, the non-cationic lipid is oleic acid or a compound of Formula I, II, or IV of US2018/0028664, incorporated herein by reference in its entirety. The non-cationic lipid can comprise, for example, 0-30% (mol) of the total lipid present in the lipid nanoparticle. In some embodiments, the non-cationic lipid content is 5-20% (mol) or 10-15% (mol) of the total lipid present in the lipid nanoparticle. In embodiments, the molar ratio of ionizable lipid to the neutral lipid ranges from about 2:1 to about 8:1 (e.g., about 2:1, 3:1, 4:1, 5:1, 6:1, 7:1, or 8:1).
In some embodiments, the lipid nanoparticles do not comprise any phospholipids.
In some aspects, the lipid nanoparticle can further comprise a component, such as a sterol, to provide membrane integrity. One exemplary sterol that can be used in the lipid nanoparticle is cholesterol and derivatives thereof. Non-limiting examples of cholesterol derivatives include polar analogues such as 5a-choiestanol, 53-coprostanol, choiesteryl-(2,-hydroxy)-ethyl ether, choiesteryl-(4″-hydroxy)-butyl ether, and 6-ketocholestanol; non-polar analogues such as 5a-cholestane, cholestenone, 5a-cholestanone, 5p-cholestanone, and cholesteryl decanoate; and mixtures thereof. In some embodiments, the cholesterol derivative is a polar analogue, e.g., choiesteryl-(4′-hydroxy)-butyl ether. Exemplary cholesterol derivatives are described in PCT publication WO2009/127060 and US patent publication US2010/0130588, each of which is incorporated herein by reference in its entirety.
In some embodiments, the component providing membrane integrity, such as a sterol, can comprise 0-50% (mol) (e.g., 0-10%, 10-20%, 20-30%, 30-40%, or 40-50%) of the total lipid present in the lipid nanoparticle. In some embodiments, such a component is 20-50% (mol) 30-40% (mol) of the total lipid content of the lipid nanoparticle.
In some embodiments, the lipid nanoparticle can comprise a polyethylene glycol (PEG) or a conjugated lipid molecule. Generally, these are used to inhibit aggregation of lipid nanoparticles and/or provide steric stabilization. Exemplary conjugated lipids include, but are not limited to, PEG-lipid conjugates, polyoxazoline (POZ)-lipid conjugates, polyamide-lipid conjugates (such as ATTA-lipid conjugates), cationic-polymer lipid (CPL) conjugates, and mixtures thereof. In some embodiments, the conjugated lipid molecule is a PEG-lipid conjugate, for example, a (methoxy polyethylene glycol)-conjugated lipid.
Exemplary PEG-lipid conjugates include, but are not limited to, PEG-diacylglycerol (DAG) (such as I-(monomethoxy-polyethyleneglycol)-2,3-dimyristoylglycerol (PEG-DMG)), PEG-dialkyloxypropyl (DAA), PEG-phospholipid, PEG-ceramide (Cer), a pegylated phosphatidylethanoloamine (PEG-PE), PEG succinate diacylglycerol (PEGS-DAG) (such as 4-0-(2′,3′-di(tetradecanoyloxy)propyl-1-0-(w-methoxy(polyethoxy)ethyl) butanedioate (PEG-S-DMG)), PEG dialkoxypropylcarbam, N-(carbonyl-methoxypolyethylene glycol 2000)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine sodium salt, or a mixture thereof. Additional exemplary PEG-lipid conjugates are described, for example, in U.S. Pat. No. 5,885,6I3, U.S. Pat. No. 6,287,59I,
US2003/0077829, US2003/0077829, US2005/0175682, US2008/0020058, US2011/0117125, US2010/0130588, US2016/0376224, US2017/0119904, and US/099823, the contents of all of which are incorporated herein by reference in their entirety. In some embodiments, a PEG-lipid is a compound of Formula III, III-a-2, III-b-1, III-b-2, or V of US2018/0028664, the content of which is incorporated herein by reference in its entirety. In some embodiments, a PEG-lipid is of Formula II of US20150376115 or US2016/0376224, the content of both of which is incorporated herein by reference in its entirety. In some embodiments, the PEG-DAA conjugate can be, for example, PEG-dilauryloxypropyl, PEG-dimyristyloxypropyl, PEG-dipalmityloxypropyl, or PEG-distearyloxypropyl. The PEG-lipid can be one or more of PEG-DMG, PEG-dilaurylglycerol, PEG-dipalmitoylglycerol, PEG-disterylglycerol, PEG-dilaurylglycamide, PEG-dimyristylglycamide, PEG-dipalmitoylglycamide, PEG-disterylglycamide, PEG-cholesterol (I-[8′-(Cholest-5-en-3[beta]-oxy)carboxamido-3′,6′-dioxaoctanyl] carbamoyl-[omega]-methyl-poly(ethylene glycol), PEG-DMB (3,4-Ditetradecoxylbenzyl-[omega]-methyl-poly(ethylene glycol) ether), and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000]. In some embodiments, the PEG-lipid comprises PEG-DMG, 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000]. In some embodiments, the PEG-lipid comprises a structure selected from:
In some embodiments, lipids conjugated with a molecule other than a PEG can also be used in place of PEG-lipid. For example, polyoxazoline (POZ)-lipid conjugates, polyamide-lipid conjugates (such as ATTA-lipid conjugates), and cationic-polymer lipid (GPL) conjugates can be used in place of or in addition to the PEG-lipid.
Exemplary conjugated lipids, i.e., PEG-lipids, (POZ)-lipid conjugates, ATTA-lipid conjugates and cationic polymer-lipids are described in the PCT and LIS patent applications listed in Table 2 of WO2019051289A9, the contents of all of which are incorporated herein by reference in their entirety.
In some embodiments, the PEG or the conjugated lipid can comprise 0-20% (mol) of the total lipid present in the lipid nanoparticle. In some embodiments, PEG or the conjugated lipid content is 0.5-10% or 2-5% (mol) of the total lipid present in the lipid nanoparticle. Molar ratios of the ionizable lipid, non-cationic-lipid, sterol, and PEG/conjugated lipid can be varied as needed. For example, the lipid particle can comprise 30-70% ionizable lipid by mole or by total weight of the composition, 0-60% cholesterol by mole or by total weight of the composition, 0-30% non-cationic-lipid by mole or by total weight of the composition and 1-10% conjugated lipid by mole or by total weight of the composition. Preferably, the composition comprises 30-40% ionizable lipid by mole or by total weight of the composition, 40-50% cholesterol by mole or by total weight of the composition, and 10-20% non-cationic-lipid by mole or by total weight of the composition. In some other embodiments, the composition is 50-75% ionizable lipid by mole or by total weight of the composition, 20-40% cholesterol by mole or by total weight of the composition, and 5 to 10% non-cationic-lipid, by mole or by total weight of the composition and 1-10% conjugated lipid by mole or by total weight of the composition. The composition may contain 60-70% ionizable lipid by mole or by total weight of the composition, 25-35% cholesterol by mole or by total weight of the composition, and 5-10% non-cationic-lipid by mole or by total weight of the composition. The composition may also contain up to 90% ionizable lipid by mole or by total weight of the composition and 2 to 15% non-cationic lipid by mole or by total weight of the composition. The formulation may also be a lipid nanoparticle formulation, for example comprising 8-30% ionizable lipid by mole or by total weight of the composition, 5-30% non-cationic lipid by mole or by total weight of the composition, and 0-20% cholesterol by mole or by total weight of the composition; 4-25% ionizable lipid by mole or by total weight of the composition, 4-25% non-cationic lipid by mole or by total weight of the composition, 2 to 25% cholesterol by mole or by total weight of the composition, 10 to 35% conjugate lipid by mole or by total weight of the composition, and 5% cholesterol by mole or by total weight of the composition; or 2-30% ionizable lipid by mole or by total weight of the composition, 2-30% non-cationic lipid by mole or by total weight of the composition, 1 to 15% cholesterol by mole or by total weight of the composition, 2 to 35% conjugate lipid by mole or by total weight of the composition, and 1-20% cholesterol by mole or by total weight of the composition; or even up to 90% ionizable lipid by mole or by total weight of the composition and 2-10% non-cationic lipids by mole or by total weight of the composition, or even 100% cationic lipid by mole or by total weight of the composition. In some embodiments, the lipid particle formulation comprises ionizable lipid, phospholipid, cholesterol and a PEG-ylated lipid in a molar ratio of 50:10:38.5:1.5. In some other embodiments, the lipid particle formulation comprises ionizable lipid, cholesterol and a PEG-ylated lipid in a molar ratio of 60:38.5:1.5.
In some embodiments, the lipid particle comprises ionizable lipid, non-cationic lipid (e.g. phospholipid), a sterol (e.g., cholesterol) and a PEG-ylated lipid, where the molar ratio of lipids ranges from 20 to 70 mole percent for the ionizable lipid, with a target of 40-60, the mole percent of non-cationic lipid ranges from 0 to 30, with a target of 0 to 15, the mole percent of sterol ranges from 20 to 70, with a target of 30 to 50, and the mole percent of PEG-ylated lipid ranges from 1 to 6, with a target of 2 to 5.
In some embodiments, the lipid particle comprises ionizable lipid/non-cationic-lipid/sterol/conjugated lipid at a molar ratio of 50:10:38.5:1.5.
In an aspect, the disclosure provides a lipid nanoparticle formulation comprising phospholipids, lecithin, phosphatidylcholine and phosphatidylethanolamine.
In some embodiments, one or more additional compounds can also be included. Those compounds can be administered separately, or the additional compounds can be included in the lipid nanoparticles of the invention. In other words, the lipid nanoparticles can contain other compounds in addition to the nucleic acid or at least a second nucleic acid, different than the first. Without limitations, other additional compounds can be selected from the group consisting of small or large organic or inorganic molecules, monosaccharides, disaccharides, trisaccharides, oligosaccharides, polysaccharides, peptides, proteins, peptide analogs and derivatives thereof, peptidomimetics, nucleic acids, nucleic acid analogs and derivatives, an extract made from biological materials, or any combinations thereof.
In some embodiments, LNPs are directed to specific tissues by the addition of LNP targeting domains. For example, biological ligands may be displayed on the surface of LNPs to enhance interaction with cells displaying cognate receptors, thus driving association with and cargo delivery to tissues wherein cells express the receptor. In some embodiments, the biological ligand may be a ligand that drives delivery to the liver, e.g., LNPs that display GalNAc result in delivery of nucleic acid cargo to hepatocytes that display asialoglycoprotein receptor (ASGPR). The work of Akinc et al. Mol Ther 18(7):1357-1364 (2010) teaches the conjugation of a trivalent GalNAc ligand to a PEG-lipid (GalNAc-PEG-DSG) to yield LNPs dependent on ASGPR for observable LNP cargo effect (see, e.g.,
In some embodiments, LNPs are selected for tissue-specific activity by the addition of a Selective ORgan Targeting (SORT) molecule to a formulation comprising traditional components, such as ionizable cationic lipids, amphipathic phospholipids, cholesterol and poly(ethylene glycol) (PEG) lipids. The teachings of Cheng et al. Nat Nanotechnol 15(4):313-320 (2020) demonstrate that the addition of a supplemental “SORT” component precisely alters the in vivo RNA delivery profile and mediates tissue-specific (e.g., lungs, liver, spleen) gene delivery and editing as a function of the percentage and biophysical property of the SORT molecule.
In some embodiments, the LNPs comprise biodegradable, ionizable lipids. In some embodiments, the LNPs comprise (9Z,I2Z)-3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl)oxy)methyl)propyl octadeca-9,I2-dienoate, also called 3-((4,4-bis(octyloxy)butanoyl)oxy)-2-((((3-(diethylamino)propoxy)carbonyl)oxy)methyl)propyl (9Z,12Z)-octadeca-9,12-dienoate) or another ionizable lipid. See, e.g, lipids of WO2019/067992, WO/2017/173054, WO2015/095340, and WO2014/136086, as well as references provided therein. In some embodiments, the term cationic and ionizable in the context of LNP lipids is interchangeable, e.g., wherein ionizable lipids are cationic depending on the pH.
In some embodiments, the average LNP diameter of the LNP formulation may be between 10s of nm and 100s of nm, e.g., measured by dynamic light scattering (DLS). In some embodiments, the average LNP diameter of the LNP formulation may be from about 40 nm to about 150 nm, such as about 40 nm, 45 nm, 50 nm, 55 nm, 60 nm, 65 nm, 70 nm, 75 nm, 80 nm, 85 nm, 90 nm, 95 nm, 100 nm, 105 nm, 110 nm, 115 nm, 120 nm, 125 nm, 130 nm, 135 nm, 140 nm, 145 nm, or 150 nm. In some embodiments, the average LNP diameter of the LNP formulation may be from about 50 nm to about 100 nm, from about 50 nm to about 90 nm, from about 50 nm to about 80 nm, from about 50 nm to about 70 nm, from about 50 nm to about 60 nm, from about 60 nm to about 100 nm, from about 60 nm to about 90 nm, from about 60 nm to about 80 nm, from about 60 nm to about 70 nm, from about 70 nm to about 100 nm, from about 70 nm to about 90 nm, from about 70 nm to about 80 nm, from about 80 nm to about 100 nm, from about 80 nm to about 90 nm, or from about 90 nm to about 100 nm. In some embodiments, the average LNP diameter of the LNP formulation may be from about 70 nm to about 100 nm. In a particular embodiment, the average LNP diameter of the LNP formulation may be about 80 nm. In some embodiments, the average LNP diameter of the LNP formulation may be about 100 nm. In some embodiments, the average LNP diameter of the LNP formulation ranges from about I mm to about 500 mm, from about 5 mm to about 200 mm, from about 10 mm to about 100 mm, from about 20 mm to about 80 mm, from about 25 mm to about 60 mm, from about 30 mm to about 55 mm, from about 35 mm to about 50 mm, or from about 38 mm to about 42 mm.
A LNP may, in some instances, be relatively homogenous. A polydispersity index may be used to indicate the homogeneity of a LNP, e.g., the particle size distribution of the lipid nanoparticles. A small (e.g., less than 0.3) polydispersity index generally indicates a narrow particle size distribution. A LNP may have a polydispersity index from about 0 to about 0.25, such as 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, or 0.25. In some embodiments, the polydispersity index of a LNP may be from about 0.10 to about 0.20.
The zeta potential of a LNP may be used to indicate the electrokinetic potential of the composition. In some embodiments, the zeta potential may describe the surface charge of an LNP. Lipid nanoparticles with relatively low charges, positive or negative, are generally desirable, as more highly charged species may interact undesirably with cells, tissues, and other elements in the body. In some embodiments, the zeta potential of a LNP may be from about −10 mV to about +20 mV, from about −10 mV to about +15 mV, from about −10 mV to about +10 mV, from about −10 mV to about +5 mV, from about −10 mV to about 0 mV, from about −10 mV to about −5 mV, from about −5 mV to about +20 mV, from about −5 mV to about +15 mV, from about −5 mV to about +10 mV, from about −5 mV to about +5 mV, from about −5 mV to about 0 mV, from about 0 mV to about +20 mV, from about 0 mV to about +15 mV, from about 0 mV to about +10 mV, from about 0 mV to about +5 mV, from about +5 mV to about +20 mV, from about +5 mV to about +15 mV, or from about +5 mV to about +10 mV.
The efficiency of encapsulation of a protein and/or nucleic acid, describes the amount of protein and/or nucleic acid that is encapsulated or otherwise associated with a LNP after preparation, relative to the initial amount provided. The encapsulation efficiency is desirably high (e.g., close to 100%). The encapsulation efficiency may be measured, for example, by comparing the amount of protein or nucleic acid in a solution containing the lipid nanoparticle before and after breaking up the lipid nanoparticle with one or more organic solvents or detergents. An anion exchange resin may be used to measure the amount of free protein or nucleic acid (e.g., RNA) in a solution. Fluorescence may be used to measure the amount of free protein and/or nucleic acid (e.g., RNA) in a solution. For the lipid nanoparticles described herein, the encapsulation efficiency of a protein and/or nucleic acid may be at least 50%, for example 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%. In some embodiments, the encapsulation efficiency may be at least 80%. In some embodiments, the encapsulation efficiency may be at least 90%. In some embodiments, the encapsulation efficiency may be at least 95%.
A LNP may optionally comprise one or more coatings. In some embodiments, a LNP may be formulated in a capsule, film, or table having a coating. A capsule, film, or tablet including a composition described herein may have any useful size, tensile strength, hardness or density.
Additional exemplary lipids, formulations, methods, and characterization of LNPs are taught by WO2020061457, which is incorporated herein by reference in its entirety.
In some embodiments, in vitro or ex vivo cell lipofections are performed using Lipofectamine MessengerMax (Thermo Fisher) or TransIT-mRNA Transfection Reagent (Mirus Bio). In certain embodiments, LNPs are formulated using the GenVoy_ILM ionizable lipid mix (Precision NanoSystems). In certain embodiments, LNPs are formulated using 2,2-dilinoleyl-4-dimethylaminoethyl-[1,3]-dioxolane (DLin-KC2-DMA) or dilinoleylmethyl-4-dimethylaminobutyrate (DLin-MC3-DMA or MC3), the formulation and in vivo use of which are taught in Jayaraman et al. Angew Chem Int Ed Engl 51(34):8529-8533 (2012), incorporated herein by reference in its entirety.
LNP formulations optimized for the delivery of CRISPR-Cas systems, e.g., Cas9-g RNA RNP, gRNA, Cas9 mRNA, are described in WO2019067992 and WO2019067910, both incorporated by reference.
Additional specific LNP formulations useful for delivery of nucleic acids are described in U.S. Pat. Nos. 8,158,601 and 8,168,775, both incorporated by reference, which include formulations used in patisiran, sold under the name ONPATTRO.
Exemplary dosing of LNPs comprising the RNA compositions described herein may include about 0.1, 0.25, 0.3, 0.5, 1, 2, 3, 4, 5, 6, 8, 10, or 100 mg/kg (RNA). Exemplary dosing of AAV comprising a nucleic acid encoding one or more components of the system may include an MOI of about 1011, 1012, 1013, and 1014 vg/kg.
In some embodiments, the invention includes a lipid nanoparticle (LNP) comprising the ANDbody polypeptide (or RNA encoding the same), nucleic acid molecule, or DNA encoding an ANDbody described herein. In embodiments, the LNP comprises a cationic lipid. In some embodiments, the LNP further comprises one or more neutral lipid, e.g., DSPC, DPPC, DMPC, DOPC, POPC, DOPE, SM, a steroid, e.g., cholesterol, and/or one or more polymer conjugated lipid, e.g., a pegylated lipid, e.g., PEG-DAG, PEG-PE, PEG-S-DAG, PEG-cer or a PEG dialkyoxypropylcarbamate. In some embodiments, the cationic lipid of the LNP has a structure according to:
For a review of LNP, see also, e.g., Li et al. 2017, Nanomaterials 7, 122; doi:10.3390/nano7060122.
Viral Vectors
The compositions described herein (e.g., polypeptide or RNA ANDbody compositions), can be delivered by a viral vector (e.g., a viral vector expressing an RNA). A viral vector may be administered to a cell or to a subject (e.g., a human subject or non-human animal). A viral vector may be locally or systemically administered.
Examples of viral vectors include a retrovirus (e.g., Retroviridae family viral vector), adenovirus (e.g., Ad5, Ad26, Ad34, Ad35, and Ad48), parvovirus (e.g., adeno-associated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g., measles and Sendai), positive strand RNA viruses, such as picornavirus and alphavirus, and double stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus, replication deficient herpes virus), and poxvirus (e.g., vaccinia, modified vaccinia Ankara (MVA), fowlpox and canarypox). Other viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, human papilloma virus, human foamy virus, and hepatitis virus, for example. Examples of retroviruses include: avian leukosis-sarcoma, avian C-type viruses, mammalian C-type, B-type viruses, D-type viruses, oncoretroviruses, HTLV-BLV group, lentivirus, alpharetrovirus, gammaretrovirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, Virology (Third Edition) Lippincott-Raven, Philadelphia, 1996). Other examples include murine leukemia viruses, murine sarcoma viruses, mouse mammary tumor virus, bovine leukemia virus, feline leukemia virus, feline sarcoma virus, avian leukemia virus, human T-cell leukemia virus, baboon endogenous virus, Gibbon ape leukemia virus, Mason Pfizer monkey virus, simian immunodeficiency virus, simian sarcoma virus, Rous sarcoma virus and lentiviruses. Other examples of vectors are described, for example, in U.S. Pat. No. 5,801,030, the teachings of which are incorporated herein by reference.
Anellovirus vectors can also be used for delivering an ANDbody composition described herein. Anellovectors are known in the art and described, e.g., in WO2020123773, WO2020123816, WO2018232017, and WO2020123773. In certain embodiments, an anellovector composition comprises a genomic element that comprises a promoter operably linked to a nucleic acid sequence encoding an ANDbody described herein, the genetic element encapsulated by a proteinaceous exterior comprising an Anellovirus ORF1, e.g., an anellovirus capsid protein.
Cell and Vesicle-Based Carriers
A composition described herein (e.g., polypeptide or RNA ANDbody compositions), described herein can be administered to a cell in a cell, vesicle or other membrane-based carrier. In one embodiment, the compositions and systems described herein can be formulated in liposomes or other similar vesicles. Liposomes are spherical vesicle structures composed of a uni- or multilamellar lipid bilayer surrounding internal aqueous compartments and a relatively impermeable outer lipophilic phospholipid bilayer. Liposomes may be anionic, neutral or cationic. Liposomes are biocompatible, nontoxic, can deliver both hydrophilic and lipophilic drug molecules, protect their cargo from degradation by plasma enzymes, and transport their load across biological membranes and the blood brain barrier (BBB) (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol. 2011, Article ID 469679, 12 pages, 2011. doi:10.1155/2011/469679 for review). Vesicles can be made from several different types of lipids; however, phospholipids are most commonly used to generate liposomes as drug carriers. Methods for preparation of multilamellar vesicle lipids are known in the art (see for example U.S. Pat. No. 6,693,086, the teachings of which relating to multilamellar vesicle lipid preparation are incorporated herein by reference). Although vesicle formation can be spontaneous when a lipid film is mixed with an aqueous solution, it can also be expedited by applying force in the form of shaking by using a homogenizer, sonicator, or an extrusion apparatus (see, e.g., Spuch and Navarro, Journal of Drug Delivery, vol. 2011, Article ID 469679, 12 pages, 2011. doi:10.1155/2011/469679 for review). Extruded lipids can be prepared by extruding through filters of decreasing size, as described in Templeton et al., Nature Biotech, 15:647-652, 1997, the teachings of which relating to extruded lipid preparation are incorporated herein by reference.
Exosomes can also be used as drug delivery vehicles for the compositions and systems described herein. For a review, see Ha et al. July 2016. Acta Pharmaceutica Sinica B. Volume 6, Issue 4, Pages 287-296; https://doi.org/10.1016/j.apsb.2016.02.001.
Ex vivo differentiated red blood cells can also be used as a carrier for an agent (e.g., an inhibitor) described herein, e.g., an antibody or a nucleic acid described herein. See, e.g., WO2015073587; WO2017123646; WO2017123644; WO2018102740; w02016183482; WO2015153102; WO2018151829; WO2018009838; Shi et al. 2014. Proc Natl Acad Sci USA. 111(28): 10131-10136; U.S. Pat. No. 9,644,180; Huang et al. 2017. Nature Communications 8: 423; Shi et al. 2014. Proc Natl Acad Sci USA. 111(28): 10131-10136.
Fusosome compositions, e.g., as described in WO2018208728, can also be used as carriers to deliver the [agent] or preparation described herein.
Plant nanovesicles and plant messenger packs (PMPs), e.g., as described in WO2011097480, WO2013070324, WO2017004526, or WO2020041784 can also be used as carriers to deliver the compositions described herein.
Without further elaboration, it is believed that one skilled in the art can, based on the above description, utilize the present invention to its fullest extent. The following specific embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever. All publications and sections thereof cited herein are herein incorporated by reference for the purposes or subject matter referenced herein.
The invention will be further illustrated in the following non-limiting examples.
1.1 Vaccination to Create Anti-RAGE Antibodies
Antibodies against human RAGE extracellular domain, an exemplary address target of the present technology, are created by immunization. The extracellular domain of human RAGE (NCBI protein accession 015109 positions N24-A344) (huRAGE) fused to the Fc region of human IgG1 (UniProt ID P01857 positions P100-K330) is expressed in HEK293F cells. Briefly, DNA sequences are codon optimized for mammalian expression and ordered in the pcDNA3.4-TOPO expression vector (ThermoFisher Scientific). Proteins are transiently transfected into HEK293 cells and purified using rProtein A Sepharose Fast Flow resin according to manufacturer's instructions (GE Healthcare) similar to prior methods (Rothschilds et al. 2019). 50 ug of the huRAGE-Fc fusion protein is used to immunize female BALB/c mice by i.p. injection in CFA/IFA (Millipore Sigma, catalog #F5881-10ML and F5506-10ML) adjuvant. Subsequently, hybridomas are generated (Listek et al. 2020). Clones are initially screened for IgG reactivity specific for the huRAGE-Fc fusion protein used for immunization in an ELISA format followed by flow cytometry studies using cells stably (CHO) or transiently (HEK293F) transfected with full-length huRAGE. Anti-RAGE hybridoma clones are next evaluated based on murine cross-reactivity. Flow cytometry studies are done using cells stably (CHO) or transiently (HEK293F) transfected with full-length mouse RAGE (mRAGE), and clones are selected that bind to mRAGE. Positive clones expressing anti-RAGE mAbs cross-reactive between human and mouse are then further purified by limited dilution cloning. The hybridomas are grown in DMEM/2% ultra low IgG serum and the mAbs are purified by protein G chromatography according to manufacturer's instructions using (Millipore Sigma, P3296-1 ML).
1.2 Selecting for Inert Anti-RAGE Antibodies
Address target binding sites of the present technology are designed to not influence signaling upon binding the address target, such as the exemplary RAGE address target. Accordingly, anti-RAGE hybridoma clones produces as described above are further evaluated based on their inability to block RAGE ligand binding. Human RAGE ligands tested included HMGB1 (full-length, from Creative BioMart catalog #HMGB1-29332TH), Advanced Glycation Endproduct (fused to bovine serum albumin, Millipore Sigma catalog #121800-10MG-M), S100A12 (full-length, from R&D Systems catalog #1052-ER-050), S100A1 (full-length, from R&D Systems catalog #9705-S1-100), S100A4 (R&D Systems catalog #4137-S4-050), S100A10 (full-length, from Creative BioMart catalog #S100A10-157H), S100A11 (R&D Systems catalog #9015-S11-050), S100A13 (R&D Systems catalog #4327-SA-050), S100B (R&D Systems catalog #1820-SB-050), amyloid-β-peptide (DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA (SEQ ID NO: 76) from NM_000484.2, Millipore Sigma catalog #AG912-1MG) and Mac-1 (F17-N1105 from NP_001139280 and Q23-N700 from UniProt P05107, R&D Systems catalog #4047-AM-050). ELISAs are used to quantify ability of ligands to bind in the presence of anti-RAGE antibodies. HuRAGE-Fc is adsorbed to ELISA plates, then after blocking, the plates are incubated with concentrations of 10 fM up to 10 uM of anti-RAGE antibody clones from the hybridomas (one condition per concentration and per clone). After washing the plates, ligands are each biotinylated according to manufacturer's instructions (ThermoFisher catalog #21435), and then incubated on the plates at concentrations ranging from 10 fM up to 10 uM. After washing, SA-linked HRP secondary antibodies are added, followed by TMB substrate and colorimetric readout quantified by absorbance. Ligand binding is compared within a given ligand with versus without anti-RAGE antibodies to isolate anti-RAGE clones that are inert and do not affect binding of one or more ligands.
The inability of anti-RAGE antibodies to inhibit IFNα-induced gene signature is also evaluated, and anti-RAGE hybridoma clones are chosen that do not change cellular signaling based on an IFNα-induced gene signature assay. PBMCs from healthy human donors are stimulated for 4 h with 50% sera from SLE patients. The assay is completed either in the presence of anti-RAGE antibodies or unrelated (negative) isotype control human IgG1 antibodies (Bio X Cell catalog #BE0297) at antibody concentrations ranging from 10 fM up to 10 uM. In addition a huRAGE-Fc fusion molecule is used as a positive control. Total RNA is purified and expression of type I IFN-inducible genes, including DDX58, G1P2, MXI, OAS3, RSAD2, IFITI, IF135 are measured by real-time qRT-PCR analysis as in prior methods (WO 2008/137552 A2, https://patentimages.storage.googleapis.com/94/26/c8/7b9f27f693c4b6/WO2008137552A2.pdf). The inhibition values of gene expression are normalized to the negative control Ab.
1.3 Vaccination to Create Anti-Notch2 Antibodies
Antibodies against the extracellular domain of human Notch2 (huNotch2) fused to the Fc region of human IgG1, an exemplary effector target of the present technology, are created by immunization similar to RAGE as described above. After immunization and hybridoma generation, clones are screened exactly as above but for binding to full length human and mouse Notch2 (instead of RAGE). Positive clones expressing anti-Notch2 mAbs cross-reactive between human and mouse are then further purified by limited dilution cloning. The hybridomas are grown in DMEM/2% ultra low IgG serum and the mAbs are purified by protein G chromatography.
1.4 Selecting for Active Anti-Notch2 Antibodies at Wide IC50 Ranges
Effector target binding sites of the present technology, such as Notch2, are designed to not influence signaling upon binding the effector target, unless they are localized to a target tissue by an address target binding site, such as RAGE. Accordingly, the binding affinities of effector target (e.g., Notch2) binding sites are analyzed. Specifically, the IC50 s of Notch2 antibodies on the ligand human Jagged-2-Fc fusion protein (Creative BioMart, JAG2-382H) binding to surface Notch2 are evaluated using flow cytometry to choose antibodies at IC50's ranging from less than 1 nM up to 5 uM. Jagged-2-Fc is labeled with alexa fluor 647 (AF647) according to manufacturer's instructions (ThermoFisher, A20186) and methods previously described (Tzeng et al. 2015).
HEK293F cells are transiently transfected with full-length huNotch2. The cells are incubated with anti-Notch2 antibodies at concentrations increasing from 1 pM up to 50 uM. Subsequently (and without washing the cells), the cells are then incubated for 1 hour at 4 degrees Celsius with a constant concentration of AF647 labeled Jagged-2-Fc, ranging (for different IC50 assays) from 1 pM up to 50 uM. For each IC50 assay, one constant concentration of AF647 Jagged-2-Fc is chosen with varied anti-Notch2. Binding of AF647 Jagged-2-Fc with increasing anti-Notch2 antibody concentrations is quantified on the cells by flow cytometry using a ThermoFisher Attune N×T (B2R3Y3V6).
1.5 Expressing and Purifying ANDbodies as Bispecifics
DNA sequences from 10 RAGE antibodies and 10 Notch2 antibodies ranging in IC50 (from <1 nM up to 5 uM) are cloned using In-Fusion HD Cloning (Takara Bio, catalog #638911) into human IgG1 framework with single matching point mutations in the CH3 domain Fc region according to the ‘Controlled Fab-Arm Exchange’ (cFAE) method (Labrijn et al. 2014). After separately expressing antibodies from transient HEK293 expressions and purifying each antibody using protein A affinity resin, parental antibodies (combinations of 1 RAGE antibody with 1 Notch2 antibody) are made into bispecific RAGE/Notch2 ANDbodies according to the cFAE method. Briefly, parental antibodies are mixed under permissive redox conditions to enable recombination of half-molecules. Subsequently, the reductant is removed to allow for reoxidation of interchain disulfide bonds. Lastly, exchange efficiency is quantified using chromatography-based or mass spectrometry-based methods. Around 100 variant ANDbodies of RAGE×Notch2 are made.
1.6 Affinity of Andbody Variants
To identify ANDbody™ variants that meet desired effector target and address target binding affinity criteria, SPR-based affinity measurements are carried out on BIAcore model 2000 or T100 (Biacore/GE Healthcare, Piscataway, N.J.) at 25° C. using HBS-EP+ buffer (Cytiva catalog #BR100669) with 0.1 mg/ml BSA (Millipore Sigma catalog #A9418) as a running buffer. A Sensor Chip Protein A (Cytiva catalog #29127557) is used to capture mouse RAGE-Fc, human RAGE-Fc, mouse Notch2-Fc, or human Notch2-Fc. ANDbody is injected in a 3-fold dilution series from 60 to 0.74 nM, and dissociation is monitored for 10 min for all proteins. Kinetic analysis is done by simultaneously fitting the association and dissociation phases of the sensorgram using the 1:1 Langmuir binding model in BIAevaluation software (Biacore) as supplied by the manufacturer. Double referencing is applied in each analysis to eliminate background responses from the reference surface and buffer only control.
This assay can quantitatively assess the affinities of every ANDbody variant for RAGE and Notch2. ANDbody variants with higher affinity for RAGE than Notch2 as well as variants with no affinity differences or higher affinity for Notch2 are used in subsequent in vitro and in vivo experiments.
1.7 In Vitro Assays for Notch2 Antagonism on Cells with or without RAGE Expression
To analyze ANDbody characteristics, in vitro, HEK293F cells are transiently transfected with full length huRAGE (R+) or full length huNotch2 (N+), or co-transfected with both (RN+). The many variant RAGE×Notch2 ANDbodies are fluorophore-labeled with alexa fluor 647 (AF647) according to manufacturer's instructions (ThermoFisher, A20186) and methods previously described (Tzeng et al. 2015). Subsequently, ANDbodies are incubated with R+, N+, RN+, or combined R+ plus N+ cells at ANDbody concentrations ranging from 10 fM up to 10 uM. The parental anti-Notch2 mono-specific antibodies (one from each variant) are fluorophore labeled with FITC according to manufacturer's instructions (ThermoFisher, 53027). In some conditions, the parental anti-Notch2 FITC labeled antibodies are incubated with the cells pre-bound with AF647 RAGE×Notch2 (matching Notch2 variants) at concentrations of 10 fM up to 10 uM to saturate the remaining binding sites for Notch2. The binding EC50s of both the AF647 labeled RAGE×Notch2 ANDbody variants and the parental FITC labeled parental anti-Notch2 antibodies are quantified using flow cytometry. When the FITC Notch2 antibody is added after the AF647 RAGE×Notch2, the FITC signal from those cells is subtracted from the FITC signal from FITC Notch2 alone on cells (then normalized to the Notch2 alone signal) to quantify the % Notch2 bound by RAGE×Notch2. These numbers at different concentrations of the RAGE×Notch2 ANDbody are used to create EC50 curves. The assay is also run replacing the AF647-labeled ANDbody with AF647-labeled anti-Notch2 antibody.
A difference in observed EC50s on N+ cells vs RN+ cells reveals an enhanced Notch2 blockade when RAGE is present and identifies cells expressing the RAGE×Notch2 ANDbodies.
1.8 Biodistribution (In Vivo) for ANDbody and Parental Antibodies
To analyze ANDbody distribution, in vivo, the biodistribution of the RAGE×Notch2 ANDbody as well as each of the parental antibodies (anti-Notch2 or anti-RAGE used for the cFAE of the ANDbody) is quantified in female Balb/c and C57BL/6 mice.
To quantify the cellular biodistribution, the proteins (ANDbody and antibodies) are first individually labeled with AF647 according to manufacturer's instructions (ThermoFisher, A20186) and methods previously described (Tzeng et al. 2015). Then, each labeled antibody is injected individually at doses of 10 ug, 100 ug, and 500 ug IV (tail vein). Saline (PBS) is also injected as a control at equal volume.
For cellular biodistribution, at time points of 12 hours, 1 day, 2 days, 3 days, 7 days, and 14 days after injection, mice are euthanized using CO2 and tissues including heart, lung, spleen, blood, kidney, liver, and intestines are processed into single cell suspensions according to methods previously described (Tzeng et al. 2015). Briefly, blood is collected by cardiac puncture into EDTA-treated tubes (BD catalog #365974), and other tissues are harvested, weighed, mechanically dissociated between frosted glass slides, and rendered into single-cell suspensions by filtration through 70-μm mesh screens (Millipore Sigma, catalot #CLS431751-50EA). Splenocytes, whole blood, and lung are treated with ammonium-chloride-potassium (ACK) lysing buffer (Thermofisher Scientific, catalog #A1049201). Heart is digested with collagenase and processed into single cell suspension according to previous methods (Covarrubias et al. 2019). Flow cytometry is performed on immune cells using markers for CD8 T cells (CD3e+ CD8+), CD4 T cells (CD3e+ CD4+ Foxp3−), regulatory T cells (CD4+ CD25+ FOXP3+), monocytes/macrophages (CD3e− CD11 b+ CD11c−/lo NK1.1− Ly6G− SSClo), dendritic cells (CD3e− CD11chi), NK cells (NK1.1+ CD3e−), and NKT cells (NK1.1+ CD3e+) as previously described (Tzeng et al. 2015). Lung cells including epithelial (CD326+CD31−CD45−), endothelial (CD326− CD31+ CD45−), and hematopoietic lineages (CD326−CD31−CD45+) are also analyzed as previously defined (Singer et al. 2016). Antibodies are purchased from Biolegend, and flow cytometry is run on a ThermoFisher Attune N×T (B2R3Y3V6). Presence of the labeled ANDbody or other labeled antibody on the cell surface is defined by fluorescence of AF647 (and this fluorophore was avoided in the flow panels).
To quantify the tissue biodistribution, the proteins (ANDbody and antibodies) are first individually labeled with NHS-5/6-FAM (Thermofisher Scientific, catalog #46409) as per the manufacturer's instructions.
For tissue biodistribution, at time points of 12 hours, 1 day, 2 days, 3 days, 7 days, and 14 days after injection, mice are euthanized using CO2 and tissues including lung, spleen, blood, kidney, liver, and intestines are harvested, weighed, and imaged on an IVIS Spectrum imaging system (Caliper Life Sciences; excitation, 500 nm; emission, 540 nm). Images are analyzed using the Living Image software.
1.9 In Vivo Bioactivity Quantifying Gene Expression Changes
To analyze ANDbody activity, in vivo, bioactivity is quantified using using female Balb/c and C57BL/6 mice. To quantify bioactivity across tissues, the RAGE×Notch2 ANDbody or each of the respective parental antibodies (anti-Notch2 or anti-RAGE used for the cFAE of the ANDbody) is injected at doses of 10 ug, 100 ug, and 500 ug IV (tail vein). Saline (PBS) is also injected as a control at equal volume.
At time points of 12 hours, 1 day, 2 days, 3 days, 7 days, and 14 days after injection, tissues including lung, spleen, blood, kidney, liver, heart, and intestines are processed into single cell suspensions according to methods previously described (Tzeng et al. 2015). Briefly, blood is collected by cardiac puncture into EDTA-treated tubes (BD catalog #365974), and other tissues are harvested, weighed, mechanically dissociated between frosted glass slides, and rendered into single-cell suspensions by filtration through 70-μm mesh screens (Millipore Sigma, catalot #CLS431751-50EA). Splenocytes and whole blood are treated with ammonium-chloride-potassium (ACK) lysing buffer (Thermofisher Scientific, catalog #A1049201).
qRT-PCR is performed using methods previously described (Nandagopal et al. 2018). RNA is prepared using the rNeasy kit (QIAGEN). cDNA is prepared from 500 ng RNA using the iScript cDNA synthesis kit (Bio-Rad). 0.5 μL cDNA is used per 10 μL RT-qPCR reaction mix containing 1× iqSYBR Green Supermix (Bio-Rad) and 450 nM total forward and reverse primers. Reactions are performed on a BioRad CFX Real-Time PCR Detection System using a 2-step amplification protocol, with the following thermocycling parameters: 95 C, 3 min followed by 40 cycles of 95 C, 10 s (melting) and 55 C, 30 s (annealing+extension). All reactions are performed in duplicate.
Genes related to Notch2 signaling are mouse Hes1, Hey1, and HeyL, and the reference gene is SdhA. Primers used for amplification are the mouse Hes1 primer set (Forward, 5′-CAACACGACACCGGACAAAC-3′ (SEQ ID NO: 77) and Reverse, 5′-AAGAATAAATGAAAGTCTAAGCCAA-3′ (SEQ ID NO: 78)), mouse Hey1 primer set (Forward, 5′-GCCGAAGTTG CCCGTTATCT-3′ (SEQ ID NO: 79) and Reverse, 5′-CGCTGGGATG CGTAGTTGTT-3′ (SEQ ID NO: 80)), mouse HeyL primer set (Forward, 5′-GAGCTGAC TTCCCACAACCA-3′ (SEQ ID NO: 81) and Reverse, 5′-GAGAGG TGCCTTTGCGTAGA-3′ (SEQ ID NO: 82)), and mouse SdhA primer set (Forward, 5′-AGTGGGCT GTCTTCCTTAAC-3′ (SEQ ID NO: 83) and Reverse, 5′-GGATTGCTTCT GTTTGCTTGG-3′ (SEQ ID NO: 84)) previously described (Nandagopal et al. 2018). All primers are purchased from IDT DNA.
Hes1, Hey1, and HeyL gene expression is measured in the ANDbody treated mice, untreated mice, and anti-Notch2 treated mice, including in the lungs.
1.10 In Vivo Bioactivity Using Weights and Histology
Using female Balb/c and C57BL/6 mice, histology is done on organs such as the spleen, kidney, liver, heart, intestines, teeth, and lungs to compare pathology with ANDbody treatment, with treatment with anti-Notch2 alone, or saline (PBS). Starting at 8 weeks of age, 10 ug, 100 ug, and 500 ug of the ANDbody or of the corresponding Notch2 antibody (prior to cFAE) is injected IV (tail vein) 1× or 2× per week. Saline (PBS) is also injected as a control at equal volume 1× or 2× per week. Mice are weighed 2× per week starting prior to the first treatment. After 2 weeks, 4 weeks, and 6 weeks of treatment, mice are euthanized and organs are processed for histology.
Unless otherwise noted, organs are removed into cassettes and then placed directly into 10% neutral-buffered formalin (Sigma-Aldrich) for 12-24 hours prior to embedding in paraffin. Lungs are perfused with 10% neutral-buffered formalin prior to being placed in cassettes for soaking in neutral-buffered formalin. Intestines are thoroughly rinsed before being put in cassettes for soaking in 10% neutral-buffered formalin. Paraffin sections (1-2 μm) are cut and de-waxed prior to histochemical staining. Sections are stained with hematoxylin/eosin (H&E; Merck, Darmstadt, Germany) and scored blindly according to immune infiltrates and tissue morphology.
In addition to lung morphology, weight loss (or not) of ANDbody treated mice over the course of treatment is compared with weight loss (or not) of mice treated with anti-Notch2, and weight loss (or not) of untreated mice.
2.1 Yeast Surface Display to Create Anti-UMOD Antibodies
Yeast surface display (Chao et al. 2006) is used to engineer antibodies to mouse UMOD (Creative BioMart, catalog #UMOD-17835M, untagged), an exemplary address target of the present technology. This is done by using methods described previously (Angelini et al. 2015) and summarized below. The yeast display starts with a synthetic antibody library from the Sidhu laboratory that is based off of natural frameworks, library ‘G’ (Van Deventer et al. 2015). scFvs displayed on the yeast surface are selected for binding to mouse UMOD. Subsequent sorts can be done against the human UMOD antigen (Creative BioMart, catalog #UMOD-001 H, untagged), such that binders can be cross-reactive between human and mouse forms. To increase affinity of the scFv binders, affinity maturation is performed using error-prone PCR as described previously (Angelini et al. 2015) and the resulting library is re-sorted for binding to both mouse and human UMOD. Subsequent to engineering, many scFvs that are multi-species cross-reactive are cloned back into human IgG1 antibody format.
2.2 Selecting for Inert Anti-UMOD Antibodies
Address target binding sites of the present technology are designed to not influence signaling upon binding the address target, such as the exemplary UMOD address target. Accordingly, anti-UMOD antibodies are further evaluated based on their inability to block UMOD ligand binding, in an assay such as the one described above for RAGE antibodies or an in vivo assay. Inert UMOD antibodies may be identified in such assays whereby kidney architecture is not affected or modified by the screened UMOD antibody.
2.3 Vaccination to Create Anti-Notch2 Antibodies
Antibodies cross-reactive to mouse and human Notch2 are created, cloned, and expressed into the human IgG1 framework according to prior methods as described above.
2.4 Selecting for Active Notch2 Antibodies at Wide IC50 Ranges
Antibodies against Notch2 will be selected at wide IC50 ranges as described above.
2.5 Expressing and Purifying ANDbodies as Bispecifics
DNA sequences from 10 UMOD antibodies and 10 Notch2 antibodies ranging in IC50 (from <1 nM up to 5 uM) are made into about 100 variant ANDbodies as described above.
2.6 Affinity of ANDbody Variants for UMOD and Notch2
ANDbody affinities for UMOD and Notch2 are evaluated similarly to above using a BIAcore (as described above). In this case, human and mouse versions of His-tagged UMOD are immobilized on a Sensor Chip NTA (Cytiva catalog #BR100034). Human and mouse notch2-Fc are immobilized as described above.
2.7 Biodistribution (In Vivo) for ANDbody and Parental Antibodies
Cellular and tissue biodistribution studies are done using methods described above (as described above). However, the ANDbody used in this case is UMOD×Notch2, and the parental antibodies correspond to anti-UMOD and anti-Notch2.
2.8 In Vivo Bioactivity Quantifying Gene Expression Changes
The in vivo bioactivity of UMOD×Notch2 ANDbodies is quantified using gene expression methods described above.
2.9 In Vivo Bioactivity Using Weights and Histology
The in vivo bioactivity of UMOD×Notch2 ANDbodies is quantified using weight and histology methods described above.
3.1 Yeast Surface Display to Create Anti-MEP1B Antibodies
Yeast surface display (Chao et al. 2006) is used to engineer antibodies to mouse MEP1B (Cusabio, CSB-MP730755M0), an exemplary address target of the present technology. Yeast display is performed as described above (0) to get cross-reactive mouse/human MEP1B binders (human MEP1B, Cusabio, CSB-MP618098HU). Subsequent to engineering, many scFv's cross-reactive to mouse and human MEP1B are cloned into human IgG1, transiently transfected into HEK293F cells, and purified using protein A resin as described above.
3.2 Vaccination to Create Anti-Notch2 Antibodies
Antibodies cross-reactive to mouse and human Notch2 are created, cloned, and expressed into the human IgG1 framework according to prior methods described above.
3.3 Selecting for Active Notch2 Antibodies at Wide IC50 Ranges
Antibodies against Notch2 are selected at wide IC50 ranges as described above.
3.4 Expressing and Purifying ANDbodies as Bispecifics
DNA sequences from 10 MEP1B antibodies and 10 Notch2 antibodies ranging in IC50 (from <1 nM up to 5 uM) are made into about 100 variant ANDbodies as described above.
3.5 Affinity of ANDbody Variants for MEP1B and Notch2
ANDbody affinities for MEP1B and Notch2 are evaluated similarly to above using a BIAcore. In this case, human and mouse versions of His-tagged MEP1B are immobilized on a Sensor Chip NTA (Cytiva catalog #BR100034). Human and mouse notch2-Fc are immobilized as described above.
3.6 Biodistribution (In Vivo) for ANDbody and Parental Antibodies
Cellular and tissue biodistribution studies are done using methods described above. However, the ANDbody used in this case is MEP1B×Notch2, and the parental antibodies correspond to anti-MEP1B and anti-Notch2.
3.7 In Vivo Bioactivity Quantifying Gene Expression Changes
The in vivo bioactivity of MEP1B×Notch2 ANDbodies is quantified using the gene expression methods described above.
3.8 In Vivo Bioactivity Using Weights and Histology
The in vivo bioactivity of MEP1B×Notch2 ANDbodies is quantified using weight and histology methods described above.
4.1 Vaccination to Create Anti-RAGE Antibodies
Methods are described above to vaccinate in order to create mouse/human cross-reactive anti-RAGE antibodies.
4.2 Selecting for Inert Anti-RAGE Antibodies
Methods are described above to select for inert anti-RAGE antibodies.
4.3 Yeast Surface Display to Create Anti-IL11Ra Antibodies
Yeast surface display is used similar to above to create antibodies of varying affinities cross-reactive with mouse and human IL11Ra, an exemplary effector target of the present technology. The DNA sequences coding for extracellular domains of mouse IL11Ra (positions 24-372 of UniProt ID Q64385) and human IL11Ra (positions 24-370 of UniProt ID 014626) are codon optimized for mammalian expression and ordered with a C-terminal His tag in the pcDNA3.4-TOPO expression vector (ThermoFisher Scientific). Proteins are transiently transfected into HEK293F cells and purified using TALON® Metal Affinity Resin according to manufacturer's instructions (Clontech) similar to prior methods (Rothschilds et al. 2019). These soluble recombinant mouse and human IL11 Ra are used as the antigens for yeast surface display.
ScFv's cross-reactive to mouse and human IL11 Ra are cloned into human IgG1, transiently transfected into HEK293F cells, and purified using protein A resin as described above.
4.4 Selecting for Active Anti-IL11Ra Antibodies at Wide IC50 Ranges
The IC50s of IL11 Ra antibodies on the ligand human IL11 (R&D Systems, catalog #218-IL-025/CF) binding to surface IL11 Ra are evaluated using flow cytometry to choose antibodies at IC50's ranging from less than 1 nM up to 5 uM, as described above. In this current example, full length human IL11 Ra is transiently transfected to the surface of HEK293F cells. The methods from the prior example are used by replacing IL11 Ra antibodies in place of Notch2 antibodies, and IL11 in place of Jagged-2-Fc.
4.5 Expressing and Purifying ANDbodies as Bispecifics
DNA sequences from 10 RAGE antibodies and 10 IL11 Ra antibodies ranging in IC50 (from <1 nM up to 5 uM) are made into about 100 variant ANDbodies as described above.
4.6 Affinity of ANDbody Variants for RAGE and IL11Ra
ANDbody affinities for RAGE and IL11 Ra are evaluated similarly to above using a BIAcore. In this case, human and mouse versions of His-tagged IL11 Ra are immobilized on a Sensor Chip NTA (Cytiva catalog #BR100034), and human and mouse versions of RAGE-Fc are captured on a Sensor Chip Protein A (Cytiva catalog #29127557).
4.7 In Vitro Assays for IL11Ra Antagonism on Cells with or without RAGE Expression
This assay is done as described above, except substituting full length human IL11 Ra instead of Notch2, as well as substituting anti-IL11 Ra antibodies for anti-Notch antibodies. The corresponding RAGE×IL11Ra ANDbodies are also used.
4.8 Biodistribution (In Vivo) for ANDbody and Parental Antibodies
Cellular and tissue biodistribution studies are done using methods described above. However, the ANDbody used in this case is RAGE×IL11Ra, and the parental antibodies correspond to anti-RAGE and anti-IL11 Ra.
4.9 In Vivo Bioactivity of RAGE×IL11Ra ANDbodies
In response to mouse treatment with murine IL11, there is an increase in collagen content in both the ventricle and the kidney (Schafer et al. 2017). Accordingly, collagen content is measured to quantify amount of IL11 Ra bioactivity after ANDbody treatment.
Similar to prior methods (Schafer et al. 2017), 10-week-old male C57BL/6 mice are injected with 2 ug mouse IL11 daily subcutaneously or an identical volume of saline for 21 days. The mouse IL11 is recombinantly made by synthesizing codon-optimized DNA using the sequence for mouse IL11 (UniProt ID P47873) with a C-terminal His tag, doing HEK293F transient transfections, and purifying the His tagged IL11 with TALON resin as described above. Starting 3 days before the first IL11 injection and then 2× per week thereafter, IL11- and saline-treated mice receive therapeutic injections IP constituting 250 ug of ANDbody RAGE×IL11Ra, parental anti-IL11 Ra alone, or saline (PBS) in equal volume.
At the end of 21 days of IL11 treatment, mice are euthanized and the amounts of total collagen in the lung, spleen, blood, kidney, liver, heart, and intestines are quantified on the basis of colorimetric detection of hydroxyproline using a Quickzyme Total Collagen assay kit (Quickzyme Biosciences) and similar to prior methods (Schafer et al. 2017).
5.1 Yeast Surface Display to Create Anti-UMOD Antibodies
Anti-UMOD (e.g., address target) antibodies are selected for as above and cloned into human IgG1.
5.2 Selecting for Inert Anti-UMOD Antibodies
Anti-UMOD antibodies are further evaluated based on their inability to block UMOD ligand binding, in an assay such as the ones described above.
5.3 Yeast Surface Display to Create Anti-IL11Ra Antibodies
The same IL11 Ra antibodies generated above in yeast surface display will be used here as described above. ScFv's cross-reactive to mouse and human IL11 Ra are cloned into human IgG1, transiently transfected into HEK293F cells, and purified using protein A resin as described above.
5.4 Selecting for Active IL11Ra Antibodies at Wide IC50 Ranges
The method described above is used to select for IL11 Ra antibodies at varied IC50s.
5.5 Expressing and Purifying ANDbodies as Bispecifics
DNA sequences from 10 UMOD antibodies and 10 IL11 Ra antibodies ranging in IC50 (from <1 nM up to 5 uM) are made into about 100 variant ANDbodies as described above.
5.6 Affinity of ANDbody Variants for UMOD and IL11Ra
ANDbody affinities for UMOD and IL11 Ra are evaluated similarly to above using a BIAcore. In this case, human and mouse versions of His-tagged UMOD and His-tagged IL11 Ra are immobilized on a Sensor Chip NTA (Cytiva catalog #BR100034). It is expected that some ANDbody variants have higher affinity for UMOD than for IL11 Ra, although all variants are tested in future assays.
5.7 Biodistribution (In Vivo) for ANDbody and Parental Antibodies
Cellular and tissue biodistribution studies are done using methods described above. However, the ANDbody used in this example is UMOD×IL11Ra, and the parental antibodies correspond to anti-UMOD and anti-IL11Ra.
5.8 In Vivo Bioactivity of UMOD×IL11Ra ANDbodies
The in vivo bioactivity of UMOD×IL11Ra ANDbodies is quantified using the same methods described above.
6.1 Yeast Surface Display to Create Anti-MEP1B Antibodies
Anti-MEP1B (e.g., address target) antibodies are selected for as above and cloned into human IgG1.
6.2 Yeast Surface Display to Create Anti-IL11Ra Antibodies
The same IL11Ra (e.g., effector target) antibodies generated above in yeast surface display will be used here. ScFv's cross-reactive to mouse and human IL11Ra are cloned into human IgG2, transiently transfected into HEK293F cells, and purified using protein A resin as described above.
6.3 Selecting for Active Anti-IL11Ra Antibodies at Wide IC50 Ranges
The method described above is used to select for IL11Ra antibodies at varied IC50s.
6.4 Expressing and Purifying ANDbodies as Fusion Proteins into Human IgG2
The 10 highest affinity MEP1B scFv's and 10 IL11Ra antibodies ranging in affinity (from <1 nM up to 5 uM) are made as ANDbodies with human IgG2 Fc regions. To do this, the scFv sequences from MEP1B variants are cloned respectively onto the IgG2 IL11Ra antibody variants. The MEP1B scFvs are separated by a flexible linker (3×GGGGS (SEQ ID NO: 85)) from either the N or C terminal of either the light or heavy chains of IL11Ra antibodies (each ANDbody has 2 MEP1B scFvs). Variants are made with 4 total MEP1B scFvs per ANDbody by cloning MEP1B scFvs (always separated by the linker) before the N terminal and after the C terminal of the heavy chain or the light chain, respectively. Other variants with 4 or more MEP1B scFvs per IL11Ra antibody on the MEP1B×IL11Ra ANDbody by mixing and matching the locations of the scFv on the IL11Ra antibodies: at N terminal of both heavy and light chains; at C terminal of both heavy and light chains; at N terminal of heavy chain and C terminal of light chain; at C terminal of heavy chain and N terminal of light chain; and other variants with scFvs in 3 or 4 different locations (resulting in 6 or 8 total scFvs per ANDbody, respectively).
6.5 Affinity of ANDbody Variants for MEP1B and IL11Ra
ANDbody affinities for MEP1B and IL11Ra are evaluated similarly to above using a BIAcore. In this case, human and mouse versions of His-tagged MEP1B and His-tagged IL11Ra are immobilized on a Sensor Chip NTA (Cytiva catalog #BR100034).
6.6 Biodistribution (In Vivo) for ANDbody and Parental Antibodies
Cellular and tissue biodistribution studies are done using methods described above. However, the ANDbody used in this case is MEP1B×IL11Ra, and the parental antibodies correspond to anti-MEP1B and anti-IL11Ra.
6.7 In Vivo Bioactivity of MEP1B×IL11Ra ANDbodies
The in vivo bioactivity of MEP1B×IL11Ra ANDbodies is quantified using the same methods described above.
This example demonstrates the restricted expression of an anti-DSG1 antibody (address binder) in skin.
7.1 Anti-DSG1 Monoclonal Antibody Expression and Purification
Sequences encoding the variable heavy chain regions (HC: SEQ ID NO: 24 and SEQ ID NO: 26, shown in Table 4) of two anti-desmoglein-1 (anti-DSG1) antibodies named 3-09*5 and 3-07/1e (Yamagami et al., J Immunol., 183(9): 5615-5621, 2009) were fused to a human IgG1 (hulgG1) backbone with the effector null mutations L234A, L235A, and P329G (LALA-PG) and cloned into a PCDNA3.4™ vector (ThermoFisher Scientific). The variable light chain regions (SEQ ID NO: 25 and SEQ ID NO: 27) were fused to a constant kappa light chain (for 3-09*5) (SEQ ID NO: 22) or a constant lambda light chain (for 3-07/1e) (SEQ ID NO: 23) and cloned into PCDNA3.4™
To express and purify the antibodies, a 1:1 ratio of heavy chain to light chain DNA was transfected into EXPI293F™ cells (ThermoFisher Scientific) using the EXPIFECTAMINE™ 293 Transfection Kit (ThermoFisher Scientific) following manufacturer's recommendations. Transiently expressed antibodies were purified from conditioned media 5 days post-transfection by filtering out the transfected cells. Conditioned media was incubated with protein A agarose beads for 1 hour. The bound beads were washed with Phosphate Buffered Saline (PBS) pH 7.4 followed by elution of the bound antibody with 0.1 M Glycine pH 2.5 and neutralized with 1/10 volume of Tris pH 8.5. The neutralized eluate was buffer exchanged into PBS. The resulting mAbs were designated as PRO003 (3-09*5 HC) (heavy chain sequence: SEQ ID NO: 28; light chain sequence: SEQ ID NO: 29) and PRO004 (3-07/1e HC) (heavy chain sequence: SEQ ID NO: 30; light chain sequence: SEQ ID NO: 31).
The purified mAbs were analyzed by analytical size exclusion chromatography (SEC) for monodispersity and by SDS-PAGE for purity.
7.2 Anti-DSG1 Antibodies PRO003 and PRO004 Bind to Murine DSG1 Expressed on Cells
Murine DSG1 (NCBI accession NP_034209.2) with a c-Myc epitope tag at the protein C terminus was transiently expressed in RAW 264.7 cells using LIPOFECTAMINE™ 3000 (ThermoFisher Scientific) according to the manufacturer's protocol. Expression of DSG1 was confirmed by fixing and permeabilizing the cells, followed by staining with an anti-c-Myc antibody (Life Technologies A-21281) and analysis by flow cytometry. PRO003 and PRO004 bound specifically to the cells transfected with mouse DSG1, confirming that they have the expected binding specificity and are suitable for studies in mice.
7.3 Anti-DSG1 Antibodies Injected into Mice Accumulate Preferentially in Skin
To demonstrate that binding to a skin address can cause accumulation of an antibody in the skin, the anti-DSG1 antibodies PRO003 and PRO004 were chemically conjugated to the near-infrared (IR) dye IRDYE® 800CW using according to the manufacturer's instructions (LI-COR® 928-38044).
The labeled antibodies were each administered to mice by tail vein injection at a dose level of 3 mg/kg. Each antibody was administered to two groups of 3 mice, which were euthanized at 3 days and 7 days after dosing. Following euthanization, 9 organs were collected (heart, lung, pancreas, kidney, small intestine, large intestine, skin, liver, stomach), and the near-IR fluorescence of each tissue was measured on a IVIS® imager (PERKINELMER®). To image the skin, a patch of skin was shaved and approximately 1 cm2 was collected for imaging. Samples from each mouse were arranged in a standard format and total fluorescence intensity was measured. Fluorescence intensity from each organ was quantified and averaged across each tissue by measuring total signal and subtracting the local background. High background signal was observed in the livers from all treated mice, so livers were excluded from the analysis. Without wishing to be bound by theory, it is believed that the liver may take up the flourescent dye independent of antibody targeting. Similarly, background signal was observed in the stomach from all groups, including mice that were not treated with any antibody. Fluorescence was observed from the food fed to the mice, so the stomach was excluded from analysis.
This example demonstrates the restricted expression of an anti-RAGE antibody (address binder) in the lung.
8.1 Anti-RAGE Monoclonal Antibody Expression and Purification
Sequences encoding the variable heavy chain regions (SEQ ID NO: 32 and SEQ ID NO: 34, shown in Table 5) of two anti-RAGE mAbs named h11E6.8 and XT-M4 (Creative Biolabs) were fused to a hulgG1 backbone with the effector null mutations L234A, L235A, and P329G (LALA-PG) and cloned into a PCDNA3.4™ vector (ThermoFisher Scientific). Sequences encoding the variable light chain regions (SEQ ID NO: 33 and SEQ ID NO: 35) were fused to constant kappa light chains and cloned into PCDNA3.4™.
For expression and purification, a 1:1 ratio of heavy chain to light chain DNA was transfected into EXPI293F™ Cells (ThermoFisher Scientific) using the EXPIFECTAMINE™ 293 Transfection Kit (ThermoFisher Scientific) following the manufacturer's recommendations. Transiently expressed antibodies were purified from conditioned media 5 days post-transfection by filtering out the transfected cells. Conditioned media was incubated with protein A agarose beads for 1 hour. The bound beads were washed with Phosphate Buffered Saline (PBS) pH 7.4 followed by elution of the bound antibody with 0.1 M Glycine pH 2.5 and neutralized with 1/10 volume of Tris pH8.5. The neutralized eluate was buffer exchanged into PBS. The resulting mAbs were designated PRO001 (h11E6.8) (heavy chain sequence: SEQ ID NO: 36; light chain sequence: SEQ ID NO: 37) and PRO002 (XT-M4) (heavy chain sequence: SEQ ID NO: 38; light chain sequence: SEQ ID NO: 39).
The purified mAbs were analyzed by analytical size exclusion chromatography for monodispersity and by SDS-PAGE for purity. PRO001 and PRO002 expressed highly monodispered and resolved on SDS-PAGE at the expected molecular weight. Binding studies confirmed binding to the RAGE antigen (not shown).
To test the binding of the anti-RAGE antibodies by ELISA, recombinant His-tagged murine RAGE protein (ab276858 from Abcam) was coated on NUNC-IMMUNO™ MAXISORP™ ELISA plates at 1 μg/mL concentration overnight. The next day, coated antigen was removed and the wells were blocked with 1% IgG-free bovine serum albumin (BSA) followed by incubation with 11 four-fold serially diluted anti-RAGE antibodies (PRO001 and PRO002) with a starting concentration of 20 nM. Bound antibodies were detected with peroxidase-conjugated anti-human IgG antibodies with tetramethylbenzidine (TMB) and acid stop reagents. Both PRO001 and PRO002 bound murine RAGE antigen at similar affinities by ELISA around 90 pM apparent affinity, suggesting that both antibodies are tight binders.
8.2 Anti-RAGE Antibodies PRO001 and PRO002 Bind to Murine RAGE Expressed on Cells
PRO001 and PRO002 were tested for binding to mouse RAGE in cell culture. To confirm binding activity and specificity of the two antibodies, mouse RAGE (NCBI accession NP 031451.2) with a c-Myc epitope tag at the protein C terminus was transiently expressed in EXPI293™ cells (ThermoFisher Scientific) using EXPIFECTAMINE™ (ThermoFisher Scientific) according to the manufacturer's protocol. Expression of RAGE was confirmed by fixing and permeabilizing the cells, followed by staining with anti-c-Myc antibody (Life Technologies A-21281) and analysis by flow cytometry. Both antibodies bound specifically to murine RAGE expressed on cells, confirming that they have the expected binding specificity and are suitable for studies in mice.
8.3 Anti-RAGE Antibodies Injected into Mice Accumulate Preferentially in Lungs
To demonstrate that binding to a lung address can cause accumulation of an antibody in the lungs, the anti-RAGE antibodies PRO001 and PRO002 were chemically conjugated to the near-IR dye as described in Example 7.
The labeled antibodies were each administered to mice by tail vein injection and imaged as described in Example 7.
8.4 An Anti-RAGE Antibody Accumulates Specifically on Alveolar Cells
Single-cell expression analysis indicated that RAGE is expressed specifically in type 1 alveolar cells, with lower expression in type 2 alveolar cells. To test the hypothesis that the antibodies can address a specific cell type, three Balb/C mice were treated by tail vein injection with 3 mg/kg of PRO002. Three untreated mice were used as negative control. Three days after dosing, the mice were euthanized, lungs and other tissues were collected, and all tissues were fixed in formalin. Sections from each tissue were analyzed by immunohistochemistry (IHC) using an anti-human secondary antibody conjugated to horseradish peroxidase.
This example demonstrates the restricted expression of an anti-CDH16 antibody (address binder) in the kidney.
9.1 Anti-CDH16 Monoclonal Antibody Expression and Purification
A sequence encoding the variable heavy chain region (SEQ ID NO: 40; shown in Table 6) of the anti-cadherin 16 (anti-CDH16) mAb Ab270263 (Abcam) was fused to a hulgG1 backbone with the effector null mutations L234A, L235A, and P329G (LALA-PG) and cloned into a PCDNA3.4™ vector (ThermoFisher Scientific). A sequence encoding the variable light chain region (SEQ ID NO: 41) was fused to a constant kappa light chain and cloned into PCDNA3.4™.
For expression and purification, a 1:1 ratio of heavy chain to light chain DNA was transfected into EXPI293F™ Cells (ThermoFisher Scientific) using the EXPIFECTAMINE™ Transfection Kit (ThermoFisher Scientific) following the manufacturer's recommendations. Transiently expressed antibodies were purified from conditioned media 5 days post-transfection by filtering out the transfected cells. Conditioned media was incubated with protein A agarose beads for 1 hour. The bound beads were washed with Phosphate Buffered Saline (PBS) pH 7.4 followed by elution of the bound antibody with 0.1 M Glycine pH 2.5 and neutralized with 1/10 volume of Tris pH 8.5. The neutralized eluate was buffer exchanged into PBS. The resulting mAb was designated as PRO056 (heavy chain sequence: SEQ ID NO: 42; light chain sequence: SEQ ID NO: 43).
The purified mAb was analyzed by analytical size exclusion chromatography for monodispersity and by SDS-PAGE for purity. PRO056 expressed highly monodispered and resolved on SDS-PAGE at the expected molecular weight.
To test the binding of the anti-CDH16 antibodies by ELISA, recombinant His-tagged murine CDH16 protein, expressed and purified in house, was coated on NUNC-IMMUNO™ MAXISORP™ ELISA plates at 1 μg/mL concentration overnight. The next day, coated antigen was removed and the wells were blocked with 1% IgG-free BSA followed by incubation with 11 three-fold serially diluted anti-CDH16 antibody (PRO056) with a starting concentration of 533 nM. Bound antibody was detected with peroxidase-conjugated anti-human IgG antibodies with TMB and acid stop reagents. PRO056 bound murine CDH16 antigen at an affinity of 200 pM by ELISA.
9.2 Anti-CDH16 Antibody Accumulates Preferentially in the Kidney
The anti-CDH16 antibody PRO056 was chemically conjugated to near-IR fluorescent dye IRDYE® 800CW, as described in Example 7. The labeled antibody was administered to mice by tail vein injection at a dose level of 3 mg/kg. Two groups of 3 mice were used, which were euthanized at 3 days and 7 days after dosing. Following euthanization, organs were collected, and the near-IR fluorescence of each tissue was measured on a model IVIS® imager (PERKINELMER®), as above. Fluorescence intensity from each organ was quantified and averaged across each tissue by measuring total signal and subtracting the local background.
The distribution is strongly skewed to the kidney when compared to the antibodies provided herein that target addresses in the skin, lung, or kidney. These data show that an antibody binding to CDH16 accumulates preferentially in kidney, demonstrating they can be used as an address bidding domain for preferential kidney targeting of an ANDbody.
This example demonstrates the restricted expression of an anti-CDH17 antibody (address binder) in the intestine.
10.1 Anti-CDH17 Monoclonal Antibody Expression and Purification
A sequence encoding the variable heavy chain region (SEQ ID NO: 44; shown in Table 7) of the anti-cadherin 17 (anti-CDH17) mAb MAB8524 (R&D Systems) was fused to a hulgG1 backbone with the effector null mutations L234A, L235A, P329G (LALA-PG) and cloned into a PCDNA3.4™ vector (ThermoFisher Scientific). A sequence encoding the variable light chain region (SEQ ID NO: 45) was fused to a constant kappa light chain and cloned into PCDNA3.4™
For expression and purification, a 1:1 ratio of heavy chain to light chain DNA was transfected into EXPI293F™ cells (ThermoFisher Scientific) using the EXPIFECTAMINE™ 293 Transfection Kit (ThermoFisher Scientific) following the manufacturer's recommendations. Transiently expressed antibodies were purified from conditioned media 5 days post-transfection by filtering out the transfected cells. Conditioned media was incubated with protein A agarose beads for 1 hour. The bound beads were washed with Phosphate Buffered Saline (PBS) pH 7.4 followed by elution of the bound antibody with 0.1 M Glycine pH 2.5 and neutralized with 1/10 volume of Tris pH 8.5. The neutralized eluate was buffer exchanged into PBS. The resulting mAb was designated as PRO061 (heavy chain sequence: SEQ ID NO: 46; light chain sequence: SEQ ID NO: 47).
The purified mAb was analyzed by analytical size exclusion chromatography for monodispersity and by SDS-PAGE for purity. PRO061 expressed highly monodispered and resolved on SDS-PAGE at the expected molecular weight.
To confirm binding activity and specificity, mouse CDH17 (NCBI accession NP 062727.1) with a c-Myc epitope tag at the protein C terminus was transiently expressed in RAW 264.7 cells using LIPOFECTAMINE™ 3000 (ThermoFisher Scientific) according to the manufacturer's protocol. Expression of CDH17 was confirmed by fixing and permeabilizing the cells, followed by staining with an anti-c-Myc antibody (Life Technologies A-21281) and analysis by flow cytometry. PRO061 bound specifically to the cells transfected with mouse CDH17, confirming that it has the expected binding specificity and is suitable for studies in mice.
10.2 Anti-CDH17 Antibody Injected into Mice Accumulates Preferentially in the Intestine
PRO061 was chemically conjugated to near-IR fluorescent dye IRDYE® 800CW, as described in Example 7. The labeled antibody was administered to mice by tail vein injection at a dose level of 3 mg/kg. Two groups of 3 mice were used, which were euthanized at 3 days and 7 days after dosing. Following euthanization, organs were collected, and the near-IR fluorescence of each tissue was measured on a model IVIS® imager (PERKINELMER®), as above. Fluorescence intensity from each organ was quantified and averaged across each tissue by measuring total signal and subtracting the local background.
Immunohistochemistry (IHC) on fresh frozen (FF) healthy mouse tissue microarray (TMA) sections mounted onto glass slides was used for assaying whether predicted organ-specific or preferentially expressed addresses were actually of highest abundance in the predetermined organs, and for determining which monoclonal antibody clones (mAbs) bound with greatest preference to the desired organ.
Glass slides coated with FF TMA were generated by first assembling a fresh frozen tissue microarray block. To enable TMA block formation, individual organs from freshly sacrificed C57BL/6 mice were embedded in optimal cutting (OCT) medium in separate cryomolds and frozen. Cylindrical cores of tissue were then taken from each block and placed into a block to create the final FF TMA. Layers of the TMA were then cut off using a cryostat, mounted onto positively charged microscopy glass slides, and stored at −80° C. until stained.
Addresses were validated by direct binding of FF TMA-coated slides with either polyclonal antibodies or mAbs raised against the address in question. These address-specific antibodies were detected with horseradish peroxidase (HRP)-conjugated antibodies specific for the IgG of the host in which the primary address specific antibody was raised. Location and intensity of binding was determined by the addition of the HRP substrate 3,3′Diaminobenzidine (DAB), which yields a brown color at the site of primary antibody binding, proportional to the abundance of deposited antibody. Nuclei were counterstained with hematoxylin to yield a blue color. For each of the respective addresses, a range of different mAb clones was assayed for tissue specificity, and their patterns of tissue binding were assessed by performing IHC on the same FF TMAs described above.
Table 8 summarizes observed binding of the antibodies tested. All the antibodies tested reacted primarily with the expected target tissue, with varying degrees of weaker reactivity on other tissues. Without wishing to be bound by theory, much of the off-tissue reactivity may reflect non-specific binding by the antibody. For example, four antibodies tested for binding to RAGE each show binding to the lung, but 3 show variable low-level binding to other tissues.
This example demonstrates the production of an exemplary ANDbody that blocks Notch2 and binds RAGE as an address.
12.1 Anti-Notch2 Monoclonal Antibody Expression and Purification
Sequences encoding the variable heavy chain regions (SEQ ID NOs: 48, 50, 52 and 54; shown in Table 9) of four anti-Notch2 mAbs (Wu et al., Nature, 464: 1052-1057, 2010) were each individually fused to a hulgG1 backbone with the effector null mutations L234A, L235A, and P329G (LALA-PG) and cloned into a PCDNA3.4™ vector (ThermoFisher Scientific). Sequences encoding the corresponding variable light chain regions (SEQ ID NOs: 49, 51, 53, and 55) were fused to constant kappa light chains and cloned into PCDNA3.4™
For expression and purification, a 1:1 ratio of heavy chain to light chain DNA was transfected into EXPI293F™ cells (ThermoFisher Scientific) using the EXPIFECTAMINE™ 293 Transfection Kit (ThermoFisher Scientific) following the manufacturer's recommendations. Transiently expressed antibodies were purified from conditioned media 5 days post-transfection by filtering out the transfected cells. Conditioned media was incubated with protein A agarose beads for 1 hour. The bound beads were washed with Phosphate Buffered Saline (PBS) pH 7.4 followed by elution of the bound antibody with 0.1 M Glycine pH 2.5 and neutralized with 1/10 volume of Tris pH 8.5. The neutralized eluate was buffer exchanged into PBS. The resulting mAbs were designated as PRO034 (heavy chain sequence: SEQ ID NO: 56; light chain sequence: SEQ ID NO: 57), PRO035 (heavy chain sequence: SEQ ID NO: 58; light chain sequence: SEQ ID NO: 59), PRO036 (heavy chain sequence: SEQ ID NO: 60; light chain sequence: SEQ ID NO: 61), and PRO037 (heavy chain sequence: SEQ ID NO: 62; light chain sequence: SEQ ID NO: 63).
12. 2 Anti Notch2 Binding and Affinity Testing
To test the binding of the anti-Notch2 antibodies by ELISA, recombinant His-tagged human and murine Notch2 NRR domains, expressed and purified in house, were coated on NUNC-IMMUNO™ MAXISORP™ ELISA plates at 1 μg/mL concentration overnight. The next day, coated antigen was removed and the wells were blocked with 1% IgG-free BSA followed by incubation with 11 three-fold serially diluted anti-Notch2 antibodies (PRO034, PRO035, PRO036 and PRO037) with a starting concentration of 200 nM for PRO035 and PRO037 and 666 nM for PRO034 and PRO036. Bound antibody was detected with peroxidase-conjugated anti-human IgG antibodies with TMB and acid stop reagents. Each of the antibodies bound human and murine NRR domain of Notch2 with affinities between 47 pM and 140 nM.
To test the binding affinity of the anti-Notch2 antibodies by biolayer interferometry (BLI), each of PRO034, PRO035, PRO036 and PRO037 were immobilized on anti-human IgG Fc biosensors and dipped into the recombinant His-tagged murine and human Notch2 NRR protein at various concentrations from 1000 nM to 31 nM to measure the rate of association with the antigen. The dissociation rate was then measured by dipping the biosensors into buffer. The binding affinity was calculated as a ratio of the dissociation rate to the association rate. The intrinsic affinities determined by BLI were all in the nM range, suggesting that avidity improves affinity in an ELISA format.
12. 3 Design and Production of Notch2/RAGE ANDbodies
ANDbodies containing a first fragment antigen-binding (Fab) arm of a anti-Notch2 antibody described above (PRO034, PRO035, and PRO036) and a second Fab arm of the anti-RAGE antibody PRO002 (Example 8) were generated using a controlled Fab arm exchange (cFAE) reaction (Labrijn et al., Proc Natl Acad Sci U.S.A., 110(13): 5145-5150, 2013). Site-directed mutagenesis was performed to introduce a F405L amino acid substitution mutation in the Fc fragment of the anti-RAGE antibody (PRO002) and a K409R amino acid substitution mutation in the Fc fragment of each of the anti-Notch2 antibodies (PRO034, PRO035, and PRO036). These antibodies were expressed and purified as described previously for the parental antibodies. The individual monoclonal antibodies were then mixed in an equimolar ratio in a controlled reduction and reoxidation reaction that drives recombination of the bispecific antibody guided by the matching point mutations (F405L-K409R). The formation of the ANDbody was analyzed by analytical chromatography and SDS-PAGE. The resulting ANDbodies were designated as PRO051, PRO052 and PRO053 (comprising PRO034, PRO035, and PRO036, respectively).
SDS-PAGE and analytical size exclusion chromatography showed that the major product formed after cFAE reaction had a molecular weight of a typical IgG1 (150 kDa), suggesting complete reoxidation. Analytical hydrophobic interaction chromatography indicated the formation of a new product, the desired heterodimeric antibody.
12.4 Notch2/RAGE ANDbodies are Shown to Bind Simultaneously to Notch2 and RAGE by BLI
To test simultaneous dual antigen binding of the Notch2/RAGE ANDbodies by BLI, PRO051, PRO052 and PRO053, along with monovalent parental antibody controls were immobilized on anti-human IgG Fc biosensors and dipped into the recombinant His-tagged murine RAGE protein at 150 nM, followed by a second association step into wells containing recombinant murine Notch2 NRR at 150 nM to measure dual antigen binding. The dissociation rate was then measured by dipping the biosensors into buffer.
The sensorgrams showed that the ANDbodies PRO051, PRO052 and PRO053 were able to bind both RAGE and Notch2 antigens simultaneously, but the monovalent parental antibodies bound only one of RAGE and Notch2 NRR. This supports the conclusion that the ANDbodies were the correct composition and were functional in binding both antigens simultaneously.
12.5 Notch2/RAGE ANDbody are Shown to Bind Preferentially to Human Lung Tissue by Immunohistochemistry
Immunohistochemistry (IHC) on fresh frozen healthy mouse tissue microarray (FF TMA) sections mounted onto glass slides was used to evaluate tissue binding by ANDbodies containing the Notch2 inhibitory antibodies described above. TMAs were constructed and stained as described in Example 11.
12.6 A Notch2/RAGE ANDbody Distributes Preferentially to the Lungs Compared to a Matched Non-Targeted Anti-Notch2 Antibody
To evaluate how an ANDbody targeting Notch2 and RAGE behaves in vivo, mice were treated by IV dosing with the PRO051, PRO052, and PRO053 antibodies at 3 mg/kg. All groups contained 3 mice. At 3, 7, 14, and 21 days after dosing, tissues were collected from each mouse. The accumulation of each antibody in the lungs was measured by homogenizing a fixed amount of lung tissue, normalizing each sample to a fixed amount of extracted protein, and then detecting the human antibody by sandwich ELISA.
This example describes the production of an exemplary ANDbody that (i) comprises a ligand effector that targets the IL-10 pathway and (ii) binds DSG1 as an address.
13.1 Description, Design and Production of IL-10/DSG1 ANDbodies
To test formats of IL-10/anti-DSG1 ANDbodies, three parameters were explored: valency of IL-10 (1 or 2 moieties of IL-10), valency of the anti-DSG1 arm (1 or 2 Fab arms) and two versions of IL-10 (dimeric or monomeric IL-10). Formats that represent different combinations of IL-10 molecules, IL-10 valency, and antibody valency were assessed. Wild-type (WT) IL-10 (accession number P22301), a monomeric engineered IL-10 sequence (Josephson et al., J Biol Chem., 275(18): 13552-7, 2000), and a dimeric engineered IL-10 sequence (Minshawi et al., Front Immunol., 11: 1794, 2020) were fused to PRO003 sequences (Example 7) at the C-terminus of heavy chain for the bivalent formats. For monovalent formats, monomeric and dimeric IL-10 were fused at the N-terminus of the Fc and co-expressed with PRO003. The monovalent formats are asymmetric, and mutations in the Fc domain (chain A: S364K/K409S; chain B: K370S/F405K (WO 2017/106462 A1)) are used to enforce asymmetric pairing.
To express and purify the antibodies, a 1:1 ratio of heavy chain to light chain DNA or a 1:1:1 ratio of heavy chain to light chain to IL-10-Fc (listed below) was transfected into EXPI293F™ cells (ThermoFisher Scientific) using the EXPIFECTAMINE™ 293 Transfection Kit (ThermoFisher Scientific) following the manufacturer's recommendations. Transiently expressed antibodies were purified from conditioned media 5 days post-transfection by filtering out the transfected cells. Conditioned media was incubated with protein A agarose beads for 1 hour. The bound beads were washed with Phosphate Buffered Saline (PBS) pH 7.4 followed by elution of the bound antibody with 0.1 M Glycine pH 2.5 and neutralized with 1/10 volume of Tris pH 8.5. The neutralized eluate was buffer exchanged into PBS.
The resulting mAbs were designated as PRO023, PRO024, PRO025, PRO026 and PRO027 (
PRO023 comprises (a) a heavy chain sequence (SEQ ID NO: 67) comprising the heavy chain sequence of PRO003 (SEQ ID NO: 28) and the wild-type human IL-10 sequence (SEQ ID NO: 64) and (b) the light chain sequence of PRO003 (SEQ ID NO: 29).
PRO024 comprises (a) a heavy chain sequence (SEQ ID NO: 68) comprising the heavy chain sequence of PRO003 (SEQ ID NO: 28) and the monomeric human IL-10 sequence (SEQ ID NO:64) and (b) the light chain sequence of PRO003 (SEQ ID NO: 29).
PRO025 comprises (a) a heavy chain sequence (SEQ ID NO: 69) comprising the heavy chain sequence of PRO003 (SEQ ID NO: 28) and the dimeric human IL-10 sequence (SEQ ID NO:66) and (b) the light chain sequence of PRO003 (SEQ ID NO: 29).
PRO026 comprises (a) the heavy chain sequence of PRO003, further comprising mutations in the Fc domain to enforce asymmetric pairing (SEQ ID NO: 70), (b) the light chain sequence of PRO003 (SEQ ID NO: 29), and (c) an IL-10-Fc fusion protein (SEQ ID NO: 72) comprising an Fc region including mutations to enforce asymmetric pairing (SEQ ID NO: 71) and a monomeric human IL-10 sequence (SEQ ID NO:64).
PRO027 comprises (a) the heavy chain sequence of PRO003, further comprising mutations in the Fc domain to enforce asymmetric pairing (SEQ ID NO: 70), (b) the light chain sequence of PRO003 (SEQ ID NO: 29), and (c) an IL-10-Fc fusion protein (SEQ ID NO: 73) comprising an Fc region including mutations to enforce asymmetric pairing (SEQ ID NO: 71) and the dimeric human IL-10 sequence (SEQ ID NO:66).
The purified ANDbodies were analyzed by analytical size exclusion chromatography for monodispersity and by SDS-PAGE for purity. PRO024 and PRO026 had the highest yields and monodispersity after single-step purification. PRO023 and PRO027 had moderate yields and were ˜70% monodispersed. PRO025 had lower yields with ˜89% monodispersity.
13.2 IL-10/DSG1 ANDbodies Bind to Both IL-10 Receptors
To test the binding of the IL-10/anti-DSG1 ANDbodies to IL-10 receptor alpha (IL-10Ra) by ELISA, recombinant His-tagged human IL-10Ra (Creative Biomart) was coated on NUNC-IMMUNO™ MAXISORP™ ELISA plates at 1 μg/mL concentration overnight. The next day, coated antigen was removed and the wells were blocked with 1% IgG-free BSA followed by incubation with 11 three-fold serially diluted anti-IL-10/anti-DSG1 ANDbodies (as provided above) with a starting concentration of 30 μg/mL. Bound antibody was detected with peroxidase-conjugated anti-human IgG antibodies with TMB and acid stop reagents.
Of the molecules tested, only those containing an IL-10 moiety (PRO023, PRO024, PRO025, PRO026, PRO027, and the positive control IL-10 Fc) (Creative Biomart IL10-326H) bound IL-10Ra, demonstrating that the binding was driven by IL-10 and not the negative control anti-DSG1 antibody (PRO003) and that the IL-10 moiety was functional in binding its receptor.
13.3 IL-10/DSG1 ANDbodies Activate the IL-10 Signaling Pathway
To show that IL-10 retains its biological activity as a part of the various ANDbodies described above, the ability to each IL-10/DSG1 ANDbody to activate the IL-10 signaling pathway was tested. HEK-BLUE™ IL-10 cells (InvivoGen) were used to evaluate the signaling activity and relative potency of each molecule. These cells express all the components of the IL-10 signaling pathway, including an IL-10-inducible gene encoding secreted embryonic alkaline phosphatase (SEAP). When IL-10 signaling is activated in these cells, they express and secrete SEAP in to the cell culture media. The degree of IL-10 signal is measured by adding QUANTI-BLUE™ solution colorimetric reagent (InvivoGen) to the cell culture media, followed by reading absorbance at 630 nm.
In this experiment, each of PRO023, PRO024, PRO025, PRO026, and PRO027 was titrated from 1 pM to >1 nM with overnight incubation in cell culture.
13.4 IL-10/DSG1 ANDbodies Suppress the Inflammatory Response in Primary Mouse Macrophages
To show that IL-10/DSG1 ANDbodies are able to inhibit inflammatory immune responses, the effects of IL-10/DSG1 ANDbodies on mouse peripheral blood mononucleocytes (PBMCs) and macrophages treated with lipid polysaccharide (LPS) as an inflammatory stimulus were evaluated. In these experiments, PBMCs were isolated from blood and macrophages were isolated from the spleens of Balb/C mice by negative enrichment on magnetic beads (Miltenyi Biotech #130-110-434). Macrophage activation was assayed by measuring the level of TNFα cytokine present in the media after 3 hours and 5-6 hours of stimulation with LPS.
13.5 Engagement of an Address Target Enhances the Activity/Potency of the Effector Function of an ANDbody
The combination of addressing (e.g., using an address targeting domain) with a biologically active molecule has the potential to enhance a biological activity in a variety of ways. One exemplary enhancement is by increasing the potency of the effector moiety on specific cells where the address target is also present.
To test whether signaling potency of the effector targeting domain can be enhanced by the presence of an address targeting domain, human DSG1 was expressed on the HEK-BLUE™ IL-10 cells using stable expression with a lentivirus (the stable expressing cells are denoted HEKBLUE™ IL-10/DSG1). The DSG1 gene (NP_034209.2) was cloned into a suitable lentiviral plasmid backbone, packaged into viral particles using the VIRAPOWER™ Lentiviral Packing Mix (ThermoFisher Scientific) and transduced according to the manufacturer's instructions. Expression of DSG1 was confirmed by qPCR.
The potency of recombinant human IL-10, an ANDbody in which monomeric IL-10 replaces one Fab of the anti-DSG1 mAb (PRO058, functionally equivalent to PRO026), and a matched control in which the antibody sequence contains Motavizumab as a negative control were evaluated. Activity was tested on HEK-BLUE™ IL-10 cells and on HEK-BLUE™ IL-10 cells stably expressing DSG1.
13.6 IL-10/DSG1 ANDbodies Retain the Pharmacokinetic and Tissue Distribution Properties of the Parental Anti-DSG1 Antibody
In some ANDbodies the targeting moiety is intended to impart the tissue or cellular targeting of a parental mAb or other targeting molecule onto a biologically active moiety that would otherwise have undesirable pharmacokinetics or tissue distribution.
The IL-10/DSG1 ANDbodies are intended to direct IL-10 activity to the skin. In Example 7, it was shown that this anti-DSG1 antibody distributes preferentially into the skin of mice. In contrast, IL-10 is reported to clear from circulation in humans with a half-life of approximately 2 hours (Radwanski et al, Pharm Res. 1998 December; 15(12):1895-901. We therefore evaluated whether IL-10/DSG1 ANDbodies retain the skin targeting capability of the parental antibody.
BALB/c mice were dosed by tail vein injection with 3 mg/kg of PRO003, PRO024, or PRO058. PRO058 is functionally equivalent to PRO026, with a substitution in the Fc domain to improve purification of the recombinant protein. PRO058 comprises (a) the heavy chain sequence of PRO0026 (SEQ ID NO: 70), (b) the light chain sequence of PRO003 (SEQ ID NO: 29), and (c) an IL-10-Fc fusion protein (SEQ ID NO: 75) comprising an Fc region (SEQ ID NO: 74) and a monomeric human IL-10 sequence (SEQ ID NO:64).
Serum samples were collected at time points from 1 hour to 48 hours. Tissue samples were collected at 1, 2, 4 and 7 days after dosing. The amount of anti-DSG1 or ANDbody in each serum or tissue sample was measured by ELISA.
This example describes the production of exemplary ANDbodies that block TNFα and bind DSG1 as an address.
14.1 Anti TNFα Monoclonal Antibody Expression and Purification
Anti TNFα antibodies having VH and VL sequences from a commercial antibody fused to a hulgG1 backbone with effector null mutations L234A, L235A, P329G (LALA-PG) were produced and their binding and affinity to TNFα was characterized as described above. The resulting mAbs were designated as PRO076 and PRO078.
14.2 Anti TNFα—DSG1 ANDbody Design, Expression and Purification
ANDbodies were designed by combining PRO004 (Example 7) with a previously reported dominant-negative TNFα (Steed et al. Science. 2003 Sep. 26; 301(5641) or clinically validated anti-TNFα antibodies listed below with the aim of locally downmodulating TNFα in the extracellular milieu of the inflamed skin. The TNFα-blocking anti-DSG1 ANDbody designs explored various formats and valencies, including cytokine/antibody and TNF receptor 2 (TNFR2)/antibody fusions.
To express and purify the antibodies, a 1:1 ratio of heavy chain to light chain DNA was transfected into EXPI293F™ Cells (ThermoFisher Scientific) using the EXPIFECTAMINE™ 293 Transfection Kit (ThermoFisher Scientific) following the manufacturer's recommendations. Transiently expressed antibodies were purified from conditioned media 5 days post-transfection by filtering out the transfected cells. Conditioned media was incubated with protein A agarose beads for 1 hour. The bound beads were washed with Phosphate Buffered Saline (PBS) pH 7.4 followed by elution of the bound antibody with 0.1 M Glycine pH 2.5 and neutralized with 1/10 volume of Tris pH 8.5. The neutralized eluate was buffer exchanged into PBS. The resulting mAbs were designated as PRO070, PRO074, PRO075 and PRO077 (
The purified ANDbodies were analyzed by analytical size exclusion chromatography for monodispersity and by SDS-PAGE for purity. Standard additional purification steps were performed to remove aggregation. PRO077 had the highest final yield, followed by PRO074 and PRO075, while PRO070 had the lowest final yield. The polished ANDbodies were pure and of the correct composition as seen by SDS-PAGE.
14.3 Anti TNFα—DSG1 ANDbody Binding and Affinity Testing
ELISA binding assays demonstrated that all constructs were active in binding human and murine TNFα with varying affinities. PRO074 and PRO075 had similar affinities to both human and murine TNFα, which was within two/three-fold difference to the parent antibody. PRO077 had a 5-fold and a 12-fold decrease in binding affinity to human and murine TNFα, respectively, when compared to the parent antibody. This reduction in affinity is probably due to the change of format from Fab to single-chain variable fragment (scFv).
14.4 Anti TNFα—DSG1 ANDbody In Vitro Activity Assays
The ability of each anti-TNFα/anti-DSG1 ANDbody to inhibit TNFα signaling was evaluated using HEK-BLUE™ TNFα cells (InvivoGen). These cells are engineered to express secreted embryonic alkaline phosphatase (SEAP) in response to signaling to TNFα signaling. TNFα was measured according to the manufacturer's instructions. To evaluate inhibitory activity, the concentration of TNFα was fixed at 225 pm (approximately the EC80 of a recombinant human TNFα in this assay), and cells were pre-incubated with concentrations of TNFα blocking molecules from 10 nM to approximately 10 pM. Table 12 shows the IC50 of each anti-TNFα/DSG1 ANDbody alongside matched parent antibodies as positive controls. These data show that the ANDbodies retain TNFα blocking activity comparable to the original anti-TNFα parent antibodies.
Some embodiments of the technology described herein can be defined according to any of the following numbered embodiments:
1. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein:
(i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell;
(ii) the second binding site does not substantially influence signaling upon binding the address target; and
(iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site.
2. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein:
(i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell;
(ii) the second binding site does not substantially influence signaling upon binding the address target; and
(iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site;
and wherein localization of the macromolecule to a non-target tissue or cell is substantially reduced relative to localization of a reference macromolecule lacking the second binding site.
3. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein:
(i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell;
(ii) the second binding site does not substantially influence signaling upon binding the address target; and
(iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site;
and wherein localization of the macromolecule to a target tissue or cell is substantially increased relative to localization of a reference macromolecule lacking the second binding site.
4. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein:
(i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell;
(ii) the second binding site does not substantially influence signaling upon binding the address target; and
(iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site;
and wherein at least 25% of the macromolecule administered to a subject is detected at the target tissue or cell at a time point between 1 and 7 days following administration.
5. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein:
(i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell;
(ii) the second binding site does not substantially influence signaling upon binding the address target; and
(iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site;
and wherein the affinity of the first binding site for the effector target is lower than the affinity of the second binding site for the address target.
6. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein:
(i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell;
(ii) the second binding site does not substantially influence signaling upon binding the address target; and
(iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site;
and wherein the avidity of the first binding site for the effector target is lower than the avidity of the second binding site for the address target.
7. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein:
(i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell;
(ii) the second binding site does not substantially influence signaling upon binding the address target; and
(iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site;
and wherein the potency of the first binding site at the target tissue or cell is substantially increased relative to a reference macromolecule lacking the second binding site.
8. The macromolecule of any one of embodiments 1-7, wherein the first binding site has a low affinity for the effector target.
9. The macromolecule of any one of embodiments 1-7, wherein the first binding site has a low avidity for the effector target.
10. The macromolecule of any one of embodiments 1˜4 and 6-9, wherein the affinity of the first binding site for the effector target is lower than the affinity of the second binding site for the address target.
11. The macromolecule of any one of embodiments 1-10, wherein the avidity of the first binding site for the effector target is lower than the avidity of the second binding site for the address target.
12. The macromolecule of any one of embodiments 1-11, wherein:
(a) the Kd of the first binding site for the effector target is higher than the Kd of the second binding site for the address target;
(b) the EC50 of the first binding site for the effector target is higher than the EC50 of the second binding site for the address target; or
(c) the IC50 of the first binding site for the effector target is higher than the IC50 of the second binding site for the address target.
13. The macromolecule of any one of embodiments 1-12, wherein the first binding site has an affinity to the effector target of at least about 2 times, at least about 5 times, or at least about 10 times less than the affinity of the second binding site to the address target.
14. The macromolecule of any one of embodiments 1-13, wherein the affinity of the second binding site to the address target has a Kd of greater than about 1 nM, greater than about 2 nM, or greater than about 50 nm.
15. The macromolecule of any one of embodiments 1-14, wherein the effector target is a protein, lipid, or sugar.
16. The macromolecule of any one of embodiments 1-15, wherein the effector target is a cell membrane-associated target.
17. The macromolecule of embodiment 15 or 16, wherein the effector target is a protein.
18. The macromolecule of embodiment 17, wherein the effector target is a secreted protein.
19. The macromolecule of embodiment 17 or 18, wherein the effector target is encoded by a gene selected from the group consisting of the genes recited in Table 1.
20. The macromolecule of any one of embodiments 1-19, wherein the macromolecule agonizes the effector target.
21. The macromolecule of any one of embodiments 1-19, wherein the macromolecule antagonizes the effector target.
22. The macromolecule of any one of embodiments 1-21, wherein the address target is a protein, lipid, or sugar.
23. The macromolecule of embodiment 22, wherein the address target is a protein.
24. The macromolecule of any one of embodiments 17-23, wherein expression of the effector target or the address target is expression of an RNA sequence encoding the effector target or the address target.
25. The macromolecule of embodiment 24, wherein the expression level of the effector target or the address target is assessed by using a RNA sequence dataset.
26. The macromolecule of embodiment 25, wherein the RNA sequence dataset is a Genotype-Tissue Expression (GTEx) dataset or a Human Protein Atlas (HPA) dataset.
27. The macromolecule of embodiment 23, wherein expression of the effector target or the address target is protein expression.
28. The macromolecule of any one of embodiments 1-27, wherein the effector target is systemically expressed in the subject.
29. The macromolecule of any one of embodiments 1-27, wherein the effector target is regionally expressed in the subject.
30. The macromolecule of any one of embodiments 1-27, wherein the effector target is locally expressed in the subject.
31. The macromolecule of any one of embodiments 1-30, wherein the address target is regionally expressed in the subject.
32. The macromolecule of any one of embodiments 1-30, wherein the address target is locally expressed in the subject.
33. The macromolecule of any one of embodiments 1-30, wherein the expression of the address target is restricted to a cell type in the subject.
34. The macromolecule of any one of embodiments 1-33, wherein the address target is a soluble protein or an extracellular matrix (ECM)-associated protein and is not present in detectable amounts on the cell surface.
35. The macromolecule of embodiment 34, wherein the address target is expressed in the ECM and is not present in detectable amounts elsewhere in the subject.
36. The macromolecule of any one of embodiments 1-35, wherein the address target is expressed only by a cell in the subject when in a specific cell state.
37. The macromolecule of any one of embodiments 1-36, wherein the address target is expressed only by a cell in the subject when in a disease state.
38. The macromolecule of any one of embodiments 1-37, wherein the address target is not expressed in a tissue in which binding of the second binding site to the effector target is deleterious to the subject.
39. The macromolecule of any one of embodiments 1-38, wherein the binding site for the address target does not bind in detectable amounts to the binding site of a natural ligand of the address target.
40. The macromolecule of any one of embodiments 1-39, wherein expression of the effector target or address target includes expression in one or more of minor salivary gland, thyroid, lung, breast, mammary tissue, pancreas, adrenal gland, liver, kidney, kidney cortex, kidney medulla, adipose-visceral tissue, omentum, small intestine, terminal ileum, fallopian tube, ovary, uterus, skin, skin not sun exposed, suprapubic skin, cervix, endocervix, ectocervix, vagina, skin sun exposed, lower leg skin, eneanterior cingulate cortex, Brodmann area 24 (BA24), basal ganglia, caudate nucleus, putamen, nucleus acumbens, hypothalamus, amygdala, hippocampus, cerebellum, cerebellar hemisphere, substantia nigra, pituitary gland, spinal cord, cervical spinal cord, artery, aorta, heart, atrial appendage, coronary artery, left ventricle, esophagus, esophagus mucosa, esophagus muscularis, gastroesophageal junction, spleen, stomach, colon, transverse colon, sigmoid colon, testis, whole blood cells, EBV-transformed lymphocytes, artery-tibial, or nerve-tibial tissues.
41. The macromolecule of embodiment 40, wherein expression of the effector target or address target includes expression in skin tissue, lung tissue, kidney tissue, or intestine tissue.
42. The macromolecule of embodiment 41, wherein expression of the address target is substantially higher in skin tissue, lung tissue, kidney tissue, or intestine tissue than in any other tissue.
43. The macromolecule of any one of embodiments 1-42, wherein the effector target and/or the address target is expressed on a structural tissue in the subject.
44. The macromolecule of any one of embodiments 1-43, wherein the effector target and address target are on the same cell.
45. The macromolecule of any one of embodiments 1-43, wherein the effector target and address target are on different cells.
46. The macromolecule of embodiment 45, wherein the effector target and address target are on different cells of the same cell type.
47. The macromolecule of embodiment 45, wherein the effector target and address target are on different cells of different cell types.
48. The macromolecule of embodiment 45, wherein the effector target and address target are on different cells in the same tissue.
49. The macromolecule of any one of embodiments 45, 47, and 48, wherein:
(a) the effector target is on a circulating cell and the address target is on a tissue-restricted cell; or
(b) the effector target is on a tissue-restricted cell and the address target is on a circulating cell.
50. The macromolecule of any one of embodiments 45-49, wherein the effector target and address target are on different cells located within 100 nm of each other in the subject.
51. The macromolecule of any one of embodiments 45-49, wherein either the effector target or the address target is present on a cell surface.
52. The macromolecule of any one of embodiments 1-51, wherein the macromolecule is a DNA polynucleotide.
53. The macromolecule of any one of embodiments 1-51, wherein the macromolecule comprises an RNA or RNA-polypeptide conjugate.
54. The macromolecule of any one of embodiments 1-51 and 53, wherein the macromolecule comprises a polypeptide.
55. The macromolecule of any one of embodiments 1-51, wherein the macromolecule is a polypeptide.
56. The macromolecule of embodiment 54 or 55, wherein the polypeptide is an antibody or antigen-binding fragment thereof.
57. The macromolecule of embodiment 56, wherein the first binding site and the second binding site each comprise a VH and/or a VL.
58. The macromolecule of embodiment 57, wherein the macromolecule is an antibody comprising a first binding site that is specific for the effector target in the subject and a second binding site that is specific for the address target.
59. The macromolecule of embodiment 57 or 58, wherein the macromolecule is an asymmetric antibody or a symmetric antibody.
60. The macromolecule of any one of embodiments 56-59, wherein the antibody or antigen-binding fragment thereof comprises an scFv, BsIgG, a BsAb fragment, a BiTE, a dual-affinity re-targeting protein (DART), a tandem diabody (TandAb), a diabody, an Fab2, a di-scFv, chemically linked F(ab′)2, an Ig molecule with 2, 3 or 4 different antigen binding sites, a DVI-IgG four-in-one, an ImmTac, an HSAbody, an IgG-IgG, a Cov-X-Body, an scFv1-PEG-scFv2, an appended IgG, an DVD-IgG, an affibody, an affilin, an affimer, an affitin, an alphabody, an anticalin, an avimer, a DARPin, a Fynomer, a monobody, a nanoCLAMP, a bis-Fab, an Fv, a Fab, a Fab′-SH, a linear antibody, an scFv, an antibody with only a heavy chain (Humabody), an ScFab, an IgG antibody fragment, a single-chain variable region antibody, a single-domain heavy chain antibody. a bispecific triplebody, a BiKE, a CrossMAb, a dsDb, an scDb, tandem a dAb/VHH, a triple dAb VHH, a tetravalent dAb/VHH, a Fab-scFv, a Fab-Fv, or a DART-Fc, an adnectin, a Kunitz-type inhibitor, or a receptor decoy.
61. The macromolecule of embodiment 54, wherein the polypeptide is a ligand of the effector target or a ligand of the address target.
62. The macromolecule of embodiment 61, wherein the ligand is a natural ligand, a modified ligand, or a synthetic ligand.
63. The macromolecule of embodiment 61 or 62, wherein the effector target or address target is a receptor and the polypeptide is a ligand thereof.
64. The macromolecule of any one of embodiments 61-63, wherein the first binding site comprises an antibody or antigen-binding fragment thereof and the second binding site comprises a ligand of the address target.
65. The macromolecule of any one of embodiments 61-63, wherein the first binding site comprises a ligand of the effector target and the second binding site comprises an antibody or antigen-binding fragment thereof.
66. The macromolecule of any one of embodiments 1-51 and 54-65, wherein the amino acid sequences of the first and second binding sites are at least about 10% identical, at least about 20% identical, at least about 30% identical, at least about 40% identical, at least about 50% identical, at least about 60% identical, or at least about 70% identical.
67. The macromolecule of any one of embodiments 1-66, wherein the address target has a Gini coefficient higher than about 0.4, about 0.5, about 0.57, about 0.65, about 0.7, about 0.85, about 0.90, or about 0.95.
68. The macromolecule of any one of embodiments 1-67, wherein the address target has a Tau coefficient higher than about 0.67, about 0.75, about 0.8, about 0.85, about 0.90, or about 0.95.
69. The macromolecule of any one of embodiments 1-68, wherein the effector target has a Gini coefficient lower than about 0.25, about 0.20, or about 0.15.
70. The macromolecule of any one of embodiments 1-69, wherein the effector target has a Tau coefficient lower than about 0.25, about 0.20, or about 0.15.
71. The macromolecule of any one of embodiments 1-70, further comprising a third binding site.
72. The macromolecule of embodiment 71, wherein the third binding site is the same as the first binding site.
73. The macromolecule of embodiment 71, wherein the third binding site is the same as the second binding site.
74. The macromolecule of any one of embodiments 1-73, wherein the first binding site and second binding site are directly joined to each other in the macromolecule.
75. The macromolecule of any one of embodiments 1-73, wherein the first binding site and the second binding site in the macromolecule are joined by a stable domain.
76. The macromolecule of any one of embodiments 1-75, wherein the effector target is Notch2 and the address target is RAGE.
77. The macromolecule of embodiment 76, wherein RAGE signaling is not influenced by the second site binding the RAGE address target.
78. The macromolecule of any one of embodiments 1-75, wherein the effector target is Notch2 and the address target is uromodulin (UMOD).
79. The macromolecule of embodiment 78, wherein UMOD signaling is not influenced by the second site binding the UMOD address target.
80. The macromolecule of any one of embodiments 1-75, wherein the effector target is Notch2 and the address target is meprin A subunit beta (MEP1B).
81. The macromolecule of embodiment 80, wherein MEP1B signaling is not influenced by the second site binding the MEP1B address target.
82. The macromolecule of any one of embodiments 1-75, wherein the effector target is IL11Ra and the address target is RAGE.
83. The macromolecule of embodiment 82, wherein RAGE signaling is not influenced by the second site binding the RAGE address target.
84. The macromolecule of any one of embodiments 1-75, wherein the effector target is IL 11 Ra and the address target is UMOD.
85. The macromolecule of embodiment 84, wherein UMOD signaling is not influenced by the second site binding the UMOD address target.
86. The macromolecule of any one of embodiments 1-85, wherein the subject is a human.
87. A method of delivering a moiety to a target tissue or cell in a subject, comprising administering to the subject a macromolecule of any one of embodiments 1-86, wherein the target tissue comprises the address target.
88. The method of embodiment 87, wherein the moiety is a molecule.
89. The method of embodiment 87 or 88, wherein the moiety is not a toxin.
90. The method of embodiment 87, wherein the moiety is a cell.
91. The method of embodiment 90, wherein the moiety is not a T cell or an NK cell.
92. The method of any one of embodiments 87-91, wherein the target tissue is not a tumor.
93. A method of modulating an effector target in a target tissue, comprising administering to the tissue a macromolecule of any one of embodiments 1-86, wherein the target tissue comprises the address target and the effector target.
94. A method of biasing a binding agent away from binding an effector target when the effector target is found in the heart or lungs, comprising administering the macromolecule of any one of embodiments 1-86, wherein the address target is not substantially expressed in the heart or lungs.
95. A method of modulating a target tissue in a subject, comprising administering to the subject a macromolecule of any one of embodiments 1-86, wherein the target tissue comprises the address target and the effector target.
96. A method of treating a subject having a disease or condition associated with an effector target, comprising administering to the subject a macromolecule of any one of embodiments 1-86, wherein the first binding site of the macromolecule binds the effector target.
97. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject;
wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell,
wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site, and
wherein the second binding site does not bind to the binding site of the natural ligand of the address target.
98. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject;
wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell,
wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site, and
wherein the first binding site and second binding site are directly joined to each other in the macromolecule.
99. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject;
wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell,
wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site, and
wherein the first binding site and second binding are joined to each other by a stable domain.
100. A macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject;
wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell,
wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site, and wherein the effector target and/or the address target is expressed on a structural tissue in a host.
101. A pharmaceutical composition comprising the macromolecule of any one of embodiments 1-86.
102. A pharmaceutical composition comprising a macromolecule and one or more pharmaceutically acceptable excipients,
wherein the macromolecule comprises a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject;
wherein the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell, and
wherein the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site.
103. The pharmaceutical composition of embodiment 101 or 102, wherein the pharmaceutical composition is an RNA pharmaceutical composition.
104. The pharmaceutical composition of any one of embodiments 101-103, further comprising a carrier.
105. The pharmaceutical composition of embodiment 104, wherein the carrier is a lipid nanoparticle.
106. The pharmaceutical composition of embodiment 104, wherein the carrier is a viral vector.
107. The pharmaceutical composition of embodiment 104, wherein the carrier is a membrane-based carrier.
108. The pharmaceutical composition of embodiment 107, wherein the membrane-based carrier is a cell.
109. The pharmaceutical composition of embodiment 107, wherein the membrane-based carrier is a vesicle.
110. A method for modulating activity of an effector target in the skin of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in the subject, and
(b) the second binding site is specific for desmoglein-1 (DSG-1).
111. A method for modulating activity of an effector target in the lung of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in the subject, and
(b) the second binding site is specific for RAGE.
112. A method for modulating activity of an effector target in the kidney of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in the subject, and
(b) the second binding site is specific for cadherin 16 (CDH16).
113. A method for modulating activity of an effector target in the intestine of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in the subject, and
(b) the second binding site is specific for cadherin 17 (CDH17).
114. A method of localizing a macromolecule at a target tissue or cell of a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in the subject, and
(b) the second binding site is specific for an address target expressed in the target tissue or cell in the subject; wherein:
(i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell;
(ii) the second binding site does not substantially influence signaling upon binding the address target; and
(iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site; and
allowing the macromolecule to localize at the target tissue or cell of the subject.
115. A method of concentrating a macromolecule in a target tissue or cell in a subject, the method comprising administering to the subject a macromolecule comprising a first binding site and a second binding site, wherein:
(a) the first binding site is specific for an effector target in a subject, and
(b) the second binding site is specific for an address target expressed in a target tissue or cell in the subject; wherein:
(i) the second binding site localizes the first binding site to the address target such that the first binding site influences effector target signaling in the target tissue or cell;
(ii) the second binding site does not substantially influence signaling upon binding the address target; and
(iii) the first binding site does not substantially influence effector target signaling in the absence of localization by the second binding site;
and allowing the macromolecule to concentrate at the target tissue or cell of the subject, wherein at least 25% of the macromolecule detectable in the subject is detected at the target tissue or cell at a time point between 1 and 7 days following administration of the macromolecule to the subject.
116. The method of embodiment 114 or 115, wherein the potency of the first binding site at the target tissue or cell is substantially increased relative to a reference macromolecule lacking the second binding site.
117. The method of embodiment 114 or 115, wherein effector target signaling by the macromolecule in a non-target tissue or cell of the subject is substantially decreased relative to a reference macromolecule lacking the second binding site.
118. The method of embodiments 110-117, wherein the macromolecule is a macromolecule of any one of embodiments 1-86.
Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, the descriptions and examples should not be construed as limiting the scope of the invention.
| Number | Date | Country | |
|---|---|---|---|
| 63197928 | Jun 2021 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/US22/32561 | Jun 2022 | US |
| Child | 18055992 | US |
