Patent Application
20220362366
Cancer is now the primary cause of death in developed countries and world-wide. The financial burden of this disease, and more importantly, the suffering it causes, is immense. There is an obvious and urgent need to speed the development and application of new, more efficacious anti-cancer therapies. The field of oncology is vast and comprises several indications, including some rare/orphan forms. Although oncology continues to be one of the most active areas in terms of drug development, there is still a significant unmet need.
Recent advances in cancer immunology have documented the importance of T cell-mediated anti-tumor immunity against human cancers, and inhibitory receptors expressed by T cells have become important targets for cancer immunotherapy. Signaling through the immune checkpoint programmed cell death protein-1 (PD-1) enables tumor progression by dampening antitumor immune responses. Therapeutic blockade of the signaling axis between PD-1 and its ligand programmed cell death ligand-1 (PD-L1) with monoclonal antibodies has shown remarkable clinical success in the treatment of cancer and demonstrated impressive activity across a broad set of cancer subtypes, even at advanced and metastatic stages of disease. Therapeutics targeting this pathway are currently in clinical trials. Pembrolizumab and nivolumab are the first of this anti-PD-1 pathway family of checkpoint inhibitors to gain accelerated approval from the US Food and Drug Administration (FDA) for the treatment of ipilimumab-refractory melanoma.
Monoclonal antibodies targeting immunologic checkpoints and especially the PD-1/PD-L1 axis provided spectacular results in cancer therapy in the recent years. Despite their proven utility, antibodies have specific drawbacks as therapeutics, including poor tissue/tumor penetrance which may be especially pertinent when targeting the PD-1:PD-L1 signaling pathway. For example, PD-1-expressing effector T cells are found infiltrated within solid tissue of PD-L1-expressing tumors. This is problematic for antibodies, which are impeded from entering tumors due to their large size. It follows that antibodies may therefore fail to completely antagonize PD-1:PD-L1 signaling at the intended therapeutic site within tumors, leading to suboptimal efficacy.
Checkpoint blockades turn on a new paradigm shift in immunotherapy for cancer. However, a lot of cancer patients failed to respond to the PD-1/PD-L1 checkpoint blockades. What are needed are new PD-1/PD-L1 checkpoint inhibitors for the treatment of cancer, viral infections, autoimmune diseases and Alzheimer's disease.
Disclosed are methods and compositions related to synthetic PD-L1 peptides.
In one aspect, disclosed herein are PD-L1 chimeric peptides for stimulating an immune response to a PD-L1 protein comprising one or more PD-L1 B cell epitopes, a T helper (Th) epitope (for example, a measles virus fusion protein peptide such as SEQ ID NO: 6), and a linker (such as, for example, SEQ ID NO: 7) joining the PD-L1 B cell epitope to the Th epitope, wherein the one or more PD-L1 B cell epitopes consist of a sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, and SEQ ID NO:5. For example, disclosed herein are chimeric peptides of any preceding aspect, wherein the peptide comprises the amino acid sequence as set forth in SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO:10 or SEQ ID NO:11.
Also disclosed herein are synthetic PD-L1 peptides for stimulating an immune response to a PD-L1 protein comprising one or more of the sequences as set forth in SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15 including the D enantiomer of the disclosed sequences. In one aspect, the synthetic peptide can be acetylated.
In one aspect disclosed herein are chimeric peptides comprising the synthetic peptide of any preceding aspect, further comprising a Th epitope (for example, a measles virus fusion protein peptide such as SEQ ID NO: 6), and a linker (such as, for example, SEQ ID NO: 7) joining the synthetic PD-L1 peptide to the Th epitope. For example, disclosed herein are chimeric peptides of any preceding aspect, wherein the peptide comprises the amino acid sequence as set forth in SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, or SEQ ID NO: 19.
Also disclosed herein are pharmaceutical compositions comprising one or more chimeric or synthetic peptides of any preceding and a pharmaceutically acceptable vehicle (such as, for example, a vehicle that is biodegradable including, but not limited to adjuvants (such as for example, a water in oil adjuvant including but not limited to Montanide).
In one aspect disclosed are pharmaceutical compositions of any preceding aspect further comprising one or more HER-2 B cell epitopes (such as for example, SEQ ID NO: 27, or SEQ ID NO: 29), one or more chimeric HER 2 peptides (such as for example, SEQ ID NO: 28, or SEQ ID NO: 30), and/or one or more anti-Her-2 antibodies.
Also disclosed herein are HER-2 chimeric peptides for stimulating an immune response to a HER-2 comprising one or more HER-2 B cell epitopes, a T helper (Th) epitope (including, but not limited to measles virus fusion protein peptide (such as, for example SEQ ID NO: 6), and a linker (such as, for example, SEQ ID NO: 7) joining the HER-2 B cell epitope to the Th epitope, wherein the one or more HER-2 B cell epitopes consist of a sequence selected from the group consisting of SEQ ID NO: 27 and SEQ ID NO: 29. For example, a HER-2 chimeric peptide comprising the amino acid sequence as set forth in SEQ ID NO:28 or SEQ ID NO: 30.
In one aspect, disclosed herein are antibodies that specifically bind to a chimeric peptides or synthetic peptides of any preceding aspect.
Also disclosed herein are methods of treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer and/or metastasis (such as, for example, breast cancer, ovarian cancer, endometrial cancer, colon cancer, non-small cell lung cancer, prostate cancer, and cervical cancer), Alzheimer's disease, or an autoimmune disease in a subject comprising administering to the subject any of the peptides or compositions of any preceding aspect.
The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate several embodiments and together with the description illustrate the disclosed compositions and methods.
Before the present compounds, compositions, articles, devices, and/or methods are disclosed and described, it is to be understood that they are not limited to specific synthetic methods or specific recombinant biotechnology methods unless otherwise specified, or to particular reagents unless otherwise specified, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
As used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a pharmaceutical carrier” includes mixtures of two or more such carriers, and the like.
Ranges can be expressed herein as from “about” one particular value, and/or to “about” another particular value. When such a range is expressed, another embodiment includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another embodiment. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint. 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 when a value is disclosed that “less than or equal to” the value, “greater than or equal to the value” and possible ranges between values are also disclosed, as appropriately understood by the skilled artisan. For example, if the value “10” is disclosed the “less than or equal to 10” as well as “greater than or equal to 10” is also disclosed. It is also understood that the throughout the application, data is provided in a number of different formats, and that this data, represents endpoints and starting points, and ranges for any combination of the data points. For example, if a particular data point “10” and a particular data point 15 are disclosed, it is understood that greater than, greater than or equal to, less than, less than or equal to, and equal to and 15 are considered disclosed as well as between 10 and 15. 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.
In this specification and in the claims which follow, reference will be made to a number of terms which shall be defined to have the following meanings:
“Optional” or “optionally” means that the subsequently described event or circumstance may or may not occur, and that the description includes instances where said event or circumstance occurs and instances where it does not.
The term “administering” refers to an administration that is oral, topical, intravenous, subcutaneous, transcutaneous, transdermal, intramuscular, intra-joint, parenteral, intra-arteriole, intradermal, intraventricular, intracranial, intraperitoneal, intralesional, intranasal, rectal, vaginal, by inhalation or via an implanted reservoir. The term “parenteral” includes subcutaneous, intravenous, intramuscular, intra-articular, intra-synovial, intrasternal, intrathecal, intrahepatic, intralesional, and intracranial injections or infusion techniques.
As used herein, the term “comprising” is intended to mean that the compositions and methods include the recited elements, but not excluding others. “Consisting essentially of” when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination. Thus, a composition consisting essentially of the elements as defined herein would not exclude trace contaminants from the isolation and purification method and pharmaceutically acceptable carriers, such as phosphate buffered saline, preservatives, and the like. Embodiments defined by each of these transition terms are within the scope of this invention.
An “effective amount” is an amount sufficient to effect beneficial or desired results. An effective amount can be administered in one or more administrations, applications or dosages.
The terms “treat”, “treating”, “treatment” and grammatical variations thereof as used herein, include partially or completely delaying, alleviating, mitigating or reducing the intensity of one or more attendant symptoms of a disorder or condition and/or alleviating, mitigating or impeding one or more causes of a disorder or condition. Treatments according to the invention may be applied preventively, prophylactically, pallatively or remedially. In some instances, the terms “treat”, “treating”, “treatment” and grammatical variations thereof, include partially or completely reducing the size of a tumor, reducing the number of tumors, and reducing the severity/metastatic ability of a tumor as compared with prior to treatment of the subject or as compared with the incidence of such symptom in a general or study population.
References in the specification and concluding claims to parts by weight of a particular element or component in a composition denotes the weight relationship between the element or component and any other elements or components in the composition or article for which a part by weight is expressed. Thus, in a compound containing 2 parts by weight of component X and 5 parts by weight component Y, X and Y are present at a weight ratio of 2:5, and are present in such ratio regardless of whether additional components are contained in the compound. As used herein, a “wt. %” or “weight percent” or “percent by weight” of a component, unless specifically stated to the contrary, refers to the ratio of the weight of the component to the total weight of the composition in which the component is included, expressed as a percentage.
Throughout this application, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this pertains. The references disclosed are also individually and specifically incorporated by reference herein for the material contained in them that is discussed in the sentence in which the reference is relied upon.
Disclosed are the components to be used to prepare the disclosed compositions as well as the compositions themselves to be used within the methods disclosed herein. These and other materials are disclosed herein, and it is understood that when combinations, subsets, interactions, groups, etc. of these materials are disclosed that while specific reference of each various individual and collective combinations and permutation of these compounds may not be explicitly disclosed, each is specifically contemplated and described herein. For example, if a particular synthetic or chimeric PD-L1 peptide is disclosed and discussed and a number of modifications that can be made to a number of molecules including the synthetic or chimeric PD-L1 peptide are discussed, specifically contemplated is each and every combination and permutation of the synthetic or chimeric PD-L1 peptide and the modifications that are possible unless specifically indicated to the contrary. Thus, if a class of molecules A, B, and C are disclosed as well as a class of molecules D, E, and F and an example of a combination molecule, A-D is disclosed, then even if each is not individually recited each is individually and collectively contemplated meaning combinations, A-E, A-F, B-D, B-E, B-F, C-D, C-E, and C-F are considered disclosed. Likewise, any subset or combination of these is also disclosed. Thus, for example, the sub-group of A-E, B-F, and C-E would be considered disclosed. This concept applies to all aspects of this application including, but not limited to, steps in methods of making and using the disclosed compositions. Thus, if there are a variety of additional steps that can be performed it is understood that each of these additional steps can be performed with any specific embodiment or combination of embodiments of the disclosed methods.
The PD-1 gene, which belongs to the immunoglobulin super family, encodes a 55 kDa type I transmembrane protein. Both mouse PD-1 and human PD-1 consist of 288 amino acids, and have signal peptide at N terminal (20 amino acid) and hydrophobic region in the middle part, which is a transmembrane region. Human and murine PD-1 proteins share about 60%-80% amino acid identity with conservation of four potential N-glycosylation sites, and residues that define the Ig-V domain. PD-1 is expressed on T cells, B cells, and macrophages. The ligands for PD-1 are the B7 family members PD-L1 (B7-H1) and PD-L2 (B7-DC). Signaling through the immune checkpoint programmed cell death protein-1 (PD-1) enables tumor progression by dampening antitumor immune responses. Therapeutic blockade of the signaling axis between PD-1 and its ligand programmed cell death ligand-1 (PD-L1) with monoclonal antibodies has shown remarkable clinical success in the treatment of cancer and demonstrated impressive activity across a broad set of cancer subtypes. Disclosed herein, are improvements on traditional PD-1/PD-L1 blockades using smaller, non-antibody peptide therapeutics and peptide vaccines which directly block the interaction of PD-1 and PD-L1 or can stimulate host immune responses to generate antibodies to PD-L1 that block the PD-1/PD-L1 interaction.
Using computer aided analysis of PD-L1 B cell epitopes, sequences corresponding to PD-L1 (SEQ ID NO: 1) residues 36-53, 50-67, 95-112, and 130-147 were derived. Thus, in one aspect, disclosed herein are synthetic PD-L1 peptides for stimulating an immune response to a PD-L1 protein comprising residues 36-53, 50-67, 95-112, and/or 130-147 of PD-L1. For example, disclosed herein are synthetic PD-L1 peptides for stimulating an immune response to a PD-L1 protein comprising LIVYWEMEDKNIIQFVHG (SEQ ID NO: 2), FVHGEEDLKVQHSSYRQR (SEQ ID NO: 3), YRCMISYGGADYKRITVK (SEQ ID NO: 4), and/or VTSEHELTCQAEGYPKAE (SEQ ID NO: 5). In one aspect, the peptides can acylated and/or amidated. Thus, disclosed herein are synthetic PD-L1 peptides for stimulating an immune response to a PD-L1 protein comprising (SEQ ID NO: 2), (SEQ ID NO: 3), (SEQ ID NO: 4), and/or (SEQ ID NO: 5); wherein the synthetic peptide is acylated and/or amidated.
In some instances, uses of an analog of the L-amino sequence can advantages to the base sequence such as resistance to degradation, stability, ease of synthesis, or have greater efficacy. In one aspect, it is understood and herein contemplated that the disclosed synthetic sequences can be comprise the L-amino sequence in reverse order from amino to carboxy end. For example, the retro sequence of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5, are GHVFQIINKDEMEWYVIL (SEQ ID NO: 12), RQRYSSHQVKLDEEGHVF (SEQ ID NO: 13), KVTIRKYDAGGYSIMCRY (SEQ ID NO: 14), and EAKPYGEAQCTLEHESTV (SEQ ID NO: 15), respectively. These retro sequences can also have the mirror conformation of the base sequence. Thus, disclosed herein are synthetic PD-L1 peptides comprising one or more of the sequences as set forth in SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, and/or SEQ ID NO: 15. As with SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5; synthetic peptides comprising SEQ ID NO 12, SEQ ID NO: 13, SEQ ID NO: 14 and/or SEQ ID NO: 15 can be acetylated and/or amidated.
In addition to retro analogs of the L-amino acid sequence set forth in SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5 which are set forth in SEQ ID NO 12, SEQ ID NO: 13, SEQ ID NO: 14 and SEQ ID NO: 15 are D enantiomer analogs of the forward L-amino (SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5) and retro L-amino sequence (SEQ ID NO 12, SEQ ID NO: 13, SEQ ID NO: 14 and SEQ ID NO: 15) which can possess increased resistance to degradation and proteolysis allowing for better oral administration, extended efficacy, and increased ease of synthesis. Accordingly, in one aspect, disclosed herein are synthetic PD-L1 peptides comprising one or more of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO 12, SEQ ID NO: 13, SEQ ID NO: 14 and/or SEQ ID NO: 15; wherein the amino acids comprising the sequence are D amino acids.
In one aspect, it is understood and herein contemplated that the disclosed synthetic PD-L1 peptides can have increased B cell stimulation by linking the synthetic PD-L1 peptides to a helper T (Th) cell epitope that promotes the release of cytokines that assist in bypassing MHC restriction (i.e., a promiscuous Th cell epitope) to form a chimeric PD-L1 peptide. For example, disclosed herein, in one aspect are PD-L1 chimeric peptides for stimulating an immune response to a PD-L1 protein comprising one or more PD-L1 B cell epitopes further comprising a T helper (Th) epitope (for example, a measles virus fusion protein peptide such as SEQ ID NO: 6), wherein the one or more PD-L1 B cell epitopes consist of a sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, and/or SEQ ID NO: 15. It is understood and herein contemplated that the B cell epitope (i.e., the PD-L1 synthetic peptide) can comprise D amino acids.
The Th epitope can be from about 14 to about 22, more preferably about 15 to 21, most preferably 16 amino acids in length. Preferably, the Th cell epitope has one of the following amino acid sequences provided in Table 1.
To join the synthetic PD-L1 peptide and the Th cell epitope, an amino acid linker can be used. Preferably the linker is a peptide of from about 2 to about 15 amino acids, more preferably from about 2 to about 10 amino acids, most preferably from about 2 to about 6 amino acids in length. The most preferred linker comprises the amino acid sequence Gly-Pro-Ser-Leu (SEQ ID NO: 7). Thus, in one aspect, also disclosed herein are chimeric peptides comprising the synthetic peptide of any preceding aspect, further comprising a Th epitope (for example, a measles virus fusion protein peptide such as SEQ ID NO: 6), and a linker (such as, for example, SEQ ID NO: 7) joining the synthetic PD-L1 peptide to the Th epitope. For example, disclosed herein, in one aspect, are chimeric PD-L1 peptides for stimulating an immune response to a PD-L1 protein comprising one or more PD-L1 B cell epitopes, a T helper (Th) epitope (for example, a measles virus fusion protein peptide such as SEQ ID NO: 6), and a linker (such as, for example, SEQ ID NO: 7) joining the PD-L1 B cell epitope to the Th epitope; wherein the chimeric PD-L1 peptide comprises the amino acid sequence as set forth in
As with the synthetic peptides, it is understood and herein contemplated that the amino acids of the synthetic PD-L1 peptides comprised within the chimeric PD-L1 peptides can be a D amino acid analogs of the L-amino acids in the sequence. Accordingly, in one aspect, disclosed herein are chimeric peptides comprising any of the synthetic PD-L1 peptides disclosed herein, further comprising a Th epitope (for example, a measles virus fusion protein peptide such as SEQ ID NO: 6), and a linker (such as, for example, SEQ ID NO: 7) joining the synthetic PD-L 1 peptide to the Th epitope. For example, disclosed herein, in one aspect, are chimeric PD-L1 peptides comprising the amino acid sequence as set forth in SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, and/or SEQ ID NO: 19; wherein the synthetic PD-L1 peptide sequence (i.e., the B cell epitope) comprises D amino acids.
As disclosed herein, the disclosed synthetic and chimeric PD-L1 peptides can be combined with targeted therapies using peptide-based B-cell epitopes and peptide immuno-therapeutics that block the growth and spread of cancer by inhibiting oncogenic signaling pathways, such as, HER-2. The human epidermal growth factor receptor 2 (HER-2) also known as HER2, HER-2/neu, p185neu, ERBB2 or CD340 family of receptors plays a central role in the pathogenesis of several human cancers including breast, ovarian, renal, colon and lung carcinomas cancers and is associated with more aggressive forms of cancer, increased risk of metastasis, increased tumor invasion and decreased overall survival. Therefore, HER-2 is a key therapeutic target in several cancers that are binding sites of trastuzumab (HERCEPTIN®) and pertuzumab (PERJECTA®). Trastuzumab was the first humanized mAb targeting HER-2 in combination with chemotherapy to be approved for clinical use in patients with metastatic HER-2 positive breast cancer. The addition of pertuzumab, a humanized mAb that blocks the dimerization of HER-2 with other HER family members, to docetaxel and trastuzumab in patients with untreated HER-2 positive breast cancer, resulted in improvement in progression-free survival from 12.4 months to 18.5 months and in overall survival from 40.8 to 56.5 months. Despite the benefit observed from trastuzumab approximately one-third of patients with metastatic, HER-2 positive breast cancer initially respond and the majority of responding patients eventually develop acquired resistance within one year of therapy. Targeted therapies with humanized mAb to HER-2 (trastuzumab, pertuzumab) or the chimeric mAb specific targeting EGFR (cetuximab, ERBITUX®) have markedly improved survival in the adjuvant setting but still demonstrate toxicities, intrinsic or acquired resistance, and the majority of patients with advanced cancer finally succumb to their disease.
Also disclosed herein are HER-2 chimeric peptides for stimulating an immune response to a HER-2 comprising one or more HER-2 B cell epitopes, a T helper (Th) epitope (including, but not limited to measles virus fusion protein peptide (such as, for example SEQ ID NO: 6), and a linker (such as, for example, SEQ ID NO: 7) joining the HER-2 B cell epitope to the Th epitope, wherein the one or more HER-2 B cell epitopes consist of a sequence selected from the group consisting of SEQ ID NO: 27 and SEQ ID NO: 29. For example, a HER-2 chimeric peptide comprising the amino acid sequence as set forth in SEQ ID NO:28 or SEQ ID NO: 30.
It is understood and herein contemplated that any of the PD-L1 peptides, synthetic PD-L1 peptides, chimeric PD-L1 peptides (for example any of the peptides as set forth in SEQ ID NOs: 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, and/or 19) and/or any of the HER-2 peptides or chimeric HER-2 peptides (for example, any of the peptides as set forth in SEQ ID NO: 27, 28, 29, or 30) can be formulated as a vaccine or pharmaceutical composition which can be administered therapeutically or prophylactically to a subject having or at risk of developing a cancer (such as, for example, breast cancer, ovarian cancer, endometrial cancer, colon cancer, non-small cell lung cancer, prostate cancer, and cervical cancer), autoimmune disease, and/or Alzheimer's disease. In one aspect, the vaccine or pharmaceutical composition can comprise one or more chimeric or synthetic peptides of any preceding and a pharmaceutically acceptable vehicle (such as, for example, a vehicle that is biodegradable including, but not limited to an emulsion comprising a pharmaceutically acceptable adjuvant. As used herein, the term “adjuvant” typically refers to a class of substance that can increase the magnitude of the immune response elicited by the programmed cell death ligand-1 (PD-L1) chimeric peptides beyond that which would be expected, either from the chimeric peptides alone or from the chimeric peptides as herein described in the absence of an adjuvant.
Suitable adjuvants will be known to persons skilled in the art. Non-limiting examples of suitable adjuvants include aluminium salts (e.g. aluminium hydroxide, aluminium phosphate and potassium aluminium sulfate (also referred to as Alum)), liposomes, virosomes, water-in-oil or oil-in-water emulsions (e.g. Freund's adjuvant, Montanide®, MF59® and AS03), 3-O-desacyl-4′-monophosphoryl lipid A (MPL) and adjuvants containing MPL (e.g. AS01, AS02 and AS04) and saponin-based adjuvants. Saponin-based adjuvants include saponins or saponin derivatives from, for example, Quillaja saponaria, Panax ginseng Panax notoginseng, Panax quinquefolium, Platycodon grandiflonim, Polygala senega, Polygala tenuifolia, Quillaja brasiliensis, Astragalus membranaceus and Achyranthes bidentata. Exemplary saponin-based adjuvants include iscoms, iscom matrix, ISCOMATRIX™ adjuvant, Matrix M™ adjuvant, Matrix C™ adjuvant, Matrix Q™ adjuvant, AbISCO®-100 adjuvant, AbISCO®-300 adjuvant, ISCOPREP™, an ISCOPREP™ derivative, adjuvant containing ISCOPREP™ or an ISCOPREP™ derivative, QS-21, a QS-21 derivative, and an adjuvant containing QS-21 or a QS21 derivative. The vaccine composition as herein described can also be associated with immumodulatory agents, including, for example, cytokines, chemokines and growth factors. Mixtures of two or more adjuvants within the same vaccine composition are also contemplated herein. In an embodiment, the adjuvant is water in oil adjuvant Montanide. For example, disclosed herein are PD-L1 peptide, synthetic PD-L1 peptide, and/or chimeric PD-L1 peptide (for example any of the peptides as set forth in SEQ ID NOs: 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, and/or 19) comprising pharmaceutical compositions further comprising one or more HER-2 B cell epitopes (such as for example, SEQ ID NO: 27, or SEQ ID NO: 29), one or more chimeric HER 2 peptides (such as for example, SEQ ID NO: 28, or SEQ ID NO: 30), and/or one or more anti-Her-2 antibodies. In one aspect, disclosed herein are pharmaceutical compositions comprising any of the PD-L1 peptide, synthetic PD-L1 peptide, and/or chimeric PD-L1 peptide (for example any of the peptides as set forth in SEQ ID NOs: 2, 3, 4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, and/or 19) with or without HER-2 B cell epitopes further comprising an adjuvant selected from the group consisting of aluminium hydroxide, aluminium phosphate, potassium aluminium sulfate, calcium phosphate hydroxide, Freund's complete adjuvant, Montanide®, Freund's incomplete adjuvant, iscoms, iscom matrix, ISCOMATRIX™ adjuvant, Matrix M™ adjuvant, Matrix C™ adjuvant, Matrix Q™ adjuvant, AbISCO®-100 adjuvant, AbISCO®-300 adjuvant, ISCOPREP™, an ISCOPREP™ derivative, adjuvant containing ISCOPREP™ or an ISCOPREP™ derivative, QS-21, a QS-21 derivative, and an adjuvant containing QS-21 or a QS21 derivative.
In one aspect, disclosed herein are antibodies that specifically bind to any of the PD-L1 chimeric peptides, PD-L1 synthetic peptides, HER-2 chimeric peptides, HER-2 synthetic peptides disclosed herein.
1. Sequence Similarities
It is understood that as discussed herein the use of the terms homology and identity mean the same thing as similarity. Thus, for example, if the use of the word homology is used between two non-natural sequences it is understood that this is not necessarily indicating an evolutionary relationship between these two sequences, but rather is looking at the similarity or relatedness between their nucleic acid sequences. Many of the methods for determining homology between two evolutionarily related molecules are routinely applied to any two or more nucleic acids or proteins for the purpose of measuring sequence similarity regardless of whether they are evolutionarily related or not.
In general, it is understood that one way to define any known variants and derivatives or those that might arise, of the disclosed genes and proteins herein, is through defining the variants and derivatives in terms of homology to specific known sequences. This identity of particular sequences disclosed herein is also discussed elsewhere herein. In general, variants of genes and proteins herein disclosed typically have at least, about 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99 percent homology to the stated sequence or the native sequence. Those of skill in the art readily understand how to determine the homology of two proteins or nucleic acids, such as genes. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level.
Another way of calculating homology can be performed by published algorithms.
Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. MoL Biol. 48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by inspection.
It is understood that any of the methods typically can be used and that in certain instances the results of these various methods may differ, but the skilled artisan understands if identity is found with at least one of these methods, the sequences would be said to have the stated identity, and be disclosed herein.
For example, as used herein, a sequence recited as having a particular percent homology to another sequence refers to sequences that have the recited homology as calculated by any one or more of the calculation methods described above. For example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using the Zuker calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by any of the other calculation methods. As another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using both the Zuker calculation method and the Pearson and Lipman calculation method even if the first sequence does not have 80 percent homology to the second sequence as calculated by the Smith and Waterman calculation method, the Needleman and Wunsch calculation method, the Jaeger calculation methods, or any of the other calculation methods. As yet another example, a first sequence has 80 percent homology, as defined herein, to a second sequence if the first sequence is calculated to have 80 percent homology to the second sequence using each of calculation methods (although, in practice, the different calculation methods will often result in different calculated homology percentages).
2. Peptides
a) Protein and Peptide Variants
As discussed herein there are numerous variants of the synthetic PD-L1 peptides and chimeric PD-L1 peptides that are known and herein contemplated. In addition, to the known functional PD-L1 strain variants there are derivatives of the synthetic PD-L1 peptides and chimeric PD-L1 peptides which also function in the disclosed methods and compositions. Protein variants and derivatives are well understood to those of skill in the art and in can involve amino acid sequence modifications. For example, amino acid sequence modifications typically fall into one or more of three classes: substitutional, insertional or deletional variants. Insertions include amino and/or carboxyl terminal fusions as well as intrasequence insertions of single or multiple amino acid residues. Insertions ordinarily will be smaller insertions than those of amino or carboxyl terminal fusions, for example, on the order of one to four residues. Immunogenic fusion protein derivatives, such as those described in the examples, are made by fusing a polypeptide sufficiently large to confer immunogenicity to the target sequence by cross-linking in vitro or by recombinant cell culture transformed with DNA encoding the fusion. Deletions are characterized by the removal of one or more amino acid residues from the protein sequence. Typically, no more than about from 2 to 6 residues are deleted at any one site within the protein molecule. These variants ordinarily are prepared by site specific mutagenesis of nucleotides in the DNA encoding the protein, thereby producing DNA encoding the variant, and thereafter expressing the DNA in recombinant cell culture. Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, for example M13 primer mutagenesis and PCR mutagenesis. Amino acid substitutions are typically of single residues, but can occur at a number of different locations at once; insertions usually will be on the order of about from 1 to 10 amino acid residues; and deletions will range about from 1 to 30 residues. Deletions or insertions preferably are made in adjacent pairs, i.e. a deletion of 2 residues or insertion of 2 residues. Substitutions, deletions, insertions or any combination thereof may be combined to arrive at a final construct. The mutations must not place the sequence out of reading frame and preferably will not create complementary regions that could produce secondary mRNA structure. Substitutional variants are those in which at least one residue has been removed and a different residue inserted in its place. Such substitutions generally are made in accordance with the following Tables 2 and 3 and are referred to as conservative substitutions.
Substantial changes in function or immunological identity are made by selecting substitutions that are less conservative than those in Table 3, i.e., selecting residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site or (c) the bulk of the side chain. The substitutions which in general are expected to produce the greatest changes in the protein properties will be those in which (a) a hydrophilic residue, e.g. seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g. leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine or proline is substituted for (or by) any other residue; (c) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) an electronegative residue, e.g., glutamyl or aspartyl; or (d) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having a side chain, e.g., glycine, in this case, (e) by increasing the number of sites for sulfation and/or glycosylation.
For example, the replacement of one amino acid residue with another that is biologically and/or chemically similar is known to those skilled in the art as a conservative substitution. For example, a conservative substitution would be replacing one hydrophobic residue for another, or one polar residue for another. The substitutions include combinations such as, for example, Gly, Ala; Val, Ile, Leu; Asp, Glu; Asn, Gln; Ser, Thr; Lys, Arg; and Phe, Tyr. Such conservatively substituted variations of each explicitly disclosed sequence are included within the mosaic polypeptides provided herein.
Substitutional or deletional mutagenesis can be employed to insert sites for N-glycosylation (Asn-X-Thr/Ser) or O-glycosylation (Ser or Thr). Deletions of cysteine or other labile residues also may be desirable. Deletions or substitutions of potential proteolysis sites, e.g. Arg, is accomplished for example by deleting one of the basic residues or substituting one by glutaminyl or histidyl residues.
Certain post-translational derivatizations are the result of the action of recombinant host cells on the expressed polypeptide. Glutaminyl and asparaginyl residues are frequently post-translationally deamidated to the corresponding glutamyl and asparyl residues.
Alternatively, these residues are deamidated under mildly acidic conditions. Other post-translational modifications include hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the o-amino groups of lysine, arginine, and histidine side chains (T. E. Creighton, Proteins: Structure and Molecular Properties, W. H. Freeman & Co., San Francisco pp 79-86 [1983]), acetylation of the N-terminal amine and, in some instances, amidation of the C-terminal carboxyl.
It is understood that one way to define the variants and derivatives of the disclosed proteins herein is through defining the variants and derivatives in terms of homology/identity to specific known sequences. Specifically disclosed are variants of these and other proteins herein disclosed which have at least, 70% or 75% or 80% or 85% or 900% or 95% identity to the stated sequence. Those of skill in the art readily understand how to determine the homology of two proteins. For example, the homology can be calculated after aligning the two sequences so that the homology is at its highest level.
Another way of calculating homology can be performed by published algorithms. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2: 482 (1981), by the homology alignment algorithm of Needleman and Wunsch, J. MoL Biol. 48: 443 (1970), by the search for similarity method of Pearson and Lipman, Proc. Natl. Acad. Sci. U.S.A. 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by inspection.
The same types of homology can be obtained for nucleic acids by for example the algorithms disclosed in Zuker, M. Science 244:48-52, 1989, Jaeger et al. Proc. Natl. Acad. Sci. USA 86:7706-7710, 1989, Jaeger et al. Methods Enzymol. 183:281-306, 1989.
It is understood that the description of conservative mutations and homology can be combined together in any combination, such as embodiments that have at least 70% homology to a particular sequence wherein the variants are conservative mutations.
As this specification discusses various proteins and protein sequences it is understood that the nucleic acids that can encode those protein sequences are also disclosed. This would include all degenerate sequences related to a specific protein sequence, i.e. all nucleic acids having a sequence that encodes one particular protein sequence as well as all nucleic acids, including degenerate nucleic acids, encoding the disclosed variants and derivatives of the protein sequences. Thus, while each particular nucleic acid sequence may not be written out herein, it is understood that each and every sequence is in fact disclosed and described herein through the disclosed protein sequence. It is also understood that while no amino acid sequence indicates what particular DNA sequence encodes that protein within an organism, where particular variants of a disclosed protein are disclosed herein, the known nucleic acid sequence that encodes that peptide or protein is also known and herein disclosed and described.
It is understood that there are numerous amino acid and peptide analogs which can be incorporated into the disclosed compositions. For example, there are numerous D amino acids or amino acids which have a different functional substituent then the amino acids shown in Table 2 and Table 3. The opposite stereo isomers of naturally occurring peptides are disclosed, as well as the stereo isomers of peptide analogs. These amino acids can readily be incorporated into polypeptide chains by charging tRNA molecules with the amino acid of choice and engineering genetic constructs that utilize, for example, amber codons, to insert the analog amino acid into a peptide chain in a site specific way.
Molecules can be produced that resemble peptides, but which are not connected via a natural peptide linkage. For example, linkages for amino acids or amino acid analogs can include CH2NH—, —CH2S—, —CH2—CH2—, —CH═CH— (cis and trans), —COCH2—, —CH(OH)CH2—, and —CHH2SO— (These and others can be found in Spatola, A. F. in Chemistry and Biochemistry of Amino Acids, Peptides, and Proteins, B. Weinstein, eds., Marcel Dekker, New York, p. 267 (1983); Spatola, A. F., Vega Data (March 1983), Vol. 1, Issue 3, Peptide Backbone Modifications (general review); Morley, Trends Pharm Sci (1980) pp. 463-468; Hudson, D. et al., Int J Pept Prot Res 14:177-185 (1979) (—CH2NH—, CH2CH2—); Spatola et al. Life Sci 38:1243-1249 (1986) (—CH H2—S); Hann J. Chem. Soc Perkin Trans. I 307-314 (1982) (—CH—CH—, cis and trans); Almquist et al. J. Med. Chem. 23:1392-1398 (1980) (—COCH2—); Jennings-White et al. Tetrahedron Lett 23:2533 (1982) (—COCH2—); Szelke et al. European Appln, EP 45665 CA (1982): 97:39405 (1982) (—CH(OH)CH2—); Holladay et al. Tetrahedron. Lett 24:4401-4404 (1983) (—C(OH)CH2—); and Hruby Life Sci 31:189-199 (1982) (—CH2—S—); each of which is incorporated herein by reference. A particularly preferred non-peptide linkage is —CH2NH—. It is understood that peptide analogs can have more than one atom between the bond atoms, such as b-alanine, g-aminobutyric acid, and the like.
Amino acid analogs and analogs and peptide analogs often have enhanced or desirable properties, such as, more economical production, greater chemical stability, enhanced pharmacological properties (half-life, absorption, potency, efficacy, etc.), altered specificity (e.g., a broad-spectrum of biological activities), reduced antigenicity, and others.
D-amino acids can be used to generate more stable peptides, because D amino acids are not recognized by peptidases and such. Systematic substitution of one or more amino acids of a consensus sequence with a D-amino acid of the same type (e.g., D-lysine in place of L-lysine) can be used to generate more stable peptides. In other words, contemplated herein is the inverso (i.e., the D-amino acid substitution) of any disclosed sequence. Cysteine residues can be used to cyclize or attach two or more peptides together. This can be beneficial to constrain peptides into particular conformations. In one aspect, disclosed herein are synthetic PD-L1 peptides comprising one or more of the sequences as set forth in SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, or SEQ ID NO:5; wherein the amino acids of the peptide are the D enantiomer.
In one aspect, the disclosed synthetic peptides can be in reverse order such that the amino to carboxy end of the peptide is reversed (i.e., the retro sequence). In one aspect, disclosed herein are the retro sequences of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5, which comprises, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, and SEQ ID NO: 15, respectively. These retro sequences can also have the mirror conformation of the base sequence. In one aspect, the retro sequence can also comprise a D amino acid substitution (i.e., the retro-inverso) sequence. Thus, disclosed herein are synthetic PD-L1 peptides comprising one or more of the sequences as set forth in SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, and SEQ ID NO: 15; wherein the amino acids of the peptide are the D enantiomer.
It is understood that any of the D amino acid substituted synthetic peptides disclosed herein can be used in as the PD-L1 epitope in the disclosed PD-L1 chimeric peptides. For example, disclosed herein are chimeric PD-L1 peptides comprising one or more PD-L1 B cell epitopes, a T helper (Th) epitope, and a linker joining the PD-L1 B cell epitope to the Th epitope, wherein the one or more PD-L1 B cell epitopes consist of a sequence selected from the group consisting of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, and SEQ ID NO: 15; and wherein the amino acids of the peptide are the D enantiomer. In one aspect, disclosed herein are chimeric PD-L1 peptides, wherein the peptide comprises the amino acid sequence as set forth in SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10 SEQ ID NO: 11, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, or SEQ ID NO: 19; and wherein the amino acids of the synthetic PD-L1 peptide are the D enantiomer.
3. Pharmaceutical Carriers/Delivery of Pharmaceutical Products
As described above, the synthetic PD-L1 peptides, chimeric PD-L1 peptides, synthetic HER-2 peptides, and/or chimeric HER-2 peptides disclosed herein can also be administered in vivo in a pharmaceutically acceptable carrier. Thus, in one aspect, disclosed herein are pharmaceutical composition comprising any one or more of the PD-L1 peptides as set forth in SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19. SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, and/or SEQ ID NO: 30.
By “pharmaceutically acceptable” is meant a material that is not biologically or otherwise undesirable, i.e., the material may be administered to a subject, along with the nucleic acid or vector, without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained. The carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art.
It is understood and herein contemplated that the disclosed PD-L1 peptides comprising pharmaceutical compositions are particularly useful in the treatment, inhibition, reduction, decrease, amelioration, and/or prevention of diseases or conditions where PD-L1 mediated immune suppression occurs. Over the past two decades, another cancer treatment paradigm has evolved: selective, mechanism-based targeted therapies using peptide-based B-cell epitopes and peptide immuno-therapeutics that block the growth and spread of cancer by inhibiting oncogenic signaling pathways; these targeted therapies tend to have fewer side effects than non-specific chemotherapies. Hence, peptide-based and small molecule inhibitors have received attention in recent years in drug development strategies. However, compare to monoclonal antibodies, small molecule immune checkpoint inhibitors need substantial improvements. Thus, in one aspect, the disclosed pharmaceutical composition comprising one or more of the PD-L1 peptides disclosed herein can be combined with a disease-specific treatment or vaccine to further increase the efficacy of the PD-L1 peptides. For example, a pharmaceutical composition comprising one or more of the PD-L1 peptides can be combined with anti-HER2 antibodies, HER-2 chimeric peptides, and/or HER-2 B cell epitopes for use in treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer and/or metastasis (such as, for example, breast cancer, ovarian cancer, endometrial cancer, colon cancer, non-small cell lung cancer, prostate cancer, and cervical cancer).
In one aspect, disclosed herein are pharmaceutical compositions comprising one or more of the PD-L1 peptide, synthetic peptides, or chimeric peptides disclosed herein (for example, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, and/or SEQ ID NO: 19) further comprising one or more HER-2 B cell epitopes (for example SEQ ID NO: 27 or 29 or chimeric epitopes SEQ ID NO: 28 or 30) and/or anti-Her-2 antibodies. In one aspect, specifically disclosed herein are pharmaceutic compositions comprising MVF-PD-L1 (36-53) as set forth in SEQ ID NO: 8, MVF-PD-L1 (50-67) as set forth in SEQ ID NO: 9, MVF-PD-L1 (95-112) as set forth in SEQ ID NO: 10, and/or MVF-PD-L1 (130-147) as set forth in SEQ ID NO: 11; a MVF-HER-2 (266-296) peptide (for example as set forth in SEQ ID NO: 28), and a MVF-HER-2 (597-626) peptide (for example as set forth in SEQ ID NO: 30).
The compositions may be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by intraperitoneal injection, transdermally, extracorporeally, topically or the like, including topical intranasal administration or administration by inhalant. As used herein, “topical intranasal administration” means delivery of the compositions into the nose and nasal passages through one or both of the nares and can comprise delivery by a spraying mechanism or droplet mechanism, or through aerosolization of the nucleic acid or vector. Administration of the compositions by inhalant can be through the nose or mouth via delivery by a spraying or droplet mechanism. Delivery can also be directly to any area of the respiratory system (e.g., lungs) via intubation. The exact amount of the compositions required will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity of the allergic disorder being treated, the particular nucleic acid or vector used, its mode of administration and the like. Thus, it is not possible to specify an exact amount for every composition. However, an appropriate amount can be determined by one of ordinary skill in the art using only routine experimentation given the teachings herein.
Parenteral administration of the composition, if used, is generally characterized by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution of suspension in liquid prior to injection, or as emulsions. A more recently revised approach for parenteral administration involves use of a slow release or sustained release system such that a constant dosage is maintained. See, e.g., U.S. Pat. No. 3,610,795, which is incorporated by reference herein.
The materials may be in solution, suspension (for example, incorporated into microparticles, liposomes, or cells). These may be targeted to a particular cell type via antibodies, receptors, or receptor ligands. The following references are examples of the use of this technology to target specific proteins to tumor tissue (Senter, et al., Bioconjugate Chem., 2:447-451, (1991); Bagshawe, K. D., Br. J. Cancer, 60:275-281, (1989); Bagshawe, et al., Br. J. Cancer, 58:700-703, (1988); Senter, et al., Bioconjugate Chem., 4:3-9, (1993); Battelli, et al., Cancer Immunol. Immunother., 35:421-425, (1992); Pietersz and McKenzie, Immunolog. Reviews, 129:57-80, (1992); and Roffler, et al., Biochem. Pharmacol, 42:2062-2065, (1991)). Vehicles such as “stealth” and other antibody conjugated liposomes (including lipid mediated drug targeting to colonic carcinoma), receptor mediated targeting of DNA through cell specific ligands, lymphocyte directed tumor targeting, and highly specific therapeutic retroviral targeting of murine glioma cells in vivo. The following references are examples of the use of this technology to target specific proteins to tumor tissue (Hughes et al., Cancer Research, 49:6214-6220, (1989); and Litzinger and Huang, Biochimica et Biophysica Acta, 1104:179-187, (1992)). In general, receptors are involved in pathways of endocytosis, either constitutive or ligand induced. These receptors cluster in clathrin-coated pits, enter the cell via clathrin-coated vesicles, pass through an acidified endosome in which the receptors are sorted, and then either recycle to the cell surface, become stored intracellularly, or are degraded in lysosomes. The internalization pathways serve a variety of functions, such as nutrient uptake, removal of activated proteins, clearance of macromolecules, opportunistic entry of viruses and toxins, dissociation and degradation of ligand, and receptor-level regulation. Many receptors follow more than one intracellular pathway, depending on the cell type, receptor concentration, type of ligand, ligand valency, and ligand concentration. Molecular and cellular mechanisms of receptor-mediated endocytosis has been reviewed (Brown and Greene, DNA and Cell Biology 10:6, 399-409 (1991)).
a) Pharmaceutically Acceptable Carriers
The compositions, including antibodies, can be used therapeutically in combination with a pharmaceutically acceptable carrier.
Suitable carriers and their formulations are described in Remington: The Science and Practice of Pharmacy (19th ed.) ed. A. R. Gennaro, Mack Publishing Company, Easton, Pa. 1995. Typically, an appropriate amount of a pharmaceutically-acceptable salt is used in the formulation to render the formulation isotonic. Examples of the pharmaceutically-acceptable carrier include, but are not limited to, saline, Ringer's solution and dextrose solution. The pH of the solution is preferably from about 5 to about 8, and more preferably from about 7 to about 7.5. Further carriers include sustained release preparations such as semipermeable matrices of solid hydrophobic polymers containing the antibody, which matrices are in the form of shaped articles, e.g., films, liposomes or microparticles. It will be apparent to those persons skilled in the art that certain carriers may be more preferable depending upon, for instance, the route of administration and concentration of composition being administered.
Pharmaceutical carriers are known to those skilled in the art. These most typically would be standard carriers for administration of drugs to humans, including solutions such as sterile water, saline, and buffered solutions at physiological pH. The compositions can be administered intramuscularly or subcutaneously. Other compounds will be administered according to standard procedures used by those skilled in the art.
Pharmaceutical compositions may include carriers, thickeners, diluents, buffers, preservatives, surface active agents and the like in addition to the molecule of choice. Pharmaceutical compositions may also include one or more active ingredients such as antimicrobial agents, antiinflammatory agents, anesthetics, and the like.
The pharmaceutical composition may be administered in a number of ways depending on whether local or systemic treatment is desired, and on the area to be treated. Administration may be topically (including ophthalmically, vaginally, rectally, intranasally), orally, by inhalation, or parenterally, for example by intravenous drip, subcutaneous, intraperitoneal or intramuscular injection. The disclosed antibodies can be administered intravenously, intraperitoneally, intramuscularly, subcutaneously, intracavity, or transdermally.
Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose), and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, anti-oxidants, chelating agents, and inert gases and the like.
Formulations for topical administration may include ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable.
Compositions for oral administration include powders or granules, suspensions or solutions in water or non-aqueous media, capsules, sachets, or tablets. Thickeners, flavorings, diluents, emulsifiers, dispersing aids or binders may be desirable.
Some of the compositions may potentially be administered as a pharmaceutically acceptable acid- or base-addition salt, formed by reaction with inorganic acids such as hydrochloric acid, hydrobromic acid, perchloric acid, nitric acid, thiocyanic acid, sulfuric acid, and phosphoric acid, and organic acids such as formic acid, acetic acid, propionic acid, glycolic acid, lactic acid, pyruvic acid, oxalic acid, malonic acid, succinic acid, maleic acid, and fumaric acid, or by reaction with an inorganic base such as sodium hydroxide, ammonium hydroxide, potassium hydroxide, and organic bases such as mono-, di-, trialkyl and aryl amines and substituted ethanolamines.
b) Therapeutic Uses
Effective dosages and schedules for administering the compositions may be determined empirically, and making such determinations is within the skill in the art. The dosage ranges for the administration of the compositions are those large enough to produce the desired effect in which the symptoms of the disorder are effected. The dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like. Generally, the dosage will vary with the age, condition, sex and extent of the disease in the patient, route of administration, or whether other drugs are included in the regimen, and can be determined by one of skill in the art. The dosage can be adjusted by the individual physician in the event of any counterindications. Dosage can vary, and can be administered in one or more dose administrations daily, for one or several days. Guidance can be found in the literature for appropriate dosages for given classes of pharmaceutical products. For example, guidance in selecting appropriate doses for antibodies can be found in the literature on therapeutic uses of antibodies, e.g., Handbook of Monoclonal Antibodies, Ferrone et al., eds., Noges Publications, Park Ridge, N.J., (1985) ch. 22 and pp. 303-357; Smith et al., Antibodies in Human Diagnosis and Therapy, Haber et al., eds., Raven Press, New York (1977) pp. 365-389. A typical daily dosage of the antibody used alone might range from about 1 μg/kg to up to 100 mg/kg of body weight or more per day, depending on the factors mentioned above.
The synthetic PD-L1 peptides, chimeras, and antibodies disclosed herein that inhibit the interaction of PD-1 and PD-L1 can be administered prophylactically to patients or subjects who are at risk for developing a cancer, autoimmune disease, of Alzheimer's disease or therapeutically (i.e., after diagnosis of a disease or onset of symptoms) for treatment, inhibition, reduction, amelioration, and/or prevention of a cancer (such as, for example, breast cancer, ovarian cancer, endometrial cancer, colon cancer, non-small cell lung cancer, prostate cancer, and cervical cancer), autoimmune disease, of Alzheimer's disease.
Other molecules or antibodies that interact with PD-1 or PD-L1 to inhibit PD-1/PD-L1 interactions (for example, Pembrolixumab and nivolumab) can be used in combination with the disclosed synthetic PD-L1 peptides, chimeric PD-L1 peptides, or anti-PD-L1 antibodies to treat, inhibit, reduce, decrease, ameliorate, and/or prevent a cancer, autoimmune disease or Alzheimer's disease in a subject.
4. Antibodies
(1) Antibodies Generally
The term “antibodies” is used herein in a broad sense and includes both polyclonal and monoclonal antibodies. In addition to intact immunoglobulin molecules, also included in the term “antibodies” are fragments or polymers of those immunoglobulin molecules, and human or humanized versions of immunoglobulin molecules or fragments thereof, as long as they are chosen for their ability to interact with PD-L1 such that PD-1 is inhibited from interacting with PD-L1 or the HER-2 receptor is inhibited. Antibodies that bind SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, and/or SEQ ID NO: 19 involved in the interaction between PD-1 and PD-L1 are also disclosed. Also disclosed herein are antibodies that bind SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, and/or SEQ ID NO: 30 of HER-2 are also disclosed. The antibodies can be tested for their desired activity using the in vitro assays described herein, or by analogous methods, after which their in vivo therapeutic and/or prophylactic activities are tested according to known clinical testing methods. There are five major classes of human immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG-1, IgG-2, IgG-3, and IgG-4; IgA-1 and IgA-2. One skilled in the art would recognize the comparable classes for mouse. The heavy chain constant domains that correspond to the different classes of immunoglobulins are called alpha, delta, epsilon, gamma, and mu, respectively.
The term “monoclonal antibody” as used herein refers to an antibody obtained from a substantially homogeneous population of antibodies, i.e., the individual antibodies within the population are identical except for possible naturally occurring mutations that may be present in a small subset of the antibody molecules. The monoclonal antibodies herein specifically include “chimeric” antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, as long as they exhibit the desired antagonistic activity.
The disclosed monoclonal antibodies can be made using any procedure which produces mono clonal antibodies. For example, disclosed monoclonal antibodies can be prepared using hybridoma methods, such as those described by Kohler and Milstein, Nature, 256:495 (1975). In a hybridoma method, a mouse or other appropriate host animal is typically immunized with an immunizing agent to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the immunizing agent. Alternatively, the lymphocytes may be immunized in vitro.
The monoclonal antibodies may also be made by recombinant DNA methods. DNA encoding the disclosed monoclonal antibodies can be readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of murine antibodies). Libraries of antibodies or active antibody fragments can also be generated and screened using phage display techniques, e.g., as described in U.S. Pat. No. 5,804,440 to Burton et al. and U.S. Pat. No. 6,096,441 to Barbas et al.
In vitro methods are also suitable for preparing monovalent antibodies. Digestion of antibodies to produce fragments thereof, particularly, Fab fragments, can be accomplished using routine techniques known in the art. For instance, digestion can be performed using papain. Examples of papain digestion are described in WO 94/29348 published Dec. 22, 1994 and U.S. Pat. No. 4,342,566. Papain digestion of antibodies typically produces two identical antigen binding fragments, called Fab fragments, each with a single antigen binding site, and a residual Fc fragment. Pepsin treatment yields a fragment that has two antigen combining sites and is still capable of cross-linking antigen.
As used herein, the term “antibody or fragments thereof” encompasses chimeric antibodies and hybrid antibodies, with dual or multiple antigen or epitope specificities, and fragments, such as F(ab′)2, Fab′, Fab, Fv, sFv, and the like, including hybrid fragments. Thus, fragments of the antibodies that retain the ability to bind their specific antigens are provided. For example, fragments of antibodies which maintain PD-L1 binding activity or bind SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, and/or SEQ ID NO: 19 are included within the meaning of the term “antibody or fragment thereof.” Such antibodies and fragments can be made by techniques known in the art and can be screened for specificity and activity according to the methods set forth in the Examples and in general methods for producing antibodies and screening antibodies for specificity and activity (See Harlow and Lane. Antibodies, A Laboratory Manual. Cold Spring Harbor Publications, New York, (1988)).
Also included within the meaning of “antibody or fragments thereof” are conjugates of antibody fragments and antigen binding proteins (single chain antibodies).
The fragments, whether attached to other sequences or not, can also include insertions, deletions, substitutions, or other selected modifications of particular regions or specific amino acids residues, provided the activity of the antibody or antibody fragment is not significantly altered or impaired compared to the non-modified antibody or antibody fragment. These modifications can provide for some additional property, such as to remove/add amino acids capable of disulfide bonding, to increase its bio-longevity, to alter its secretory characteristics, etc. In any case, the antibody or antibody fragment must possess a bioactive property, such as specific binding to its cognate antigen. Functional or active regions of the antibody or antibody fragment may be identified by mutagenesis of a specific region of the protein, followed by expression and testing of the expressed polypeptide. Such methods are readily apparent to a skilled practitioner in the art and can include site-specific mutagenesis of the nucleic acid encoding the antibody or antibody fragment. (Zoller, M. J. Curr. Opin. Biotechnol. 3:348-354, 1992).
As used herein, the term “antibody” or “antibodies” can also refer to a human antibody and/or a humanized antibody. Many non-human antibodies (e.g., those derived from mice, rats, or rabbits) are naturally antigenic in humans, and thus can give rise to undesirable immune responses when administered to humans. Therefore, the use of human or humanized antibodies in the methods serves to lessen the chance that an antibody administered to a human will evoke an undesirable immune response.
(2) Human Antibodies
The disclosed human antibodies can be prepared using any technique. The disclosed human antibodies can also be obtained from transgenic animals. For example, transgenic, mutant mice that are capable of producing a full repertoire of human antibodies, in response to immunization, have been described (see, e.g., Jakobovits et al., Proc. Natl. Acad. Sci. USA, 90:2551-255 (1993); Jakobovits et al., Nature, 362:255-258 (1993); Bruggermann et al., Year in Immunol., 7:33 (1993)). Specifically, the homozygous deletion of the antibody heavy chain joining region (J(H)) gene in these chimeric and germ-line mutant mice results in complete inhibition of endogenous antibody production, and the successful transfer of the human germ-line antibody gene array into such germ-line mutant mice results in the production of human antibodies upon antigen challenge. Antibodies having the desired activity are selected using Env-CD4-co-receptor complexes as described herein.
(3) Humanized Antibodies
Antibody humanization techniques generally involve the use of recombinant DNA technology to manipulate the DNA sequence encoding one or more polypeptide chains of an antibody molecule. Accordingly, a humanized form of a non-human antibody (or a fragment thereof) is a chimeric antibody or antibody chain (or a fragment thereof, such as an sFv, Fv, Fab, Fab′, F(ab′)2, or other antigen-binding portion of an antibody) which contains a portion of an antigen binding site from a non-human (donor) antibody integrated into the framework of a human (recipient) antibody.
To generate a humanized antibody, residues from one or more complementarity determining regions (CDRs) of a recipient (human) antibody molecule are replaced by residues from one or more CDRs of a donor (non-human) antibody molecule that is known to have desired antigen binding characteristics (e.g., a certain level of specificity and affinity for the target antigen). In some instances, Fv framework (FR) residues of the human antibody are replaced by corresponding non-human residues. Humanized antibodies may also contain residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. Generally, a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. In practice, humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies. Humanized antibodies generally contain at least a portion of an antibody constant region (Fc), typically that of a human antibody.
(4) Administration of Antibodies
Administration of the antibodies can be done as disclosed herein. Nucleic acid approaches for antibody delivery also exist. The broadly neutralizing anti-PD-L1 antibodies and antibody fragments (including any antibody that binds to SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, and/or SEQ ID NO: 19) can also be administered to patients or subjects as a nucleic acid preparation (e.g., DNA or RNA) that encodes the antibody or antibody fragment, such that the patient's or subject's own cells take up the nucleic acid and produce and secrete the encoded antibody or antibody fragment. The delivery of the nucleic acid can be by any means, as disclosed herein, for example.
It is understood and herein contemplated that the disclosed compositions, synthetic PD-L1 peptides, and chimeric PD-L1 peptides can be used to treat, inhibit, reduce, decrease, ameliorate, and/or prevent any disease where immune suppression and prevention of programmed cell death is advantageous to the disease, such as Alzheimer's disease, autoimmune diseases, or any disease where uncontrolled cellular proliferation occurs such as cancers.
A non-limiting list of different types of autoimmune disease that can be treated, inhibited, reduced, decreased, ameliorated, and/or prevented using the chimeric or synthetic peptides or pharmaceutical compositions disclosed herein includes, but is not limited to, Psoriasis, Alopecia Areata, Primary biliary cirrhosis, Autoimmune polyendocrine syndrome, Diabetes mellitus type 1, autoimmune thyroiditis, Systemic Lupus Erythematosus, Multiple sclerosis, Guillain-Barre syndrome, Grave's disease, Sjogren's syndrome, ulcerative colitis, Autoimmune hemolytic anemia, Pernicious anemia, Psoriatic arthritis, rheumatoid arthritis, relapsing polychondritis, myasthenia gravis, Acute disseminated encephalomyelitis, and Granulomatosis with polyangiitis.
A non-limiting list of different types of cancers that can be treated, inhibited, reduced, decreased, ameliorated, and/or prevented using the chimeric or synthetic peptides or pharmaceutical compositions disclosed herein includes, but is not limited to lymphoma, B cell lymphoma, T cell lymphoma, mycosis fungoides, Hodgkin's Disease, myeloid leukemia, bladder cancer, brain cancer, nervous system cancer, head and neck cancer, squamous cell carcinoma of head and neck, kidney cancer, lung cancers such as small cell lung cancer and non-small cell lung cancer, endometrial cancer, neuroblastoma/glioblastoma, ovarian cancer, pancreatic cancer, prostate cancer, skin cancer, liver cancer, melanoma, squamous cell carcinomas of the mouth, throat, larynx, and lung, colon cancer, cervical cancer, cervical carcinoma, breast cancer, and epithelial cancer, renal cancer, genitourinary cancer, pulmonary cancer, esophageal carcinoma, head and neck carcinoma, large bowel cancer, hematopoietic cancers; testicular cancer; colon and rectal cancers, prostatic cancer, ipilimumab-refractory melanoma, or pancreatic cancer.
Accordingly, in one aspect, disclosed herein are methods of treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer, Alzheimer's disease, or an autoimmune disease in a subject comprising administering to a subject a PD-L1 synthetic peptide, wherein the PD-L1 synthetic peptide comprises one or more of the sequences as set forth in SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, or SEQ ID NO: 15. It is understood and herein contemplated that the synthetic peptides can comprise be acetylated, amidated, and/or the D enantiomer. Accordingly, in one aspect, disclosed herein are methods of treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer (such as, for example, breast cancer, ovarian cancer, endometrial cancer, colon cancer, non-small cell lung cancer, prostate cancer, and cervical cancer), Alzheimer's disease, or an autoimmune disease in a subject comprising administering to a subject a PD-L1 synthetic peptide wherein the PD-L1 synthetic peptide comprises the D enantiomer and or D enantiomer retro inverso of SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO: 18, SEQ ID NO: 9, SEQ ID NO: 10, or SEQ ID NO: 11 as set forth in SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, and SEQ ID NO: 19, respectively.
In one aspect, it is understood that the disclosed compositions can be combined with other treatments for a given disease or condition. For example, in one aspect, disclosed herein are methods of treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer and/or metastasis comprising administering to a subject a PD-L1 peptide, PD-L1 synthetic peptide, or PD-L1 chimeric peptide; wherein the disease or condition is cancer (such as, for example breast cancer, ovarian cancer, endometrial cancer, colon cancer, non-small cell lung cancer, prostate cancer, and cervical cancer), and wherein the method further comprises administering to the subject one or more HER-2 B cell epitopes (for example, one or more of the HER-2 peptides as set forth in SEQ ID NO: 27 or 29 or chimeric MVF-HER-2 peptides as set forth in SEQ ID NO: 28 or 30) and/or one or more anti-HER-2 antibodies. It is understood that where a HER-2 B cell epitope or anti-HER-2 antibody is administered to the subject, the administration can be as a separate concurrent administration, prior administration of the HER-2 B cell epitope or anti-HER-2 antibody, subsequent administration of the HER-2 B cell epitope or anti-HER-2 antibody, or a HER-2 B cell epitope or anti-HER-2 antibody that is a component in the same pharmaceutical formulation as the PD-L1 peptide, PD-L1 synthetic peptide, or PD-L1 chimeric peptide. For example, a method of treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer and/or metastasis (such as, for example, breast cancer, ovarian cancer, endometrial cancer, colon cancer, non-small cell lung cancer, prostate cancer, and cervical cancer) can comprise administering to a subject a pharmaceutical composition comprising one or more of the PD-L1 peptides set forth in SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 4, and SEQ ID NO: 5; chimeric PD-L1 peptides as set forth in SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10 and SEQ ID NO: 11; and/or retro inverso PD-L1 peptide as set forth in SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, and SEQ ID NO: 19; the method further comprising administering to the subject one or more HER-2 B cell epitopes HER-2 (266-296) as set forth in SEQ ID NO: 27 and/or HER-2 (597-626) as set forth in SEQ ID NO: 29 and/or chimeric epitopes MVF-HER-2 (266-296) peptide (for example as set forth in SEQ ID NO: 28, and a MVF-HER-2 (597-626) peptide (for example as set forth in SEQ ID NO: 30). Accordingly, in one aspect, disclosed herein is a method of treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer and/or metastasis (such as, for example, breast cancer, ovarian cancer, endometrial cancer, colon cancer, non-small cell lung cancer, prostate cancer, and cervical cancer) comprising administering to a subject with a cancer a pharmaceutical composition comprising an MVF-PD-L1 (36-53) as set forth in SEQ ID NO: 8, MVF-PD-L1 (50-67) as set forth in SEQ ID NO: 9, MVF-PD-L1 (95-112) as set forth in SEQ ID NO: 10, and/or MVF-PD-L1 (130-147) as set forth in SEQ ID NO: 11; a MVF-HER-2 (266-296) peptide (for example as set forth in SEQ ID NO: 28), and a MVF-HER-2 (597-626) peptide (for example as set forth in SEQ ID NO: 30).
It is further understood and herein contemplated that the synthetic peptides for use in treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer, autoimmune disease or Alzheimer's disease can be a component of a chimeric peptide. Thus, in one aspect, disclosed herein are methods of treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer, Alzheimer's disease, or an autoimmune disease in a subject comprising administering to a subject a PD-L1 chimeric peptide wherein the chimeric peptide comprises one or more PD-L1 B cell epitopes, a T helper (Th) epitope, and a linker joining the PD-L1 B cell epitope to the Th epitope, wherein the one or more PD-L1 B cell epitopes consist of a sequence selected from the group consisting of SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, and SEQ ID NO: 15. It is understood and herein contemplated that the synthetic PD-L1 peptides (i.e., the PD-L1 B cell epitopes) used in the chimeric peptides can comprise be acetylated, amidated, and/or the D enantiomer. In one aspect, for example, disclosed herein are methods of treating, inhibiting, reducing, decreasing, ameliorating, and/or preventing a cancer (such as, for example, breast cancer, ovarian cancer, endometrial cancer, colon cancer, non-small cell lung cancer, prostate cancer, and cervical cancer), Alzheimer's disease, or an autoimmune disease in a subject comprising administering to a subject a PD-L1 chimeric peptide wherein the chimeric peptide comprises SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, or SEQ ID NO: 19.
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compounds, compositions, articles, devices and/or methods claimed herein are made and evaluated, and are intended to be purely exemplary and are not intended to limit the disclosure. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.), but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in ° C. or is at ambient temperature, and pressure is at or near atmospheric.
The selection of candidate B-cell epitopes expressed on the surface of PD-L1 was accomplished by an in-house (Peptide Companion™, 5x.com) computer-aided analysis using six correlates of antigenicity, described as follows: (a) The profiles of chain flexibility and mobility of individual sequences were calculated; (b) Hydropathy profiles were generated over a seven residue span setting and then smoothed with a three-residue span using the scale of Kyte and Doolittle; (c) Hydrophilicity profiles over a six-residue window were generated using the program of Hopp and Woods; (d) Analysis of the exposure of an amino acid residue to water (1.4A probe) was carried out by the solvent exposure algorithm; (e) Protrusion indices were calculated that predicts portions of proteins that are accessible and protrude into the solvent; (f) The probability that a five-residue sequence is antigenic was determined by the method of Welling et al. Sequences were given a score of 1 to 6 based on their respective index values and were ranked: the highest ranking sequences had the highest individual score for the analyses examined, and successive candidates had the next highest score, etc.
The best scoring epitopes were further ranked by correlation with their secondary structural attributes; e.g., an amphiphilic α-helical sequence or a β-turn loop regions are preferred over a random coil fragments. Computer programs by Chou and Fasman and Novotny et al. were used to predict the secondary structure (α-helix, β-strand/sheet, β-turn/loop, random coil) and α-helical amphiphilic moment. Finally, consideration was given to the individual amino acid sequence. Electrostatic ion pairs and helix dipole interaction in helical segment were also considered (e.g., hydrophobic/hydrophilic balance).
Peptide epitope mapping using algorithms of immunogenicity/antigenicity was used to identify 4 epitopes of PD-L1 and the analysis of these epitopes was combined with crystal structures complex of human PD-1/human PD-L1 (hPD-1/hPD-L1) as disclosed by Zak et al. in 2015 (PDB ID: 4ZQK) to engineer a chimeric B-cell vaccine based on the extracellular domain of PD-1. The selection was further enhanced by examining the 3-D structure of PD-1 (PDB ID code: 4Z18, 4ZQK, 3BIK). All the four epitopes were modelled using PyMOL 3-D modeling software DeLano WL (2002) The PvMOL User's Manual. The sequences receiving the highest scores are displayed in Table 4. Employing this method, four of the twelve highest scoring B-cell epitope sequences of human PD-L1, amino acid 36-53, 50-67, 95-112 and 130-147 were chosen for evaluation in combination with information from the crystal structure of PD-1:PDL1.
The structures of human PD-1 (PDB 3RRQ) and human PD-L1 (PDB 3BIS, 3FN3, 4Z18, 5C3T) have been determined, but those in turn did not account for significant plasticity within the human PD-1 upon complex formation demonstrated only very recently by the structure of the fully human PD-1/PD-L1 complex. Although the above structures provided a complete description of the interaction, the flat surface of the protein-protein interface still complicates drug design efforts in the absence of structural information on the small-molecule inhibitors in complex with either PD-1 or PD-L1 to guide further rational drug development. The crystal structure demonstrates that the receptor-ligand interaction is mediated in its major part by residues of C0CFG strands within both PD-1 and PDL1 (
Four novel peptide sequences that were identified to target human PD-L1 were then synthesized using a 9600 Milligen/Biosearch solid-phase peptide synthesizer (Millipore, Bedford, Mass., USA) with Fmoc/t-Butyl chemistry and PyBOP/6C1-HOBT coupling reagents on CLEAR amide resin (Peptides International, Louisville, Ky., USA). Some peptide samples were acetylated using 1-Acetylimidazole (Sigma-Aldrich St. Lois, Mo., USA) before cleavage. All peptides were synthesized as chimeric constructs with a promiscuous T helper epitope derived from the measles virus fusion protein (MVF, amino acids 288-302) using a four residue linker (GPSL). Peptides were cleaved from the resin using cleavage reagent R (TFA)/thioanisole/EDT/anisole (90/5/3/2), and crude peptides were purified by semi preparative (C4 Vydac columns) reversed-phase-high performance liquid chromatography (RP-HPLC; Waters, Bedford, Mass., USA). RP-HPLC fractions showing the same retention time were pooled together and lyophilized. All peptides showed purity in excess of 95%. Samples were then characterized by MALDI (Matrix Assisted Laser Desorption Ionization mass spectroscopy at the CCIC (Campus Chemical Instrumentation Center, The Ohio State University, Columbus, Ohio, USA) and analyzed on an analytical RP-HPLC system (Waters, Bedford, Mass., USA). All peptides had the correct molecular mass.
For each peptide, vaccine antibodies were raised using New Zealand white rabbits purchased from Charles River Laboratories (Wilmington, Mass., USA). Rabbits were immunized with 1 mg of MVF chimeric peptide emulsified in Montanide ISA 720 (Seppic, Paris, France) and nor-MDP adjuvant (N-acetyl-glucosamine-3 yl-acetyl 1-alanyl-d-isoglutamine) and boosted twice at three-week intervals. Antibody titers were monitored by direct ELISA against the peptide immunogen, the peptide B cell epitope, and an acetylated version of the B-cell epitope. Sera was collected weekly and animals were sacrificed at nine weeks. Peptide vaccine antibodies were purified by affinity chromatography using a protein A/G column and the concentration was measured by Coomassie protein assay. All experiments were performed in accordance with the U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals and approved by the Ohio State University Institutional Animals Care and Use Committee and detailed in the accepted protocol.
The peptide vaccines were dissolved in water and emulsified in Montanide ISA 720 (1:1) and 100 μg nor-MDP (N-acetylglucosamine-3yl-acetyl-1-alanyl-d-isoglutamine). Female Balb/c mice (Charles River Laboratories) at the age of 5 to 6 weeks were immunized three times at 3-week intervals with 100 μg peptide vaccine, and 15 days after the third immunization, the mice were challenged s.c. with CT-26 tumor cells (100,000 per mouse). Mice immunized with an irrelevant MVF peptide chimera were used as a negative control.
Mice treated twice a week with anti-mouse PD-L1 MAb (Bio X Cell, West Lebanon, N.H.) 200 ug/dose was used as a positive control. Tumor growth was monitored for up to 18 days after challenge. During immunization, blood was drawn biweekly and used in ELISA to monitor Ab titers. The mice were euthanized at the end of treatment and tumors extracted and weighed samples of the tumors were saved for further study and for histological examination. The spleens were also collected for further examination.
Vaccines were dissolved in water and emulsified in Montanide ISA 720 (1:1) and 50 μg nor-MDP (N-acetylglucosamine-3yl-acetyl-1-alanyl-d-isoglutamine). Female Balb/c mice (Charles River Laboratories) at the age of 5 to 6 week were immunized three times at 3-week intervals with 100 μg of each peptide vaccine, and 2 weeks after the third immunization, the mice were challenged s.c. with CT-26-HER2 neu tumor cells (100,000 per mouse).
Mice treated twice a week with anti-mouse PD-L1 MAb 10F.9G2 (Bio X Cell, West Lebanon, N.H.) 200 ug/dose was used as a positive control or purified mouse IgG from mouse sera (Sigma-Aldrich, St. Louis, Mo.) as a negative control. Tumor growth was monitored for up to 21 days after challenge. During immunization, blood was drawn biweekly and used in ELISA to monitor Ab titers. The mice were euthanized at the end of treatment and tumors extracted and weighed samples of the tumors were saved for further study and for histological examination.
Organs (spleen, liver, heart, lung, lymph node, brown adipose tissue, kidney, and tumor) from Balb/c mice vaccinated with combination peptides (HER-2, PD-1 and PD-L1) were collected from mice and submitted for analysis at the Comparative Pathology & Mouse Phenotyping Core facility of the Comprehensive cancer center department of Veterinary Biosciences (Pathologist: Krista M. D. La Perle, D V M, PhD, Dipl. ACVP)
All experiments were performed in accordance with the U.S. Public Health Service Policy on Humane Care and Use of Laboratory Animals and approved by the Ohio State University Institutional Animals Care and Use Committee and detailed in the accepted protocol.
The human immune system is comprised of a complex network of immune checkpoint molecules that facilitate the elimination of cells expressing foreign antigens while maintaining tolerance to self-antigen. Immune checkpoint receptors are promising new immunotherapy targets for the treatment of a variety of diseases, including cancer and autoimmune-mediated disorders. Programmed cell death protein 1, also known as PD-1 (CD279), is an immune inhibitory receptor expressed on activated T cells and B cells and plays a critical role in regulating immune responses to tumor antigens. Engagement of PD-1 by either of its ligands, PD-L1 (B7-H1) or PD-L2 (B7-DC) on an adjacent cell inhibits T-cell receptor (TCR) signaling and TCR-mediated proliferation, transcriptional activation and cytokine production. Therapeutic antibodies and Fc fusion proteins designed to block the PD-1/PD-L1 interaction show promising results in clinical trials for the treatment of a variety of cancers.
Antibody-dependent cell-mediated cytotoxicity (ADCC) is a mechanism of action of antibodies through which virus-infected or other diseased cells are targeted for destruction by components of the cell-mediated immune system. ADCC is a desirable mechanism for killing target cancer cells using antibody-based drugs. The antibody binds to target antigens on the cell surface. When the Fc effector portion of target-bound antibodies also binds to FcγRIIIa receptors on the cell surface of effector cells (natural killer cells predominantly), multiple cross-linking of the two cell types occurs, leading to pathway activation of ADCC. Killing of target cells is an endpoint of this pathway activation and is used in ADCC bioassays.
A new paradigm in immunotherapy is advanced herein that focuses on humoral responses based on conformational B-cell epitope vaccines, with the goal of circumventing intrinsic drug resistance whilst providing the possibility of a durable cure. Specifically, two novel B-cell epitope specific vaccines (B-Vaxx) were developed: a trastuzumab-binding epitope and the pertuzumab-binding epitope designed specifically using the X-ray structures of the HER-2-trastuzumab and HER-2-pertuzumab complexes. The clinical results of the first-in-human, dose escalation portion of the Phase I study with B-Vaxx were recently reported. The study vaccine was safe, well tolerated, exhibited anti-tumor activity and showed preliminary indication that peptide vaccination may avoid therapeutic resistance and offer a promising alternative to mAb therapies.
Herein is presented the characterization and development of a new B-cell peptide epitope targeting the human PD-L1, which elicits polyclonal antibodies in vivo that can block PD-1/PD-L1 interaction, that potentially mimics the effects of Atezolizumab. Using sophisticated methods of peptide mapping and predictive antigenicity algorithms based on 3D structure of PD-L1, we show the preclinical development of the PD-L1 vaccine to design a chimeric B-cell vaccine based on the extracellular domain of PD-L1, which we linked to a promiscuous T helper cell measles virus fusion protein (MVF).
The immunogenicity of each peptide epitopes was first evaluated in rabbits and Balb/c mice, which elicited antibodies that recognized the immunogenic synthetic peptides as well as the recombinant human PD-L1 protein. The syngeneic colorectal CT-26 wt Balb/c mouse tumor model was used to evaluate the efficacy of vaccination with the four MVF-PD-L1 peptides as growth inhibitors of CT-26 tumor cells. The PD-L1 (130-147), PD-L1 (50-67) and the PD-L1 mAb epitope showed significant inhibition of tumor growth as compared to PBS. We then expanded the experiments in the another syngeneic CT26/HER-2 Balb/c carcinoma model. The antitumor effects of all 4 MVF-PD-L1 epitopes vaccination were examined in the syngeneic Balb/c colon carcinoma mouse model challenged with CT26/HER-2 cell line. Interestingly, treatment with PD-L1 (130-147) demonstrated greater inhibition of tumor growth exhibited superior tumor growth inhibition as compared to PBS and the commercially available standard mouse anti-PD-L1 antibody
a) Results
(1) The Design and Purification of Four Novel Human PD-L1 (hPD-L1) Peptide Epitopes
The tertiary structure of PD-L1 is composed of an extracellular domain, a transmembrane domain, and an intracellular region. Because the extracellular domain is responsible for binding of PD-1, as well as being accessible for anti-peptides antibodies, we have chosen this domain as an immunogenic region. B-cell epitopes were ranked based on six correlates of antigenicity and correlated with their secondary structure, combined analysis of these epitopes with crystal structures complex of human PD-1/human PD-L1 (hPD-1/hPD-L1). From this analysis, four B-cell epitope sequences of human PD-L1 were identified for further investigation: amino acid: 36-53, 50-67, 95-112 and 130-147 (
(2) In Vivo Immunization with PD-L1 Epitopes Results in Robust Antibody Response in Rabbits.
Immunogenicity of all four peptides were evaluated in outbred rabbits (
(3) Efficacy of the PD-L1 Vaccine Epitopes Versus Anti-Mouse PD-L1 (B7-H1) mAb Clone 10F.9G2 in Inhibiting Tumor Growth in a Syngeneic Balb/c Model Challenged with CT26 Colon Carcinoma Cell Line.
In order to verify the efficacy of the PD-L1 epitope vaccines in vivo in the CT26 carcinoma cell line, Balb/c mice (10 mice/group) were immunized with 100 μg each of MVF-PD-L1 (36-53), MVF-PD-L1 (50-67), MVF-PD-L1 (95-112) and MVF-PD-L1 (130-147) emulsified with nor-MDP and Montanide 720 (1:1 ratio) SCHEME 1A (
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Two weeks after the third immunization (3Y), the mice were inoculated subcutaneously (s.c) with CT26 carcinoma cells (1×105 cells per mouse) and tumor formation was monitored on a daily basis afterwards. Mice treated with PBS served as negative control, and twice weekly treated mice with 200 μg/dose injections of anti-mouse PD-L1 monoclonal antibody (mAb clone 10F.9G2) served as positive control. Tumor growth was monitored daily and measured by caliper. Tumor growth (Tumor volume; LWW mm3) pattern for each individual mouse is shown in
(a) Antibody Isotypes.
We also analyzed the different isotypes of antibodies being generated by vaccination. The isotypes of antibodies elicited in the mice were determined to be predominantly of the IgG1 class (Data shown in
(b) Anti-MVF-PD-L1 130 Antibody is Capable of Blocking Pd-1/Pd-L1 Interaction.
The bioluminescent cell-based PD-1/PD-L1 blockade bioassays provide a good option for rapid screening of therapeutic antibodies or other compounds developed to interfere with PD-1-signaling interaction. PD1/PD-L1 blockade assay was used to test the functionality of 3 anti-PD-L1 antibodies. It was observed that purified polyclonal anti-PD-L1 antibody from the rabbits was able to block PD1/PD-L1 interaction similar to commercial anti-human PD-L1 antibody (
(c) Apoptosis Determination by Caspase Activity Assay.
The potential for disease-specific targeting and low toxicity profiles have made monoclonal antibodies attractive therapeutic drug candidates. Antibody-mediated target cell killing is frequently associated with immune effector mechanisms such as antibody-directed cellular cytotoxicity, but they can also be induced by apoptotic processes. Antibody-directed mechanisms, including antigen crosslinking, activation of death receptors, and blockade of ligand-receptor growth or survival pathways, can elicit the induction of apoptosis in targeted cells. Depending on their mechanism of action, monoclonal antibodies can induce targeted cell-specific killing alone or can enhance target cell susceptibility to chemo- or radio-therapeutics by effecting the modulation of anti-apoptotic pathways. To further examine this, we evaluated whether anti-PD-L1 peptide vaccine antibodies were capable of inducing apoptosis of cancer cells via a caspase activation assay. MC38 (as PD-L1 expressing cells) and CT26WT cancer cells were seeded in 96-well plates and incubated overnight at 37° C. The following day, Low serum growth media containing peptide vaccine antibodies as well as reference antibody Atezolizumab and β-Lapachone as apoptosis inducer were added to the wells. The plates were then incubated for an additional 24 hours at 37° C. The caspase-Glo reagent was then added, and caspase 9 release was determined using an illuminometer as a measure of apoptotic induction. Caspase-9 is a member of cysteine aspartic acid specific protease (caspase) family, which plays a key initiator role in the intrinsic apoptotic pathway of mammalian cells. We found that the PD-L1 antibody caused a significant increase in the amount of caspase activity in treated cells as compared to negative controls (PBS) and comparable to mAb Atezolizumab. The increased caspase release was more than 3 fold (
(d) ADCC Activity.
Antibody-dependent cell-mediated cytotoxicity (ADCC) is the critical mechanism of action of anti-cancer mAbs, through which antibodies recruit FcγR-bearing effector cells to target “diseased” cells for destruction by components of the cell-mediated immune system, such as natural killer cells. However, it is known that most of PD-1/PD-L1 antibodies in clinical development do not mediate antibody-dependent cell mediated cytotoxicity, like atezolizumab (MPDL3280A), which is an FcγR-binding deficient IgG1 isotype humanized monoclonal antibody engineered to eliminate ADCC activity. While ADCC induction could potentially enhance tumor death by inducing apoptosis, it can also result in depletion of PD-L1-expressing T cells, thereby blunting the immune response. In order to eliminate ADCC and CDC at clinically relevant doses, the Fc (the fragment crystallizable) domain of atezolizumab is engineered to reduce its interaction with the FcγR.
To evaluate ADCC activity of the purified polyclonal antibodies, we used MC38 cells treated for 16 h with 25 ng/ml IFN-γ, and WIL2-S target cells together with Jurkat effector cells. A linearity test for ADCC response was performed at various concentration of antibody as shown in
(4) Efficacy of the PD-L1 Vaccine Epitopes Versus Anti-Mouse PD-L1 (B7-H1) mAb Clone 10F.9G2 in Inhibiting Tumor Growth in a Syngeneic Balb/c Model Challenged CT26 Colon Carcinoma Cell Line Expressing HER-2
In order to verify the efficacy of the PD-L1 epitope vaccines in vivo in the CT26-HER-2 carcinoma cell line, Balb/c mice (10 mice/group) were immunized with 100 μg each of MVF-PD-L1 (36-53), MVF-PD-L1 (50-67), MVF-PD-L1 (95-112) and MVF-PD-L1 (130-147) emulsified with nor-MDP and Montanide 720 (1:1 ratio) SCHEME 2A (
Two weeks after the third immunization (3Y), the mice were inoculated subcutaneously (s.c) with CT26 carcinoma cells (1×105 cells per mouse) and tumor formation was monitored on a daily basis afterwards. Mice treated with PBS served as negative control, and twice weekly treated mice with 200 μg/dose injections of anti-mouse PD-L1 monoclonal antibody (mAb clone 10F.9G2) served as positive control. Tumor growth was monitored daily and measured by caliper. Tumor growth (Tumor volume; LWW mm3) pattern for each individual mouse is shown in
We also analyzed the different isotypes of antibodies being generated by vaccination. The isotypes of antibodies elicited in the mice were determined to be predominantly of the IgG1 class (Data shown in
(5) Combination Treatment with the Peptide Vaccine PD-L1 and HER-2 Epitopes Results in Robust HER-2 and PD-L1 Antibody Response and Inhibition of Tumor Growth in Balb/c CT26/HER-2 Model
Next, CT26/HER-2 tumor model in Balb/c was used to test for synergistic effects of anti-PD-L1 immunization therapy in combination with anti-HER-2 immunization therapy to determine whether this combination could increase immunogenicity, enhance anti-tumor responses and provide synergistic benefit in inhibiting tumor growth. Balb/c mice (10 mice/group) were immunized 3 times at 3 week's intervals with MVF-PD-L1 (36-53, 50-67, 95-112, 130-147) in combination with MVF-HER-2 (266-296)+MVF-HER-2 (597-626) peptide vaccine constructs emulsified with ISA 720 (1:1 ratio) summarized in SCHEME 3A-3C (
1
16
0
91
)
0
1
)
)
2
0
4
indicates data missing or illegible when filed
7
4
2
05
00
1
38
98
8
4
4
1
19
indicates data missing or illegible when filed
indicates data missing or illegible when filed
5
62
0
73
03
5
0
3
9
1
4
2
2
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5
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b) Discussion
Current enthusiasm about cancer immunotherapy stems from the success of some agents targeting immune checkpoint molecules such as programmed cell death 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4. Currently over a dozen immune checkpoint antibodies targeting CTLA-4 and PD-1/PD-L1 have received FDA regulatory approval worldwide, and there are numerous of ongoing clinical trials for checkpoint inhibitors targeting PD-1 and PD-L1. These therapies have led to exceptional successes in only a minority of patients. Mechanisms underpinning innate and acquired resistance are responsible in part to for the lack of response to PD-1/PD-L1 blockade, highlighting the rationale that well-designed combination therapies may extend the use and clinical impact. For example, the combination of ipilimumab and nivolumab was approved by the FDA because of positive results for patients with unresectable melanoma and promising Phase I & II trials, however the combination also showed increased toxicity compared to monotherapy.
Compared to PD-1 inhibitors, PD-L1 inhibitors can reduce the incidence of side effects resulting from immune disorders. The FDA has approved one humanized mAb (atezolizumab, TECENTRIC®) and two fully human mAb (avelumab, BAVENCIO® and durvalumab, IMFINZI®) targeting PD-L1. The recently reported avelumab/hPD-L1 complex structures have provided clear structural information on how the therapeutic mAbs abrogate the binding of PD-1/PD-L1. The PD-L1 targeting antibody, avelumab is now in multiple phase III clinical trials against non-small cell lung cancer (NSCLC) (NCT02395172), advanced renal cell cancer (NCT02684006) and gastric cancer (NCT02625610).
A vaccine targeting PD-L1 consisting of the extracellular domain of PD-L1 (PD-L1E) fused to the C-terminal of the translocation domain of diphtheria toxin (DTT) was recently reported. The therapeutic efficacy of the DPDL1E vaccine was evaluated in B16-F10 tumor-bearing C57BL/6 mice. The authors concluded that the DPDL1E vaccine targeting PD-L1 induced a PD-L1-specific immune response and delayed tumor growth in vivo. These results indicate a promising avenue for future research in the quest for cancer vaccine design.
Overall, the rational development of various immune strategies for managing certain cancers holds substantial promise for transforming the therapeutic landscape and improving disease management in human beings. This study also draws attention to the benefits of using a multi-targeted approach, thus it is increasingly appreciated that only use of drugs that affect multiple signaling modalities results in strong anti-proliferative effects and delay the onset of drug resistance. However, in this current study, it was demonstrated that it is possible to generate vaccine combinations that can serve as powerful tools to interrogate oncogenic drivers in cancer cells. At present, there are no B-cell epitope vaccines available for purchase that target the human PD-1/PD-L1 axis.
c) Materials and Methods
(1) Identification and Synthesis of Peptide Epitopes for hPD-L1.
The selection of candidate B-cell epitopes expressed on the surface of PD-L1 was accomplished by an in-house computer-aided analysis (Peptide Companion™, 5z.com) using six correlates of antigenicity, described as follows: (a) The profiles of chain flexibility and mobility of individual sequences were calculated according to Karplus and Schultz; (b) Hydropathic profiles were generated over a seven residue span setting and then smoothed with a three residue span using the scale of Kyte and Doolittle; (c) Hydrophilicity profiles over a six residue window were generated using the program of Hopp and Woods; (d) Analysis of the exposure of an amino acid residue to water was carried out by the solvent exposure algorithm of Rose et al.; (e) Protrusion indices were calculated by the method of Thornton et al. that predicts portions of proteins that are accessible and protrude into the solvent; (f) The probability that a five-residue sequence is antigenic was determined by the method of Welling et al.; Sequences were given a score of 1 to 6 based on their respective index values and were ranked: the highest ranking sequences had the highest individual score for the analyses examined, and successive candidates had the next highest score, etc. The best scoring epitopes were further ranked by correlation with their secondary structural attributes; e.g., an amphiphilic α-helical sequence or a β-turn loop region are preferred over a random coil fragment. Computer programs by Chou and Fasman and Novotny et al. were used to predict the secondary structure (α-helix, β-strand/sheet, β-turn/loop, random coil) and α-helical amphiphilic moment. Finally, consideration was given to the individual amino acid sequence. Electrostatic ion pairs and helix dipole interaction in helical segment were also considered (e.g., hydrophobic/hydrophilic balance). We used peptide epitope mapping using algorithms of immunogenicity/antigenicity to identify four epitopes of PD-L1. We have modelled all the four epitopes using PyMOL 3-D modeling software (DeLano WL 2002, The PyMOL User's Manual).
Four novel peptide sequences were then synthesized using a 9600 Milligen/Biosearch solid-phase peptide synthesizer (Millipore, Bedford, Mass., USA) with Fmoc/BOP chemistry and PyBOP/HOBT coupling reagents (PB Biosystems, Louisville, Ky., USA) on CLEAR amide resin (Peptides International, Louisville, Ky., USA). Some peptide samples were acetylated using 1-Acetylimidazole (Sigma-Aldrich St. Lois, Mo., USA) before cleavage. All peptides were synthesized as chimeric constructs with a promiscuous T helper epitope derived from the measles virus fusion protein (MVF, amino acids 288-302) using a four residue linker (GPSL). Peptides were cleaved from the resin using cleavage reagent R (TFA)/thioanisole/EDT/anisole (90/5/3/2), and crude peptides were purified by semi preparative (C-4 Vydac columns) reversed phase high performance liquid chromatography (RP-HPLC; Waters, Bedford, Mass., USA). RPHPLC fractions showing the same retention time were pooled together and lyophilized. All peptides showed purity in excess of 95%. Samples were then characterized by MALDI (Matrix Assisted Laser Desorption Ionization mass spectroscopy at the CCIC (Campus Chemical Instrumentation Center, The Ohio State University, Columbus, Ohio, USA) and analyzed on an analytical RP-HPLC system (Waters, Bedford, Mass., USA). All peptides had the correct molecular mass.
(2) Immunization with hPD-L1 Peptide Epitopes.
For each peptide, vaccine antibodies were raised in New Zealand white rabbits, purchased from Charles River Laboratories (Wilmington, Mass., USA). Rabbits were immunized with 1 mg of MVF chimeric peptide emulsified in Montanide ISA 720 (Seppic, Paris, France) and boosted 3 times at three week intervals. For mouse experiments, mice, 6-8 weeks old, were immunized with 0.1 mg of peptide emulsified in ISA720 (1:1 ratio). Mice were boosted with the respective doses at 3-week intervals. Blood was then collected and sera were tested for antibody titers. Sera were collected weekly and peptide vaccine antibodies were purified by affinity chromatography using a protein A/G column and the concentration was measured using Spectrophometer. All experiments were performed in accordance with the U.S. Public Health Service Policy on Humane Care and Use of Laboratory animals and approved by the Ohio State University Institutional Animals Care and Use Committee, detailed in the accepted protocol.
(3) In Vivo Studies of Four Peptide Vaccine hPD-L1 Epitopes: CT-26 and CT26/HER-2 Tumor Model in Mice.
6-8 weeks old BALB/c mice (Charles River, Wilmington, Mass.) were used as standard animal models. Mouse CT26 colon carcinoma cell line was purchased from American Type Culture Collection Cells and were regularly cultured in RPMI1640 medium containing 10% FBS. CT26/HER2 cells were kindly provided by M. Penichet. Vaccines were dissolved in sterile water and emulsified in Montanide ISA 720 (1:1). Female Balb/c mice (Charles River Laboratories) at the age of 6-8 weeks were immunized three times at 3-week intervals with 100 μg of each peptide vaccine, and 2 weeks after the third immunization, the mice were challenged with CT26 and/or CT26/HER-2 tumor cells, which were implanted subcutaneously (s.c) on the right flank (1×105 per mouse). 200 μg of rat α-mouse PD-L1 mAb 10F.9G2 (Bio X Cell, West Lebanon, N.H.) were administered intraperitoneally (i.p.), twice weekly following tumor inoculation in the control group. Mice were monitored and scored for the formation of palpable tumors on a daily basis and sacrificed if tumors became necrotic or exceeded the predetermined size of 2,000 mm3. Tumor volumes were measured in cubic millimeters with calipers and calculated with the following formula: A×B2×0.5, where A is the largest diameter, and B is the widest point perpendicular to length. During immunization, blood was drawn weekly and used in ELISA to monitor antibody titers.
(4) Antibody-Dependent Cell-Mediated Cytotoxicity (ADCC) Reporter Bioassay.
ADCC Reporter Bioassay (Promega) was used per the manufacturer's instruction to assess ADCC activity. Briefly, the target WIL2-S and MC38 cells were seeded in each well of a 96-well assay plate one day prior. The MC38 cells were treated with IFN-γ (25 ng/ml for 16 hr at 37° C.) to ensure induction of PD-L1 expression. The next day, either serially diluted reference antibody (Atezolizumab) or CD20 control antibody, and serially diluted purified PD-L1 130 polyclonal antibody were added to the assay plate. Next, Jurkat cells (immortalized T-lymphocyte cells engineered to stably express FcγRIIIa receptors, as effector cells) were co-cultured with antibody treated target cells at an effector cell to target cell ratio of 4:1 for 6 h at 37° C. in a humidified 5% CO2 incubator. Once bound to the antibody, engineered Jurkat T-lymphocyte cells activated gene transcription through the nuclear factor of activated T-cells (NFAT) pathway, inducing the expression of firefly luciferase. Lastly, luciferase activity was quantified using luciferase assay reagent by a SpectraMax M3 plate reader (Molecular Devices).
(5) Apoptosis (Caspase 9 Assay).
The Caspase-Glo 9 assay kit (Promega, Madison, Wis.) was used for caspase detection in treated cells in vitro. The reagent provides a proluminescent caspase-9 substrate, in combination with luciferase and a cell-lysing agent. Cells were plated in 96-well plates at 1×104 cells per well and cultured in complete media overnight. Then, the cells were treated with anti-PD-L1 antibodies as well as reference antibody Atezolizumab and β-Lapachone (10 uM, Sigma Aldrich) for 24 hours. Caspase activity was measured by adding 50 μl of CASPASE-GLO® 9 reagent directly to the assay well which results in cell lysis, followed by caspase cleavage of the substrate, and the generation of luminescence. The luminescence was detected using a microplate reader (Molecular Devices). The amount displayed on the readout is proportional to the amount of caspase activity in the sample.
(6) PD-1/PD-L1 Bioassay.
The assay was performed following the manufacturer's protocol for the PD-1/PD-L1 blockade bioassay (Promega). In brief, 4×105 aAPC/CHO-K1 or PD-L1 aAPC/CHO-K1 cells were seeded into 96-well plates in RPMI-1640 with 10% FBS. After overnight culturing, the medium was aspirated, and serially diluted purified PD-L1 or PD-1 antibodies, as well as Nivolumab and Atezolizumab antibodies (as reference antibodies) were added. Next, PD-1 effector cells were co-cultured and plate was kept for 5 h at 37° C. in a humidified 5% C02 incubator. Following mixing with Bio-Glo Reagent, the luminescence was measured with a luminescence plate reader, SpectraMax M3 plate reader (Molecular Devices).
(7) Mouse Isotyping Assay.
Antibody isotypes (i.e. IgA, IgM, IgG1, IgG2a, IgG2b, IgG3) were determined using the Mouse Typer Isotyping Kit (BIO-RAD, Hercules, Calif.). Briefly, wells of a 96-well assay plate were coated with 200 ng peptide antigen in ddH2O, and incubated at 4° C. overnight. The plate was washed with washing buffer (0.05% Tween-20 and 1% horse sera in PBS). The plate was then blocked with 1% BSA in PBS at room temperature for 1 hour. 100 ul of diluted mice sera was added to each well for 2 hours and after washing the wells, 100 μl ready to use rabbit anti-mouse subclasses antibodies were added to each well respectively and incubated at room temperature for another 2 hours. The wells were washed again, 100 μl of 1/3000 dilution of goat anti-rabbit conjugated to HRP antibody (BIO-RAD, Hercules, Calif.) was added to each well and incubated for 1 hour at room temperature in dark. The plate was then washed and 50 μl prepared substrate solution was added to each well. The reaction was stopped with 25 μl 5% SDS stopping buffer. Absorbance at 415 nm was determined using an ELISA plate reader. Dilutions of each sera samples were determined by the ELISA titers shown in absorbance of 0.4 or higher after subtracting the background.
(8) Statistical Analysis.
Tumor sizes were observed daily and measured by caliper. Tumor volumes were calculated by formula: Volume=(Length*Width*Width)/2. Data statistical analysis was performed using GraphPad Prism 8.1.2 (GraphPad Software, Inc.). One-way analysis of variance (one-way ANOVA) followed by the Tukey's multiple comparisons test were used to compare data in multiple groups or data between groups in multiple groups. p-value or adjusted p-value less than 0.05 was accepted as statistically significant different. * indicates p<0.05, ** indicates p<0.01.
a) Experiments Design: There are Two Parts of this Experiments (10 Mice/Group, 6-8w):
(1) Part One: From G0 to G4, these Four Groups of Mice are Challenged with D2F2 WT Cancer Cells.
G0, G1 and G2 are control groups, mice in these groups were not treated before tumor cells challenge. Following challenge with D2F2 WT tumor cells, G0 mice were treated with PBS (i.p.) twice per week start from day 2 post challenge served as negative control, G1 and G2 mice were treated with anti-PD-1 mAb (29F.1A12) or anti-PD-L1 mAb (1° F.9G2), respectively. Treatment for G1 and G2 mouse groups was also started from day 2 post tumor challenge, with 100 ug administered/mouse twice a week. G1 and G2 served as positive control. By contrast, G3 and G4 mice were immunized with 100 ug MVF-PD-1 (92-110)+ISA720 or 100 ug MVF-PD-L1 (130-147)+ISA720 per mouse, respectively. The mice were immunized up to 4 times before tumor challenge. And mice did not receive further treatment after challenged with D2F2 WT tumor cells. All the mice had been monitored at least twice per week, and the tumors were measured with calipers as data indicated (
(2) Part Two from G10 to G15, these Five Groups of Mice Planned to be Challenged with D2F2/E2 Cancer Cells.
G10, G11 and G12 are control groups, which did not receive treatment before tumor cells challenge. After challenging the mice with D2F2/E2 tumor cells, G10 mice were treated with PBS (i.p.) twice per week start form day 2 post challenge served as negative control, G11 and G12 mice were treated with anti-PD-1 mAb (29F.1A12) or anti-PD-L1 mAb (1° F.9G2), respectively. For G1 and G12, treatments started from day 2 post tumor challenge, with 100 ug/mouse twice a week. G11 and G12 served as positive control. G13, G14 and G15 mice were immunized with 100 ug MVF-HER-2 (266-296)+100 ug MVF-HER-2 (597-626)+ISA720 per mouse for G13, 100 ug MVF-PD-1 (92-110)+100 ug MVF-HER-2 (266-296)+100 ug MVF-HER-2 (597-626)+ISA720 per mouse for G14 and 100 ug MVF-PD-L1 (130-147)+100 ug MVF-HER-2 (266-296)+100 ug MVF-HER-2 (597-626)+ISA720 per mouse for G15. The mice were immunized up to 4 times before tumor challenge. And mice did not receive further treatment after challenged with D2F2/E2 tumor cells. All the mice had been monitored at least twice per week, and the tumors were measured with calipers as data indicated (
b) Scheme of the Experiment:
Mice were immunized with designed peptides vaccines as descripted in
c) Results
(1) Immunogenicity of G3 Mice which Immunized with 100 Ug MVF-PD-1(92-110)+ISA720 Per Mouse.
The bleed were collected as indicated in
To detect the antibody against MVF-PD-1(92-110) in the mice sera, we coated the MVF-PD-1(92-110) peptide on the 96-well assay plate (COSTAR) with 100p of 2 μg/ml peptide as antigen in ddiH2O, and incubated at 4° C. overnight. The plate was washed with washing buffer (0.05% tween-20 and 1% horse sera in PBS). And then the plate was blocked with 200 ul of 1% BSA in PBS at room temperature for 1 hr. After incubation, 100 ul of 2-fold serial diluted sera was added to each well and incubated at room temperature for 2 hrs. The wells were washed again, 100 μl of 1/500 dilution of goat anti-mice conjugated to HRP antibody (0.8 mg/ml, Invitrogen) was added to each well and incubated for 1 hr at room temperature in dark. The plate received a final wash and 50 μl prepared ABTS substrate solution was added to each well. The reaction was stopped with 25 μl 1% SDS in ddi water. Absorbance at 415 nm was determined using an ELISA plate reader. Dilutions of each sera samples were determined by the highest antibody ELISA titers shown in absorbance of higher than 0.2.
(2) Immunogenicity of G4 Mice which Immunized with 100 Ug MVF-PD-L1 (130-147)+ISA720 Per Mouse.
The bleed were collected as indicated in
To detect the antibody against MVF-PD-L1 (130-147) in the mice sera, we coated the MVF-PD-L1 (130-147) peptide on the 96-well assay plate (COSTAR) with 100 μl of 2 μg/ml peptide as antigen in ddiH2O, and incubated at 4° C. overnight. The plate was washed with washing buffer (0.05% tween-20 and 1% horse sera in PBS). And then the plate was blocked with 200 ul of 1% BSA in PBS at room temperature for 1 hr. After incubation, 100 ul of 2-fold serial diluted sera was added to each well and incubated at room temperature for 2 hrs. The wells were washed again, 100 μl of 1/500 dilution of goat anti-mice conjugated to HRP antibody (0.8 mg/ml, Invitrogen) was added to each well and incubated for 1 hr at room temperature in dark. The plate received a final wash and 50 μl prepared ABTS substrate solution was added to each well. The reaction was stopped with 25 μl 1% SDS in ddi water. Absorbance at 415 nm was determined using an ELISA plate reader. Dilutions of each sera samples were determined by the highest antibody ELISA titers shown in absorbance of higher than 0.2.
(3) Immunogenicity of G13 Mice which Immunized with 100 Ug MVF-HER-2 (266-296)+100 Ug MVF-HER-2 (597-626)+ISA720 Per Mouse.
The bleed were collected as indicated in
To detect the antibody against MVF-HER-2 (266-296) in the mice sera, we coated the MVF-HER-2 (266-296) peptide on the 96-well assay plate (COSTAR) with 100 μl of 2 μg/ml peptide as antigen in ddiH2O, and incubated at 4° C. overnight. The plate was washed with washing buffer (0.05% tween-20 and 1% horse sera in PBS). And then the plate was blocked with 200 ul of 1% BSA in PBS at room temperature for 1 hr. After incubation, 100 ul of 2-fold serial diluted sera was added to each well and incubated at room temperature for 2 hrs. The wells were washed again, 100 μl of 1/500 dilution of goat anti-mice conjugated to HRP antibody (0.8 mg/ml, Invitrogen) was added to each well and incubated for 1 hr at room temperature in dark. The plate received a final wash and 50 μl prepared ABTS substrate solution was added to each well. The reaction was stopped with 25 μl 1% SDS in ddi water. Absorbance at 415 nm was determined using an ELISA plate reader. Dilutions of each sera samples were determined by the highest antibody ELISA titers shown in absorbance of higher than 0.2. The same procedure was performed to detect the antibody against MVF-HER-2 (597-626) in the mice sera. At 4Y+13, the results indicated that the CR mice which mice without tumor or very small tumor the antibody titers are relatively higher than those of mice with big tumor.
(4) Immunogenicity of G14 Mice which Immunized with 100 Ug MVF-PD-1 (92-110)+100 Ug MVF-HER-2 (266-296)+100 Ug MVF-HER-2 (597-626)+ISA720 Per Mouse.
The bleed were collected as indicated in
To detect the antibody against MVF-PD-1 (92-110) in the mice sera, we coated the MVF-PD-1 (92-110) peptide on the 96-well assay plate (COSTAR) with 100 μl of 2 μg/ml peptide as antigen in ddiH2O, and incubated at 4° C. overnight. The plate was washed with washing buffer (0.05% tween-20 and 1% horse sera in PBS). And then the plate was blocked with 200 ul of 1% BSA in PBS at room temperature for 1 hr. After incubation, 100 ul of 2-fold serial diluted sera was added to each well and incubated at room temperature for 2 hrs. The wells were washed again, 100 μl of 1/500 dilution of goat anti-mice conjugated to HRP antibody (0.8 mg/ml, Invitrogen) was added to each well and incubated for 1 hr at room temperature in dark. The plate received a final wash and 50 μl prepared ABTS substrate solution was added to each well. The reaction was stopped with 25 μl 1% SDS in ddi water. Absorbance at 415 nm was determined using an ELISA plate reader. Dilutions of each sera samples were determined by the highest antibody ELISA titers shown in absorbance of higher than 0.2. The same procedure was performed to detect the antibody against MVF-HER-2 (266-296) and MVF-HER-2 (597-626) in the mice sera. At 4Y+13, the results indicated that the CR mice which mice without tumor or very small tumor the antibody titers are relatively higher than those of mice with big tumor.
(5) Immunogenicity of G15 Mice which Immunized with 100 Ug MVF-PD-L1 (130-147)+100 Ug MVF-HER-2 (266-296)+100 Ug MVF-HER-2 (597-626)+ISA720 Per Mouse.
The bleed were collected as indicated in
To detect the antibody against MVF-PD-L1 (130-147) in the mice sera, we coated the MVF-PD-L1 (130-147) peptide on the 96-well assay plate (COSTAR) with 100 μl of 2 μg/ml peptide as antigen in ddiH2O, and incubated at 4° C. overnight. The plate was washed with washing buffer (0.05% tween-20 and 1% horse sera in PBS). And then the plate was blocked with 200 ul of 1% BSA in PBS at room temperature for 1 hr. After incubation, 100 ul of 2-fold serial diluted sera was added to each well and incubated at room temperature for 2 hrs. The wells were washed again, 100 μl of 1/500 dilution of goat anti-mice conjugated to HRP antibody (0.8 mg/ml, Invitrogen) was added to each well and incubated for 1 hr at room temperature in dark. The plate received a final wash and 50 μl prepared ABTS substrate solution was added to each well. The reaction was stopped with 25 μl 1% SDS in ddi water. Absorbance at 415 nm was determined using an ELISA plate reader. Dilutions of each sera samples were determined by the highest antibody ELISA titers shown in absorbance of higher than 0.2. The same procedure was performed to detect the antibody against MVF-HER-2 (266-296) and MVF-HER-2 (597-626) in the mice sera. At 4Y+13, the results indicated that the CR mice which mice without tumor or very small tumor the antibody titers are relatively higher than those of mice with big tumor.
(6) Tumor Growth and Survival
Log-rank (Mantel-Cox) test was also used to analyze the percentage of survival as the mice were treated with the designed groups (
At day 21 and day 28, with one-way ANOVA tested all the six groups the all the p values less than 0.01. And all the peptide treated groups MVF-HER-2 (266-296)+MVF-HER-2(597-626); MVF-PD-1 (92-110)+MVF-HER-2 (266-296)+MVF-HER-2 (597-626) and MVF-PD-L1 (130-147)+MVF-HER-2 (266-296)+MVF-HER-2 (597-626) with much smaller tumor volume than PBS negative control group and both of mAbs positive control groups as well. All the mice in peptides immunized groups with small tumor or most of them without any tumor at day 21 and day 28, respectively.
Additionally, log-rank (Mantel-Cox) test was used to analysis the percentage of survival as the mice were treated with the designed groups (
This application claims the benefit of U.S. Provisional Application No. 62/901,727, filed on Sep. 17, 2019, which is incorporated herein by reference in its entirety.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2020/051240 | 9/17/2020 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 62901727 | Sep 2019 | US |
