Patent Application
20230287365
The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. The ASCII copy, created on Aug. 13, 2021, is named 01948-281WO2_Sequence_Listing_08_13_21_ST25.txt and is 95,537 bytes in size.
Damaged cells, activated immune cells, platelets and stressed cells release large amounts of adenosine 5′-triphosphate (ATP) and adenosine 5′ diphosphate (ADP) during tissue injury, inflammation, hypoxia, apoptosis, vascular thrombosis and mechanical perturbation. Besides passively via ruptured cell membranes, nucleotide release can be done actively through exocytosis of intracellular vesicles or transport by membrane-bound channels or transporters. These extracellular nucleotides serve as potent signaling molecules and stimulate various ligand-gated ion channel P2X receptors (P2XR) and G-protein-coupled P2Y receptors (P2YR) to drive inflammation, platelet activation, clotting, immune response regulation, tissue blood flow control, and neuronal signaling. This form of purinergic signaling is also crucial to the activation of inflammasomes, via P2X7R, with subsequent proinflammatory cytokine release in response to damage-associated molecular patterns and pathogen-associated molecular patterns. To prevent overstimulation or desensitization of P2XRs and P2YRs, ATP and ADP are quickly hydrolyzed to produce adenosine 5′ monophosphate (AMP), and eventually nucleoside adenosine.
The conversion from pro-inflammatory ATP or ADP to anti-inflammatory adenosine is regulated by the spatial and temporal expression patterns, enzymatic activity variation, enzyme concentration, exposure duration, and localization of ectonucleotidases, a group of enzymes responsible for hydrolysis of extracellular nucleotides under varied biological conditions. Due to the complex regulatory network of these enzymes, impairment of nucleotide hydrolysis can disrupt the desired equilibrium of ATP, ADP, and AMP during inflammatory responses. Accordingly, new compositions and methods are needed to better regulate the hydrolysis of ATP and ADP to AMP in order to reduce inflammation.
The present invention features bifunctional enzymes that are engineered to hydrolyze nucleotide triphosphates (e.g., ATP) completely to form nucleosides (e.g., adenosine), through the fusion of the ectodomains (ECD) of an ecto-nucleoside triphosphate diphosphohydrolase (E-NTPDase)/CD39 family member and an ectonucleotidase (NMPase), such as an ecto-5′ nucleotidase (eN)/CD73, an alkaline phosphatase (AP), or an acid phosphatase (AP). Described herein are polypeptides that include an E-NTPDase CD39 family member with an NMPase (e.g., eN, ALP, or AP) and methods of use thereof, e.g., for decreasing inflammation.
In one aspect, the invention features a polypeptide that includes an E-NTPDase (e.g., NTPDase1, NTPDase2, NTPDase3, NTPDase4, NTPDase5, NTPDase6, NTPDase7, and NTPDase8, or a variant thereof, as described herein) and an NMPase, such as eN, ALP, or AP (e.g., a fusion protein containing the ECD of an E-NTPDase fused to the ECD of an eN, in either order). In particular embodiments, the ECD of the E-NTPDase corresponds to the extracellular catalytic domain. The extracellular catalytic domain may be a region that shares homology or sequence identity to the extracellular catalytic domain of CD39, which is set forth in SEQ ID NO: 1. Homology or sequence identity can be determined using standard sequence alignment or other homology-determining tools known in the art. The polypeptide may have a structure from N-terminus to C-terminus of A-(E-NTPDase)-L-eN-B; or A-eN-L-(E-NTPDase)-B; wherein A is absent or is an amino acid sequence of one or more amino acids; B is absent or is an amino acid sequence of one or more amino acids; and L is absent or is a linker, e.g., a chemical linker or a polypeptide linker of one or more amino acids.
The polypeptide may have a structure from N-terminus to C-terminus of A-(E-NTPDase)-L-ALP-B; or A-ALP-L-(E-NTPDase)-B; wherein A is absent or is an amino acid sequence of one or more amino acids; B is absent or is an amino acid sequence of one or more amino acids; and L is absent or is a linker, e.g., a chemical linker or a polypeptide linker of one or more amino acids.
The polypeptide may have a structure from N-terminus to C-terminus of A-(E-NTPDase)-L-AP-B; or A-AP-L-(E-NTPDase)-B; wherein A is absent or is an amino acid sequence of one or more amino acids; B is absent or is an amino acid sequence of one or more amino acids; and L is absent or is a linker, e.g., a chemical linker or a polypeptide linker of one or more amino acids.
The E-NTPDase may be ectonucleoside triphosphate diphosphohydrolase-1 (NTPDase1; CD39) or a biologically active truncation, mutant, or derivative thereof. The CD39 may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NO: 1. The CD39 may include or consist of the sequence of SEQ ID NO: 1.
The eN may be ecto-5′-nucleotidase (CD73) or a biologically active truncation, mutant, or derivative thereof. The CD73 may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NO: 2. The CD73 may include or consist of the sequence of SEQ ID NO: 2.
The ALP may be intestinal alkaline phosphatase, e.g., human intestinal alkaline phosphatase. The AP may be human prostatic acid phosphatase.
In some embodiments, A, B, and/or L includes a fragment crystallizable (Fc) domain. The Fc domain may be an IgG1 Fc domain. The Fc domain may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NO: 5. The Fc domain may include or consist of the sequence of SEQ ID NO: 5.
In some embodiments, A, B, and/or L include or consist of one or more glycines, serines, or a combination thereof (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 or more glycines, serines, or a combination thereof). For example, A, B, and/or L may include a polyglycine linker. The polyglycine linker may include or consist of the sequence of GGGG (SEQ ID NO: 3). The linker, L, may also be selected from any of a number of known polypeptide linkers with 1-20 amino acids or more in length.
The polypeptides described herein may have a structure from N-terminus to C-terminus of A-CD39-L-CD73-B; or A-CD73-L-CD39-B; wherein A is absent or is an amino acid sequence of one or more amino acids; B is absent or is an amino acid sequence of one or more amino acids; and L is absent or is a linker of, e.g., one or more amino acids.
A, B, and/or L may include a polyglycine linker and an Fc domain. A, B, and/or L may include GGGG-Fc and/or GGGG-Fc-GGGG. For example, A, B, and/or L may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NOs: 6 or 7. A, B, and/or L may include or consists of the sequence of SEQ ID NOs: 6 or 7. A, B, and/or L may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NO: 4. For example, A may include or consist of the sequence of SEQ ID NO: 4. L may include or consist of GGGG (SEQ ID NO: 3) and B may include GGGG-Fc.
In some embodiments, the polypeptide has at least 80% (e.g., at least 80%, 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NOs: 8 or 9. For example, the polypeptide may include or consist of the sequence of SEQ ID NOs: 8 or 9 (i.e., A-CD39-L-CD73-Fc (construct 2 in
In some embodiments, L includes GGGG-Fc-GGGG. The polypeptide may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NOs: 10 or 11. For example, the polypeptide may include or consist of the sequence of SEQ ID NOs: 10 or 11 (i.e., A-CD39-Fc-CD73-B (construct 1 in
Another aspect of the disclosure features a polynucleotide encoding the polypeptide of any of the above aspects. Also featured are a vector that includes the polynucleotide and a cell that includes the polynucleotide or the vector.
Yet another aspect of the disclosure features a method of producing a polypeptide as described herein. The method includes providing a cell transformed with a polynucleotide encoding the polypeptide or a vector that includes the polynucleotide; culturing the transformed cell under conditions for expressing the polynucleotide, wherein the culturing results in expression of the polypeptide. The method may further include purifying and/or isolating the polypeptide.
In another aspect, the invention features a method of hydrolyzing a nucleotide triphosphate (NTP) or nucleotide diphosphate (NDP) to a nucleoside. The method includes providing the polypeptide of any of the above aspects and the NTP or NDP and allowing the polypeptide to hydrolyze the NTP or NDP to a nucleoside. The NTP may be adenosine 5′ triphosphate (ATP). The NDP may be adenosine 5′ diphosphate (ADP). The nucleoside may be adenosine. The method may include providing a polynucleotide encoding the polypeptide, a vector containing the polynucleotide, or a cell containing the polynucleotide or vector (or a composition containing any one or more of these components) rather than the polypeptide.
In another aspect, the invention features a method of inhibiting platelet aggregation (e.g., in a subject, such as a human, in need thereof) by providing the polypeptide of any one of any of the above aspects, or a composition containing the same, and allowing the polypeptide to hydrolyze ATP and ADP to adenosine. The method may include providing a polynucleotide encoding the polypeptide, a vector containing the polynucleotide, or a cell containing the polynucleotide or vector (or a composition containing any one or more of these components) rather than the polypeptide. The subject may be at risk of forming a blood clot, e.g., a pulmonary embolism.
In another aspect, the invention features a method of decreasing (e.g., by 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97, 99%, or more) inflammation (e.g., as measured by a blood test, e.g., by using a blood test for C-reactive protein (hs-CRP) in a subject (e.g., a human) by providing the polypeptide of any of the above aspects and allowing the polypeptide to hydrolyze ATP and ADP to adenosine. The method may include providing a polynucleotide encoding the polypeptide, a vector containing the polynucleotide, or a cell containing the polynucleotide or vector (or a composition containing any one or more of these components) rather than the polypeptide.
In another aspect, the invention features a method of treating a disease characterized by high levels of ATP and/or tissue damage, such as an acute inflammatory disease or cancer, by providing the polypeptide of any one of any of the above aspects, or a composition containing the same, thereby hydrolyzing ATP and ADP to adenosine in the subject. The disease may be selected from a cardiovascular or cerebrovascular illness, such as an illness associated with or linked to vascular endothelial and platelet activation with thrombosis, ischemia reperfusion injury, transplantation graft preservation and reperfusion, reperfusion injury to native organs, such as the heart, brain, liver, and gut, unstable angina and myocardial infarction, stroke, pulmonary embolism, deep vein thrombosis (DVT), acute surgical and nonsurgical trauma, a pulmonary illness (e.g., acute respiratory distress syndrome (ARDS) or a pulmonary illness caused by, e.g., lung injury resulting from trauma, a surgical procedure, an infection, pulmonary embolism, asthma, primary pulmonary hypertension, and pulmonary fibrosis), a neurodegenerative disease, multiple sclerosis, a rheumatological or autoimmune disease (e.g., acute tophaceous gout, seropositive rheumatoid arthritis, juvenile rheumatoid arthritis, psoriasis, lupus, and dermatomyositis), a gastrointestinal or liver disease (e.g., inflammatory bowel disease, celiac disease, Clostridium difficile and pseudomembranous colitis, mesenteric ischemia, fatty liver disorder and non-alcoholic steatohepatitis, acute toxic liver injury as with acetaminophen and mushroom poisoning, acute viral hepatitis, fulminant liver failure, and acute renal failure), septicemia and end-organ failure with purine starvation, COVID-19, acute diabetic ketoacidosis and metabolic perturbation, and pregnancy conditions, such as pre-eclampsia, toxemia, and acute fatty liver of pregnancy. The method can promote a decrease of inflammation (e.g., by 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97, 99%, or more, e.g., as relative to an untreated subject), e.g., as measured by a blood test, e.g., via a blood test for C-reactive protein (hs-CRP) in the subject (e.g., a human). The method may include providing a polynucleotide encoding the polypeptide, a vector containing the polynucleotide, or a cell containing the polynucleotide or vector (or a composition containing any one or more of these components) rather than the polypeptide.
In some embodiments of the methods described herein, the method reduces (e.g., by 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97, 99%, or more) blood pressure (e.g., as measured by diastolic and/or systolic pressure or ambulatory blood pressure monitoring (ABPM)) in the subject (e.g., a human). The method may be used to reduce vascular thrombosis and/or mechanical perturbation. The method may be used to reduce ischemia. The method may be used to treat a cancer.
In some embodiments, the methods described herein may be used to reduce inflammation in a tissue injury (e.g., injury to the epidermis, arm, leg, torso, head, foot, hand, finger), e.g., as measured by a blood test for hs-CRP or a volume of swelling in the subject.
The method may be used to reduce (e.g., by 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97, 99%, or more) hypoxia, e.g., as measured using pulse oximetry.
The method may be used to reduce (e.g., by 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97, 99%, or more) apoptosis, e.g., as determined via flow cytometry or externalization of phosphatidylserine on the plasma membrane using fluorescent-tagged annexin V.
In another aspect, the invention features a pharmaceutical composition that includes, the polypeptide, polynucleotide, vector, or cell of any of the above embodiments and a pharmaceutically acceptable carrier.
In another aspect, featured is a kit that includes the pharmaceutical composition and instructions for use thereof. The instructions may be used to instruct a user to perform a method as described herein.
As used herein, the term “about” refers to a value that is 10% above or below the value being described.
As used herein, the terms “conservative mutation,” “conservative substitution,” “conservative amino acid substitution,” and the like refer to a substitution of one or more amino acids for one or more different amino acids that exhibit similar physicochemical properties, such as polarity, electrostatic charge, and steric volume. These properties are summarized for each of the twenty naturally occurring amino acids in Table 1 below.
†based on volume in A3: 50-100 is small, 100-150 is intermediate, 150-200 is large, and >200 is bulky
From this table it is appreciated that the conservative amino acid families include (i) G, A, V, L and I; (ii) D and E; (iii) C, S and T; (iv) H, K and R; (v) N and Q; and (vi) F, Y and W. A conservative mutation or substitution is therefore one that substitutes one amino acid for a member of the same amino acid family (e.g., a substitution of Ser for Thr or Lys for Arg).
As used herein, the terms “ectonucleoside triphosphate diphosphohydrolase,” “E-NTPDase,” and (“NTPDase”) refer to enzymes that catalyze the hydrolysis of γ- and β-phosphate residues of triphospho- and diphosphonucleosides to the monophosphonucleoside derivative. Examples of E-NTPDases include (alternative names in parentheses), e.g., NTPDase1 (CD39, ATPDase, ecto-apyrase), NTPDase2 (CD39L1, ecto-ATPase), NTPDase3 (CD39L3, HB6), NTPDase4 (UDPase, LALP70), NTPDase5 (CD39L4, ER-UDPase, PCPH), NTPDase6 (CD39L2), NTPDase7 (LALP1), and NTPDase8 (liver canalicular ecto-ATPase, hATPDase). The genes encoding human NTPDase1-NTPDase8 (UniProt P49961, Q9Y5L3, 075355, Q9Y227, 075356, 075354, Q9NQZ7, Q5MY95) are ENTPD1-ENTPD8, respectively (GenBank accession numbers U87697, AF144748, AF034840, AF016032, AF039918, AY327581, AF2692655, and AY430414). The genes encoding murine NTPDase1-NTPDase8 (UniProt P55772, 055026, Q8BFW6, Q9DBT4, Q9WUZ9, Q3UOP5, Q3TCT4, Q8K0L2) are Entpd1-Entpd8, respectively (GenBank accession numbers NM_009848, AY376711, AY376710, NM_026174, AJ238636, NM_172117, AF2888221, and AY36442). The term E-NTPDase includes all biologically active fragments, truncations, mutants, variants, substitutions, or derivatives thereof, e.g., of any of the foregoing protein or gene sequences. The term E-NTPDase also includes homologs from other species, such as rat, pig, chicken, bovine, and the like. Other sequences would be readily apparent to the skilled artisan, e.g., using publicly available databases known in the art. E-NTPDases are described, e.g., in Robson et al. (Pur. Sign. 2:409-430, 2006), which is hereby incorporated by reference in its entirety.
One example of an E-NTPDase is ectonucleoside triphosphate diphosphohydrolase-1 (also known as NTPDase1 and CD39). CD39 hydrolyzes nucleoside triphosphates and disphosphates, such as ATP, UTP, ADP, and UDP to their monophosphate form. CD39 is multi-pass transmembrane domain and contains an extracellular catalytic domain. Full-length human CD39 has the following amino acid sequence (UniProt P49961):
CD39 encompasses all biologically active fragments, truncations, mutants, variants, substitutions, or derivatives thereof. An exemplary CD39 fragment is the polypeptide of SEQ ID NO: 1, which corresponds to the extracellular catalytic domain. CD39 includes all polypeptides having at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 99%, or 100% sequence identity to SEQ ID NO: 12 or to SEQ ID NO: 1. The term CD39 also includes homologs from other species, such as mouse, rat, pig, chicken, bovine, and the like (see, e.g., UniProt sequences P55772, P9767, Q9MYU4, P79784, and 018956). Other sequences would be readily apparent to the skilled artisan, e.g., using publicly available databases known in the art.
As used herein, the terms “nucleotide monophosphatase” and “NMPase” refer to enzymes that catalyze the removal of a phosphate group to convert a nucleotide monophosphate to a nucleoside. Examples of NMPases are “ecto-5′ nucleotidase” and “eN,” which refer to enzymes that catalyze the 5′ hydrolysis of nucleotide monophosphates to nucleosides. One example of eN is ecto-5′-nucleotidase (CD73). CD73 hydrolyzes nucleotide monophosphates, such as adenosine monophosphate (AMP), nicotinamide adenine dinucleotide (NAD), and nicotinamide mononucleotide (NMN) to remove the phosphate groups, e.g., to adenosine, nicotinamide adenine dinucleoside, and nicotinamide mononucleoside, respectively. CD73 is a GPI-anchored protein and contains an extracellular catalytic domain. Full-length human CD73 has the following amino acid sequence (UniProt P21589):
Full-length CD73 includes an N-terminal 26 amino acid signal peptide and a C-terminal 25 amino acid propeptide that are removed during maturation, yielding a 523 amino acid fragment, corresponding to residues 27-549 (SEQ ID NO: 2). CD73 encompasses all biologically active fragments, truncations, mutants, variants, substitutions, or derivatives thereof. An exemplary CD73 fragment is the polypeptide of SEQ ID NO: 1. CD73 includes all polypeptides having at least 50%, 60%, 70%, 80%, 85%, 90%, 95%, 97%, 99%, or 100% sequence identity to SEQ ID NO: 13 or to SEQ ID NO: 2. The term cd73 also includes homologs from other species, such as mouse, rat, pig, chicken, bovine, and the like (see, e.g., UniProt sequences Q61503, P21588, Q05927, and H2QTC9). Other sequences would be readily apparent to the skilled artisan, e.g., using publicly available databases known in the art.
Other Examples of NMPases are alkaline phosphatase (ALP) and acid phosphatase (AP). ALPs include, for example, intestinal alkaline phosphatase (IALP, e.g., human IALP UniProt P09923, A0A024R4A2), placental alkaline phosphatase (PALP, e.g., human PALP UniProt P05187), tissue nonspecific alkaline phosphatase (TNSALP, e.g., human TNSALP UniProt P05186), and germ cell alkaline phosphatase (GALP, e.g., human GALP P10696). Acid phosphatase includes, for example, prostatic acid phosphatase (PAP, e.g., human PAP UniProt P15309).
The term NMPase includes all biologically active fragments, truncations, mutants, variants, substitutions, or derivatives thereof, e.g., of any of the foregoing protein or gene sequences. The term NMPase also includes homologs from other species, such as mouse, rat, pig, chicken, bovine, and the like. Other sequences would be readily apparent to the skilled artisan, e.g., using publicly available databases known in the art. NMPases are described, e.g., in Melo et al. (Am J Physiol Gastointest Liver Physiol 15:G826-838, 2014) and Pettengil et al. (J Biol Chem 20:27315-27316, 2013), which are hereby incorporated by reference in their entirety.
As used herein, the term “fragment” is meant a portion of a polypeptide or nucleic acid molecule that contains, preferably, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain, e.g., 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 400, 500, or more amino acid residues, up to the entire length of the polypeptide. Exemplary fragments include the CD39 fragment of SEQ ID NO: 1 and the CD73 fragment of SEQ ID NO: 2, which are soluble fragments that include their respective catalytic domains.
As used herein, the term “nucleoside” refers to molecules containing a nucleobase (nitrogenous base) and a five-carbon sugar, such as ribose or 2′-deoxyribose. Examples of nucleosides include cytidine, uridine, adenosine, guanosine, thymidine, and inosine. As used herein, the term “nucleotide” refers to a nucleoside a phosphate group, generally of one to three phosphates. Examples of nucleotides include nucleoside triphosphates, such as adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP), thymidine triphosphate (TTP), and uridine triphosphate (UTP). In some instances, the terms “nucleoside” and “nucleotide” may be used interchangeably and would be well understood to the skilled artisan as context will dictate.
As used herein, the term “percent (%) identity” refers to the percentage of amino acid residues of a candidate sequence, e.g., a mutant NMPase (e.g., eN) or an E-NTPDase, that are identical to the amino acid residues of a reference sequence, e.g., a wild-type Melittin polypeptide, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent identity (i.e., gaps can be introduced in one or both of the candidate and reference sequences for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). Alignment for purposes of determining percent identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, ALIGN, or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. In some embodiments, the percent amino acid sequence identity of a given candidate sequence to, with, or against a given reference sequence (which can alternatively be phrased as a given candidate sequence that has or includes a certain percent amino acid sequence identity to, with, or against a given reference sequence) is calculated as follows:
100×(fraction of A/B)
where A is the number of amino acid residues scored as identical in the alignment of the candidate sequence and the reference sequence, and where B is the total number of amino acid residues in the reference sequence. In some embodiments where the length of the candidate sequence does not equal to the length of the reference sequence, the percent amino acid sequence identity of the candidate sequence to the reference sequence would not equal to the percent amino acid sequence identity of the reference sequence to the candidate sequence.
As used herein, the term “pharmaceutically acceptable carrier” refers to an excipient or diluent in a pharmaceutical composition. The pharmaceutically acceptable carrier is compatible with the other ingredients of the formulation and not deleterious to the recipient. The pharmaceutically acceptable carrier may provide pharmaceutical stability to the pore forming polypeptide or may impart another beneficial characteristic (e.g., sustained release characteristics). The nature of the carrier differs with the mode of administration. For example, for intravenous administration, an aqueous solution carrier is generally used; for oral administration, a solid carrier is preferred.
As used herein, the term “pharmaceutical composition” refers to a medicinal or pharmaceutical formulation that contains an active ingredient at a pharmaceutically acceptable purity as well as one or more excipients and diluents to enable the active ingredient suitable for the method of administration. The pharmaceutical composition includes pharmaceutically acceptable components that are compatible with, for example, a polypeptide. The pharmaceutical composition may be in aqueous form, for example, for intravenous or subcutaneous administration or in tablet or capsule form, for example, for oral administration.
As used herein, the term “subject” refers to a mammal, e.g., a human.
As used herein, the term “therapeutically effective amount” refers to an amount, e.g., a pharmaceutical dose, effective in inducing a desired biological effect in a subject or patient or in treating a patient having a condition or disorder described herein. It is also to be understood herein that a “therapeutically effective amount” may be interpreted as an amount giving a desired therapeutic effect, either taken in one dose or in any dosage or route, taken alone or in combination with other therapeutic agents.
As used herein, the terms “treatment” or “treating” refer to reducing or ameliorating a disorder and/or one or more symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder or symptoms associated therewith be completely eliminated. Reducing or decreasing the side effects of a disease or condition or the risk or progression of the disease or condition may be relative to a subject who did not receive treatment, e.g., a control, a baseline, or a known control level or measurement. The reduction or decrease may be, e.g., by about 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 99%, or about 100% relative to the subject who did not receive treatment or the control, baseline, or known control level or measurement. Various assays or efficacy metrics for a given disorder or disease are described in more detail below.
Extracellular di- and tri-phosphate nucleotides are released from activated or injured cells to trigger vascular and immune P2 purinergic receptors, provoking inflammation and vascular thrombosis. These metabokines are scavenged by ecto-nucleoside triphosphate diphosphohydrolase-1 (E-NTPDase1; CD39). Further degradation of the mono-phosphate nucleoside end-products occurs by surface ecto-5′-nucleotidase (NMPase; CD73). These ecto-enzymatic processes, in tandem, promote adenosinergic responses, which are immunosuppressive and antithrombotic. However, such homeostatic ecto-enzymatic mechanisms are lost in a setting of oxidative stress, which consequently boosts inflammatory processes.
Described herein are bifunctional enzymes containing ectodomains (ECDs) of an E-NTPDase (e.g., NTPDase 1 (CD39), NTPDase2, NTPDase3, NTPDase4, NTPDase5, NTPDase6, NTPDase7, or NTPDase8, e.g., CD39) and an NMPase, such as eN (e.g., CD73), alkaline phosphatase (ALP), or acid phosphatase (AP) within a single polypeptide. The polypeptides containing these bifunctional enzymes are capable of hydrolyzing extracellular tri- and di-phosphate nucleotides directly to nucleosides and can be used therapeutically to ameliorate inflammatory diseases. Surprisingly, these bifunctional polypeptides were superior in catalyzing conversion tri- and di-phosphate nucleotides into nucleosides when compared to alkaline phosphatase and acid phosphatase fusion proteins or single polypeptide enzymes in combination (i.e., not as a fusion protein). Furthermore, the polypeptides described herein were shown to have beneficial impacts on platelet activation in vitro, confirming their therapeutic utility for converting pro-inflammatory ATP into anti-inflammatory adenosine. The polypeptides and methods of use thereof of the present disclosure are described in more detail below.
The polypeptides described herein include an ectonucleoside triphosphate diphosphohydrolase (E-NTPDase) and an NMPase, such as ecto-5′ nucleotidase (eN), ALP, or AP. The E-NTPDase and eN may be connected, e.g., by a linker of, e.g., at least one amino acid. The polypeptide may also include additional amino acid residues, e.g., spacers, at the N- or C-termini of the polypeptide or anywhere therebetween. For example, the polypeptide may have a structure from N-terminus to C-terminus of A-(E-NTPDase)-L-eN-B; or A-eN-L-(E-NTPDase)-B, in which A is absent or is an amino acid sequence of one or more amino acids, B is absent or is an amino acid sequence of one or more amino acids, and L is absent or is a linker, e.g., a chemical linker or a polypeptide linker of one or more (e.g., 1 to 20) amino acids.
The polypeptide may have a structure from N-terminus to C-terminus of A-(E-NTPDase)-L-ALP-B; or A-ALP-L-(E-NTPDase)-B; wherein A is absent or is an amino acid sequence of one or more amino acids; B is absent or is an amino acid sequence of one or more amino acids; and L is absent or is a linker, e.g., a chemical linker or a polypeptide linker of one or more amino acids.
The polypeptide may have a structure from N-terminus to C-terminus of A-(E-NTPDase)-L-AP-B; or A-AP-L-(E-NTPDase)-B; wherein A is absent or is an amino acid sequence of one or more amino acids; B is absent or is an amino acid sequence of one or more amino acids; and L is absent or is a linker, e.g., a chemical linker or a polypeptide linker of one or more amino acids.
The E-NTPDase may be ectonucleoside triphosphate diphosphohydrolase-1 (NTPDase1, E-NTPase1, CD39), NTPDase2, NTPDase3, NTPDase4, NTPDase5, NTPDase6, NTPDase7, or NTPDase8 or a biologically active truncation, mutant, or derivative thereof. In particular, the E-NTPDase is an ECD of a known E-NTPDase. The E-NTPDase can also be a variant of a known E-NTPDase, such as those described herein, that has at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to the amino acid or nucleic acid sequence of the known E-NTPDase sequence. The variant E-NTPDase may contain only the region corresponding to the ECD of the known E-NTPDase.
The E-NTPDase may be CD39 or a biologically active truncation, mutant, or derivative thereof. The CD39 may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NO: 1 or 12. The CD39 may include or consist of the sequence of SEQ ID NO: 1 or 12.
The eN may be ecto-5′-nucleotidase (CD73) or a biologically active truncation, mutant, or derivative thereof. The CD73 may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NO: 2 or 13. The CD73 may include or consist of the sequence of SEQ ID NO: 2 or 13.
The polypeptides described herein may have a structure from N-terminus to C-terminus of A-CD39-L-CD73-B; or A-CD73-L-CD39-B; wherein A is absent or is an amino acid sequence of one or more amino acids; B is absent or is an amino acid sequence of one or more amino acids; and L is absent or is a linker, e.g., a chemical linker or a polypeptide linker of one or more (e.g., 1 to 20) amino acids.
In some embodiments, the polypeptide has at least 80% (e.g., at least 80%, 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NOs: 8 or 9 (i.e., A-CD39-L-CD73-Fc; or A-CD73-L-CD39-Fc). For example, the polypeptide may include or consist of the sequence of SEQ ID NOs: 8 or 9 (i.e., A-CD39-L-CD73-Fc; or A-CD73-L-CD39-Fc). The polypeptide may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NOs: 10 or 11 (i.e., A-CD39-Fc-CD73-B; or A-CD73-Fc-CD39-B). For example, the polypeptide may include or consist of the sequence of SEQ ID NOs: 10 or 11 (i.e., A-CD39-Fc-CD73-B; or A-CD73-Fc-CD39-B).
Other polypeptides described herein include fusions of CD39 or CD73 and an FC domain (e.g., the polypeptides of SEQ ID NOs: 46 and 47 and variants thereof having at least 80% sequence identity thereto). The polypeptides may be formulated as a combination.
The polypeptides described herein may optionally include a linker, spacer, and or terminal regions. The polypeptides may include a linker between the E-NTPDase (e.g., CD39 or fragment thereof) and the NMPase, e.g., eN (e.g., CD73 or a fragment thereof), ALP, and AP. The linker may be a polypeptide linker or a chemical linker. Alternatively, the linker may be absent.
The polypeptide may also include additional amino acid residues, e.g., spacers or terminal regions, at the N- or C-termini of the polypeptide or anywhere therebetween. For example, A and/or B, may each be, independently, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, or more amino acids long. A and/or B may each be, independently, e.g., from about 1 to about 500 amino acids (e.g., about 1 to about 400, about 1 to about 300, about 5 to about 300, about 5 to about 200, about 5 to about 100, about 5 to about 50, about 5 to about 30, about 10 to about 30, about 10 to about 20) long.
In some embodiments, A, B, and/or L includes one or more glycines, serines, or a combination thereof (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 or more glycines, serines, or a combination thereof). For example, A, B, and/or L may include a polyglycine linker. The polyglycine linker may consist of the sequence of GGGG (SEQ ID NO: 3).
In some embodiments, A, B, and/or L includes a fragment crystallizable (Fc) domain. The Fc domain may be, e.g., IgG-1, IgG-2, IgG-3, IgG-3 or IgG-4, including the CH2 and CH3 domains of the immunoglobulin heavy chain. The Fc may also include any portion of the hinge region joining the Fab and Fc regions. The Fc can be of any mammal, including human, and may be post-translationally modified (e.g., by glycosylation). The Fc domain may be an IgG1 Fc domain. The Fc domain may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NO: 5. The Fc domain may include or consist of the sequence of SEQ ID NO: 5.
In some embodiments, A, B, and/or L includes a half-life extending moiety, such as albumin (e.g., human serum albumin).
A, B, and/or L may include a polyglycine linker and an Fc domain. A, B, and/or L may include GGGG-Fc and/or GGGG-Fc-GGGG. For example, A, B, and/or L may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NOs: 6 or 7. A, B, and/or L may include or consists of the sequence of SEQ ID NOs: 6 or 7. A, B, and/or L may have at least 80% (e.g., at least 85%, 90%, 95%, 97%, or 99%) sequence identity to SEQ ID NO: 4. For example, A may include or consist of the sequence of SEQ ID NO: 4. L may include or consist of GGGG (SEQ ID NO: 3) and B may include GGGG-Fc. In some embodiments, L includes GGGG-Fc-GGGG.
Peptide Linkers
A linker may be, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, or more amino acids long. The linker may be, e.g., from about 1 to about 500 amino acids (e.g., about 1 to about 400, about 1 to about 300, about 1 to about 20, about 5 to about 300, about 5 to about 200, about 5 to about 100, about 5 to about 50, about 5 to about 30, about 10 to about 30, about 10 to about 20) long.
Suitable peptide linkers are known in the art, and include, for example, peptide linkers containing flexible amino acid residues such as glycine and serine. In certain embodiments, a linker can contain motifs, e.g., multiple or repeating motifs, of GS, GGS, GGGGS (SEQ ID NO: 14), GGSG (SEQ ID NO: 15), or SGGG (SEQ ID NO: 16). In certain embodiments, a linker can contain 2 to 12 amino acids including motifs of GS, e.g., GS, GSGS (SEQ ID NO: 17), GSGSGS (SEQ ID NO: 18), GSGSGSGS (SEQ ID NO: 19), GSGSGSGSGS (SEQ ID NO: 20), or GSGSGSGSGSGS (SEQ ID NO: 21). In certain other embodiments, a linker can contain 3 to 12 amino acids including motifs of GGS, e.g., GGS, GGSGGS (SEQ ID NO: 22), GGSGGSGGS (SEQ ID NO: 23), and GGSGGSGGSGGS (SEQ ID NO: 24). In yet other embodiments, a linker can contain 4 to 12 amino acids including motifs of GGSG (SEQ ID NO: 15), e.g., GGSGGGSG (SEQ ID NO: 25), or GGSGGGSGGGSG (SEQ ID NO: 26). In other embodiments, a linker can contain motifs of GGGGS (SEQ ID NO: 14), e.g., GGGGSGGGGSGGGGS (SEQ ID NO: 27). In certain embodiments, a linker is SGGGSGGGSGGGSGGGSGGG (SEQ ID NO: 28).
In some embodiments, a peptide linker is a peptide linker including the amino acid sequence of any one of (GS)x, (GGS)x, (GGGGS)x, (GGSG)x, (SGGG)x, wherein x is an integer from 1 to 50 (e.g., 1-40, 1-30, 1-20, 1-10, or 1-5). In some embodiments, the peptide linker has the amino acid sequence (GGGGS)x, wherein x is an integer selected from 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.
In some embodiments, a peptide linker contains only glycine residues, e.g., at least 4 glycine residues (e.g., 4-200, 4-180, 4-160, 4-140, 4-40, 4-100, 4-90, 4-80, 4-70, 4-60, 4-50, 4-40, 4-30, 4-20, 4-19, 4-18, 4-17, 4-16, 4-15, 4-14, 4-13, 4-12, 4-11, 4-10, 4-9, 4-8, 4-7, 4-6 or 4-5 glycine residues) (e.g., 4-200, 6-200, 8-200, 10-200, 12-200, 14-200, 16-200, 18-200, 20-200, 30-200, 40-200, 50-200, 60-200, 70-200, 80-200, 90-200, 100-200, 120-200, 140-200, 160-200, 180-200, or 190-200 glycine residues). In certain embodiments, a linker has 4-30 glycine residues (e.g., 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 glycine residues). In some embodiments, a linker containing only glycine residues may not be glycosylated (e.g., O-linked glycosylation, also referred to as O-glycosylation) or may have a decreased level of glycosylation (e.g., a decreased level of O-glycosylation) (e.g., a decreased level of O-glycosylation with glycans such as xylose, mannose, sialic acids, fucose (Fuc), and/or galactose (Gal) (e.g., xylose)) as compared to, e.g., a linker containing one or more serine residues.
In some embodiments, a linker containing only glycine residues may not be O-glycosylated (e.g., O-xylosylation) or may have a decreased level of O-glycosylation (e.g., a decreased level of O-xylosylation) as compared to, e.g., a linker containing one or more serine residues.
In some embodiments, a linker containing only glycine residues may not undergo proteolysis or may have a decreased rate of proteolysis as compared to, e.g., a linker containing one or more serine residues.
In certain embodiments, a linker can contain motifs of GGGG (SEQ ID NO: 3), e.g., GGGGGGGG (SEQ ID NO: 29), GGGGGGGGGGGG (SEQ ID NO: 30), GGGGGGGGGGGGGGGG (SEQ ID NO: 31), or GGGGGGGGGGGGGGGGGGGG (SEQ ID NO: 32). In certain embodiments, a linker can contain motifs of GGGGG (SEQ ID NO: 33), e.g., GGGGGGGGGG (SEQ ID NO: 34) or GGGGGGGGGGGGGGG (SEQ ID NO: 35).
In other embodiments, a linker can also contain amino acids other than glycine and serine, e.g., GENLYFQSGG (SEQ ID NO: 36), SACYCELS (SEQ ID NO: 37), RSIAT (SEQ ID NO: 38), RPACKIPNDLKQKVMNH (SEQ ID NO: 39), GGSAGGSGSGSSGGSSGASGTGTAGGTGSGSGTGSG (SEQ ID NO: 40), AAANSSIDLISVPVDSR (SEQ ID NO: 41), or GGSGGGSEGGGSEGGGSEGGGSEGGGSEGGGSGGGS (SEQ ID NO: 42).
Chemical Linkers
In some embodiments, the two polypeptide domains are connected via a chemical linker. A chemical linker provides space, rigidity, and/or flexibility between two or more components of the fusion protein or conjugate. In some embodiments, a linker may be a bond, e.g., a covalent bond, e.g., an amide bond, a disulfide bond, a C—O bond, a C—N bond, a N—N bond, a C—S bond, or any kind of bond created from a chemical reaction, e.g., chemical conjugation. In some embodiments, a linker includes no more than 250 atoms (e.g., 1-2, 1-4, 1-6, 1-8, 1-10, 1-12, 1-14, 1-16, 1-18, 1-20, 1-25, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, 1-60, 1-65, 1-70, 1-75, 1-80, 1-85, 1-90, 1-95, 1-100, 1-110, 1-120, 1-130, 1-140, 1-150, 1-160, 1-170, 1-180, 1-190, 1-200, 1-210, 1-220, 1-230, 1-240, or 1-250 atom(s); 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 95, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 28, 26, 24, 22, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 atom(s)). In some embodiments, a linker includes no more than 250 non-hydrogen atoms (e.g., 1-2, 1-4, 1-6, 1-8, 1-10, 1-12, 1-14, 1-16, 1-18, 1-20, 1-25, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, 1-60, 1-65, 1-70, 1-75, 1-80, 1-85, 1-90, 1-95, 1-100, 1-110, 1-120, 1-130, 1-140, 1-150, 1-160, 1-170, 1-180, 1-190, 1-200, 1-210, 1-220, 1-230, 1-240, or 1-250 non-hydrogen atom(s); 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 95, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 28, 26, 24, 22, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 non-hydrogen atom(s)). In some embodiments, the backbone of a linker includes no more than 250 atoms (e.g., 1-2, 1-4, 1-6, 1-8, 1-10, 1-12, 1-14, 1-16, 1-18, 1-20, 1-25, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, 1-60, 1-65, 1-70, 1-75, 1-80, 1-85, 1-90, 1-95, 1-100, 1-110, 1-120, 1-130, 1-140, 1-150, 1-160, 1-170, 1-180, 1-190, 1-200, 1-210, 1-220, 1-230, 1-240, or 1-250 atom(s); 250, 240, 230, 220, 210, 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 95, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 28, 26, 24, 22, 20, 18, 16, 14, 12, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 atom(s)). The “backbone” of a linker refers to the atoms in the linker that together form the shortest path from one part of the conjugate to another part of the conjugate. The atoms in the backbone of the linker are directly involved in linking one part of the conjugate to another part of the conjugate. For examples, hydrogen atoms attached to carbons in the backbone of the linker are not considered as directly involved in linking one part of the conjugate to another part of the conjugate.
Molecules that may be used to make linkers include at least two functional groups, e.g., two carboxylic acid groups. In some embodiments of a divalent linker, the divalent linker may contain two carboxylic acids, in which the first carboxylic acid may form a covalent linkage with one component in the conjugate and the second carboxylic acid may form a covalent linkage (e.g., a C—S bond or a C—N bond) with another component in the conjugate.
In some embodiments, dicarboxylic acid molecules may be used as linkers (e.g., a dicarboxylic acid linker). Examples of dicarboxylic acids molecules that may be used to form linkers include, but are not limited to,
wherein n is an integer from 1 to 20 (e.g., n is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20).
Other examples of dicarboxylic acids molecules that may be used to form linkers include, but are not limited to,
In some embodiments, dicarboxylic acid molecules, such as the ones described herein, may be further functionalized to contain one or more additional functional groups.
In some embodiments, the linking group may include a moiety including a carboxylic acid moiety and an amino moiety that are spaced by from 1 to 25 atoms. Examples of such linking groups include, but are not limited to,
wherein n is an integer from 1 to 20 (e.g., n is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20).
In some embodiments, a linking group may include a moiety including a carboxylic acid moiety and an amino moiety, such as the ones described herein, may be further functionalized to contain one or more additional functional groups. Such linking groups may be further functionalized, for example, to provide an attachment point to a polypeptide as described herein (e.g., by way of a linker, such as a PEG linker).
In some embodiments, the linking group may include a moiety including two amino moieties (e.g., a diamino moiety) that are spaced by from 1 to 25 atoms. Examples of such linking groups include, but are not limited to,
wherein n is an integer from 1 to 20 (e.g., n is 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20).
In some embodiments, a linking group may include a diamino moiety, such as the ones described herein, may be further functionalized to contain one or more additional functional groups. Such diamino linking groups may be further functionalized, for example, to provide an attachment point to a polypeptide as described herein (e.g., by way of a linker, such as a PEG linker).
In some embodiments, a molecule containing an azide group may be used to form a linker, in which the azide group may undergo cycloaddition with an alkyne to form a 1,2,3-triazole linkage. In some embodiments, a molecule containing an alkyne group may be used to form a linker, in which the alkyne group may undergo cycloaddition with an azide to form a 1,2,3-triazole linkage. In some embodiments, a molecule containing a maleimide group may be used to form a linker, in which the maleimide group may react with a cysteine to form a C—S linkage. In some embodiments, a molecule containing one or more haloalkyl groups may be used to form a linker, in which the haloalkyl group may form a covalent linkage, e.g., C—N and C—O linkage.
In some embodiments, a linker may include a synthetic group derived from, e.g., a synthetic polymer (e.g., a polyethylene glycol (PEG) polymer). In some embodiments, a linker may include one or more amino acid residues. In some embodiments, a linker may be an amino acid sequence (e.g., a 1-25 amino acid, 1-10 amino acid, 1-9 amino acid, 1-8 amino acid, 1-7 amino acid, 1-6 amino acid, 1-5 amino acid, 1-4 amino acid, 1-3 amino acid, 1-2 amino acid, or 1 amino acid sequence). In some embodiments, a linker (L or L′) may include one or more optionally substituted C1-C20 alkylene, optionally substituted C1-C20 heteroalkylene (e.g., a PEG unit), optionally substituted C2-C20 alkenylene (e.g., C2 alkenylene), optionally substituted C2-C20 heteroalkenylene, optionally substituted C2-C20 alkynylene, optionally substituted C2-C20 heteroalkynylene, optionally substituted C3-C20 cycloalkylene (e.g., cyclopropylene, cyclobutylene), optionally substituted C2-C20 heterocycloalkylene, optionally substituted C4-C20 cycloalkenylene, optionally substituted C4-C20 heterocycloalkenylene, optionally substituted C8-C20 cycloalkynylene, optionally substituted C8-C20 heterocycloalkynylene, optionally substituted C5-C15 arylene (e.g., C6 arylene), optionally substituted C3-C15 heteroarylene (e.g., imidazole, pyridine), O, S, NRi (Ri is H, optionally substituted C1-C20 alkyl, optionally substituted C1-C20 heteroalkyl, optionally substituted C2-C20 alkenyl, optionally substituted C2-C20 heteroalkenyl, optionally substituted C2-C20 alkynyl, optionally substituted C2-C20 heteroalkynyl, optionally substituted C3-C20cycloalkyl, optionally substituted C2-C20 heterocycloalkyl, optionally substituted C4-C20 cycloalkenyl, optionally substituted C4-C20 heterocycloalkenyl, optionally substituted C8-C20 cycloalkynyl, optionally substituted C8-C20 heterocycloalkynyl, optionally substituted C5-C15 aryl, or optionally substituted C3-C15 heteroaryl), P, carbonyl, thiocarbonyl, sulfonyl, phosphate, phosphoryl, or imino.
Covalent conjugation of two or more components in a conjugate using a linker may be accomplished using well-known organic chemical synthesis techniques and methods. Complementary functional groups on two components may react with each other to form a covalent bond. Examples of complementary reactive functional groups include, but are not limited to, e.g., maleimide and cysteine, amine and activated carboxylic acid, thiol and maleimide, activated sulfonic acid and amine, isocyanate and amine, azide and alkyne, and alkene and tetrazine. Site-specific conjugation to a polypeptide may accomplished using techniques known in the art. Exemplary techniques for site-specific conjugation to an Fc domain are provided in Agarwall. P., et al. Bioconjugate Chem. 26:176-192 (2015).
Other examples of functional groups capable of reacting with amino groups include, e.g., alkylating and acylating agents. Representative alkylating agents include: (i) an α-haloacetyl group, e.g., XCH2CO— (where X=Br, Cl, or I); (ii) a N-maleimide group, which may react with amino groups either through a Michael type reaction or through acylation by addition to the ring carbonyl group; (iii) an aryl halide, e.g., a nitrohaloaromatic group; (iv) an alkyl halide; (v) an aldehyde or ketone capable of Schiff's base formation with amino groups; (vi) an epoxide, e.g., an epichlorohydrin and a bisoxirane, which may react with amino, sulfhydryl, or phenolic hydroxyl groups; (vii) a chlorine-containing of s-triazine, which is reactive towards nucleophiles such as amino, sufhydryl, and hydroxyl groups; (viii) an aziridine, which is reactive towards nucleophiles such as amino groups by ring opening; (ix) a squaric acid diethyl ester; and (x) an α-haloalkyl ether.
Examples of amino-reactive acylating groups include, e.g., (i) an isocyanate and an isothiocyanate; (ii) a sulfonyl chloride; (iii) an acid halide; (iv) an active ester, e.g., a nitrophenylester or N-hydroxysuccinimidyl ester; (v) an acid anhydride, e.g., a mixed, symmetrical, or N-carboxyanhydride; (vi) an acylazide; and (vii) an imidoester. Aldehydes and ketones may be reacted with amines to form Schiff's bases, which may be stabilized through reductive amination.
It will be appreciated that certain functional groups may be converted to other functional groups prior to reaction, for example, to confer additional reactivity or selectivity. Examples of methods useful for this purpose include conversion of amines to carboxyls using reagents such as dicarboxylic anhydrides; conversion of amines to thiols using reagents such as N-acetylhomocysteine thiolactone, S-acetylmercaptosuccinic anhydride, 2-iminothiolane, or thiol-containing succinimidyl derivatives; conversion of thiols to carboxyls using reagents such as α-haloacetates; conversion of thiols to amines using reagents such as ethylenimine or 2-bromoethylamine; conversion of carboxyls to amines using reagents such as carbodiimides followed by diamines; and conversion of alcohols to thiols using reagents such as tosyl chloride followed by transesterification with thioacetate and hydrolysis to the thiol with sodium acetate.
In some embodiments, a linker of the invention, is conjugated (e.g., by any of the methods described herein) to a fusion protein, for example the Fc portion of a fusion protein. In some embodiments of the invention, the linker is conjugated by way of: (a) a thiourea linkage (i.e., —NH(C═S)NH—) to a lysine; (b) a carbamate linkage (i.e., —NH(C═O)—O) to a lysine; (c) an amine linkage by reductive amination (i.e., —NHCH2) to a lysine; (d) an amide (i.e., —NH—(C═O)CH2) to a lysine; (e) a cysteine-maleimide conjugate between a maleimide of the linker to a cysteine; (f) an amine linkage by reductive amination (i.e., —NHCH2) between the linker and a carbohydrate (e.g., a glycosyl group of an Fc domain monomer or an Fc domain); (g) a rebridged cysteine conjugate, wherein the linker is conjugated to two cysteines; (h) an oxime linkage between the linker and a carbohydrate (e.g., a glycosyl group of an Fc domain monomer or an Fc domain); (i) an oxime linkage between the linker and an amino acid residue; (j) an azido linkage between the linker; (k) direct acylation of a linker; or (I) a thioether linkage between the linker.
The invention also features polynucleotides encoding a polypeptide as described herein. Also featured is a vector that includes the polynucleotide encoding the polypeptide. Also contemplated herein is a cell that includes the polynucleotide or the vector.
The polypeptides may be produced according to routine methods known to one of skill in the art. The invention also features a method of producing a polypeptide as described herein by providing a cell transformed with a polynucleotide encoding the polypeptide or a vector that includes the polynucleotide and culturing the transformed cell under conditions for expressing the polynucleotide. The culturing results in expression of the polypeptide. The polypeptide may further be isolated from the remainder of the cell culture and/or cellular debris.
Also featured are viral vectors encoding the polypeptide that are suitable for administration to a subject, e.g., as a delivery vehicle or as a gene therapy.
Viral genomes provide a rich source of vectors that can be used for the efficient delivery of exogenous genes into a mammalian cell. Viral genomes are particularly useful vectors for gene delivery as the polynucleotides contained within such genomes are typically incorporated into the nuclear genome of a mammalian cell by generalized or specialized transduction. These processes occur as part of the natural viral replication cycle, and do not require added proteins or reagents in order to induce gene integration. Examples of viral vectors are a retrovirus (e.g., Retroviridae family viral vector), adenovirus (e.g., Ad5, Ad26, Ad34, Ad35, and Ad48), parvovirus, coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g. measles and Sendai), positive strand RNA viruses, such as picornavirus and alphavirus, and double stranded DNA viruses including adenovirus, herpesvirus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, modified vaccinia Ankara (MVA), fowlpox and canarypox). Other viruses include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, human papilloma virus, human foamy virus, and hepatitis virus, for example. Examples of retroviruses are avian leukosis-sarcoma, avian C-type viruses, mammalian C-type, B-type viruses, D-type viruses, oncoretroviruses, HTLV-BLV group, lentivirus, alpharetrovirus, gammaretrovirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, Virology, Third Edition (Lippincott-Raven, Philadelphia, (1996))). Other examples are murine leukemia viruses, murine sarcoma viruses, mouse mammary tumor virus, bovine leukemia virus, feline leukemia virus, feline sarcoma virus, avian leukemia virus, human T-cell leukemia virus, baboon endogenous virus, Gibbon ape leukemia virus, Mason Pfizer monkey virus, simian immunodeficiency virus, simian sarcoma virus, Rous sarcoma virus and lentiviruses. Other examples of vectors are described, for example, in McVey et al., (U.S. Pat. No. 5,801,030), the teachings of which are incorporated herein by reference.
Retroviral Vectors
The delivery vector used in the methods and compositions described herein may be a retroviral vector. One type of retroviral vector that may be used in the methods and compositions described herein is a lentiviral vector. Lentiviral vectors (LVs), a subset of retroviruses, transduce a wide range of dividing and non-dividing cell types with high efficiency, conferring stable, long-term expression of the transgene encoding the polypeptide or RNA. An overview of optimization strategies for packaging and transducing LVs is provided in Delenda, The Journal of Gene Medicine 6: S125 (2004), the disclosure of which is incorporated herein by reference.
The use of lentivirus-based gene transfer techniques relies on the in vitro production of recombinant lentiviral particles carrying a highly deleted viral genome in which the agent of interest is accommodated. In particular, the recombinant lentivirus are recovered through the in trans coexpression in a permissive cell line of (1) the packaging constructs, i.e., a vector expressing the Gag-Pol precursors together with Rev (alternatively expressed in trans); (2) a vector expressing an envelope receptor, generally of an heterologous nature; and (3) the transfer vector, consisting in the viral cDNA deprived of all open reading frames, but maintaining the sequences required for replication, encapsidation, and expression, in which the sequences to be expressed are inserted.
A LV used in the methods and compositions described herein may include one or more of a 5′-Long terminal repeat (LTR), HIV signal sequence, HIV Psi signal 5′-splice site (SD), delta-GAG element, Rev Responsive Element (RRE), 3′-splice site (SA), elongation factor (EF) 1-alpha promoter and 3′-self inactivating LTR (SIN-LTR). The lentiviral vector optionally includes a central polypurine tract (cPPT) and a woodchuck hepatitis virus post-transcriptional regulatory element (WPRE), as described in U.S. Pat. No. 6,136,597, the disclosure of which is incorporated herein by reference as it pertains to WPRE. The lentiviral vector may further include a pHR′ backbone, which may include for example as provided below.
The Lentigen LV described in Lu et al., Journal of Gene Medicine 6:963 (2004) may be used to express the DNA molecules and/or transduce cells. A LV used in the methods and compositions described herein may a 5′-Long terminal repeat (LTR), HIV signal sequence, HIV Psi signal 5′-splice site (SD), delta-GAG element, Rev Responsive Element (RRE), 3′-splice site (SA), elongation factor (EF) 1-alpha promoter and 3′-self inactivating L TR (SIN-LTR). It will be readily apparent to one skilled in the art that optionally one or more of these regions is substituted with another region performing a similar function.
Enhancer elements can be used to increase expression of modified DNA molecules or increase the lentiviral integration efficiency. The LV used in the methods and compositions described herein may include a nef sequence. The LV used in the methods and compositions described herein may include a cPPT sequence which enhances vector integration. The cPPT acts as a second origin of the (+)-strand DNA synthesis and introduces a partial strand overlap in the middle of its native HIV genome. The introduction of the cPPT sequence in the transfer vector backbone strongly increased the nuclear transport and the total amount of genome integrated into the DNA of target cells. The LV used in the methods and compositions described herein may include a Woodchuck Posttranscriptional Regulatory Element (W PRE). The WPRE acts at the transcriptional level, by promoting nuclear export of transcripts and/or by increasing the efficiency of polyadenylation of the nascent transcript, thus increasing the total amount of mRNA in the cells. The addition of the WPRE to LV results in a substantial improvement in the level of expression from several different promoters, both in vitro and in vivo. The LV used in the methods and compositions described herein may include both a cPPT sequence and WPRE sequence. The vector may also include an IRES sequence that permits the expression of multiple polypeptides from a single promoter.
In addition to IRES sequences, other elements which permit expression of multiple polypeptides are useful. The vector used in the methods and compositions described herein may include multiple promoters that permit expression more than one polypeptide. The vector used in the methods and compositions described herein may include a protein cleavage site that allows expression of more than one polypeptide. Examples of protein cleavage sites that allow expression of more than one polypeptide are described in Klump et al., Gene Ther.; 8:811 (2001), Osborn et al., Molecular Therapy 12:569 (2005), Szymczak and Vignali, Expert Opin Biol Ther. 5:627 (2005), and Szymczak et al., Nat Biotechnol. 22:589 (2004), the disclosures of which are incorporated herein by reference as they pertain to protein cleavage sites that allow expression of more than one polypeptide. It will be readily apparent to one skilled in the art that other elements that permit expression of multiple polypeptides identified in the future are useful and may be utilized in the vectors suitable for use with the compositions and methods described herein.
The viral vectors (e.g., retroviral vectors, e.g., lentiviral vectors) may include a promoter operably coupled to the transgene encoding the polypeptide or the polynucleotide encoding the RNA to control expression. The promoter may be a ubiquitous promoter. Alternatively, the promoter may be a tissue specific promoter.
The polypeptides described herein (e.g., polypeptides that include an ectonucleoside triphosphate diphosphohydrolase (E-NTPDase) and an NMPase, such as eN, ALP, or AP, such as the polypeptides of any one of SEQ ID NOs: 8-11 and variants thereof having at least 80% sequence identity thereto) may be used to hydrolyze a nucleotide triphosphate (NTP) or nucleotide diphosphate (NDP) to a nucleoside. The method includes providing a polypeptide as described herein and the NTP or NDP and allowing the polypeptide to hydrolyze the NTP or NDP to the nucleoside. The NTP may be adenosine 5′ triphosphate (ATP). The NDP may be adenosine 5′ diphosphate (ADP), and the nucleoside may be adenosine.
The polypeptide may be provided directly or may be provided, e.g., as a polynucleotide or a vector or cell comprising the same, e.g., as a delivery vehicle or as a gene therapy.
The polypeptides, polynucleotides, vectors, or cells described herein may be formulated into pharmaceutical compositions for administration to human subjects for the treatment of a disease or condition, such as a disease or condition related to inflammation.
The compositions and methods described herein may be used to reduce a level of inflammation, e.g., in a subject, such as a human, in need thereof. For example, the methods may decrease (e.g., by 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97, 99%, or more) a level of inflammation as compared to a reference (e.g., the subject before onset of inflammation or a healthy subject without inflammation. For example, the inflammation may decrease by about 5%, about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, or about 100% following administration of the composition. The level of inflammation may be measured e.g., by using a blood test for C-reactive protein (hs-CRP) in a subject.
The compositions described herein may be used for inhibiting or reducing (e.g., by 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97, 99%, or more) platelet aggregation. Platelet aggregation can be measured by a Lumi-aggregometor (Chrono-Log, Havertown, PA) as described in Enjyoji et al. Nat Med 5: 1010-1017, 1999, which is hereby incorporated by reference. Platelets may be incubated at 37° C. and the percent light transmission can be measured, e.g., following administration of the polypeptide. The subject may be at risk of forming a blood clot, e.g., a pulmonary embolism.
The compositions described herein may be used to reduce (e.g., by 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, or more, e.g., by about 0.1 mmHg, 0.2 mmHg, 0.3 mmHg, 0.4 mmHg, 0.5 mmHg, 1 mmHg, 2 mmHg, 3 mmHg, 4 mmHg, 5 mmHg, or more) blood pressure in a subject. Blood pressure may be measured by diastolic and/or systolic pressure or ambulatory blood pressure monitoring (ABPM), as would be well understood to one of skill in the art.
The method may be used to reduce vascular thrombosis and/or mechanical perturbation. The method may be used to treat ischemia.
In some embodiments, the compositions described herein may be used to reduce inflammation in a tissue injury (e.g., injury to the epidermis, arm, leg, torso, head, foot, hand, finger), e.g., as measured using a blood test for hs-CRP or by measuring a volume of swelling in the subject.
The method may be used to reduce (e.g., by 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97, 99%, or more) hypoxia, e.g., as measured using pulse oximetry.
The method may be used to reduce apoptosis, e.g., as determined via flow cytometry or externalization of phosphatidylserine on the plasma membrane using fluorescent-tagged annexin V.
The compositions may be used to treat cancer. Cancers that may be treated with the compositions described herein, include, e.g., leukemia, lymphoma, liver cancer, bone cancer, lung cancer, brain cancer, bladder cancer, gastrointestinal cancer, breast cancer, cardiac cancer, cervical cancer, uterine cancer, head and neck cancer, gallbladder cancer, laryngeal cancer, lip and oral cavity cancer, ocular cancer, melanoma, pancreatic cancer, prostate cancer, colorectal cancer, testicular cancer, throat cancer, acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), adrenocortical carcinoma, AIDS-related lymphoma, primary CNS lymphoma, anal cancer, appendix cancer, astrocytoma, atypical teratoid/rhabdoid tumor, basal cell carcinoma, bile duct cancer, extrahepatic cancer, ewing sarcoma family, osteosarcoma and malignant fibrous histiocytoma, central nervous system embryonal tumors, central nervous system germ cell tumors, craniopharyngioma, ependymoma, bronchial tumors, burkitt lymphoma, carcinoid tumor, primary lymphoma, chordoma, chronic myeloproliferative neoplasms, colon cancer, extrahepatic bile duct cancer, ductal carcinoma in situ (DCIS), endometrial cancer, ependymoma, esophageal cancer, esthesioneuroblastoma, extracranial germ cell tumor, extragonadal germ cell tumor, fallopian tube cancer, fibrous histiocytoma of bone, gastrointestinal carcinoid tumor, gastrointestinal stromal tumors (GIST), testicular germ cell tumor, gestational trophoblastic disease, glioma, childhood brain stem glioma, hairy cell leukemia, hepatocellular cancer, Langerhans cell histiocytosis, Hodgkin lymphoma, hypopharyngeal cancer, islet cell tumors, pancreatic neuroendocrine tumors, Wilms tumor and other childhood kidney tumors, Langerhans cell histiocytosis, small cell lung cancer, cutaneous T cell lymphoma, intraocular melanoma, Merkel cell carcinoma, mesothelioma, metastatic squamous neck cancer, midline tract carcinoma, multiple endocrine neoplasia syndromes, multiple myeloma/plasma cell neoplasm, myelodysplastic syndromes, nasal cavity and paranasal sinus cancer, nasopharyngeal cancer, neuroblastoma, non-Hodgkin lymphoma (NHL), non-small cell lung cancer (NSCLC), epithelial ovarian cancer, germ cell ovarian cancer, low malignant potential ovarian cancer, pancreatic neuroendocrine tumors, papillomatosis, paraganglioma, paranasal sinus and nasal cavity cancer, parathyroid cancer, penile cancer, pharyngeal cancer, pheochromocytoma, pituitary tumor, pleuropulmonary blastoma, primary peritoneal cancer, rectal cancer, retinoblastoma, rhabdomyosarcoma, salivary gland cancer, kaposi sarcoma, rhabdomyosarcoma, Sézary syndrome, small intestine cancer, soft tissue sarcoma, throat cancer, thymoma and thymic carcinoma, thyroid cancer, transitional cell cancer of the renal pelvis and ureter, urethral cancer, endometrial uterine cancer, uterine sarcoma, vaginal cancer, vulvar cancer, and Waldenström macroglobulinemia.
The method may be used to treat inflammation characterized by high levels of ATP and tissue damage and activation of immune responses.
The method may be used to treat an acute inflammatory disease, such as a cardiovascular or cerebrovascular illness associated with or linked to vascular endothelial and platelet activation with thrombosis. The method may be used to treat ischemia reperfusion injury. The method may be used to treat transplantation graft preservation and reperfusion, reperfusion injury to native organs (e.g., heart, brain, liver, and gut), and acute surgical and nonsurgical trauma.
The compositions and methods may be used to treat a pulmonary illness. The pulmonary illness may be, e.g., lung injury trauma, acute respiratory distress syndrome (ARDS), e.g., associated with a viral infection, such as that caused severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), which leads to COVID-19. Other pulmonary illnesses include, e.g., pulmonary embolism, asthma, primary pulmonary hypertension, stroke, unstable angina, myocardial infarction, deep vein thrombosis (DVT), and pulmonary fibrosis.
The compositions and methods may be used to treat gastrointestinal and/or liver disease. The compositions may be used to treat an inflammatory bowel disease (IBD), such as Crohn's disease or ulcerative colitis. Other inflammatory diseases include, e.g., celiac disease, Clostriudium difficile and pseudomembranous colitis, mesentery ischemia, fatty liver disorders and non-alcoholic steatohepatitis, acute toxic liver injury (e.g., as with acetaminophen and mushroom poisoning), acute viral hepatitis, autoimmune hepatitis, decompensated cirrhosis, and fulminant liver failure. The compositions and methods may be used to treat acute renal failure, septicemia, and end-organ failure with purine starvation.
The compositions and methods may be used to treat a neurodegenerative disease, such as multiple sclerosis.
The compositions and methods may be used to treat rheumatological and autoimmune diseases, such as acute tophaceous gout, seropositive rheumatoid arthritis, juvenile rheumatoid arthritis, psoriasis, lupus, and dermatomyositis.
The compositions and methods may be used to treat acute diabetic ketoacidosis and metabolic perturbation. The compositions and methods may be used to treat pregnancy conditions, such as preeclampsia, toxemia, and acute fatty liver of pregnancy.
Disease and conditions that may be treated with the compositions and methods described herein are described in, e.g., Eltzschig et al. (NEJM 367:2322-2333, 2012), the disclosure of which is hereby incorporated by reference.
In some embodiments, the subject that is treated is monitored for therapeutic efficacy during a course of treatment. For example, a subject that is treated for a disease or condition (e.g., high blood pressure or inflammation, e.g., IBD) may be monitored for a reduction in severity or occurrence of symptoms. If the symptoms are not sufficiently reduced (e.g., beyond a predetermined threshold, e.g., 30% reduction, 20% reduction, 10% reduction, or less), the subject may be provided an increased dose (e.g., increased frequency or higher amount per dose). If the symptoms are sufficiently reduced to a desired level (e.g., 50% reduction, 60%, reduction, 70% reduction, or more), then the dosage may remain the same or may be decreased (e.g., decreased frequency or lower amount per dose). If the disease or condition is substantially resolved, the subject may discontinue treatment.
The subject may be monitored for progression or reduction of the disease, e.g., once per day, once every two days, once every three days, once every four days, once every five days, once every six days, once a week, once every two weeks, once every three weeks, once every month, once every two months, once every three months, once every six months, once every nine months, once per year, or longer.
The polypeptides or polynucleotides, vectors, or cells comprising the same as described herein can be formulated as pharmaceutical compositions for administration to human subjects in a biologically compatible form suitable for administration in vivo.
The compositions described herein may be administered to a subject (e.g., a human) in a variety of forms depending on the selected route of administration, as will be understood by those skilled in the art. The compositions described herein may be administered, for example, by any route that allows the composition (e.g., the polypeptide or polynucleotide) to reach the target cells. The composition may be administered, for example, by oral, parenteral, intrathecal, intracerebroventricular, intraparenchymal, buccal, sublingual, nasal, rectal, patch, pump, or transdermal administration and the pharmaceutical compositions formulated accordingly. Parenteral administration includes intravenous, intraperitoneal, subcutaneous, intramuscular, transepithelial, nasal, intrapulmonary, intrathecal, intracerebroventricular, intraparenchymal, rectal, and topical modes of administration. In one embodiment, the composition is administered via aero Parenteral administration may be by continuous infusion over a selected period of time. In some preferred embodiments, the compositions described herein are administered via inhalation.
Certain compositions described herein may be administered, e.g., by inhalation. Inhalation may be oral inhalation or nasal inhalation. An inhalable composition described herein may be provided as a liquid dosage form or dry powder dosage form. A dry powder composition may be, e.g., administered by inhalation as is or after reconstitution in a vehicle (e.g., saline (e.g., isotonic saline), phosphate-buffered saline, or water).
A composition described herein may be orally administered, for example, with an inert diluent or with an assimilable edible carrier, or it may be enclosed in hard or soft shell gelatin capsules, or it may be compressed into tablets, or it may be incorporated directly with the food of the diet. For oral therapeutic administration, a composition described herein may be incorporated with an excipient and used in the form of ingestible tablets, buccal tablets, troches, capsules, elixirs, suspensions, syrups, and wafers. A composition described herein may also be administered parenterally. Solutions of a composition described herein can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, DMSO, and mixtures thereof with or without alcohol, and in oils. Under ordinary conditions of storage and use, these preparations may contain a preservative to prevent the growth of microorganisms. Conventional procedures and ingredients for the selection and preparation of suitable formulations are described, for example, in Remington's Pharmaceutical Sciences (2012, 22nd ed.) and in The United States Pharmacopeia: The National Formulary (USP 41 NF 36), published in 2018. The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that may be easily administered via syringe. Compositions suitable for buccal or sublingual administration include tablets, lozenges, and pastilles, where the active ingredient is formulated with a carrier, such as sugar, acacia, tragacanth, gelatin, and glycerin. Compositions for rectal administration are conveniently in the form of suppositories containing a conventional suppository base, such as cocoa butter.
The composition described herein may be administered to an animal, e.g., a human, alone or in combination with pharmaceutically acceptable carriers, as noted herein, the proportion of which is determined by the solubility and chemical nature of the composition, chosen route of administration, and standard pharmaceutical practice.
In general, the dosage of a pharmaceutical composition or the active agent in a pharmaceutical composition may be in the range of from about 1 pg to about 10 g (e.g., 1 pg-10 pg, e.g., 2 pg, 3 pg, 4 pg, 5 pg, 6 pg, 7 pg, 8 pg, 9 pg, 10 pg, e.g., 10 pg-100 pg, e.g., 20 pg, 30 pg, 40 pg, 50 pg, 60 pg, 70 pg, 80 pg, 90 pg, 100 pg, e.g., 100 pg-1 ng, e.g., 200 pg, 300 pg, 400 pg, 500 pg, 600 pg, 700 pg, 800 pg, 900 pg, 1 ng, e.g., 1 ng-10 ng, e.g, 2 ng, 3 ng, 4 ng, 5 ng, 6 ng, 7 ng, 8 ng, 9 ng, 10 ng, e.g., 10 ng-100 ng, e.g., 20 ng, 30 ng, 40 ng, 50 ng, 60 ng, 70 ng, 80 ng, 90 ng, 100 ng, e.g., 100 ng-1 pg, e.g., 200 ng, 300 ng, 400 ng, 500 ng, 600 ng, 700 ng, 800 ng, 900 ng, 1 μg, e.g., 1-10 μg, e.g., 1 μg, 2 μg, 3 μg, 4 μg, 5 μg, 6 μg, 7 μg, 8 μg, 9 μg, 10 μg, e.g., 10 μg-100 μg, e.g., 20 μg, 30 μg, 40 μg, 50 μg, 60 μg, 70 μg, 80 μg, 90 μg, 100 μg, e.g., 100 μg-1 mg, e.g., 200 μg, 300 μg, 400 pg, 500 μg, 600 μg, 700 μg, 800 μg, 900 μg, 1 mg, e.g., 1 mg-10 mg, e.g., 2 mg, 3 mg, 4 mg, 5 mg, 6 mg, 7 mg, 8 mg, 9 mg, 10 mg, e.g., 10 mg-100 mg, e.g., 20 mg, 30 mg, 40 mg, 50 mg, 60 mg, 70 mg, 80 mg, 90 mg, 100 mg, e.g., 100 mg-1 g, e.g., 200 mg, 300 mg, 400 mg, 500 mg, 600 mg, 700 mg, 800 mg, 900 mg, 1 g, e.g., 1 g-10 g, e.g., 2 g, 3 g, 4 g, 5 g, 6 g, 7 g, 8 g, 9 g, 10 g).
The pharmaceutical composition may also be administered as in a unit dose form or as a dose per mass or weight of the patient from about 0.01 mg/kg to about 100 mg/kg (e.g., 0.01-0.1 mg/kg, e.g., 0.02 0.03 mg/kg, 0.04 mg/kg, 0.05 mg/kg, 0.06 mg/kg, 0.07 mg/kg, 0.08 mg/kg, 0.09 mg/kg, 0.1 mg/kg, e.g., 0.1-1 mg/kg, e.g., 0.2 mg/kg, 0.3 mg/kg, 0.4 mg/kg, 0.5 mg/kg, 0.6 mg/kg, 0.7 mg/kg, 0.8 mg/kg, 0.9 mg/kg, 1 mg/kg, e.g., 1-10 mg/kg, e.g., 1 mg/kg, 2 mg/kg, 3 mg/kg, 4 mg/kg, 5 mg/kg, 6 mg/kg, 7 mg/kg, 8 mg/kg, 9 mg/kg, 10 mg/kg, e.g., 10-100 mg/kg, e.g., 20 mg/kg, 30 mg/kg, 40 mg/kg, 50 mg/kg, 60 mg/kg, 70 mg/kg, 80 mg/kg, 90 mg/kg, 100 mg/kg). The dose may also be administered as a dose per mass or weight of the patient per unit day (e.g., 0.1-10 mg/kg/day).
The dosage of the compositions (e.g., a composition including a polypeptide) described herein, can vary depending on many factors, such as the pharmacodynamic properties of the polypeptide, the mode of administration, the age, health, and weight of the recipient, the nature and extent of the symptoms, the frequency of the treatment, and the type of concurrent treatment, if any, and the clearance rate of the composition in the animal to be treated. The compositions described herein may be administered initially in a suitable dosage that may be adjusted as required, depending on the clinical response. In some embodiments, the dosage of a composition (e.g., a composition including a polypeptide) is a prophylactically or a therapeutically effective amount. Furthermore, it is understood that all dosages may be continuously given or divided into dosages given per a given time frame. The composition can be administered, for example, every hour, day, week, month, or year. In some embodiments, the composition may be administered continuously or systemically.
The pharmaceutical compositions described herein (e.g., containing a polypeptide, polynucleotide, vector, or cell described herein) may be provided in a kit that includes the pharmaceutical composition (e.g., in a container) and instructions for use thereof. The kit may contain one or more containers, in which each container contains a different composition of the invention (e.g., one container with a polypeptide of the invention and one container with a polynucleotide of the invention). The instructions enclosed with the kit may be used to instruct a user to perform a method as described herein.
The following examples are put forth so as to provide those of ordinary skill in the art with a description of how the compositions and methods described herein may be used, made, and evaluated, and are intended to be purely exemplary of the invention and are not intended to limit the scope of what the inventors regard as their invention.
Adenosine-5′-triphosphate disodium, Adenosine-5′-diphosphate disodium, Adenosine-5′-monophosphate disodium, Guanosine-5′-triphosphate disodium, Guanosine 5′-monophosphate disodium, Uridine-5′-triphosphate trisodium, Uridine 5′-diphosphate disodium, and Uridine 5′-monophosphate disodium, Guanosine 5′-diphosphate sodium, TRAP6, Chrono-log, Collagen P/N 385, malachite green hydrochloride, ammonium molybdate, Polyoxyethylene 10 Lauryl Ether, and sodium citrate·2H2O were purchased from Millipore Sigma (St. Louis, Mo.).
DNA fragments, encoding human CD39 (Thr45-Thr483; GenBank #: NP_001091645.1), human CD73 (Trp27-Ser549; GenBank #:NP_002517.1), human testicular and thymus alkaline phosphatase (ALP, Ile20-Thr502; GenBank #:NP_112603.2), human prostatic acid phosphatase (HAP, Lys33-Asp386; GenBank #:NM_001099.5) and human immunoglobulin yl Fc fragment (CH23, constant region starting with Gly236, the numbering of the EU amino acid sequence), were gene-synthesized by Blue Heron Biotech (Bothell, Wash.) and GenScript Biotech (Piscataway, N.J.). Corresponding full-length DNA fragments with an N-terminal signal sequence of glycoprotein 1 b alpha chain (MPLLLLLLLLPSPLHG; SEQ ID NO: 4) and a Gly4 linker in between each protein domain were assembled by polymerase chain reaction, and cloned into a human CMV promoter mammalian expression vector with EcoRI and BamHI (pEZ1002, HAPCH23; pEZ1006, ALPCH23; pEZ1007, CD73CH23CD39; pEZ1009, CD39CH23CD73; pEZ1010, CD39CD73CH23; pEZ1011, CD73CH23CD39; pWZ1013, CD73CH23; pWZ1014, CD39CH23). All constructs were confirmed by DNA sequencing.
Human embryonic kidney 293 (Expi293F) were grown and maintained in a humidified incubator with 5% CO2 at 37° C. in Expi293™ medium (Thermo Fisher, Waltham, Mass.). DNA transfection procedures in Expi293F cells were followed as described in ThermoFisher manufacturer's protocols. Briefly, DNA and lipofectamine complex were inoculated with 3.0×106/ml cells and expression enhancers were added 24 hrs post-transfection. Conditioned media were harvested at Day 4 and filtered with 0.2μ filters.
5 ml of Protein-A column (GE Healthcare, Piscataway, N.J.) pre-equilibrated with 50 mM Tris, 150 mM NaCl, pH 7.5 (PBS) was loaded with conditioned medium and washed with 10 column volumes (CV) of PBS, before the protein was eluted using 100% step of 150 mM Glycine pH3.5 in PBS. The protein was dialyzed overnight against 1000-fold 50 mM Tris, 150 mM NaCl, pH 7.5 (TBS) buffer overnight. Protein samples were pooled concentrated to 0.5-1.0 mg/mL using a 10 kDa MWCO centrifugal device.
The colorimetrical assay was performed as previously described (Llinas et al. J. Mol. Biol. 350: 441-451, 2005; Zhong et al. Purinergic Signal 13: 601-609, 2017). Essentially, 0.045% malachite green hydrochloride (MG), 4.2% ammonium molybdate in 4N HCl (AM), 4% solution of C12E10 (Polyoxyethylene 10 Lauryl Ether, Millipore Sigma) (CE), and 34% sodium citrate·2H2O (w/v), were prepared. Prior to the assay, MG and AM were mixed in 3:1 ratio, incubated for at least 20 min, and filtered through 0.2μ membrane. 0.1 ml of CE solution was added to every 5 ml of MG/AG solution. The NTPDase buffer contained 20 mM Tris-HCl, pH7.5, 120 mM NaCl, 5 mM KCl, 0.5 mM EDTA. 5 mM CaCl2) was added to calcium-plus reaction buffer. During the NTPDase assay, CD39 fusions or bifunctional samples (100 ng) were added to initiate the reaction at 37° C. for 10 min. 0.8 ml MG/AG/CE solution and 100 ul citrate were added sequentially to stop the reactions. A660 reading was measured by pre-blanked with 1 ml MG/AG/CE buffer. A660 reading with CaCl2) subtracted by A660 without divalent cation was converted phosphate standard curve. For NMPase assay, CD73 fusions or bifunctional samples' A660 readings were subtracted by those without enzyme. For alkaline phosphatase and acid phosphatase assays, ALP and HAP samples (200 ng) were used. A660 readings were subtracted by those without enzymes. For reaction buffer pH5.8, 200 mM Histidine, pH5.8, 120 mM NaCl, 5 mM KCl, 0.5 mM EDTA was used. For reaction buffer pH9.0, 200 mM N-cyclohexyl-2-aminoethanesulfonic acid, 120 mM NaCl, 5 mM KCl, 0.5 mM EDTA was used.
Perchloride acid (PCA)-treated samples were neutralized with 0.4 M K2HPO4 (Sigma-Aldrich, St. Louis, Mo.) and ATP, ADP, AMP and adenosine concentrations were analyzed with an Agilent 1260 Infinity HPLC system (Agilent Technologies, Santa Clara, Calif.) equipped with a G1312B binary pump, a G1367C high performance autosampler and a G1314C Variable Wavelength Detector VL+set at 254 nm. Nucleotides were separated by ion-pair reversed-phase chromatography using an Atlantis dC18 column (3 mm×150 mm, particle size 3 μm; Waters Corporation, Milford, Mass.). The samples were loaded on the column equilibrated with buffer A (0.1 M KH2PO4, 4 mM tetrabutylammonium hydrogen sulfate, pH 6). The mobile phase developed linearly from 0 to 100% buffer B (70% buffer A/30% methanol) during the first 13 min and remained isocratic at 100% buffer B for 15 min. Subsequently, the column was re-equilibrated with buffer A for 7 minutes. The flow rate was 0.5 ml/min. Adenosine, AMP, ADP and ATP were identified by their retention times and concentrations were calculated using known standards run in parallel.
Platelet aggregation was measured by a Lumi-aggregometor (Chrono-Log, Havertown, PA) as described previously (Enjyoji et al. Nat Med 5: 1010-1017, 1999). Essentially, ˜0.3 m of platelets were incubated at 37° C. and the percent light transmission was measured. Platelet agonists were tested at final concentrations of 2 μg/ml collagen or 12.5 nM Trap6. For bifunctional enzyme treatment of platelets, various amount of the protein was added as indicated.
To design a novel bifunctional enzyme that can hydrolyze tri-/diphosphate nucleotides all way down to nucleoside products (
To generate the control fusion proteins (
The resulting constructs above were transiently transfected into Expi293F cells for protein expression. The chimeric recombinant proteins, secreted into conditioned media, were purified as described in Materials and Methods. As shown in SDS-PAGE of
When the fusion proteins were analyzed in size exclusion chromatography (
Next, we set out to determine the enzymatic activities of the purified fusion proteins with colorimetrical functional assay commonly used for NTPDase enzymes. As shown in
As shown in
When the bifunctional fusion CD73CH23CD39 was measured,
As shown in
Human acidic phosphatase fusion HAPCH23 possessed ATPase (Km 9.08 mM, Vmax 2.21 μmol/nmol/min), ADPase (Km 2.1 mM, Vmax 1.91 μmol/nmol/min), and AMPase activities (Km 2.58 mM, Vmax 6.77 μmol/nmol/min) at acidic pH (
With all these data together, the bifunctional fusion enzymes exhibited robust NTPDase and NMPase activities with low Km and high Vmax. They were also active at physiological, acidic, and alkaline pHs. As measured by colorimetrical assay, the bifunctional fusions were superior over alkaline phosphatase and acid phosphatase in converting tri- and di-phosphate nucleosides into nucleosides.
To further understand the enzyme kinetics of the bifunctional fusions and the control fusion proteins, we performed a time course study on ATPase, ADPase, and AMPase at 0 min, 5 min, 10 min, 20 min, and 40 mins at 37° C. at pH7.5. 2.1 nmols of enzyme proteins were added to 100 μl reaction with 0.5 mM of ATP, ADP, or AMP. The reaction was terminated with 5 mM of perchloride acid and subjected to HPLC analysis for the accumulation or disappearance of nucleotides, as described in Materials and Methods. The peak of each corresponding nucleotides was quantified.
As shown in
As shown in
When the bifunctional enzyme CD73CH23CD39 was analyzed (
When alkaline phosphatase fusion was analyzed (
To demonstrate that the bifunctional fusion has biological efficacy, platelet aggregation assay was performed as described in Materials & Methods. When platelets were incubated at 37° C. in the presence of collagen or Trap6, aggregation occurred as determined by light transmission. As shown in
Regulating sophisticated conversion of pro-inflammatory ATP and ADP into immunosuppressive adenosine by multiple ectonucleotidase families casts a profound impact on biological processes such as inflammatory responses and thromboregulatory disturbances. By fusing the ectodomains of CD39 and CD73 into a single polypeptide, we have engineered bifunctional enzymes which hydrolyzed tri- and di-phosphate nucleotides directly into nucleosides. These engineered enzymes can be used to effectively terminate P2 receptor signaling and activate P1 receptor signaling, bypassing spatial and temporal expression patterns, enzyme activity variation, enzyme concentration and localization of CD39 and CD73 in different tissues and cell types under varied biological conditions. We have demonstrated that the bifunctional enzymes efficiently hydrolyzed ATP and ADP into adenosine via AMP intermediate, superior to human alkaline phosphatase and acid phosphatase. With the result of inhibiting platelet aggregation, these data together show that the bifunctional enzymes could be used effectively as a therapeutic, either alone or in combination with one or more additional therapeutic regimens for reducing platelet aggregation and/or inflammatory processes, for both reducing pro-inflammatory ATP and producing anti-inflammatory adenosine.
The engineered bifunctional enzymes appear well-behaved functionally and biochemically, even though they contain three different functional domains, Fc domain and ECD of CD39 and CD73. Among four versions of the fusions, the Dumbbell-shape form with CD39-ECD and CD73-ECD flanking Fc domain seems to be the better domain organization than the tandem-arrangement form. In eukaryotic cells, multidomain proteins with different functions are quite common, and our data indicate that bifunctional ectonucleotidases are functional biochemically. It is intriguing that no such enzyme exists in nature. This might implicate that separating CD73 and CD39 or other E-NTPDase family member into different individual proteins might be for the purpose of modulating purinergic signaling in different tissues and cell types. In nature, there are examples in other contexts of such a bifunctional enzyme or a two-independent-protein complex. For instance, peptide amidation is catalyzed by two critical enzymes in some organisms, peptidylglycine α-hydroxylating monooxygenase and peptidyl-α-hydroxyglycine α-amidating lyase, yet in higher organisms they exist as a bifunctional single polypeptide chain.
This study shows a head-to-head enzymatic comparison among several major ectonucleotidases. Regarding the activities toward ATP and ADP, CD39-ECD is much higher than alkaline phosphatase in all pH conditions tested. Acid phosphatase had no such activities at neutral pH while with some at acidic or alkaline pH. As expected, CD73 had no ATPDase activity. For the NMPase activity, CD73 had the highest NMPase activity among three enzymes compared, and its activity was not affected by pH. Alkaline phosphatase had a high activity at alkaline pH, lower activity at neutral pH, and little activity at acidic pH. Acid phosphatase's NMPase activity is higher than that of alkaline phosphatase in neutral and acidic pH. Acid phosphatase had no NMPase activity at alkaline pH. Based on our data, alkaline phosphatase is mainly an NMPase at alkaline and neutral pH with some activities toward ATP and ADP. The result is in line with the data from the rat and mouse alkaline phosphatase in chondrocyte. Loss of function CD73 mutant gene seems compensated by the increased expression of alkaline phosphatases, suggesting ALP is more NMPase. For acid phosphatase, it is also mostly an NMPase at neutral and acidic conditions, with some activity toward ATP and ADP at acidic and alkaline pH. During ATP hydrolysis, both alkaline phosphatase and acid phosphatase sequentially released reaction products of ADP, AMP and adenosine. Our results indicate that CD39-CD73 bifunctional fusions are the only ectonucleotidase that potently hydrolyzed ATP/ADP to adenosine through AMP intermediate under the conditions tested.
The protein engineering efforts in this study also revealed some interesting observations on the bifunctional fusions and the control proteins. We noticed a pH-sensitivity difference between the bifunctional fusion proteins and the parental fusions. For CD39CH23 fusion, ATPase activity in alkaline and acidic pH was higher than that in neutral pH, whereas its ADPase activity was opposite (
The study has confirmed that bifunctional enzymes exhibit beneficial therapeutic properties. Similar to soluble CD39, a bifunctional enzyme of the present disclosure could be used to reverse platelet activation, such as in excessive events that contribute to myocardial infarction, restenosis after angioplasty, and stroke. Because of the presence of P1 receptor in platelet, adenosine generated by a bifunctional enzyme would be expected to further modulate the inhibition. Moreover, tissue injury often results in inflammation. ATP released from damage cells activates P2 receptors on all immune cells and trigger pro-inflammatory responses. The bifunctional enzymes not only terminate these responses but also generate immunosuppressive adenosine. Bifunctional enzymes could be used, e.g., to treat patients with high blood pressure. The nucleosides generated by ectonucleotide catalysts would be expected to mediate activities in the vasculature. When sympathetic nerves release ATP, it binds to P2X receptors that result in the constriction of vascular smooth muscles. By breaking down extracellular ATP, the source of agonists for P2X receptors would be depleted, causing a stop in rising blood pressure. In addition, adenosine results in vasodilatation through the binding of adenosine to smooth muscle P1 receptors, and the dilation of blood vessels would decrease blood pressure. The bifunctional enzymes of the present disclosure could, therefore, be used to decrease blood pressure by decreasing extracellular ATP concentration while also increasing extracellular adenosine concentration.
In conclusion, we have demonstrated that a bifunctional enzyme, such as those described herein, that were engineered by fusing the ectodomains of CD39 and CD73, can be used successfully to hydrolyze ATP all the way down to adenosine. A bifunctional enzyme was shown to possess a full activity of sequentially hydrolyzing ATP or ADP mainly via AMP to adenosine. Comparing to human alkaline phosphatase and acid phosphatase, a bifunctional enzyme of the present disclosure was superior in converting tri- and di-phosphate nucleotides into nucleosides. The bifunctional enzyme exhibited a pH-sensitivity and enzymatic property difference from the parental molecules. The bifunctional enzyme was found active in platelet clotting assays, providing evidence that a bifunctional CD39/CD73 enzyme can promote therapeutic benefits in vivo by converting pro-inflammatory ATP into anti-inflammatory adenosine.
A subject at risk of a pulmonary embolism can be administered a pharmaceutical composition of the present disclosure (e.g., a polypeptide having the amino acid sequence of any one of SEQ ID NOs: 8-11 and variants thereof). The polypeptide may be formulated in a saline solution at pH 7.4 and administered intravenously to the subject. A sample of platelets from the subject is removed and assayed for platelet aggregation via a Lumi-aggregometor Platelets may be incubated at 37° C. and the percent light transmission can be measured. Following administration of the polypeptide, a sample of platelets from the subject can be removed and assayed for aggregation. Following administration of the polypeptide, the subject can be monitored for a reduction of platelet aggregation by at least about 5% to at least about 30% or more.
A subject with ulcerative colitis experiences daily episodes of bowel irritation due to chronic ulcerative colitis. The subject usually experiences 3 to 4 irritable bowel movements per day. Once a week, the subject may undergo intravenous administration of a pharmaceutical composition of the present disclosure (e.g., a polypeptide having the amino acid sequence of any one of SEQ ID NOs: 8-11 and variants thereof). The polypeptide may be formulated in 500 mL saline at a concentration of about 2 mg/kg. Following four dosage administrations of the composition over a treatment period of four weeks, the subject can be monitored for a reduction of irritable bowel movements to about 1 or 2 per day or fewer.
While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the invention that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth and follows in the scope of the claims.
Other embodiments are within the claims.
10 This invention was made with government support under Grant Nos. CA221702, CA164970, and HL094400 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US2021/045956 | 8/13/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63066117 | Aug 2020 | US |
