COMPOUNDS AND METHODS FOR USE IN CONNECTION WITH OPIOID USE DISORDERS
20210380721 · 2021-12-09
Inventors
Cpc classification
C07K2299/00
CHEMISTRY; METALLURGY
C07K2317/92
CHEMISTRY; METALLURGY
C07K2317/10
CHEMISTRY; METALLURGY
C07K16/44
CHEMISTRY; METALLURGY
G16B15/30
PHYSICS
C07K2317/33
CHEMISTRY; METALLURGY
International classification
C07K16/44
CHEMISTRY; METALLURGY
G01N33/94
PHYSICS
G16B15/30
PHYSICS
Abstract
Compositions and methods are provided for use in binding opioids, such as 6-MAM, morphine, heroin, hydrocodone, oxycodone, meperidine, and fentanyl, while avoiding binding to OUD treatment agents, such as naloxone and naltrexone. Methods are also provided for use in a systematic structure-based virtual screening and design approach for identification of such antibodies. Methods are also provided for use in treating OUD. Methods are also provided for use in detecting an opioid in a sample.
Claims
1. A method of identifying antibodies that bind an opioid without significant binding with treatment agents for opioid use disorder (OUD): (a) identifying computationally-refined structures of candidate mAbs using amino-acid sequences of variable domains of the mAbs, homology models of the antibodies, and energy-minimization; (b) superimposing X-ray crystal structures of an opioid with the computationally-refined structures of the candidate mAbs to simulate binding of opioid and antibodies to create opioid-antibody complex structures having one or more binding poses; (c) conducting energy minimization for each binding pose of each opioid-antibody complex structure; (d) calculating binding free energy of each binding pose of each opioid-antibody complex structure; and (e) select the antibodies associated with the binding pose having low binding free energy.
2. The method of claim 1, wherein the opioid is one or more of 6-MAM, morphine, heroin, hydrocodone, oxycodone, meperidine, and fentanyl.
3. The method of claim 1, and further comprising: determining actual binding affinity of each predicted antibody by preparing and testing each predicted antibody.
4. The method of claim 3, wherein the opioid is one or more of 6-MAM, morphine, heroin, hydrocodone, oxycodone, meperidine, and fentanyl.
5. The method of claim 4, and further comprising determining the binding affinity of each predicted antibody with a treatment agent for OUD.
6. The method of claim 5, wherein the treatment agent for OUD is naloxone and/or and naltrexone.
7. An isolated antibody or antigen fragment thereof that selectively binds one or more of 6-MAM, morphine, heroin, hydrocodone, oxycodone, meperidine, and fentanyl, and does not selectively bind naloxone or naltrexone, wherein the antibody is selected from the group consisting of: (a) an antibody comprising the sequence of SEQ ID NO: 5; (b) an antibody comprising the sequence of SEQ ID NO: 12; (c) an antibody comprising the sequence of SEQ ID NO: 5 and 12; (d) an antibody comprising the sequence of SEQ ID NO: 25; (e) an antibody comprising the sequence of SEQ ID NO: 51; (f) an antibody comprising the sequence of SEQ ID NO: 25 and 51; (g) an antibody comprising the sequence of (i) SEQ ID NO: 65, 66, or 67, and (ii) SEQ ID NO: 68, 69, or 70; (h) an antibody comprising the sequence of (i) SEQ ID NO: 71 or 72, (ii) GTN, STN, or DTS, and (iii) SEQ ID NO: 73, 74, or 75; and (i) an antibody comprising the sequence of (i) SEQ ID NO: 65, 66, or 67, (ii) SEQ ID NO: 68, 69, or 70, (iii) SEQ ID NO: 71 or 72, (iv) GTN, STN, or DTS, and (v) SEQ ID NO: 73, 74, or 75.
8. A method of treating an opioid use disorder (OUD), comprising: administering to a subject in need thereof an antibody according to claim 7.
9. A method of detecting an opioid in a sample, comprising: contacting the sample with an antibody according to claim 7 and detecting binding of the antibody to a ligand.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
[0023] The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are used, and the accompanying drawings of which:
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[0025]
[0026]
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[0029]
BRIEF DESCRIPTION OF THE SEQUENCE LISTING
[0030] SEQ ID NO: 1 is the sequence included in a heavy chain sequence of an antibody, which is set forth in
[0031] SEQ ID NO: 2 is the sequence included in a heavy chain sequence of an antibody, which is set forth in
[0032] SEQ ID NO: 3 is the sequence included in a heavy chain sequence of an antibody, which is set forth in
[0033] SEQ ID NO: 4 is the sequence included in a heavy chain sequence of an antibody, which is set forth in
[0034] SEQ ID NO: 5 is the sequence included in a heavy chain sequence of an antibody, which is set forth in
[0035] SEQ ID NO: 6 is the sequence included in a light chain sequence of an antibody, which is set forth in
[0036] SEQ ID NO: 7 is the sequence included in a light chain sequence of an antibody, which is set forth in
[0037] SEQ ID NO: 8 is the sequence included in a light chain sequence of an antibody, which is set forth in
[0038] SEQ ID NO: 9 is the sequence included in a light chain sequence of an antibody, which is set forth in
[0039] SEQ ID NO: 10 is the sequence included in a light chain sequence of an antibody, which is set forth in
[0040] SEQ ID NO: 11 is the sequence included in a light chain sequence of an antibody, which is set forth in
[0041] SEQ ID NO: 12 is the sequence included in a light chain sequence of an antibody, which is set forth in
[0042] SEQ ID NO: 13 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0043] SEQ ID NO: 14 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0044] SEQ ID NO: 15 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0045] SEQ ID NO: 16 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0046] SEQ ID NO: 17 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0047] SEQ ID NO: 18 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0048] SEQ ID NO: 19 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0049] SEQ ID NO: 20 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0050] SEQ ID NO: 21 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0051] SEQ ID NO: 22 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0052] SEQ ID NO: 23 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0053] SEQ ID NO: 24 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0054] SEQ ID NO: 25 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0055] SEQ ID NO: 26 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0056] SEQ ID NO: 27 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0057] SEQ ID NO: 28 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0058] SEQ ID NO: 29 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0059] SEQ ID NO: 30 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0060] SEQ ID NO: 31 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0061] SEQ ID NO: 32 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0062] SEQ ID NO: 33 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0063] SEQ ID NO: 34 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0064] SEQ ID NO: 35 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0065] SEQ ID NO: 36 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0066] SEQ ID NO: 37 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0067] SEQ ID NO: 38 is the sequence included in a heavy chain sequence of an antibody, which is set forth in Table 1.
[0068] SEQ ID NO: 39 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0069] SEQ ID NO: 40 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0070] SEQ ID NO: 41 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0071] SEQ ID NO: 42 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0072] SEQ ID NO: 43 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0073] SEQ ID NO: 44 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0074] SEQ ID NO: 45 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0075] SEQ ID NO: 46 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0076] SEQ ID NO: 47 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0077] SEQ ID NO: 48 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0078] SEQ ID NO: 49 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0079] SEQ ID NO: 50 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0080] SEQ ID NO: 51 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0081] SEQ ID NO: 52 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0082] SEQ ID NO: 53 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0083] SEQ ID NO: 54 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0084] SEQ ID NO: 55 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0085] SEQ ID NO: 56 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0086] SEQ ID NO: 57 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0087] SEQ ID NO: 58 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0088] SEQ ID NO: 59 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0089] SEQ ID NO: 60 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0090] SEQ ID NO: 61 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0091] SEQ ID NO: 62 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0092] SEQ ID NO: 63 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0093] SEQ ID NO: 64 is the sequence included in a light chain sequence of an antibody, which is set forth in Table 1.
[0094] SEQ ID NO: 65 is the sequence of a complementarity-determining regions (CDRs) of the heavy chain of an antibody as disclosed herein.
[0095] SEQ ID NO: 66 is the sequence of a complementarity-determining regions (CDRs) of the heavy chain of an antibody as disclosed herein.
[0096] SEQ ID NO: 67 is the sequence of a complementarity-determining regions (CDRs) of the heavy chain of an antibody as disclosed herein.
[0097] SEQ ID NO: 68 is the sequence of a complementarity-determining regions (CDRs) of the heavy chain of an antibody as disclosed herein.
[0098] SEQ ID NO: 69 is the sequence of a complementarity-determining regions (CDRs) of the heavy chain of an antibody as disclosed herein.
[0099] SEQ ID NO: 70 is the sequence of a complementarity-determining regions (CDRs) of the heavy chain of an antibody as disclosed herein.
[0100] SEQ ID NO: 71 is the sequence of a complementarity-determining regions (CDRs) of the light chain of an antibody as disclosed herein.
[0101] SEQ ID NO: 72 is the sequence of a complementarity-determining regions (CDRs) of the light chain of an antibody as disclosed herein.
[0102] SEQ ID NO: 73 is the sequence of a complementarity-determining regions (CDRs) of the light chain of an antibody as disclosed herein.
[0103] SEQ ID NO: 74 is the sequence of a complementarity-determining regions (CDRs) of the light chain of an antibody as disclosed herein.
[0104] SEQ ID NO: 75 is the sequence of a complementarity-determining regions (CDRs) of the light chain of an antibody as disclosed herein.
[0105] This application contains a sequence listing submitted in accordance with 37 C.F.R. 1.821, named Zhan UKRF 2462 Sequence Listing_ST25.txt, created on Jun. 1, 2021, having a size of 72 KB, which is incorporated herein by this reference.
DESCRIPTION OF EXEMPLARY EMBODIMENTS
[0106] The details of one or more embodiments of the presently-disclosed subject matter are set forth in this document. Modifications to embodiments described in this document, and other embodiments, will be evident to those of ordinary skill in the art after a study of the information provided in this document. The information provided in this document, and particularly the specific details of the described exemplary embodiments, is provided primarily for clearness of understanding and no unnecessary limitations are to be understood therefrom. In case of conflict, the specification of this document, including definitions, will control.
[0107] The presently-disclosed subject matter includes methods of identifying antibodies that bind an opioid without significant binding with treatment agents for opioid use disorder (OUD).
[0108] In some embodiments, the method involves: (a) identifying computationally-refined structures of candidate mAbs using amino-acid sequences of variable domains of the mAbs, homology models of the antibodies, and energy-minimization; (b) superimposing X-ray crystal structures of an opioid with the computationally-refined structures of the candidate mAbs to simulate binding of opioid and antibodies to create opioid-antibody complex structures having one or more binding poses; (c) conducting energy minimization for each binding pose of each opioid-antibody complex structure; (d) calculating binding free energy of each binding pose of each opioid-antibody complex structure; and (e) select the antibodies associated with the binding pose having low binding free energy. In some embodiments, the opioid is one or more of 6-MAM, morphine, heroin, hydrocodone, oxycodone, meperidine, and fentanyl.
[0109] In some embodiments, the method also involves determining actual binding affinity of each predicted antibody by preparing and testing each predicted antibody. In some embodiments, the opioid is one or more of 6-MAM, morphine, heroin, hydrocodone, oxycodone, meperidine, and fentanyl.
[0110] In some embodiments, the method also involves determining the binding affinity of each predicted antibody with a treatment agent for OUD. In some embodiments, the treatment agent for OUD is naloxone and/or and naltrexone. The presently-disclosed subject matter further includes antibodies, and compositions including such antibodies, for use in treating OUD. In some embodiments, the antibody is discovered by a method as disclosed herein. In some embodiments, the antibody is UK6Mab01 or UK6Mab02.
[0111] The presently-disclosed subject matter includes an isolated antibody or antigen fragment thereof that binds one or more of 6-MAM, morphine, heroin, hydrocodone, oxycodone, meperidine, and fentanyl, and does not bind naloxone or naltrexone. In some embodiments, the antibody is selected from the group consisting of: (a) an antibody comprising the sequence of SEQ ID NO: 5; (b) an antibody comprising the sequence of SEQ ID NO: 12; (c) an antibody comprising the sequence of SEQ ID NOs: 5 and 12; (d) an antibody comprising the sequence of SEQ ID NO: 25; (e) an antibody comprising the sequence of SEQ ID NO: 51; (f) an antibody comprising the sequence of SEQ ID NO: 25 and 51; (g) an antibody comprising the sequence of (i) SEQ ID NO: 65, 66, or 67, and (ii) SEQ ID NO: 68, 69, or 70; (h) an antibody comprising the sequence of (i) SEQ ID NO: 71 or 72, (ii) GTN, STN, or DTS, and (iii) SEQ ID NO: 73, 74, or 75; and (i) an antibody comprising the sequence of (i) SEQ ID NO: 65, 66, or 67, (ii) SEQ ID NO: 68, 69, or 70, (iii) SEQ ID NO: 71 or 72, (iv) GTN, STN, or DTS, and (v) SEQ ID NO: 73, 74, or 75. In some embodiments, the antibody comprises a sequence selected from the group consisting of the sequence of any one of SEQ ID NOS: 1-75.
[0112] The presently-disclosed subject matter further includes methods for treating OUD, which involve administering an antibody as disclosed herein to a subject in need thereof.
[0113] The presently-disclosed subject matter further includes methods for detecting an opioid in a sample, which includes contacting the sample with an antibody as disclosed herein, and detecting binding of the antibody to a ligand.
[0114] While the terms used herein are believed to be well understood by those of ordinary skill in the art, certain definitions are set forth to facilitate explanation of the presently-disclosed subject matter.
[0115] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the invention(s) belong.
[0116] All patents, patent applications, published applications and publications, GenBank sequences, databases, websites and other published materials referred to throughout the entire disclosure herein, unless noted otherwise, are incorporated by reference in their entirety.
[0117] Where reference is made to a URL or other such identifier or address, it understood that such identifiers can change and particular information on the internet can come and go, but equivalent information can be found by searching the internet. Reference thereto evidences the availability and public dissemination of such information.
[0118] As used herein, the abbreviations for any protective groups, amino acids and other compounds, are, unless indicated otherwise, in accord with their common usage, recognized abbreviations, or the IUPAC-IUB Commission on Biochemical Nomenclature (see, Biochem. (1972) 11(9):1726-1732).
[0119] Although any methods, devices, and materials similar or equivalent to those described herein can be used in the practice or testing of the presently-disclosed subject matter, representative methods, devices, and materials are described herein.
[0120] In certain instances, nucleotides and polypeptides disclosed herein are included in publicly-available databases, such as GENBANK® and SWISSPROT. Information including sequences and other information related to such nucleotides and polypeptides included in such publicly-available databases are expressly incorporated by reference. Unless otherwise indicated or apparent the references to such publicly-available databases are references to the most recent version of the database as of the filing date of this application.
[0121] The present application can “comprise” (open ended) or “consist essentially of” the components of the present invention as well as other ingredients or elements described herein. As used herein, “comprising” is open ended and means the elements recited, or their equivalent in structure or function, plus any other element or elements which are not recited. The terms “having” and “including” are also to be construed as open ended unless the context suggests otherwise.
[0122] Following long-standing patent law convention, the terms “a”, “an”, and “the” refer to “one or more” when used in this application, including the claims. Thus, for example, reference to “a cell” includes a plurality of such cells, and so forth.
[0123] Unless otherwise indicated, all numbers expressing quantities of ingredients, properties such as reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about”. Accordingly, unless indicated to the contrary, the numerical parameters set forth in this specification and claims are approximations that can vary depending upon the desired properties sought to be obtained by the presently-disclosed subject matter.
[0124] As used herein, the term “about,” when referring to a value or to an amount of mass, weight, time, volume, concentration or percentage is meant to encompass variations of in some embodiments ±20%, in some embodiments ±10%, in some embodiments ±5%, in some embodiments ±1%, in some embodiments ±0.5%, in some embodiments ±0.1%, in some embodiments ±0.01%, and in some embodiments ±0.001% from the specified amount, as such variations are appropriate to perform the disclosed method.
[0125] As used herein, ranges can be expressed as from “about” one particular value, and/or to “about” another particular value. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.
[0126] As used herein, “optional” or “optionally” means that the subsequently described event or circumstance does or does not occur and that the description includes instances where said event or circumstance occurs and instances where it does not. For example, an optionally variant portion means that the portion is variant or non-variant.
[0127] An “antibody” is an immunoglobulin molecule capable of specific binding to a target, such as a carbohydrate, polynucleotide, lipid, polypeptide, etc., through at least one antigen recognition site, located in the variable domain of the immunoglobulin molecule. As used herein, the term encompasses not only intact polyclonal or monoclonal antibodies, but also, unless otherwise specified, any antigen-binding portion thereof that competes with the intact antibody for specific binding, fusion proteins comprising an antigen-binding portion, and any other modified configuration of the immunoglobulin molecule that comprises an antigen recognition site. Antigen-binding portions include, for example, Fab, Fab′, F(ab′)2, Fd, Fv, domain antibodies (dAbs, e.g., shark and camelid antibodies), portions including complementarity determining regions (CDRs), single chain variable fragment antibodies (scFv), maxibodies, minibodies, intrabodies, diabodies, triabodies, tetrabodies, v-NAR and bis-scFv, and polypeptides that contain at least a portion of an immunoglobulin that is sufficient to confer specific antigen binding to the polypeptide. Depending on the antibody amino acid sequence of the constant region of its heavy chains, immunoglobulins can be assigned to different classes. There are five major classes (i.e., isotypes) of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, and several of these may be further divided into subclasses (subtypes), e.g., IgG.sub.1, IgG.sub.2, IgG.sub.3, IgG.sub.4, IgA.sub.1 and IgA.sub.2. The heavy-chain constant regions that correspond to the different classes of immunoglobulins are called alpha, delta, epsilon, gamma, and mu, respectively. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known.
[0128] The terms “antigen-binding portion” or “antigen-binding fragment” of an antibody (or simply “antibody portion”), as used interchangeably herein, refers to one or more portions of an antibody that retain the ability to specifically bind to an antigen (e.g., delta-CN). It has been shown that the antigen-binding function of an antibody can be performed by portions of a full-length antibody.
[0129] A “variable domain” of an antibody refers to the variable domain of the antibody light chain (VL) or the variable domain of the antibody heavy chain (VH), either alone or in combination. As known in the art, the variable domains of the heavy and light chains each consist of four framework regions (FRs) connected by three complementarity determining regions (CDRs) also known as hypervariable regions, and contribute to the formation of the antigen-binding site of antibodies. If variants of a subject variable domain are desired, particularly with substitution in amino acid residues outside a CDR (i.e., in the framework region), appropriate amino acid substitution, in some embodiments, conservative amino acid substitution, can be identified by comparing the subject variable domain to the variable domains of other antibodies which contain CDR1 and CDR2 sequences in the same canonical class as the subject variable domain.
[0130] As used herein, “monoclonal antibody” refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally-occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations, which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. The modifier “monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.
[0131] A “human antibody” is one which possesses an amino acid sequence which corresponds to that of an antibody produced by a human and/or has been made using any of the techniques for making human antibodies as disclosed herein. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen binding residues.
[0132] The term “antigen (Ag)” refers to the molecular entity used for immunization of an immunocompetent vertebrate to produce the antibody (Ab) that recognizes the Ag or to screen an expression library (e.g., phage, yeast or ribosome display library, among others). Herein, Ag is termed more broadly and is generally intended to include target molecules that are specifically recognized by the Ab, thus including portions or mimics of the molecule used in an immunization process for raising the Ab or in library screening for selecting the Ab.
[0133] Generally, the term “epitope” refers to the area or region of an antigen to which an antibody specifically binds, i.e., an area or region in physical contact with the antibody. Thus, the term “epitope” refers to that portion of a molecule capable of being recognized by and bound by an antibody at one or more of the antibody's antigen-binding regions.
[0134] An antibody that “preferentially binds” or “specifically binds” or “selectively bind” (used interchangeably herein) to an epitope is a term well understood in the art, and methods to determine such specific or preferential binding are also well known in the art. A molecule is said to exhibit “specific binding,” “selective binding,” or “preferential binding” if it reacts or associates more frequently, more rapidly, with greater duration and/or with greater affinity with a particular cell or substance than it does with alternative cells or substances. An antibody “specifically binds” or “preferentially binds” to a target if it binds with greater affinity, avidity, more readily, and/or with greater duration than it binds to other substances. Also, an antibody “specifically binds” or “preferentially binds” to a target if it binds with greater affinity, avidity, more readily, and/or with greater duration to that target in a sample than it binds to other substances present in the sample. As such, “specific binding” or “preferential binding” does not necessarily require (although it can include) exclusive binding.
[0135] As used herein, “pharmaceutically acceptable carrier” or “pharmaceutical acceptable excipient” includes any material which, when combined with an active ingredient, allows the ingredient to retain biological activity and is non-reactive with the subject's immune system. Examples include, but are not limited to, any of the standard pharmaceutical carriers such as a phosphate buffered saline solution, water, emulsions such as oil/water emulsion, and various types of wetting agents. In some embodiments, diluents for aerosol or parenteral administration are phosphate buffered saline (PBS) or normal (0.9%) saline. Compositions comprising such carriers are formulated by well-known conventional methods.
[0136] The presently-disclosed subject matter is further illustrated by the following specific but non-limiting examples. The following examples may include compilations of data that are representative of data gathered at various times during the course of development and experimentation related to the present invention.
EXAMPLES
Example 1: General Strategy of the Systematic Structure-Based Virtual Screening for mAb Selection
[0137] Antibodies, including a total of five classes, i.e. immunoglobulin (Ig)A, IgD, IgE, IgG, and IgM, are known as affinity proteins that are a key component of the adaptive immune system..sup.37 The ability of antibodies to bind to foreign invaders with high affinity and specificity is central to their functions. IgGs, including four subclasses, i.e. IgG1 to 4, are the most abundant class of antibodies, constituting approximately 75% of the serum immunoglobulin repertoire. Notably, all IgGs share the same overall architecture, with differences only in six loops known as the complementarity-determining regions (CDRs) in the antigen-binding site.
[0138] Utilizing these remarkable structural features, the general strategy of the systematic structure-based virtual screening approach to antibody selection and identification as disclosed herein starts from collection and structural modeling of all mAbs whose amino-acid sequences (particularly the six CDRs) are available, with a view toward identifying the available mAbs can meet the above-mentioned goal—capable of potently binding with all the heroin-related opioids without binding with naloxone and naltrexone. Using the modeled structure of each mAb available, one can dock each of the interested ligands (i.e. 6-MAM, heroin, morphine, naloxone, and naltrexone in the current study) to the antigen-binding site and carry out further simulations and calculations to computationally estimate the binding free energy with each ligand. Based on the computationally estimated binding free energies, one can predict which mAb most likely can meet the goal of the potency and selectivity.
[0139] Specific for the need of binding with multiple opioids, the computationally estimated binding free energies clearly indicated which mAb should have the highest overall potency for binding with 6-MAM, morphine, and heroin without significant binding affinity to naloxone and naltrexone. The computationally selected most promising mAb was modeled further for humanization, and the predicted humanized mAb was prepared and tested in vitro for its actual binding affinities with various ligands including 6-MAM, heroin, morphine, naloxone, and naltrexone etc. Described below are the detailed procedures of the used computational methods.
Example 2: Modeling of the Antibody Structures
[0140] The amino-acid sequences of variable domains of the antibodies were obtained from the IMGT/LIGM-DB database (imgt.org).sup.38 or manually collected from the references cited (see Tables 1 and 2). The homology models of antibodies were built using the PIGSpro software.sup.39 which includes known X-ray crystal structures of a number of antibodies. Using the software, for homology modeling of each antibody structure, the template (used for the framework structure modeling) was selected based on the sequence alignment with those of the known X-ray crystal structure, the loops were kept in the similar canonical structure of template for the loop modeling method, and all other parameters were set as the default of the software.
[0141] Then the initial homology models were refined by performing a series of energy minimization processes. Specifically, the Amber14SB force field.sup.40 was applied for the proteins in vacuo using AmberTools18..sup.41 The nonbonded cutoff for the real-space interactions was set to 10 Å. Two stages of energy minimization were conducted using a hybrid protocol of 8000 steps of steepest descent minimization followed by a conjugate gradient minimization until the convergence criterion (the root-mean-square of the energy gradient is less than 1.0×10.sup.−4 kcal/mol.Math.Å) was satisfied or the maximum of 2000 iteration steps was reached. During the energy minimization, a force constant of 10 kcal/mol.Math.Å.sup.2 was applied on the antibody backbone atoms. Then the final conformations were used for virtual screening described below.
Example 3: Virtual Selection of an Antibody Capable of Selectively Binding with Heroin-Related Opioids
[0142] The computationally refined antibody structures were superimposed with the X-ray crystal structure of the complex of morphine with antibody 9B1.sup.34 (PDB: 1Q0Y) using the PyMol software.sup.42 in order to transform the atomic coordinates of all proteins into the same coordinate system with a commonly defined center of box required to define for systematic molecular docking, and the MglTools.sup.43 software was used to prepare the protein and ligand pdbqt files for the docking. During the docking, the binding site was determined based on the antibody-morphine complex in 9B1 (PDB: 1Q0Y), the geometric center of the co-crystallized antibody-morphine complex was indicated as the active center of the docking box (the size_x, size_y, and size_z were set to 30, 30, and 30, respectively) which was large enough to cover the entire region of the binding site.
[0143] The docking calculations were conducted by using the AutoDock Vina software,.sup.43 and all the default parameters were adopted. For each antibody-ligand complex, the top-4 ranked binding poses of the complex were selected for further computational evaluation in multiple steps.
[0144] First, the selected complex structures were energy-minimized using the same approach as described above for the energy-minimization of antibody structures without a ligand. The general Amber force field (gaff).sup.44 was used for the ligands. Second, the energy-minimized complex structure was relaxed by performing a short (20 ps) molecular dynamics (MD) simulation using the SANDER module of the AmberTools18 software.sup.41 in vacuo with a constant temperature (T=300 K). A restrain (with a force constant of 2 kcal/mol.Math.Å.sup.2) was applied on the backbone of antibody. The SHAKE algorithm.sup.45 was used to restrain the covalent bonds with hydrogen atoms, and the time step for the MD simulation was set to 2 fs. The long-range electrostatic interactions were treated by using the particle mesh Ewald (PME) algorithm,.sup.46 and the nonbonded cutoff for the real-space interactions was set to 12 Å. Third, the last snapshots of the MD simulations were energy-minimized again using the same method described above for the energy-minimization of the free antibody structures without a ligand. Finally, the MMPBSA module of the AmberTools18 software was used to calculate the binding free energy of each antibody-ligand binding pose, leading to the identification of the antibody-ligand binding pose associated with the lowest binding free energy for each antibody-ligand complex.
[0145] With the lowest binding free energy pose for each antibody-ligand pair and the corresponding binding free energy determined, the antibody was selected with the lowest possible binding free energy (i.e. the highest possible binding affinity) with 6-MAM and with the best possible overall binding affinities with other heroin-related opioids as well as the desirable selectivity over naloxone and naltrexone.
Example 4: Antibody Humanization Design; Sequence Alignment and Modification
[0146] Humanization of the computationally selected antibody (i.e. murine antibody Ab13 in this study) was performed by using the X-ray crystal structure of Ab13 complexed with morphine.sup.34 (PDB: 1Q0Y) from PDB database (rcsb.org/pdb/home/home.do) and the immunoinformatic modelling tools made available by the IMGT database..sup.38 Briefly, the variable heavy and light chain sequences (VH and VL) of the murine antibody were compared with human germline sequences using the IMGT/DomainGapAlign tools..sup.38 The top-ranked human germline sequence was used as the template. Murine antibody residues that differ from the human sequences on the surface area were replaced, excluding the residues near the binding pocket and anchor residues. Individual residues that are clearly not involved in the binding with the ligands in the murine antibody were changed to the corresponding residues of the human antibody. The image of the aligned sequences was created using the ESPript 3.0 software..sup.47
Example 5: Antibody Humanization Design; MD Simulation and Final Sequence Selection
[0147] The above-mentioned sequence modification based on the sequence alignment and simple structural modeling led to multiple (three) possible choices of the sequence of the humanized antibody, i.e. three possible humanized antibodies denoted as H1L1, H1L2, and H1L3. The initial structures of the antibodies (generated by using the PIGSpro software.sup.39 as described above) were refined further by performing a series of energy minimization processes and restrained MD simulations in order to know which one of the three choices is most reasonable. Concerning the computational details, the Amber14SB force field.sup.40 and the generalized Amber force field (gaff).sup.44 were used for the proteins and ligands, respectively. The TIP3P water molecules.sup.48 were added as the solvent and the solute atoms were at least 10 Å away from the boundary of the water box using AmberTools18..sup.41 The counterions (i.e. Na.sup.+ ions for murine antibodies or Cl.sup.− ions for humanized antibodies) were added to neutralize the system. The long-range electrostatic interactions were handled by the particle mesh Ewald (PME) algorithm,.sup.46 and the nonbonded cutoff for the real-space interactions was set to 10 Å.
[0148] Energy minimization was performed using a hybrid protocol of 8000 steps of the steepest descent energy-minimization followed by the conjugate gradient energy-minimization until the convergence criterion (the root-mean-square of the energy gradient is less than 1.0×10.sup.−4 kcal/mol.Math.Å) was satisfied or the maximum of 2000 iteration steps was reached. During the energy minimization, a force constant of 100 kcal/mol.Math.Å.sup.2 was applied on the ligand and protein backbone atoms. Then the systems were heated up from 0 to 303.15 K linearly over a time period of 50 ps with the restraint (force constant of 10 kcal/mol.Math.Å.sup.2) on all heavy atoms in the NVT ensemble, followed by equilibrating for 325 ps with a Langevin thermostat.sup.49 in the NPT (P=1 atm and T=303.15 K) ensemble by gradually decreasing the force constant from 10 to 0.2 kcal/mol.Math.Å.sup.2. Finally, the 5-ns production run was carried out with the PMEMD module of the Amber12 in the NPT (P=1 atm and T=303.15 K) ensemble. The SHAKE algorithm was used to restrain the covalent bonds with hydrogen atoms, and the time step was set to 2 fs, the snapshots were saved every 2 ps. The RMSD values were calculated by CPPTRAJ module of AmberTools18 using the energy-minimized conformations as the references.
Example 6: Plasmid Construction
[0149] To construct the chimeric antibody (UK6Mab01) and the (fully) humanized antibody (UK6Mab02), the amino acid sequences of heavy and light chains of variable domains of UK6Mab01 and UK6Mab02 were linked with human immunoglobulin heavy constant gamma 1 (IgG1, P01857, heavy chain) and human immunoglobulin kappa constant (IGKC, P01834, light chain), respectively.
[0150] The heavy and light chains were translated to human gene sequences by using the Backtranseq provided by the EMBL-EBI,.sup.50 and the codon was optimized using the COOL..sup.51 The Kozak sequence and signal peptide sequences for heavy chain or light chain were added to optimized genes. Then the genes for heavy chain and light chain were linked by inserting an Internal Ribosome Entry Site (IRES) between them. The designed genes were synthesized by GeneArt (Invitrogen, Carlsbad, Calif.), followed by cloning the genes into the pCMV-MCS vector at the BamHI and SalI sites for the humanized antibody, and at the BamHI and XhoI sites for the chimeric antibody. The oligonucleotides were synthesized by the Eurofins Genomics (Louisville, Ky.), restriction enzymes and the KLD Enzyme Mix used for ligation were purchased from New England Biolabs (Ipswich, Mass.). The final plasmids used for transfection were verified by sequencing services provided by Eurofins Genomics (Louisville, Ky.).
Example 7: Protein Expression and Purification
[0151] CHO-S cells were grown under the condition of 37° C. and 8% CO.sub.2 in a humidified atmosphere. The constructed expression vectors for the chimeric and humanized antibodies were transfected into CHO-S cells using Minis TransIT-PRO® Transfection Kit. 400 mL cells at the density of 2×10.sup.6 cells/mL were transfected with 400 μg of expression vector and 400 μL of transfection reagent. Culture supernatants were harvested 5 days after transfection by centrifugation with 10000 rpm for 15 min at 4° C. Antibodies were purified with using a protein A resin (Mab Select SuRe™ ordered from GE Healthcare, Chicago, Ill.), as used previously..sup.52-54 Briefly, 5 mL resin was packed in a column, equilibrated with 20 mM Tris-Cl (pH=7.4), loaded the culture supernatants with flow rate of 1-2 mL/min, washed with wash buffer (20 mM Tris-Cl, 300 mM NaCl, pH=7.4), and eluted with elution buffer (50 mM citric acid, 300 mM NaCl, pH=4). Then the eluate was concentrated and stored in PB buffer. Purified proteins were analyzed by SDS-PAGE (Invitrogen, Carlsbad, Calif.).
Example 8: Antibody Binding Assays
[0152] The binding constant of the antibody with [H.sup.3]-morphine were tested using liquid scintillation counting. Briefly, 2 nM [H.sup.3]-morphine was incubated with different concentration of antibody at room temperature for 60 minutes. The total volume of mixture was 100 and pH was 7.4. Following filtration with EMD Millipore Amicon™ Ultra-0.5 Centrifugal Filter (30 kD) and EMD Millipore Amicon™ Ultra 0.5 mL vials, 50 μL of the filtrate was added to 3 mL of 3a70BTM complete counting cocktail (RPI Research Products, Mount Prospect, Ill.). After vortex, the radioactive value of the cocktail was read, the K.sub.d value was calculated using the GraphPad Prism 7 software.
[0153] The binding affinities of each antibody with other drugs were calculated from its binding constant with [H.sup.3]-morphine (K.sub.d) and IC.sub.50 values against corresponding drugs, using the IC.sub.50-to-K.sub.i converter software (umich.edu/˜shaomengwanglab/software/calc_ki/index.html>. The IC.sub.50 values of corresponding drugs were measured as follows. 100 μL of mixture (pH 7.4) containing 2 nM [H.sup.3]-morphine, 20 or 60 nM of the antibody, and a varying concentration of drug was incubated at room temperature for 60 minutes. Then the mixture was filtered with EMD Millipore Amicon™ Ultra-0.5 Centrifugal Filter (30 kD) and EMD Millipore Amicon™ Ultra 0.5 mL Vials, 50 μL of the filtrate was transferred to 3 mL of 3a70BTM complete counting cocktail (RPI Research Products, Mount Prospect, Ill.), then the radioactive value of the cocktail was read, and the IC.sub.50 value was calculated using the GraphPad Prism 7 software.
Example 9: Virtual Screening
[0154] According to the virtual screening of available antibodies, including all of those listed in Table 1 with known experimental binding affinity to any of the heroin-related opioids, 6-MAM may potentially bind with the 26 known antibodies listed in Table 1, but with different binding free energies ranging from −16.6 kcal/mol (for the most potent one, i.e. Ab13) to −2.0 kcal/mol (which represents a negligible binding affinity) (see Table 2). Hence, the binding free energies of these 26 antibodies with morphine, heroin, naloxone, and naltrexone were computationally estimated. All the calculated binding free energies are summarized in Table 2 in comparison with available experimental data.
TABLE-US-00001 TABLE 1 Variable region sequences of anti-morphine/6-MAM antibodies. Heavy Light Chain Chain Original SEQ ID SEQ ID Antibody Name HeavyChain NO: LightChain NO: Ab1 MOR131 QVQLQQSGPXLMEPGAS 13 QPVVTQESALTTSPGE 39 VKISCRASGYIFRTYWI TVTLTCRSSTGAVTTS EWIRERPGHGLEWIGEI NYANWVQEKPDHLFTG LPGSGFTKYNEKFTGKA LIGGTNNRAPGVPARF TITAEASSNTAYVQLNS SGSLIGDKAALTITGA LTSEDSAVYYCTRWGTG QIEDEALYFCVLWDSN AGIIVMDFWGRGTSVTV RLVFGGGTKLTVL SS Ab2 MOR158 QVQLQQPGXELVKPGXS 14 EIQVTQTTSSLSASLG 40 VRLSCKATGYTFATYWM DRVTISCRASQDIKNY NWVKQRPGQGLEWIGEI LNWYQQKPDGTVKLLI NPSNGRTNYNERFQNKA YYTSTLHSGVPSRFSG SLTVDKSSSTAYMQLTS SGSGTDYSLTIDNLEQ LTSEDSAVYFCARWVLR EDVATYFCQQGTTLPT PLYALDYWGQGTSVTVS WTFGGGXKVEIXRADA S A Ab3 MOR180 QVQLQQPGXELVKPGXS 15 EIQVTQTTSSLSASLG 41 VRLSCKATGYTFATYWM DRXT1XCRASQDIKNY NWVKXRPGQGLEWIGEI XNWYQQKPDGTVKLLI NPSDGRTNYNDRFKNKA YYTSSLHSGVPSRFSG TLTVDISSSTAYMQLSS SGSGTDYSLTISNLEQ LTSEDSAVYYCARWVLR EDVATYFCQQGTTLPT PLYALDYWGQGTSVTVS WTFGGGXKVEIKRADG S A Ab4 MOR8 EVKLVESGGGLVKPGGS 16 DIVLTQSPASLAVSLG 42 LKLSCAASGFTFSSYVM QRATISCKASQSVDYD SWVRQTPEKRLEWVASI GDSYMNWYQQKPGQPP SGGGTTYYPDSVKGRFT XLLIYAASNLESGIPA ISRDNARNILYLQMSSL RFSGSGSGTDFTLNIH RSEDAAMFYCAREDYYG PVEEEDAATYYCQRSN SSYWYFDVWGAGXTVTV EDPFTFGSGTKLEIK SS Ab5 MOR33 EVKLVESGXGXVKPGGS 17 DIVLTQSPASLAVSLG 43 LKLSCAASGFTFSKYVM QRATISCKASHSVDYD SWVRQTPERRLEWVASI GDGYMNWYQQKPGQPP GVSGITYFPDSVKGRFT XLLIYAASNLESGIPA ISRDNGRNVLYLQMSSL RFSGSGSGTDFTLNIH RSEDTAMYYCAREDYYG PVEEEDAATYYCQQSD SRYWYFDVWGAGTXVTV GDPFPFGSGTKLEIK SS Ab6 MOR35 EVKLVESGXXXVKPGGS 18 DIVLTQSPASLAVSLG 44 LKLSCAASGFSFSRYVL QRATISCKASQGVDFD SWVRQTPEKRLEWVASI GDAYMNWYQQKPGQPP SSGGTTYFPDSVKGRFT XLLIYAASNLESGIPA ISRDIARNILYLQLSSL RFSGSGSGTDFTLNIH RSDDTAMYYCAREDYYG PVEEEDAATYYCQQSD GRYWYFDVWGAGXTVTV GDPFPFGSGTKLEIK SS Ab7 MOR44 EVKLVESGAGVVKPGGS 19 DIVLTQSPASLAVSLG 45 LKLSCEASGFSFSRYVM QRATISCKASQSVDHD SWVRQTPEKRLEWVASI GNGYMNWYQQKPGQPP SSGGRTYYPGSEMGRFT RLLIYAASNLEYGIPV ISRDSARNILYLQMSSL RFSGSGSGTDFILNII KSEDTAMFYCAREDYYG IPVEEEDAATYYCQQS GRYWYFDVWGAGTTVTV DGDPFPFGSGTKLEIK SS Ab8 MOR83 EVICLVESGXGVVICPG 20 DIVLTQSPASLAVSLG 46 GSLKLSCAASGFSFSRY QRATISCKASQSVDHD MVSWVRQTPEKRLEWVA GNGYMNWYQQKPGQPP SISSGGRTYYPGSETGR RLLIYAASNLESGIPV FTISRDSARNILYLQMS RFRGSGSGTDFILNIH SLRSEDTAIFYCAREDY PVEEEDAATYYCQQSD YGGRYWYFDVWGXGTXV GDPFPFGSGTICLEIK TVSS Ab9 MOR76 EVKLVESGXXXVKPGGS 21 DIVLTQSPASLAVSLG 47 LKLSCAASGFSFSDYVM QRATISCKASQSVDFD SWVRQTPEKRLEWVASI GDNYMNWYQQKPGQSP SSGGRTYYPGSVKGRFT ICLLIYAASNLQSGIP ISRDDDRNILYLQMNSL ARFSGSGSGTDFTLNI RSEDTAMFYCAREDYYD EPVEEEXAATYYCQRS SSYWYFDVWGTGTTVTV NEDPFTFGSGTICLEI SS K Ab10 MOR39 QVQLQQSGPXLMKPGXS 22 QAVVTQESALTTSPGE 48 VKISCKATGYTERTYWI TVTLTCRSSTGAVTTS EWIICERPGHGLEWIGE NYANWVQEKPDHLFTG ILPGSGITKYXEKFKGK LIGGTDNRAPGVPARF AIITADTSSNTAYVQLS SGSLIGDKAALTITGA SLTSEDSAVYYCTRWGT QTEDEAVYFCVLWDSN GTGHVMDYWGQGTSVTV RLVFGGGTKLTVL SS Ab11 11C7 EVNLLESGGGLVQPGGS 23 AVVTQESILTTSPGET 49 LKVSCAASGFDFSRFWM VTLTCRSSTGAVTTSN SWVR.QAPGKGLEWIGE YANWVQQKPDHLFTSL INPSSNTINYTPSLICE IGGISNRVPGVPARFS RFIISRDNAICNTLYLQ GSLIGDKVALTIIGTQ MSKVRPEDTGLYYCAMT TEDEAIYFCALWYSNH KSVYNYGSHYYYFDVWG LVFGGGTKLTVL AGTITVTVSS Ab12 12D4 QVHLQQSGAELMKPGSS 24 AVVTQESILTTSPGET 50 VKISCKTTGYTFSNYWI VTLTCRSSTGAVTTSN EWIKERPGHGLVWIGEI YANWVQEKPDHLFTGL LPGTGRTFYSENFKVIC IGGTNNRAPGVPARFS ATFITDTSSNTAYLQLS GSLIGDKAALTITGAQ SLTSEDSAVYYCARWFR TEDEAINTCALWYSNH DLYGVDYWGQGTSVTVS LVFGGGTKLTVL S Ab13 9B1 EVQLQQSGAELMKPGAS 15 DAVVTQESALTTSPGE 51 VKISCKATGYIFSSYWI TVTLTCRSSTGAVTTS EWVKQFRPG1TGLEWIG NYANWVQEKPDHLFTG EILPGSGDTIFNEICFK LIGGTNNRAPGVPARF GICATFTADTSSNTAYM SGSLIGDICAALTITG QLSSLTSEDSAVYYCAR AQTEDEAIYFCALWSN WVLDYYGMDYWGQGTSL NKLVEGGGTKLTVL TVSS Ab14 10C3 MDFGLIFF1VALLKGVQ 26 AVVTQESALTTSPGET 52 CEVICLLESGGGLVQPG VTLTCRSSTGAVTTSN GSLKLSCAASGFDFSRY YANWVQEKPDHLFTGL WILVRQAPGKGLEWIGE IGGTNNRAPGVPARFS INPIISTTIFYTPSLMD GSLIGDKAALTITGAQ KFIISRDNAKNTLYLQM TEDEAIYFCSLWYSNH TKVRSEDTALYYCARWG LVEGGGTKLTVL DKYLFDFIWGQGTTLTV SS Ab15 368-21 EVICPLESGGGLVQPGG 27 QAVVTQESAL17SPGE 53 SLICLSCAASGEDFSRY TVTLTCRSSTGAVTTS WMSWVRQAPGKGLEWIG NYATWVQEKPDHLFTG EIHPDSSTIFYTPSLIC LIGVTNYGPPGVPSRF DICFIISRDNAICETLY SGSLIGDKAALTITGA LQMTKVRSEDTALYITA QTEEEAMYFCALWDSN RWSLRGYYFDYWGQGTT HPNTGGGTKLTVL LTVSS Ab16 402-10 EVKPLESGGGLVQPCGS 28 QAVVTQESALTTSPGE 54 LKLSCAASGFDFSRYWM TVTLTCRSSTGAVTTS SWVRQAPRKRLEWIGEI NYATWVQEKPDHLFTG NPDSSTITYTPSLICDI LIGVTNYGPPGVPSRF CFIISRDNAKNTLYLQM SGSLIGDKAALTITGA SKVRSEDTALYYCASWY QTEEEAMYFCALWDSN GLRLSYEDVWGAGTTVT LIPVEGGGTKLTVL VSS Ab17 6- EVQLVESGGGLVQPGRS 29 QSALTQPASVSGAPGQ 55 MAM- LRLSCAASGFSFGDYAI TVSISCTGWSSNIGAG 214 HMVRQAPGKGLEWVSGI YDVHWYQQLPGTAPKL SWDSYTTGYADSVKGRF LISHNTNRPSGVPDRF TVSRDNAKNSLYLQMNS SGSKSGTSASLAITGL LRPEDTAVYYCAKAPSP QAEDEADYYCQSYDST RRVIIEYFDSDYWGQGT LGVVVEGGGTICLTVL SLTVSS Ab18 6- EVQLVESGGGLVQPGRS 30 QSALTQPASVSGAPGQ 56 MAM- LRLSCAASGFSFGDYAI RVTISCTGSSSNIGAG 20 HMVRQAPGKGLEWVSGI YAVHWYQQLPGTAPKL SWDSYTTGYADSVKGRF LIYDDNNRPSGVPDRF TVSRDNAICNSLYLQMN SGSKSDTSASLAITGL SLRPEDTAVYYCAKAPS QADDEADYYCQSYDSS PRRVIIEYFDSDYWGQG LSGSVFGTGTKLTVL TSLTVSS Ab19 6- EVQLVESGGGLVQPGRS 31 QSVLTQPPSVSGAPGQ 57 MAM- LRLSCAASGFSFGDYAR RVTISCTGSSSNIGAG 219 IMVRQAPGKGLEWVSGI YDVHWYQQLPGTAPKL SWDSYTTGYADSVKGRF LIYGNSNRPSGVPDRF TVSRDNAICNSLYLQMN SGSKSGTSASLAITGL SLRPEDTAVYYCAKAPS QAEDEADYYCQSYDSS PRRVIIEYFDSDYWGGT LRGVVFGGGTKLTVL SLTVSS Ab20 6- EVQLVESGGGLVQPGRS 32 QSALTQPASVSGAPGQ 58 MAM- LRLSCAASGFSTGDYAI RVTMSCTGSSSNIGAG 102 HMVRQAPGKGLEWVSGI YDVHWYQQLPGTAPKL SWDSYTTGYADSVKGRF LIFGNTNRPSGVPDRF TVSRDNAKNSLYLQMNS SASKSGTSASLAITGL LRPEDTAVYYCAKAPSP QAEDEADYYCQSYDNS RRVHEYFDSDYWGQGTS LSGVVFGGGTKLTVL LTVSS Ab21 6- EVQLVESGGGLVQPGRS 33 QSALTQPASVSGAPGQ 59 MAM- LRLSCAASGFSFGDYAI RVTISCTGSSSNIGAG 103 HMVRQAPGKGLEWVSGI YDVHWYQQLPGTAPKL SWDSYTITGYADSVKGR LIYGNSNRPSGVPDRF FTVSRDNAICNSLYLQM SGSKSGTSASLAITGL NSLRPEDTAVYYCAKAP QAEDEADYYCQSYDSS SPRRVIIENTDSDYWGQ LSGVVFGGGTKLTVL GTSLTVSS Ab22 6- EVQLVESGGGLVQPGRS 34 QSVLTQPPSVSGAPGQ 60 MAM- LRLSCAASGFSTGDYAI RVTISCTGSSSNIGAG 108 HMVRQAPGKGLEWVSGI YDVHWYQQLPGTAPKL SWDSYTTGYADSVKGRF LWGNSNRPSGVPDRFS FVSRDNAKNSLYLQMNS GSKSGTSASLAITGLQ LRPEDTAVYYCAKAPSP AEDEADYYCQSYDSSL RRVIIEYFDSDYWGQGT SGVVFGGGTKLTVL SLTVSS Ab23 6- EVQLVESGGGLVQPGRS 35 QSALTQPASVSGAPGQ 61 MAM- LRLSCAASGFTFGDYAI TVSISCTGWSSNIGAG 49 IIMVRQAPGKGLEWVAG YDVHWYQQLPGTAPKL ISWDSYTTGYADSVKGR LISIINTNRPSGVPDR FTVSRDNAKNSLYLQMN FSGSKSGTSASLAITG SLRPEDTAVYYCAICAP LQAEDEADYYCQSYDS SPRRVIIENTQYDYWGQ TLGVVVEGGGTKLTVL GTSLTVSS Ab24 6- EVQLVESGGGLVQPGRS 36 QSALTQPASVSGAPGQ 62 MAM- LRLSCAASGFTFGDYAI RVTISCTGSSSNIGAG 120 HMVRQAPGKGLEWVAGI YDVHWYQQLPGTAPKL SWDSYTTGYADSVKGRF LIYGNSNRPSGVPDRF TVSRDNAKNSLYLQMNS SGSKSGTSASLAITGL LRPEDTAVYYCMCAPSP QAEDEADYYCQSYDSS RRVIIEYFQYDYWGQGT LSGVVFGGGTKLTVL SLTVSS Ab25 M86 DVKINESGGGINKPGGS 37 DIVLTQSPARLAVSLG 63 LKLSCAASGETSSSYAM QRATISCKASQSVDYD SWVRQSPETCRLEWVAS GDSYMNWYQQKPGQPP TSSGGSTYYPDSVKGRF ICLLIYAASNLESGIP TTSRDNARNNLYLQMSS ARFSGSGSGIDFTLNI LRSEDTAMYYCVREDYH HPVEEEDAATYYCQQS GSSYWYFDVWGAGTIVT NEDPWTFGGGTKLEIK VSS R Ab26 M3G QVQLQQSGPELMKPGAS 38 ESALTTSPGETVTLTC 64 VKISCKATGYTFSSHWI RSSTGAVTTSNYANWV EWVKQRPGHGLEWTGEI QEKPDHLFTGLIGGTN LPGSGSTKYNEKFKGKA NRAPGVPARFSGSLIG TFTADTSSNTVYMQLSS DKAALTITGAQTEDEA LTSEDSAVYHCARWSQV NFCVLWYSNEILVEGG I1VMDYWGQGTSLTVSS GTCKLTVL
TABLE-US-00002 TABLE 2 The predicted binding free energies and the activities of known anti-morphine antibodies against morphine, 6-MAM, heroin, naloxone, and naltrexone. MMPBSA (kcal/mol)/ Original Activities Antibody Name (nM).sup.a Morphine 6-MAM Heroin Naloxone Naltrexone Ab1 MOR131 MMPBSA −17.6 −11.6 −10.8 −14.4 −4.1 Activities.sup.1 0.022 (K.sub.d) nd.sup.b nd 144.9 (K.sub.d) nd Ab2 MOR158 MMPBSA −10.2 −11.6 −4.5 −12.2 −11.5 Activities.sup.1 0.118 (K.sub.d) nd nd 34.6 (K.sub.d) nd Ab3 MOR180 MMPBSA −11.7 −12.4 −20 −12.5 −15.6 Activities.sup.1 0.25 (K.sub.d) nd nd 67.6 (K.sub.d) nd Ab4 MOR8 MMPBSA −15.7 −14.8 −16.4 −10.1 −15.6 Activities.sup.1 0.143 (K.sub.d) nd nd 142.9 (K.sub.d) nd Ab5 MOR33 MMPBSA −15.4 −13.6 −13.4 −8.1 −11.5 Activities.sup.1 0.189 (K.sub.d) nd nd 145.1 (K.sub.d) nd Ab6 MOR35 MMPBSA −15.7 −14.7 −19.1 −7.6 −11.9 Activities.sup.1 0.185 (K.sub.d) nd nd 115.7 (K.sub.d) nd Ab7 MOR44 MMPBSA −12.7 −11.4 −14.2 −9.7 −15.8 Activities.sup.1 0.119 (K.sub.d) nd nd 44.82 (K.sub.d) nd Ab8 MOR83 MMPBSA −10.2 −8.5 −12.4 −12.7 −10.8 Activities.sup.1 0.103 (K.sub.d) nd nd 44.82 (K.sub.d) nd Ab9 MOR76 MMPBSA −12.9 −15.1 −17.0 −12.5 −18.8 Activities.sup.1 0.063 (K.sub.d) nd nd 32.89 (K.sub.d) nd Ab10 MOR39 MMPBSA −15.7 −10.6 −17.7 −3.8 −16.1 Activities.sup.1 2.174 (K.sub.d) nd nd 48309 (K.sub.d) nd Ab11 11C7 MMPBSA −17.8 −2.0 −10.2 −16.8 −5.4 Activities.sup.2 16.17 (K.sub.d) nd nd nd nd Ab12 12D4 MMPBSA −12.1 −10.5 −9.9 −4.3 −4.8 Activities.sup.2 13.64 (K.sub.d) nd nd >10000 (K.sub.d) nd Ab13 9B1 MMPBSA −15.1 −15.6 −16.6 −1.8 −3.2 Activities.sup.3 1 (K.sub.d) nd nd nd nd Ab14 10C3 MMPBSA −15.5 −12.9 −15.0 −9.7 −14.7 Activities.sup.2 53.83 (K.sub.d) nd nd 5105 (K.sub.d) nd Ab15 368-21 MMPBSA −17.8 −11.9 −15.2 −3.0 −10.2 Activities.sup.4 3.1 (K.sub.d) nd nd 81 (IC.sub.50) 310 (IC.sub.50) Ab16 402-10 MMPBSA −13.6 −15.4 −7.3 −5.3 −16.5 Activities.sup.4 3.5 (K.sub.d) nd nd 100 (IC.sub.50) nd Ab17 6-MAM- MMPBSA −5.0 −8.7 −5.6 −13.3 −1.7 214 Activities.sup.3 >10000 (K.sub.d) 300 (K.sub.d) nd nd nd Ab18 6-MAM- MMPBSA −9.2 −9.8 −9.9 −15.8 −10.6 20 Activities nd nd nd nd nd Ab19 6-MAM- MMPBSA −7.9 −7.1 −6.8 −17 −13.6 219 Activities.sup.5 10000 (K.sub.d) 160 (K.sub.d) nd nd nd Ab20 6-MAM- MMPBSA −3.3 −8.1 −8.5 −6.1 −8.5 102 Activities.sup.3 >10000 (K.sub.d) 170 (K.sub.d) nd nd nd Ab21 6-MAM- MMPBSA −8.0 −9.2 −11.1 −14.1 −14.9 103 Activities.sup.5 >10000 (K.sub.d) 100 (K.sub.d) nd nd nd Ab22 6-MAM- MMPBSA −2.9 −6.9 −8.6 −15.6 −13.4 108 Activities.sup.5 >10000 (K.sub.d) 170 (K.sub.d) nd nd nd Ab23 6-MAM- MMPBSA −6.9 −6.4 −9.6 −13.7 −5.6 49 Activities.sup.5 nd nd nd nd nd Ab24 6-MAM- MMPBSA −10.9 −6.7 −16.0 −4.6 −4.8 120 Activities.sup.5 >10000 (K.sub.d) 250 (K.sub.d) nd nd nd Ab25 M86 MMPBSA −11.5 −11.2 −15.1 −14.9 −20.3 Activities.sup.6 12.6 (K.sub.d) nd 5.2 (K.sub.d) nd nd Ab26 M3G MMPBSA −13.2 −12.4 −7.5 −8.7 −15.3 Activities nd nd nd nd nd .sup.aThe experimental activity data were collected from the references cited. Reported K.sub.a and IC.sub.50 values were coverted to the corresponding K.sub.d and K.sub.i, respectively. .sup.bnd (not determined) means no available experimental data. .sup.1Jun-ichi, S., et al. (1993). .sup.2Glasel, J.A., et al. (1983). .sup.3Pozharski, E., et al. (2004). .sup.4Kussie, P.H., et al. (1991). .sup.5Moghaddam, A., et al. (2003). .sup.6Matsukizono, M., et al. (2013).
[0155] Interestingly, for many of these antibodies listed in Table 2, experimental binding free energies (converted from the previously reported K.sub.d, K.sub.i, or IC.sub.50 values according to the well-known thermodynamic equation) have already been known for their binding with morphine and naloxone. According to the experimental binding affinities summarized in Table 2, the most potent anti-morphine antibodies (Ab1 to 9), Ab15, and Ab16, can also potently bind to naloxone with nanomolar K.sub.d or IC.sub.50 values (ranging from 33 nM to 145 nM). Ab15 even can potently bind with naltrexone (IC.sub.50=310 nM). A therapeutic antibody capable of binding with naloxone or naltrexone would be problematic because it would block the favorable pharmacologic action of naloxone (the currently available therapeutic agent for opioid overdose treatment) or naltrexone (the currently available therapeutic agent for opioid dependence treatment). For this reason, these potent anti-morphine antibodies would not be suitable for consideration as the desirable therapeutic candidates. Nevertheless, the available experimental data for enough number of antibodies binding with morphine and naloxone allowed us to analyze the potential correction between and computational and experimental data and, thus, validate the computational protocol. In comparison, only six antibodies have experimental data available for their binding with 6-MAM, with a very narrow range of the K.sub.d values (100 to 300 nM) that had limited the correlation analysis for 6-MAM before further experimental data was obtained to expand the range (see below).
[0156] As showed in
[0157] Within all antibodies listed Table 2, Ab13 was predicted to have the lowest binding free energy (−15.6 kcal/mol) with 6-MAM; the lowest binding free energy means the highest binding affinity. Ab13 was also predicted to have high binding affinities with morphine and heroin (corresponding to the calculated binding free energies of −15.1 and −16.6 kcal/mol, respectively). Interestingly, Ab13 was predicted to have the highest binding free energy (i.e. the lowest binding affinity) with naloxone and naltrexone (corresponding to the calculated binding free energies of −1.8 and −3.2 kcal/mol, respectively). In other words, Ab13 was predicted to be the most promising antibody capable of potently binding with 6-MAM, morphine, and heroin without significant binding affinity with naloxone and naltrexone.
Example 10: Binding Modes of Ab13 with Heroin-Related Opioids
[0158] To identify the key residues of Ab13 for the binding with 6-MAM, morphine, and heroin, the X-ray crystal structure of the complex of Ab13 with morphine was taken from the RC SB Protein Data Bank, together with the predicted binding structures of 6-MAM and heroin, were analyzed and presented in
[0159] In addition, as shown in
Example 11: Ab13 Humanization Design
[0160] Ab13 was acquired from mouse by using the hybridoma technique..sup.34 To make use of this antibody for future use in human, Ab13 must be humanized to reduce immune response. Currently, many methods have been used in antibody humanization, the most wildly used methods are complementarity determining regions (CDRs) graft and antibody resurfacing..sup.55 As CDRs graft change the framework regions (FRs) of the humanized antibody, certain key residues in FRs of Ab13 play an important role in binding with 6-MAM, heroin, and morphine according to the modelled binding structures (see
[0161] Initially, the amino-acid sequences of the variable domains of the heavy (VH) and light (VL) chains of Ab13 were analyzed using the IMGT/DomainGapAlign tools,.sup.38 and the closest human germline V and J genes were identified. As shown in
[0162] Further, for assessment of the structural stability of the humanized antibody within the above three possible choices of the humanized antibody, MD simulations were carried out to examine the fluctuation of the residues in the binding pocket and the backbone atoms of the three possible humanized antibodies (denoted as H1L1, H1L2, and H1L3). For comparison, MD simulations were also performed on the original structures of Ab13 and its complex with morphine, and the time-dependent root-mean-square deviations (RMSDs) for all the simulated structures are provided in
[0163] In comparison, the pocket residues of H1L1 were stable during the MD simulation on H1L1 without morphine bound, but less stable during the MD simulation on the H1L1-morphine complex. On the contrary, the pocket residues of H1L2 were less stable during the MD simulation on H1L2 without morphine bound, as the RMSDs continually increased during the simulation, although the simulated H1L2-morphine complex structure was relatively more stable. Within the three humanized antibodies, H1L3 has the most stable structure, as reflected by the low RMSDs (for both the pocket residues and backbone atoms, as well as morphine bound) that were stable during the MD simulations on H1L3 with or without morphine bound. So, H1L3 was the final choice of the fully humanized antibody.
[0164] Besides, for the purpose of functional comparison, a chimera antibody (a partially humanized antibody) was also designed, in which only the Fc part of the mouse Ab13 was replaced by the Fc of human IgG-1. Such a chimera antibody was expected to have the same functions with the mouse Ab13. For convenience, the chimera antibody and the fully humanized antibody (H1L3) are denoted as UK6Mab01 and UK6Mab02, respectively, in the discussion below.
Example 12: Experimental Validation of the Designed Antibodies
[0165] To prepare the designed antibodies UK6Mab01 and UK6Mab02, the sequences of heavy and light chains were assembled with human immunoglobulin heavy constant gamma 1 (IgG1, P01857) and human immunoglobulin kappa constant (IGKC, P01834), respectively. The use of internal ribosome entry site (IRES) allowed for the co-expression of a light chain and its corresponding heavy chain under the control of the same promoter. Both UK6Mab01 and UK6Mab02 proteins were expressed in the CHO-S cells and purified. A major band of approximately 75 kDa was observed, corresponding to the integrity of heavy and light chains. Two other major bands with molecular masses of approximately 50 kDa (heavy chain) and 25 kDa (light chain) were also observed (
[0166] The binding affinities of UK6Mab01 and the UK6Mab02 with various ligands were assessed by the liquid scintillation counting method. Both the UK6Mab01 and UK6Mab02 were able to potently bind to morphine with a K.sub.d value of 33.7 nM (
TABLE-US-00003 TABLE 3 Experimental binding affinities of UK6Mab01, UK6Mab02, and 9B1 with multiple drugs. K.sub.d (nM) .sup.a Drugs UK6Mab01 UK6Mab02 9B1 .sup.a morphine 33.7 127 1 6-MAM 4.8 11.9 nd .sup.b heroin 1.3 11.8 nd hydrocodone 8.2 39.3 nd meperidine 8,890 15,700 nd oxycodone 2,670 6,910 nd fentanyl 32,900 9,730 nd naloxone >10,000 >10,000 nd naltrexone >10,000 >10,000 nd .sup.a Data from reference 33. .sup.b nd (not determined) means no available experimental data.
[0167] In addition, UK6Mab01 and UK6Mab02 were examined to determine whether they can potently bind to other drugs including naloxone, naltrexone, hydrocodone, meperidine, oxycodone, methadone, amethaphetamine, ketamine, cocaine, and fentanyl (
[0168] Further, with the newly obtained binding affinity of 6-MAM with UK6Mab01, the computationally predicted binding free energies with 6-MAM were also able to be shown to excellently correlate with the corresponding experimental data (
[0169] The systematic structure-based virtual screening of available monoclonal antibodies and computational design of antibody humanization have led to discovery of promising antibodies, including the partially humanized antibody UK6Mab01 and the fully humanized antibody UK6Mab02, that can potently bind to multiple addictive opioids (including 6-MAM, morphine, heroin, and hydrocodone) without significant binding with currently available opioid overdose/dependence treatment agents naloxone and naltrexone. Specific for UK6Mab01, it was determined that K.sub.d=4.8 nM for 6-MAM, 1.3 nM for heroin, 33.7 nM for morphine, 8.2 nM for hydrocodone, and 2.7-32.9 μM for oxycodone, meperidine, and fentanyl, without significant binding affinity to other drugs tested. For UK6Mab02, it was determined that K.sub.d=11.9 nM for 6-MAM, 11.8 nM for heroin, 127 nM for morphine, 39.3 nM for hydrocodone, and 6.9-15.7 μM for oxycodone, fentanyl, and meperidine, without significant binding affinity to other drugs tested. The fully humanized antibody are contemplated for use in treatment of OUDs.
[0170] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference, including the references set forth in the following list:
REFERENCES
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[0232] It will be understood that various details of the presently disclosed subject matter can be changed without departing from the scope of the subject matter disclosed herein. Furthermore, the foregoing description is for the purpose of illustration only, and not for the purpose of limitation.