EP4719453A2 - Inhibition of metastasis with recombinant plant products - Google Patents
Inhibition of metastasis with recombinant plant productsInfo
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- EP4719453A2 EP4719453A2 EP24816474.1A EP24816474A EP4719453A2 EP 4719453 A2 EP4719453 A2 EP 4719453A2 EP 24816474 A EP24816474 A EP 24816474A EP 4719453 A2 EP4719453 A2 EP 4719453A2
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
- C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
- C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
- C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
- C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K38/00—Medicinal preparations containing peptides
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Abstract
This invention relates to an isolated recombinant protein derived from an extract of the corm of the taro plant, Colocasia esculenta. This protein has been found to have potent anti-metastatic activity against an aggressive malignancy and a higher specific activity than the prior art taro storage protein composition. The invention therefore relates to the protein compositions described herein, pharmaceutical compositions comprising the recombinant proteins, and to methods for treating cancer, for example breast cancer, using the recombinant proteins or pharmaceutical compositions comprising the recombinant proteins.
Description
Attorney Docket No.: 15024-372PC0 Patent INHIBITION OF METASTASIS WITH RECOMBINANT PLANT PRODUCTS CROSS-REFERENCE TO RELATED APPLICATIONS [0001] This application is an international application, which claims the benefit of United States provisional application serial no.63/505,048, filed 30 May 2023. The entire contents of this application is hereby incorporated by reference as if fully set forth herein. GOVERNMENT FUNDING SUPPORT [0002] This invention was made with government support under CA134274 awarded by the National Institutes of Health and VA Merit award number 101 BX00016905 awarded by the U.S. Department of Veterans Affairs. The government has certain rights in the invention. BACKGROUND OF THE INVENTION 1. Field of the Invention [0003] The invention described herein relates to the field of medicine, and in particular, to cancer and cancer metastasis treatment. In particular, a new compound has been identified as a recombinant protein with potent anti-metastatic activity, similar to the anti-metastatic activity for breast cancer previously reported for taro plant from Colocasia esculenta. This new compound is identified as recombinant Engineered Mannose-Specific Lectin 1 (rEMSL1) family. 2. Background of the Invention [0004] Breast cancer is the second leading cancer death in women in the United States. The chance of a woman having invasive breast cancer sometime during her life is about 1 in 8. Breast cancer mortality is nearly always a consequence of tumor dissemination (metastatic disease). Approximately 297,790 new cases of invasive breast cancer will be diagnosed in women in the United States this year. Nearly 43,250 women died from breast cancer during the previous year; the chance of dying from breast cancer is about 1 in 6. Women diagnosed with triple negative breast cancer (TNBC) experience the poorest overall survival of any breast cancer subtype and there are no known molecular targets in TNBC. [0005] Global Data epidemiologists forecast that the number of diagnosed incident cases of breast cancer in women in the in the eight major markets (8MM) (US, France, Germany, Italy, Spain, UK, Japan, and urban China) is expected to grow to 1.21 million cases in 2023 at
Attorney Docket No.: 15024-372PC0 Patent a rate of 4.23% per year during the forecast period. The number of five-year diagnosed prevalent cases in the 8MM is expected to increase by 43.0% over the next decade to 5.12 million cases in 2023. [0006] Furthermore, while there are many effective therapies to control primary cancers, few therapies specifically target the properties of disseminating tumor cells that transit to and expand in secondary sites. Relapse is attributed to the emergence of tumor cells with metastatic and/or stem-like properties that are inherently resistant to conventional therapies. The identification of effective therapies that specifically target metastasis are urgently needed in the art. In particular, there is an unmet need for therapies that are directed towards either metastatic or cancer cells with stem properties (CSC). [0007] The cooked product of the taro corm (an underground storage organ), poi, is a dietary staple and is used in traditional and complementary medicine. In the uncooked state, taro leaves and roots generate renal and other toxicities. A water-soluble, heat labile, high molecular weight (>5 kDa) extract of raw taro, termed taro extract (TE), has the ability to inhibit metastasis in two pre-clinical models of TNBC. This protective activity is destroyed in cooked Taro. [0008] Early studies of taro extract from Colocasia esculenta classified proteins into two major groups: two albumins, A1 and A2 (molecular masses (molecular mass 12-14 kDa and 55-60 kDa, respectively), and two globulins, G1 and G2 (molecular masses 14 k Da and 22- 24 kDa, respectively). The albumin proteins were found to accumulate at the initial stages of corm development while the globulins were more abundant in the aqueous extract. [0009] G1 was identified by N-terminal sequencing and clustered as G1a/G1c and G1b/G1d, C- and N-terminal subdomains, respectively, derived from pro-proteins. Microheterogeneity of lectins within the GNA-related superfamily has been reported. In particular, it has been reported that each subgroup was formed by several polypeptides, and that ten isoforms (pI range 5.5 to 9.5) exist. Other reports have revealed that the GNA-related lectins superfamily mostly exists as complex mixtures of 12-14 kDa polypeptides, which have been identified by 2D electrophoresis with apparent molecular masses of 12 kDa (pI range 6.5-9). Ten of these polypeptides have been identified as lectin (A5HMM7) isomers by MALDI-TOF mass spectrometry. Phylogenetic analysis of the available sequences indicated that these proteins most probably result from multiple independent domain duplication/in tandem insertion events.
Attorney Docket No.: 15024-372PC0 Patent [0010] In a similar way, the G2 group globulins are composed of two groups of proteins, G2a (molecular mass 24 kDa) and G2b (molecular mass 22 kDa), with a native molecular mass of 50 kDa. Phylogenetic analysis of G2 sequences has shown that they belong to the Kunitz family of trypsin/chymotrypsin inhibitors, which includes the sweet potato storage protein sporamin. These activities may also indicate that these proteins may have evolved from ancestral proteins with metabolic activity. The polypeptide composition of taro extracts can change slightly among distinct cultivars, as demonstrated by electrophoresis analyses. Phylogenetic analyses have indicated that multiple independent domain duplication/in tandem insertion events gives rise to distinct subgroups with a different Inter-domain sequence identity and residual sequence identity to single-domain GNA-related superfamily lectins. Evidence suggests that the two-domain lectins evolved more rapidly than their single-domain counterparts and that there was a strong tendency to generate an inter-domain sequence divergence that eventually resulted in the formation of binding sites with a totally different specificity. SUMMARY OF THE INVENTION [0011] Thus, there exists an urgent need in the art for new effective therapies that specifically target metastasis. In particular, there is an unmet need for therapies that are directed towards either metastatic or cancer cells with stem properties (CSC). [0012] In particular embodiments, the present invention relates to therapeutic agent(s) derived from edible roots of the plant Colocasia esculenta, commonly known as Taro. Specifically, the invention, in some embodiments, relates to a recombinant taro storage protein derivative. BRIEF SUMMARY OF THE DRAWINGS [0013] Certain embodiments are illustrated by way of example, and not by way of limitation, in the figures of the accompanying drawings. [0014] FIG.1A is an SDS-PAGE of untagged proteins (pET24 expression vector): rEMSL2D11 (26.9 kDa) (SEQ ID NO:38; #211), rEMSL8D11 (27.7 kDa) (SEQ ID NO:54; #811), and rEMSL1D11 (29.4 kDa) (SEQ ID NO:23; #011) overexpressed in BL21(DE3) and Rosetta cells.
Attorney Docket No.: 15024-372PC0 Patent [0015] FIG.1B is an SDS-PAGE of Sumo-fusion engineered proteins (pSumo expression vector): rEMSL2D31 (37 kDa) (SEQ ID NO:46; #231), rEMSL8D31 (38 kDa) (SEQ ID NO:62; #831), and rEMSL1D31 (39 kDa) (SEQ ID NO:31; #031) overexpressed in BL21(DE3) and Rosetta cells. [0016] FIG.1C is an SDS-PAGE of untagged proteins (pET24 expression vector): rEMSL2D11 (26.9 kDa) (SEQ ID NO:38; #211), rEMSL8D11 (27.7 kDa) (SEQ ID NO:54; #811), and rEMSL1D11 (29.4 kDa) (SEQ ID NO:23; #011) overexpressed in BL21(DE3) and Rosetta cells. [0017] FIG.1D is an SDS-PAGE of Sumo-fusion engineered proteins (pSumo expression vector): rEMSL2D31 (37 kDa) (SEQ ID NO:46; #231), rEMSL8D31 (38 kDa) (SEQ ID NO:62; #831), and rEMSL1D31 (39 kDa) (SEQ ID NO:31; #031) overexpressed in BL21(DE3) and Rosetta cells. [0018] FIG.1E shows the purification of 15N-labeled recombinant Mannose Specific Lectin 1 (rEMSL1D1(1-268)) (SEQ ID NO:9; #001) size exclusion (S200-PG) column chromatogram expressed using pSUMO expression vector (SEQ ID NO:31; #031). [0019] FIG.1F is an SDS-PAGE of fractions 8-16 eluted from the S200 column. [0020] FIG.1G provides the amino acid sequence corresponding to rEMSL1D1 (SEQ ID NO:9; #001). [0021] FIG.1H shows the 1H-15N TROSY of 15N-labeled rEMSL1D4 (residues, 28-253) by Nuclear Magnetic Resonance (NMR results) (SEQ ID NO:22; #004). [0022] FIG.1I shows that rEMSL1D11(residues 1-268) theoretical monoisotopic mass is 29542.75 Da if all cysteines are reduced (SEQ ID NO:9; #001) [0023] FIG.1J provides the sequence of EMSL1D1 (SEQ ID NO:23;#011) [0024] FIG.1K is an SDS-PAGE of 1.(eGFP)-EMSL2D23 (residues 140-216) (41,8 kDa) (SEQ ID NO.44;#223); 2. (eGFP)-EMSL2D22 (residues 24-122) (39,3 kDa) (SEQ ID NO. 43;#222); 3. (eGFP)- EMSL1D23 (residues 145-240) (41,7 kDa) (SEQ ID NO.29;#023); 4. (eGFP)- EMSL1D22 (residues 29-127) (42,3 kDa) (SEQ ID NO.28;#022); 5. (eGFP)-
Attorney Docket No.: 15024-372PC0 Patent EMSL8D23 (residues 140-239) (41.9 kDa) (SEQ ID NO.60;#023); 6. (eGFP)-EMSL8D22 (residues 24-122) (41.7 kDa) (SEQ ID NO.59;#022). [0025] FIG.2A shows TE size exclusion chromatography Superdex S200 chromatographic data. Column molecular weight calibration was performed with protein standards as described in “Methods” section. [0026] FIG.2B shows TE proteins resolved in SDS-PAGE (4-20%) on mainly 3 bands corresponding to 12, 23 and 52 kDa. [0027] FIG.2C shows an intact mass spectrum of a TE sample by MS-ESI. [0028] FIG.3A, FIG.3B, and FIG.3C shows MALDI-TOF-MS results for TE glycopeptides of 12 kD , 23 kD and 52 kD MALDI-TOF-MS, respectively. [0029] FIG.4A shows the multiple sequence alignment of EMSL1 (Q39487), EMSL2 (A5HMM7), EMSL3 (PDBID 5T20), EMSL5 (R9RL27), EMSL8 (Q43418) obtained using MUSCLE. SEQ ID NOs: SEQ ID NO:9; #001(EMSL1), SEQ ID NO:10; #201(EMSL2), SEQ ID NO:11; #301(EMSL3), SEQ ID NO:13; #501(EMSL5D1) SEQ ID NO:50; #510 (EMSL5D10), SEQ ID NO:16; #801 (EMSL8), SEQ ID NO:71; #1101 (ECTI1), and SEQ ID NO:72; #1201 (ECTI2) are shown. [0030] FIG.4B shows the pairwise sequence alignment between ETCI1 (Q39488), ETCI2 (Q39489). SEQ ID NO:71; #1101(Q39488) and SEQ ID NO:72 ;#1201(Q39489) are shown. [0031] FIG.4C shows a Neighbor Joining tree calculated from the multiple sequence alignment (FIG.4A-4A and FIG.4B-4B) of EMSL1 (SEQ ID NO:9; #001), EMSL2 (SEQ ID NO:10; #201), EMSL3 (SEQ ID NO:11; #301), EMSL5D1 (SEQ ID NO:13; #501), EMSL5D10 (SEQ ID NO:50; #510), EMSL8 (SEQ ID NO:16; #801), ECTI1 (SEQ ID NO:71; #1101), and ECTI2 (SEQ ID NO:72; #1201) proteins. [0032] FIG.4D shows unpublished X-ray structure of EMSL1D1 (residues 1-268) in ribbon highlighting the disulfide bond in yellow; the carbohydrate binding sites (CBS#1 and #2) and conserved motifs (CXLXL; SEQ ID NO:1) are highlighted in red and yellow, respectively. The structure is aligned with MSL2 (PDB ID: 5T20) represented in gray ribbon. [0033] FIG.5 is a table showing how representative N-glycan TE motifs are classified by MotiFinder, including High mannose complex N-glycans, Asymmetric biantennary Complex N-glycans, Asymmetric biantennary Complex N-glycans with terminal fucosylation, Asymmetric biantennary Complex N-glycans with core fucosylation, and Symmetric
Attorney Docket No.: 15024-372PC0 Patent biantennary Complex N-glycans. Glycans are rendered using the Symbolic Nomenclature for Glycans (SNFG). [0034] FIG.6 is a graph showing surface lung tumor colonies in mice injected with line 66.1 cells after the indicated treatments with either TE or rMLS1. [0035] FIG.7A shows the relative fluorescence units as result of TE binding to the glycan structures of the 100-glycan library (ZBiotech 100-glycan microarray). [0036] FIG.7B shows the optimization of the glycan array conditions at different TE concentrations (explored concentrations 0.2 to 150.0 µg/mL). [0037] FIG.7C also shows the calculation of an apparent KD for Man-5 and Man-6 glycans binding data to TE. [0038] FIG.7D presents a representative slide showing fluorescence (light dots) of just high- mannose N-glycans. On this microarray, we can observe TE binding specificity to high- mannose N-glycans. [0039] FIG.8A. The concentration of 0.4 µg/mL fluorescently labeled TE (NHS-Alexa555- or AF555-TE) was assessed for N-glycan recognition pattern among 100 N-glycans (ZBiotech 100N-glycan library) in replicates of 8. [0040] FIG.8B illustrates fluorescence of N-glycans on the printed 100 N-glycan microarray during the process of fluorescence detection. [0041] FIG.8C shows glycan classification analyzed by MotifFinder. [0042] FIG.9A through FIG.9E relate to TE inhibits experimental and spontaneous metastasis in two TNBC models. FIG.9A and FIG.9B show data for counted lung tumor colonies by injection of either line 66.1 tumor cells or line 410.4 cells into syngeneic mice treated with either PBS or TE. FIG.9C shows the effect of TE or PBS on spontaneous lung metastases from primary 410.4 tumors. FIG.9D shows primary tumor growth in mice from treatment in FIG.9C. FIG.9E is a Kaplan-Meier survival plot of mice injected i.v. with 66.1-luciferase cells and treated with TE or PBS. [0043] FIG.10A shows the relative fluorescence units (RFU) (y-axis) of TE (blue bar) and MSL1D34 (residues, 28-253) (red bar) on the 100 N-glycans array (x-axis). [0044] FIG.10B and FIG.10C illustrate the fluorescence of symmetric biantennary, asymmetric biantennary, and high-mannose N-glycans for TE (FIG.10B) and EMSL1D34
Attorney Docket No.: 15024-372PC0 Patent (residues, 28-253) (FIG.10C) on the printed 100 N-glycan microarray library (ZBiotechTM 100N-glycan) during the process of fluorescence detection. FIG.10C. [0045] FIG.11 examines binding of recombinant eGFP-EMSL1 (eGFP-EMSL1) in presence of unlabeled rEMSL1, rEMSL1 D1-Y64A, or rMSL1 D1-5xAla. [0046] FIG.12A and FIG.12B show bioluminescent imaging in mice injected with 66.1- luciferase cells and treated with rEMSL1D1 (SEQ ID NO:9; #001) or rEMSL1 D1-Y64A. For FIG.12A, Balb/cByJ female mice treated daily with rEMSL1 (50 µg protein) or mutant Y64A protein for 10 days. Mice injected with 1 x 10566.1-luciferase cells and bioluminescent imaging conducted on days +1, +7, +10, +14, +17 relative to tumor cell injection (p=0.018). FIG 12B shows surface lung tumor colonies at necropsy (p=0.009). [0047] FIG 13A shows the top 15 ranked N-glycan structures identified for TE (blue) and EMSL1D34 (residues, 28-253) (red) by 100 N-glycan microarray analysis. FIG.13B shows a 100 N-glycan array for EMSL1D34 CRS mutants, rEMSL1D1-Y64A (orange bar) and rEMSL1D1-5xAla (green bar), showing the absence of binding. FIG 13C is a drawing showing representative N-glycan structures showing binding to rEMSL1D34: Complex type biantennary N-linked glycans as N001; Lewis X type N-glycans as in N224 (circled in red); Terminal Type 2 N-acetyllactosamine (LacNAc) as in N6030 (circled in blue). [0048] FIG.14 presents competitive binding studies with line 66.1 cells and recombinant eGFP-EMSL1 (rEMSL1) (SEQ ID NO:27; #021) in the presence or absence of increasing concentrations of rEMSL1 (SEQ ID NO:9; #001). [0049] FIG.15A provides data on inhibition of proliferation of murine 66.1 cells by rEMSL1 (SEQ ID NO:9; #001). FIG.15B shows data on inhibition of proliferation of human breast cancer cell line MDA-MB-231 by the indicated treatments. As with TE, minor affects on proliferation were observed. [0050] FIG.16 relates to the % inhibition of proliferation of 66.1 cells, comparing the effects of TE, rEMSL1D1 (SEQ ID NO:9; #001), rEMSL1D1-Y64A (SEQ ID NO:#1001) and rEMSL1D1-5xAla (SEQ ID NO:#1001) versus vehicle-treated cells for the indicated compounds. [0051] FIG.17 shows data on the migration of line 66.1 cells under the indicated treatments. [0052] FIG.18 shows data for primary tumorsphere formation of 66.1 cells in response to TE or rEMSL1D1 (SEQ ID NO:9; #001).
Attorney Docket No.: 15024-372PC0 Patent [0053] FIG.19 provides data on the effect of rEMSL1D1 (SEQ ID NO:9; #001) on the fraction of aldehyde-dehydrogenase positive line 66.1 cells. [0054] FIG.20A and FIG.20B presents a fluorescence microarray showing rEMSL1D1 (SEQ ID NO:9;#001) (FIG.20A) and TE (FIG.20B) binding to PD-L1/PD-1. [0055] FIG.21 is a table presenting a list of protein sequences engineered EMSL1-EMSL9 and ETCI1-ETCI3 based on proteomic analysis performed on TE samples and similarity searches using UniProtTM database (uniprot.org). DETAILED DESCRIPTION OF EMBODIMENTS OF THE INVENTION 1. Overview [0056] This study has identified new therapies for breast cancer, including the most aggressive form, Triple Negative Breast Cancer (TNBC). Soluble proteins derived from an extract of the plant Colocasia esculenta, commonly known as taro, exhibit remarkably potent inhibitory effects on tumor metastasis in two orthotopic models of TNBC. Here, we describe an engineered recombinant EMSL1 (rEMSL1) protein that replicates, with high specific activity (i.e. antimetastatic activity/mg protein), the anti-metastatic, anti-proliferative, anti- migratory and anti-stem cell activity of Taro Extract (TE). This protein potently inhibits both metastatic and cancer stem cells (CSCs) with efficacy, in the absence of toxicities, and can be scaled up for commercial manufacture. 2. Definitions [0057] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. Although various methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. However, the skilled artisan understands that the methods and materials used and described are examples and may not be the only ones suitable for use in the invention. Moreover, as measurements are subject to inherent variability, any temperature, weight, volume, time interval, pH, salinity, molarity or molality, range, concentration and any other
Attorney Docket No.: 15024-372PC0 Patent measurements, quantities or numerical expressions given herein are intended to be approximate and not exact or critical figures unless expressly stated to the contrary. [0058] In the foregoing specification, the invention has been described with reference to specific embodiments thereof. It will, however, be evident that various modifications and changes may be made thereto without departing from the broader spirit and scope of the invention. The specification and drawings are, accordingly, to be regarded in an illustrative rather than a restrictive sense. [0059] Throughout this specification and the claims, unless the context requires otherwise, the word “comprise” and its variations, such as “comprises” and “comprising,” will be understood to imply the inclusion of a stated item, element or step or group of items, elements or steps but not the exclusion of any other item, element or step or group of items, elements or steps. Furthermore, the indefinite article “a” or “an” is meant to indicate one or more of the item, element or a step modified by the article. [0060] As used herein, the term “about” means plus or minus 20 percent of the recited value, so that, for example, “about 0.125” means 0.125 ±0.025, and “about 1.0” means 1.0 ±0.2. Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in specific non-limiting examples are reported as precisely as possible. Any numerical value, however, inherently contains certain errors necessarily resulting from the standard deviation found in their respective testing measurements at the time of this writing. Furthermore, unless otherwise clear from the context, a numerical value presented herein has an implied precision given by the least significant digit. Moreover, all ranges disclosed herein are to be understood to encompass any and all sub-ranges subsumed therein. For example, a range of "less than 10" can include any and all sub-ranges between (and including) the minimum value of zero and the maximum value of 10, that is, any and all sub-ranges having a minimum value of equal to or greater than zero and a maximum value of equal to or less than 10, e.g., 1 to 4. [0061] As used herein, the term “Taro Extract (TE)” refers to a composition of lectin proteins. TE contains a highly represented (>90% amino acid coverage) mannose specific lectin 2 (MSL2), previously named lectin (A5HMM7, GenBank Accession: EF541132.1) and mannose-specific lectin 1 (MSL1; SEQ ID NO:9), also known as taro storage protein TSP (Q39487, GenBank accession: D16173.1) from C. esculenta (>60 amino acid coverage).
Attorney Docket No.: 15024-372PC0 Patent Tarin or TAR1 (Q39418, GenBank accession: D16173.1) from C. esculenta also was identified with 45% amino acid sequence coverage. [0062] As used herein, the term “rTSP” or “rMSL1” and “rEMSL1” refers to recombinant proteins of the same name. [0063] As used herein, the term “engineered mannose-specific lectin 1 (EMSL1),” formerly known as “12kDa Taro Storage Protein (TSP)” refers to a 25 kDa protein from Colocasia esculenta of SEQ ID NO:9 (Uniprot: Q39487; GenBank: D16173.1; NCBI: BAA03722.1). [0064] As used herein, the term “amino acid coverage” means the percentage of amino acid sequences or peptides identified in TE sample analyzed by LC-MS/MS methods. [0065] As used herein, the term “treat,” “treatment,” and their cognates refer to administering a compound or pharmaceutical composition to obtain a desired pharmacologic and/or physiologic effect. "Treatment" therefore includes: (a) preventing or reducing the likelihood of diagnosis with the condition or disease or symptoms thereof from occurring in a subject which may be predisposed to the condition or disease but has not yet been diagnosed as having it; and/or (b) inhibiting, ameliorating, or reducing the condition or disease or symptom thereof, such as, arresting its development; and/or (c) relieving, alleviating or ameliorating the condition or disease or symptom thereof, such as, for example, causing regression of the condition or disease or symptom thereof; and/or (d) preventing or inhibiting metastasis, producing remission, diminishing of symptoms to make the disease, pathology or condition more tolerable to the patient, slowing the rate of degeneration or decline, or improving a patient's physical or mental well-being. [0066] As used herein, the term “administering” and its cognates refers to introducing an agent to a subject, and can be performed using any of the various methods or delivery systems for administering agents, pharmaceutical compositions or delivering gene vectors known to those skilled in the art. Common methods of administering agents include oral, intravenous injection or infusion, transdermal, transmucosal, intraperitoneal, intratumoral, and the like. [0067] As used herein, the term “therapy” and its cognates refer to an action taken with the intention of benefitting a patient and may comprise administration of a chemotherapeutic agent such as a drug, antibody, or the like. Therapies also include radiation therapy, surgery, dietary regimens, and the like as well. Therapy also can refer to multiple therapies that are administered concurrently or sequentially.
Attorney Docket No.: 15024-372PC0 Patent [0068] As used herein, the term “therapeutically effective amount” refers to an amount that produces a desired pharmacologic or physiologic response in a patient. The therapeutically effect amount can refer to a single dose or a number of divided doses or to a dosage regimen that can last one day, several days, weeks, months, or indefinitely. The therapeutic effect may occur immediately after administration of the amount or be delayed for hours or for a considerable time. In some embodiments, a therapeutically effective amount for an adult human includes amounts from about 1 μg/kg/day to about 50 mg/kg/day of purified protein. [0069] As used herein, the term “subject,” “individual,” “host,” and “patient,” generally are used interchangeably to refer to any animal suitable for treatment by the inventive compounds, compositions, or methods. Subjects preferably are humans, primates, simians, rodents and the like, but also include any mammal such as farm animals, companion animals, service animals, laboratory animals, and the like. [0070] A “subject in need” refers to a subject that is suspected of having, has been diagnosed as having, or is at risk of developing a disease that can be treated or prevented by administration of compounds and/or compositions described as embodiments of the invention here. In particular, such a disease or condition is a hyperproliferative disease or disorder. Other conditions amenable to treatment by the invention or which define an appropriate subject or patient will be discerned easily by the person of skill in the art based on the disclosures herein. [0071] As used herein, the term “hyperproliferative disease or disorder” refers to a benign or malignant condition, involving hyperproliferation of a cell population or tissue, including cancers, as discussed below. [0072] As used herein, the term “pharmaceutical composition” refers to a composition that comprises an active agent, preferably rEMSL1 or a pro-drug thereof, in combination with a pharmaceutically acceptable carrier or excipient. 3. Embodiments of the invention [0073] A. Introduction [0074] A recombinant protein has been produced in bacteria that partially or fully replicates activity we identified from an extract produced from the natural Taro plant. Active components of this taro extract (TE) were identified as two 12-kDa degradation products of the taro storage protein that we engineered for overexpression (termed EMSL1). A new
Attorney Docket No.: 15024-372PC0 Patent recombinant protein, termed rEMSL1, was produced to replicate inhibitory components of TE on metastasis, proliferation, migration and CSCs. This protein can be useful for treatment of hyperproliferative disorders. [0075] Taro-derived proteins, such as those in TE, can effectively target metastatic tumor cells and can inhibit CSC by direct binding to glycan ligands known to be aberrantly expressed in multiple cancers. Without wishing to be bound by theory, the TE and rEMSL1 compounds produce a blockade of glycan-dependent receptor-mediated processes, which are required for metastasis. The engineered rEMSL1 compounds and compositions of certain embodiments of the invention are designed to have higher efficacy and bioavailability. [0076] B. Methods of Isolation and Production 1. Plant Source Material [0077] Plant materials which can provide a source of the antimetastatic or anticyclooxygenase activity useful in embodiments of the invention preferably are members of the genus Colocasia, commonly referred to as taro, eddoe and dasheen. Suitable species, such as, for example, Colocasia affinis, C. bicolor, C. esculenta, C. fallax, C. fontanesii, C. formosan, C.a gaoligongensis, C. gigantean, C. gongii, C. gracilis, C. heterochroma, C. humilis, C. konishii, C. latifolia, C. lihengiae, C. macrorrhiza, C. mannii, C. marchalii, C. menglaensis, C. neocaledonica, C. obtusiloba, C. oresbia, C. rapiformis, C. tibetensis and C. yunnanensis. [0078] Additionally, members of the genus Xanthosoma, also can be used as a source for the compositions. For example, plants commonly referred to as Yautia, Malanga Blanca, Tannia, Cocoyam, Eddo, Coco, Sato-imo, Japanese Potato, Macabo, Taioba, Dasheen, Quequisque, Ape and Tannier can be used. Thus, plants belonging to species including, for example, Xanthosoma sagittifolium, X. atrovirens, X. violaceum, X. maffaffa, X. weeksii, X. roseum, X. daguense, X. poeppigii, X.a hastifolia, X. robusturn, X. caracu, X. wendlandii, X. pichinchense, X. hannoniae, X. nigrum, X. lindenii, X.a narinoense, X. eggersii, and X. yucatanensis are suitable for use. 2. Taro Extract (TE) [0079] TE is an aqueous extract of a plant, including Colocasia and Xanthosoma spp., preferably the “taro” plant Colocasia esculenta. In some embodiments, the extract or isolated polypeptides contained in the extract are made by a process comprising obtaining the
Attorney Docket No.: 15024-372PC0 Patent uncooked corm from the root (such as Taro, Malanga or Yautia), peeling the corm, combining it with an aqueous solution (such as PBS); blending the corm to liquefy it, centrifuging this liquid (e.g., at 1200 rpm for 15 minutes at 4℃) the liquid to obtain a supernatant, centrifuging the supernatant at high speed (e.g., at 15,000 rpm for 20 minutes at 4℃), and filter sterilizing the resulting supernatant to obtain a stock water-soluble extract. In some embodiments, the stock water-soluble extract is adjusted to have a protein concentration of about 1-5 mg/mL. [0080] Optionally, the stock water-soluble extract can be further purified by various techniques that are known in the art, including centrifugation, size exclusion chromatography, ion exchange chromatography, reversed phase liquid chromatography, reversed phase high performance liquid chromatography, and/or a combination of these approaches, to yield a more purified or substantially pure active agent. For example, in some embodiments, the stock extract can be centrifuged through molecular weight limit devices (such as, for example, AmiconTM Ultra 10 K (10,000) Nominal Molecular Weight Limit (NMWL) devices (MilliporeTM Corporation) at 4000 g for 45 minutes at 25℃). The upper fraction, which contains the antimetastatic activity (high molecular weight fraction) can be filter sterilized (e.g., using a 0.2 micron filter). [0081] Optionally, the stock extract can be further purified using size exclusion chromatography (SEC). For example, preparative SEC can be performed on a BiosuiteTM 250, 13 micron, 21.5 x 300 mm column (WatersTM Corp.) using Dulbecco's phosphate buffered saline with calcium and magnesium, at a flow rate of 2 ml/min. Fractions can be collected every 30 seconds and tubes can be pooled based on UV absorbance at 220 nm. In this system, the antimetastatic activity resides in an approximately 30 kD fraction (calibrated using BSA and carbonic anhydrase globular protein). [0082] In some embodiments, the 30 kD fraction from size exclusion chromatography can be further purified by ion exchange chromatography. Preparative anion exchange chromatography can be carried out using standard techniques (e.g., on an HQ/20, 10 x 100 mm column (Applied BiosystemsTM), using a 30-minute gradient of 0-30% B at a flow rate of 5 ml/min.: Buffer A = 50 mM Tris, pH 8.0; Buffer B = 50 mM Tris pH 8 + 1.0 M NaCl. Fractions can be taken every 30 seconds and tubes pooled based on UV absorbance at 220 nm). Pooled samples can be concentrated (e.g., using CentriconTM Plus 7010 K Nominal Molecular Weight Limit (NMWL) devices (MilliporeTM) and buffer exchange can be done
Attorney Docket No.: 15024-372PC0 Patent using ZebaTM Desalt Spin Columns, PireceTM Protein Research Product (Thermo ScientificTM)). [0083] In some embodiments, the active fraction obtained from ion exchange chromatography can be further purified using reversed phase chromatography (RPLC). Analytical RPLC can be done using standard techniques and equipment (e.g., using a JupiterTM C5300 Å column (PhenomenexTM), employing a 40-minute gradient of 1-100% B at 1 ml/min. Buffer A = 0.1% trifluoroacetic acid (TFA) in water; Buffer B= 0.1% TFA in water:acetonitrile (20:80), with UV detection at 215 nm using a Beckman CoulterTM HPLC systems with System Gold V8 or 32 Karat software packages). [0084] In some embodiments, additional purification of isolated proteins can be accomplished using reversed phase high performance liquid chromatography using standard techniques and equipment (e.g., on a WatersTM 2695 HPLC system; absorbance can be monitored with an Applied BiosystemsTM 785 UV detector at 214 nm; proteins can be separated, e.g., on a WatersTM Symmetry 3003 micron C41 mm x 150 mm column with a gradient of 0.1% trifluoroacetic acid (TFA) in water (solvent A) and 0.09% TFA in acetonitrile (solvent B)). 3. Production of Engineered Mannose-Specific Lectin 1 (EMSL1) [0085] A soluble extract of proteins isolated from the taro plant, e.g., Colocasia esculenta, here exhibits potent anti-metastatic activity in models of triple negative breast cancer, the most aggressive subtype of this malignancy. One of the proteins containing this activity was mannose-specific lectin 1 (MSL1), also known as taro storage protein TSP (Q39487, GenBank accession: D16173.1) from C. esculenta (>60 amino acid coverage). The sequence of EMSL1 (also known as 12kD Storage) is given below. Peptides in bold are unique to each sequence. RHIPHGQASPLPPPGHPRPPRSWLGTNYLLSGQTLETEGHLKNGDF DLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGELVINNG DGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGL NSLRFRNIPFTNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVL YGGKYGWQSNTHGNGEHCFLRLNHKGELIIEDDDFKTIWSSSYS SKQGDYVLILRDDGVAVIYGPAIWETSPQAK (EMSL1; SEQ ID NO:9)
Attorney Docket No.: 15024-372PC0 Patent [0086] TE contains highly represented (>90% amino acid coverage) mannose specific lectin 2 (MSL2), also known as lectin (A5HMM7, GenBank Accession: EF541132.1). See this sequence below. MAKLLLFLLPAILGLLIPRSAVALGTNYLLSGQTLNTDGHLKNGD FDLVMQNDCNLVLYNGNWQSNTANNGRDCKLTLTDYGELVIK NGDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFGPSVFKIDPWV PGLNSLRFRNIPFTDNLLFSGQVLYGDGRLTAKNHQLVMQGDCN LVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDDDFRPSGA AVPAPSR (MSL2; SEQ ID NO:10) [0087] We also identified peptides corresponding to tarin lectin (PDB ID 5T20), a lectin composed of EMSL2 and EMSL1, EMSL2(24-134)- EMSL1(144-253)- E212K/S223N/Y224S/V240F/P25A), with the characteristic unique peptide TIWSSNSSSK (SEQ ID NO:3), also found in TE. See also TIWSSYSSK (SEQ ID NO:5). For consistency, we will refer to this lectin as mannose-specific lectin 3 (MSL3). See below for the MSL3 sequence. Peptides in bold are unique to each sequence. MAKLLLFLLPAILGLLIPRSAVALGTNYLLSGQTLNTDGHLKNGD FDLVMQNDCNLVLYNGNWQSNTANNGRDCKLTLTDYGELVIK NGDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFGPSVFKIDPWV PGLRFRNIPFTDNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLV LYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDDDFKTIWSSN SSSKQGDYVLILRDDGFAVIYGPAIWETSA (MSL3; SEQ ID NO:11) [0088] Surprisingly, two variants of tuber agglutinin CEA from C. esculenta were found with >80% of amino acid coverage. We named them as CEA1 (R9RL27, NCBI accession: JX435122.1) and CEA2, also known as hypothetical taro protein (NCBI accession: MQM11449.1) from C. esculenta (see Table 1, below). CEA2 is a variant of CEA1 (24-252)- S164N/D209E/S217R. However, despite the close sequence similarity, these two lectins are formed by unique peptides that can be unequivocally assigned to each one of them, i.e.
Attorney Docket No.: 15024-372PC0 Patent TIWSSSSSSK (SEQ ID NO:3; from CEA1) and GELIIKEDDFK (SEQ ID NO:6; from CEA2) peptides. Peptides in bold are unique to each of the sequences, given below. CEA1: MAKLLLFLLPAILGLLVPRSAVALGTNYLLSGQTLDREGHLKNG DFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDYGELVI KNGDGSTVWRSRAQSVKGNYAAVVHPDGRLVVFGPSVFKIDP WVPGLNSLRFRNIPFTNNLLFSGQVLYGDGRLTAKSHQLVMQG DCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDDDFKT IWSSSSSSKHGDYVLILRDDGFAVIYGPAIWETSPQAK (SEQ ID NO:69) CEA2: MAKLLLFLLPAILGLLVPRSAVALGTNYLLSGQTLDREGHLKNG DFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDYGELVI KNGDGSTVWRSRAQSVKGNYAAVVHPDGRLVVFGPSVFKIDP WVPGLNSLRFRNIPFTNNLLFSGQVLYGDGRLTAKNHQLVMQG DCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKEDDFK TIWRSSSSSKHGDYVLILRDDGFAVIYGPAIWETSPQAK (SEQ ID NO:70) [0089] TAR1 (Q39418, GenBank accession: D16173.1; also known as EMSL8 or Tarin) from C. esculenta also was identified with 45% amino acid sequence coverage. Peptides in bold are unique to each sequence: MAKLLLFLLPAILGLLIPRSAVALGTNYLLSGQTLNTDGHLKNGD FDLVMQNDCNLVLYNGNWQSNTANNGRDCKLTLTDYGDLVIK NRDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFGPSVFKNDP WVPGLNSLAFRNIPSPTTCSSPQVLYGDGRLTAKNHQLGHAGRL QPGPIRLVKYGWQSNTHGNGEHCFLRLNHKGELIIRTTTSRPSGA AVPAPSRVTTFSTSRHVRRALRPAIWRPARSAPLLT (TAR1; SEQ ID NO:16)
Attorney Docket No.: 15024-372PC0 Patent [0090] Interestingly, a search of the isolated peptides outside of proteins from C. esculenta was also performed against TE homologue lectins with similar biophysical properties, i.e., curculin, miraculin, sporamin, and Kunitz trypsin inhibitors. Two 25 kDa storage proteins were recognized, called inhibitors of trypsin/chymotrypsin ITC1 (GenBank accession: D16174.1; also known as trypsin/chymotrypsin inhibitor or ECT1) and ITC2 (GenBank accession: D16175.1; also known as ECT2), with 80% and 70% amino acid coverage, respectively, and assigned the isolated peptides with high confidence (see Table 1 and Table 2). All together, we report here the most comprehensive characterization of isolectins in TE from C. esculenta. Peptides in bold are unique to each of the sequences below. ETCI1: MEFVLLLVSSLLLTARAAVASNPVLDVDGNELRRGNRYYAISL RSPNSGLTLAVRSNAPCPLNVDQAPSKDYGRPLAFFPENVDDD TVQEGSTLYIMFPEPSECRESTVWTLGRETDVVTTGGTSSSAIG PRNSRFTIRRTGDASSKGEYQIEVCPCSIGVSRAPCRLACVGSLG LTEDEANLLLNINNERPHTVRFVKVKEELAASRR (SEQ ID NO:71) ETCI2: MEFILLLVSSLLLTARAAAASNPILDVDGDELRRGHRYYAISER RPVSGLTLAARSNAPCPLNVAQTSSNDYGRPLAFFPENAEDD TVQEGNTLNIMFPEPTECRASTVWTLDRERGVVTTGGTSSSA IGPHNSRFSIRRAGDASSERERKYQIEVCPCSNGVPRPSCRMAC VGSLGLTEDEGNLLLNINNERPHAIRFVKVKEELPASRR (SEQ ID NO:72) [0091] This invention, in certain embodiments, provides a recombinant protein that replicates the therapeutic properties of EMSL1 with the added advantage of higher specific activity. It is produced and purified by a process that can be scaled up for commercial manufacture. Quality control, necessary for commercial development with an engineered
Attorney Docket No.: 15024-372PC0 Patent protein, can be facilitated and will allow safety and efficacy evaluation in human clinical trials. See examples below. 4. Recombinant EMSL1 (rEMSL1) [0092] rEMSL1 is produced by recombinant means, from a bacterium, such as, e.g. E. coli or any suitable microorganism. See below for the sequences used for production (Table 3). The sequence of the recombinant protein (Uniprot: Q39487; GenBank: D16173.1; NCBI: BAA03722.1) is provided here: RHIPHGQASPLPPPGHPRPPRSWLGTNYLLSGQTLETEGHLKNGD FDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGELVIN NGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVP GLNSLRFRNIPFTNNLLFSGQVLYGDGRLTAKNHQLVMQGDCN LVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIEDDDFKTIWSS SYSSKQGDYVLILRDDGVAVIYGPAIWETSPQAK (rEMSL1; SEQ ID NO:9) [0093] In some embodiments, the invention relates to a method for producing rEMSL1 in HEK293 cells as herein described. See Examples, below. [0094] rEMSL1, like TE, possesses high binding affinity to specific glycan motifs including Lewis X type carbohydrates, type 2 N-AcetylLactosamine (LacNAc) and core fucosylated N- glycans including the glycan motifs detected in HER-2+ or TNBC and paired metastatic specimens from the same individuals. Branched and fucosylated N-glycans (Man2- 9/HesNAc2/Fuc0-1) have been observed in primary and paired metastatic tissues, which proposed to serve as prognostic markers for patients. Like TE, rEMSL1 potently inhibits metastasis in two syngeneic models of TNBC. See Examples below. In addition, rEMSL1, like TE, shares potent anti-metastatic activity with TE in that rEMSL1 inhibits proliferation of murine and human breast cancer cells as well as tumor cell migration. Breast cancer stem cells are sensitive to rEMSL1-mediated inhibition. See Examples below. 5. Methods [0095] We examined TE protein composition and lectin specificity using LC-MS/MS methods. The LC-MS/MS spectra of tryptic digest of proteins from TE sample were searched against the fasta sequences from uniprot database for Colocasia esculenta using
Attorney Docket No.: 15024-372PC0 Patent ByonicTM software and manually with trypsin and/or chymotrypsin as digestion enzyme with specific cleavage option enabled. Carbamidomethylation as fixed modification, oxidation of methionine as variable modification, was used as search parameters. The LC-MS/MS spectra were also analyzed manually for the glycopeptides with the support of Xcalibur software. The HCD and CID MS2 spectra of glycopeptides were evaluated for the glycan neutral loss pattern, oxonium ions and the glycopeptide fragmentations to assign the sequence and the presence of glycans in the glycopeptides. [0096] Two 12-kDa degradation products of the taro storage protein (TSP), recently termed as mannose specific lectin 1 (MSL1), members of the Galanthus nivalis agglutinin (GNA) superfamily of lectins were identified via LC-MS/MS methods. Hence, we engineered EMSL1, EMSL2, EMSL3, EMSL4, EMSL5, EMSL6, EMSL7, EMSL8, EMSL9, ETCI1, ETCI2, and ETCI3 families of proteins. [0097] GNA Lectins bind glycans expressed on cell membranes. Aberrant glycosylation is associated with higher metastatic potential in breast and other malignancies. Importantly, we show evidence of TE and rEMSL1 binding to glycan profiles elevated in advanced TNBC and HER-2+ breast cancer and metastatic lesions resulting in a strong antimetastatic activity. There remains in the art a great need for additional and improved compounds, compositions, and methods for treatment of hyperproliferative disorders, including cancers. [0098] The recombinant Engineered Mannose Specific Lectins (EMSL) genes were codon optimized for the expression in E. coli and subcloned into pSUMO expression vectors. Protein recombinant Sumo-MSL overexpression was performed after induction with 1.0 mM IPTG (A600 = 0.6 - 0.8) at 20°C over 16 hours and at 37 °C for 3.5 hours. Bacterial lysates were prepared in buffer containing 50 mM Tris-HCl (pH 8), 500 mM NaCl, 8 M Urea, 5 mM beta-mercaptoethanol (BME), 0.5 mM AEBSF, DNase solution, 10 mM MgCl2, 10 mM EDTA and sonicated. Cell debris were removed by centrifugation at 15,000 x g for 45 minutes at 4 °C. [0099] The sample was filtered and loaded onto a previously equilibrated HiPrep 16/60 IMAC column with buffer A (15 mM Tris-HCl (pH8), 500 mM NaCl, 8 M Urea, 5 mM BME) and B (buffer A plus 1 M Imidazol). Sumo-MSL1 was eluted at 200 ± 20 mM Imidazole and analyzed by SDS-PAGE. Sumo-fused rEMSL1 eluted fractions (molecular weight ~45kDa) were pooled and refolded on column decreasing urea concentration step- wise using buffer 15 mM Tris-HCl (pH 8), 500 mM NaCl, 5 mM BME, 1% Glycerol.
Attorney Docket No.: 15024-372PC0 Patent [0100] Cleavage of the Sumo fusion protein was performed at 4 °C by addition of 150 μL of 1mM Ulp1 protease to refolded Sumo-MSL1 protein. The totality of the cleavage reaction was checked by SDS-PAGE. A second HiPrep 16/60 IMAC column was performed to remove the His-tagged Sumo protein and the His-tagged Ulp1 protease. MSL was collected in the flowthrough (>95% purity) as expected and verified by SDS-PAGE. [0101] As a final purification step, rMSL was concentrated and injected onto a SuperdexTM S200-PG size exclusion column previously equilibrated with buffer 10 mM Tris-HCl, pH 7.0, 150 mM NaCl, 1 mM TCEP. Fractions containing MSL (>99% pure) were eluted from the S200 column (fractions 13-15) and identified using SDS-PAGE. A size exclusion column S200 was calibrated with a gel filtration standard kit (BioradTM), containing thyroglobulin, bovine γ-globulin, chicken ovalbumin, equine myoglobin, and vitamin B12, with M.W. 670,000; 158,000; 44,000; 17,000, and 1,350 g/mol, respectively. 6. Therapeutic Agents [0102] The invention, in certain embodiments, provides the following compounds, which can be used for treatment of hyperproliferative diseases and conditions, including especially cancer. [0103] Embodiments of the invention include fusion constructs, including cloning the active components of TE into pcDNA 3.1(-) Mammalian Expression Vector) as linear fusion proteins: a. (Secretion signal peptide)-MSL1-(GGSGGLRFRGGSGG)-MSL2- (GGSGGLRFRGGSGG)-MSL3 (SEQ ID NO:74) b. (Secretion signal peptide)-MSL1-(GGSGGLRFRGGSGG)-MSL4- (GGSGGLRFRGGSGG)-MSL5D1 (SEQ ID NO:75) c. (Secretion signal peptide)-MSL1-(GGSGGLRFRGGSGG)-MSL4- (GGSGGLRFRGGSGG)-MSL5D10 (SEQ ID NO:76) d. (Secretion signal peptide)-MSL1-(GGSGGLRFRGGSGG)-MSL6- (GGSGGLRFRGGSGG)-MSL7 (SEQ ID NO77:) e. (Secretion signal peptide)-MSL1-(GGSGGLRFRGGSGG)-MSL8- (GGSGGLRFRGGSGG)-MSL9 (SEQ ID NO:78) [0104] Embodiments of the invention include fusion constructs, including cloning the active components of TE into pcDNA 3.1(-) Mammalian Expression Vector) as linear fusion proteins in combination with ETCI proteins:
Attorney Docket No.: 15024-372PC0 Patent a. (Secretion signal peptide)-ETCI1-(GGSGGLRFRGGSGG)- ETCI2- (GGSGGLRFRGGSGG)- ETCI3 (SEQ ID NO80:) b. (Secretion signal peptide)-MSL1-(GGSGGLRFRGGSGG)-ETCI1 (SEQ ID NO:81) c. (Secretion signal peptide)-MSL2-(GGSGGLRFRGGSGG)-ETCI1 (SEQ ID NO82:) d. (Secretion signal peptide)-MSL3-(GGSGGLRFRGGSGG)-ETCI1 (SEQ ID NO:83) e. (Secretion signal peptide)-MSL4-(GGSGGLRFRGGSGG)-ETCI1 (SEQ ID NO:84) f. (Secretion signal peptide)-MSL5-(GGSGGLRFRGGSGG)-ETCI1 (SEQ ID NO:85) g. (Secretion signal peptide)-MSL6-(GGSGGLRFRGGSGG)-ETCI1 (SEQ ID NO:86) h. (Secretion signal peptide)-MSL7-(GGSGGLRFRGGSGG)-ETCI1 (SEQ ID NO:87) i. (Secretion signal peptide)-MSL8-(GGSGGLRFRGGSGG)-ETCI1 (SEQ ID NO:88) j. (Secretion signal peptide)-MSL9-(GGSGGLRFRGGSGG)-ETCI1 (SEQ ID NO:89) k. (Secretion signal peptide)-MSL1-(GGSGGLRFRGGSGG)-ETCI2 (SEQ ID NO:90) l. (Secretion signal peptide)-MSL2-(GGSGGLRFRGGSGG)-ETCI2 (SEQ ID NO:91) m. (Secretion signal peptide)-MSL3-(GGSGGLRFRGGSGG)-ETCI2 (SEQ ID NO:92) n. (Secretion signal peptide)-MSL4-(GGSGGLRFRGGSGG)-ETCI2 (SEQ ID NO:93) o. (Secretion signal peptide)-MSL5-(GGSGGLRFRGGSGG)-ETCI2 (SEQ ID NO:94) p. (Secretion signal peptide)-MSL6-(GGSGGLRFRGGSGG)-ETCI2 (SEQ ID NO:95)
Attorney Docket No.: 15024-372PC0 Patent q. (Secretion signal peptide)-MSL7-(GGSGGLRFRGGSGG)-ETCI2 (SEQ ID NO:96) r. (Secretion signal peptide)-MSL8-(GGSGGLRFRGGSGG)-ETCI2 (SEQ ID NO:97) s. (Secretion signal peptide)-MSL9-(GGSGGLRFRGGSGG)-ETCI2 (SEQ ID NO:98) [0105] Embodiments of the invention include fusion constructs, including cloning the active components of TE into pcDNA 3.1(-) Mammalian Expression Vector) as a trimerization fusion protein: a. (Signal peptide for secretion)-MSL1- (GGGGSGGLRFRGGSGGGGS)-MSL2-( GGGGSGGLRFRGGSGGGGS)- MSL3- Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:99) b. (Signal peptide for secretion)-MSL1- (GGGGSGGLRFRGGSGGGGS)-MSL4-( GGGGSGGLRFRGGSGGGGS)- MSL5D1 -( GGGGSGGLRFRGGSGGGGS) Signal peptide for secretion- Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin- Strep-tag (SEQ ID NO:100) c. (Signal peptide for secretion)-MSL1- (GGGGSGGLRFRGGSGGGGS)-MSL4-( GGGGSGGLRFRGGSGGGGS)- MSL5D10 -( GGGGSGGLRFRGGSGGGGS) Signal peptide for secretion- Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin- Strep-tag (SEQ ID NO:101) d. (Signal peptide for secretion)-MSL1- (GGGGSGGLRFRGGSGGGGS)-MSL6-( GGGGSGGLRFRGGSGGGGS)- MSL7- Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:102) e. (Signal peptide for secretion)-MSL1- (GGGGSGGLRFRGGSGGGGS)-MSL8-( GGGGSGGLRFRGGSGGGGS)- MSL9- Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:103) f. (Signal peptide for secretion)-ECTI1-
Attorney Docket No.: 15024-372PC0 Patent (GGGGSGGLRFRGGSGGGGS)-ECTI2-( GGGGSGGLRFRGGSGGGGS)- ECTI3- Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:104) g. (Signal peptide for secretion)-EMSL1- (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:105) h. (Signal peptide for secretion)-EMSL2- (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:106) i. (Signal peptide for secretion)-EMSL3- (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:107) j. (Signal peptide for secretion)-EMSL4- (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:108) k. (Signal peptide for secretion)-EMSL5D1- (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:109) l. (Signal peptide for secretion)-EMSL5D10- (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:110) m. (Signal peptide for secretion)-EMSL6- (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:111) n. (Signal peptide for secretion)-EMSL7-
Attorney Docket No.: 15024-372PC0 Patent (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:112) o. (Signal peptide for secretion)-EMSL8- (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:113) p. (Signal peptide for secretion)-EMSL9- (GGGGSGGLRFRGGSGGGGS)-ECTI1 - Signal peptide for secretion-Foldon trimerization motif-HRV-3C Protease-His-tag for purification-Twin-Strep-tag (SEQ ID NO:114) [0106] Engineering of other possible combinations can be guided by initial vectors above. The invention also includes certain embodiments wherein the therapeutic agent is administered in the form of a prodrug. 7. Pharmaceutical Compositions [0107] Any of the therapeutic agents discussed herein can be used to produce a pharmaceutical composition according to embodiments of the invention. The pharmaceutical compositions can include one or more of the peptide or recombinant peptide compounds disclosed herein. In addition, the pharmaceutical compositions can include one or more inventive compound and also and further comprise one or more additional therapeutic agent known in the art, which can be determined by the skilled practitioner according to standards of care. [0108] The compounds can be administered as a base compound, and any pharmaceutically acceptable hydrate, solvate, acid or salt, and can be amorphous or in any crystalline form, or as an oil or wax. Any pharmaceutically acceptable salt can be used, as may be convenient. [0109] In certain preferred embodiments, the compounds described herein are formulated and are administered as a pharmaceutical composition that includes a pharmaceutically acceptable carrier and one or more pharmaceutical/therapeutic agent, including one or more of the compounds described herein, and including one or more of the inventive compounds described herein with an additional agent, such as drug of another class. [0110] A pharmaceutically acceptable carrier refers to any convenient compound or group
Attorney Docket No.: 15024-372PC0 Patent of compounds that is not toxic and that does not destroy or significantly diminish the pharmacological activity of the therapeutic agent with which it is formulated. Such pharmaceutically acceptable carriers or vehicles encompass any of the standard pharmaceutically accepted solid, liquid, or gaseous carriers or excipients known in the art. A suitable carrier depends on the route of administration contemplated for the pharmaceutical composition. [0111] Routes of administration are determined by the person of skill according to convenience, the health and condition of the subject to be treated, and the location and stage of the condition to be treated. Such routes can be any route which the practitioner deems to be most effective or convenient using considerations such as the patient, the patient’s general condition, and the specific condition to be treated, including local or systemic administration. For example, routes of administration can include, but are not limited to local or parenteral routes, including: oral, intravenous, intratumoral, intraarterial, intrathecal, intramuscular, subcutaneous, intradermal, intraperitoneal, rectal, vaginal, topical, nasal, local injection, buccal, transdermal, sublingual, inhalation, transmucosal, wound covering, direct injection into an area to be treated, and the like. The administration can be given by transfusion or infusion, and can be administered by an implant, an implanted pump, or an external pump, or any device known in the art. [0112] Therefore, the forms which the pharmaceutical composition can take will include, but are not limited to: tablets, capsules, caplets, lozenges, dragees, pills, granules, powders, oral solutions, powders or granules for dilution in a suitable solvent, powders for inhalation, vapors, gases, sterile solutions or other liquids for injection or infusion, transdermal patches, buccal patches, inserts and implants, rectal suppositories, vaginal suppositories, creams, lotions, oils, ointments, topical coverings (e.g., wound coverings and bandages), suspensions, emulsions, lipid vesicles, and the like. [0113] Treatment regimens of the chemical compounds contemplated for use with the invention include a single administration or a course of administrations lasting two or more days, including a week, two weeks, several weeks, a month, two months, several months, a year, or more, including indefinitely or administration for the remainder of the subject’s life. The regimen can include multiple doses per day, one dose per day or per week, for example, or one or more long infusion administration lasting for an hour, multiple hours, a full day, or longer.
Attorney Docket No.: 15024-372PC0 Patent 8. Methods of Use [0114] Suitable subjects for the invention include mammalian laboratory animals, mammalian farm animals, mammalian sport animals, mammalian zoo animals, and mammalian companion animals. Preferably, the subject is a human, but subjects can include mammals such as simians, felines, canines, equines, rats, mice, rabbits, bovines, porcines, ovines, caprines and the like. [0115] Modes of administering include, but are not limited to, any of those discussed above with respect to routes of administration. These include, for example, oral administration or intravenous, subcutaneous, intramuscular, intratumoral, peri-tumoral, or intraperitoneal injections, rectal administration by way of suppositories or enema, or local administration directly into or onto a target tissue (such as the pancreas), or administration by any route or method that delivers a therapeutically effective amount of the drug or composition to the cells or tissue to which it is targeted. See above for additional discussion of routes of administration. Administration also can refer to introducing a nucleic acid construct to the subject as DNA or mRNA, introducing a vector containing the nucleic acid to the subject, or introducing cells that have been transduced ex vivo with a construct, such as by electroporation or using a vector as described herein, to the subject. [0116] Dosage amounts per administration of these compounds include any amount determined by the practitioner and will depend on the size of the subject to be treated, the state of the health of the subject, the route of administration, the condition to be treated, the severity of the condition, and the like. In general, it is contemplated that for the majority of subjects, a dose in the range of about 0.01 mg/kg to about 100 mg/kg is suitable, preferably about 0.1 mg/kg to about 50 mg/kg, more preferably about 0.1 mg/kg to about 10 mg/kg, and most preferably about 0.2 mg/kg to about 5 mg/kg are useful. This dose can be administered weekly, daily, or multiple times per day. A dose of about 0.1 mg, 0.2 mg, 0.25 mg, 0.5 mg, 1 mg, 5 mg, 10 mg, 20 mg, 40 mg, 80 mg, 100 mg, 250 mg, 500 mg, or 1000 mg can be administered per dose or per day. [0117] The compositions of the invention can be administered in combination with (concurrently or sequentially with) existing cancer therapies. Examples of such existing cancer therapies include surgery, radiation, immune-based and chemotherapeutic agents such as alkylating agents, nitrosoureas, anti-metabolites, plant alkaloids, anti-tumor antibiotics, hormonal agents and biological response modifiers.
Attorney Docket No.: 15024-372PC0 Patent [0118] Suitable conditions or diseases for treatment using the invention include hyperproliferative diseases or conditions, including ductal carcinoma in situ, but preferably one or more cancer. Suitable cancers which can be treated using the compositions and methods of the present invention include cancer of the oral cavity and pharynx (lip, tongue, salivary gland, floor of mouth, gum and other mouth, nasopharynx, tonsil, oropharynx, hypopharynx, other oral/pharynx; i.e. head and neck cancer); cancers of the digestive system (esophagus; stomach; small intestine; colon and rectum; anus, anal canal, and anorectum; liver; intrahepatic bile duct; gallbladder; other biliary; pancreas; retroperitoneum; peritoneum, omentum, and mesentery; other digestive); cancers of the respiratory system (nasal cavity, middle ear, and sinuses; larynx; lung and bronchus; pleura; trachea, mediastinum, and other respiratory); cancers of the mesothelioma; bones and joints; and soft tissue, including heart; skin cancers, including melanomas and other non-epithelial skin cancers; Kaposi's sarcoma and breast cancer; cancer of the female genital system (cervix uteri; corpus uteri; uterus, nos; ovary; vagina; vulva; and other female genital); cancers of the male genital system (prostate gland; testis; penis; and other male genital); cancers of the urinary system (urinary bladder; kidney and renal pelvis; ureter; and other urinary); cancers of the eye and orbit; cancers of the brain and nervous system (brain; retina; and other nervous system); cancers of the endocrine system (thyroid gland and other endocrine, including thymus); cancers of the lymphomas (hodgkin's disease and non-hodgkin's lymphoma), multiple myeloma, leukemias (lymphocytic leukemia; myeloid leukemia; monocytic leukemia; and other leukemias), and the like. [0119] Other cancers that can be treated according to embodiments of the invention include, but are not limited to, Neoplasm, malignant; Carcinoma, NOS; Carcinoma, undifferentiated, NOS; Giant and spindle cell carcinoma; Small cell carcinoma, NOS; Papillary carcinoma, NOS; Squamous cell carcinoma, NOS; Lymphoepithelial carcinoma; Basal cell carcinoma, NOS; Pilomatrix carcinoma; Transitional cell carcinoma, NOS; Papillary transitional cell carcinoma; Adenocarcinoma, NOS; Gastrinoma, malignant; Cholangiocarcinoma; Hepatocellular carcinoma, NOS; Combined hepatocellular carcinoma and cholangiocarcinoma; Trabecular adenocarcinoma; Adenoid cystic carcinoma; Adenocarcinoma in adenomatous polyp; Adenocarcinoma, familial polyposis coli; Solid carcinoma, NOS; Carcinoid tumor, malignant; Branchiolo-alveolar adenocarcinoma; Papillary adenocarcinoma, NOS; Chromophobe carcinoma; Acidophil carcinoma; Oxyphilic
Attorney Docket No.: 15024-372PC0 Patent adenocarcinoma; Basophil carcinoma; Clear cell adenocarcinoma, NOS; Granular cell carcinoma; Follicular adenocarcinoma, NOS; Papillary and follicular adenocarcinoma; Nonencapsulating sclerosing carcinoma; Adrenal cortical carcinoma; Endometroid carcinoma; Skin appendage carcinoma; Apocrine adenocarcinoma; Sebaceous adenocarcinoma; Ceruminous adenocarcinoma; Mucoepidermoid carcinoma; Cystadenocarcinoma, NOS; Papillary cystadenocarcinoma, NOS; Papillary serous cystadenocarcinoma; Mucinous cystadenocarcinoma, NOS; Mucinous adenocarcinoma; Signet ring cell carcinoma; Infiltrating duct carcinoma; Medullary carcinoma, NOS; Lobular carcinoma; Inflammatory carcinoma; Paget's disease, mammary; Acinar cell carcinoma; Adenosquamous carcinoma; Adenocarcinoma w/squamous metaplasia; Thymoma, malignant; Ovarian stromal tumor, malignant; Thecoma, malignant; Granulosa cell tumor, malignant; Androblastoma, malignant; Sertoli cell carcinoma; Leydig cell tumor, malignant; Lipid cell tumor, malignant; Paraganglioma, malignant; Extra-mammary paraganglioma, malignant; Pheochromocytoma; Glomangiosarcoma; Malignant melanoma, NOS; Amelanotic melanoma; Superficial spreading melanoma; Malignant melanoma in giant pigmented nevus; Epithelioid cell melanoma; Blue nevus, malignant; Sarcoma, NOS; Fibrosarcoma, NOS; Fibrous histiocytoma, malignant; Myxosarcoma; Liposarcoma, NOS; Leiomyosarcoma, NOS; Rhabdomyosarcoma, NOS; Embryonal rhabdomyosarcoma; Alveolar rhabdomyosarcoma; Stromal sarcoma, NOS; Mixed tumor, malignant, NOS; Mullerian mixed tumor; Nephroblastoma; Hepatoblastoma; Carcinosarcoma, NOS; Mesenchymoma, malignant; Brenner tumor, malignant; Phyllodes tumor, malignant; Synovial sarcoma, NOS; Mesothelioma, malignant; Dysgerminoma; Embryonal carcinoma, NOS; Teratoma, malignant, NOS; Struma ovari, malignant; Choriocarcinoma; Mesonephroma, malignant; Hemangiosarcoma; Hemangioendothelioma, malignant; Kaposi's sarcoma; Hemangiopericytoma, malignant; Lymphangiosarcoma; Osteosarcoma, NOS; Juxtacortical osteosarcoma; Chondrosarcoma, NOS; Chondroblastoma, malignant; Mesenchymal chondrosarcoma; Giant cell tumor of bone; Ewing's sarcoma; Odontogenic tumor, malignant; Ameloblastic odontosarcoma; Ameloblastoma, malignant; Ameloblastic fibrosarcoma; Pinealoma, malignant; Chordoma; Glioma, malignant; Ependymoma, NOS; Astrocytoma, NOS; Protoplasmic astrocytoma; Fibrillary astrocytoma; Astroblastoma; Glioblastoma, NOS; Oligodendroglioma, NOS; Oligodendroblastoma; Primitive neuroectodermal; Cerebellar sarcoma, NOS; Ganglioneuroblastoma; Neuroblastoma, NOS;
Attorney Docket No.: 15024-372PC0 Patent Retinoblastoma, NOS; Olfactory neurogenic tumor; Meningioma, malignant; Neurofibrosarcoma; Neurilemmoma, malignant; Granular cell tumor, malignant; Malignant lymphoma, NOS; Hodgkin's disease, NOS; Hodgkin's; paragranuloma, NOS; Malignant lymphoma, small lymphocytic; Malignant lymphoma, large cell, diffuse; Malignant lymphoma, follicular, NOS; Mycosis fungoides; Other specified non-Hodgkin's lymphomas; Malignant histiocytosis; Multiple myeloma; Mast cell sarcoma; Immunoproliferative small intestinal disease; Leukemia, NOS; Lymphoid leukemia, NOS; Plasma cell leukemia; Erythroleukemia; Lymphosarcoma cell leukemia; Myeloid leukemia, NOS; Basophilic leukemia; Eosinophilic leukemia; Monocytic leukemia, NOS; Mast cell leukemia; Megakaryoblastic leukemia; Myeloid sarcoma; Hairy cell leukemia, and the like. [0120] In particular, breast cancer, such as TNBC, HER-2+ and HR+ breast cancer, are preferred for use with embodiments of the invention. Metastatic malignancies are particularly contemplated for use according to embodiments of the invention, including metastasis to the brain or other organs such as lung, liver, bone, and the like. The peptides disclosed here are contemplated for use in treatment of subjects for the conditions described and listed above. Particular preferred peptides include, but are not limited to SEQ ID NOs:9, 10, 11, 12, 13, 16, 71, 72 and 74-113. 9. Selected Aspects of the invention [0121] Based on examining data from our isolation and characterization of TE we engineered and claim a sequence, termed rMSL1-269, that recapitulates a large component of the lectin binding specificity identified in TE. [0122] Based on data from our laboratory, we identified bacterial expression systems, which could overproduce the rMSL1-269 sequence within multiple expression systems, one of which was superior (list here) and enabled us to produce high-yields (mg/liter) of the active and highly stable rMSL1-269 protein, which was fully sufficient for biophysical characterization and future engineering using standard methods. [0123] Based on data from, we can now improve upon the biomanufacturing of rMSL1-269 at higher yields and with further improvements in biophysical features during manufacturing scale preparations. Such an approach will also be beneficial as this process will no longer require endotoxin removal steps. The latter of eliminating the need for endotoxin removal has already been completed by engineering the rMSL1-269 sequence into mammalian
Attorney Docket No.: 15024-372PC0 Patent expression systems, including those of HEK293 and CHO cell lines. Standard screening methods will be completed to determine the optimal construct and mammalian cell line, as well as via stable or transfection strategies, as is standard in the field for optimizing production, purification, and manufacturing of an isolated biologic containing a single composition of matter identity, such as rMSL1-269. [0124] Product 1 – Full focus on rTSP - ^ renamed as rMSL1-269 (recombinant Mannose- Specific Lectin 1) to produce rMSL1-268 that is fully defined and has predictable specific
activity versus TE. The overall not be as complete as what was observed for TE. The production and manufacturing of this product is straightforward with existing technologies that are standards of the trade. [0125] Product 2 –Artificial TE – Full focus on rTSP (as above) but add in the other rMSLs we have characterized, which are listed herein, at the same mixture ratio of components as identified in TE. A mixture containing: rMSL11-269 + rMSL2 sequences + rMSL3 sequences, and the like, or more can be produced that is fully defined, mimics the ratio of components that are observed in TE, and has predictable specific activity versus TE is achievable with standard methods in the field. The specific activity of this combination of rMSLs can improve upon that observed in product 1 above and can be equal to or improved when compared to that found here for TE. Further, engineering improvements of this product can improve the product such that it further exceeds the specific activity of TE in vivo using standard protein engineering technologies in the trade for each component of the mixture, in turn (i.e., see Product 3, Product 4 below). [0126] Product 3: improved stability of artificial TE. Each component of the mixture in product 2 can be optimized using standard protein engineering techniques with the goal of improving each component of the mixture such that each on its own is more stable and thus, the mixture is more stable. [0127] Specific testing of the products and product mixtures can be subjected to additional standard testing. Some of these additional testing steps on product 2 can involve systematic removal of each rMSL component of the mixture, to identify which, if any of the rMSL# sequences can be removed from the mixture, such that improved specific activity values of the resulting product are obtained. Once each component of Product 2 is engineered to have optimal stability, and those that can be removed are identified, then a detailed engineering of
Attorney Docket No.: 15024-372PC0 Patent scale-up and biomanufacturing can be achieved for product 4 using standard methods in the field. [0128] Product 5 - Next, standard methods can be used to determine an optimal ratio for the remaining components of the mixture. This can be achieved via systematic screening of mixture ratios with standard methods established here, on a small scale. The optimal specific activity of the mixture can be identified by varying these ratios. 5. Examples [0129] This invention is not limited to the particular processes, compositions, or methodologies described, as these may vary. The terminology used in the description is for the purpose of describing the particular versions or embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the present invention, the preferred methods, devices, and materials are now described. All publications mentioned herein, are incorporated by reference in their entirety; nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention. [0130] Example 1: General Methods and Materials. [0131] A. Mass Spectroscopy. [0132] Mass spectrometry reagents were purchased from Sigma AldrichTM unless otherwise mentioned. Sequencing-grade modified trypsin was purchased from PromegaTM. Mass spectrometric data acquisition was performed on a Thermo ScientificTM LTQ OrbitrapTM Fusion Tribrid mass spectrometer attached with a DionexTM nano-LC system and on AB SCIEX MALDI TOF/TOF 5800 (Applied BiosystemTM MDS Analytical Technologies) mass spectrometer. Data analysis was performed by using Data Explorer V4.5, Xcalibur 3.0, ByonicTM software and Glycoworkbench 1.1. [0133] B. Proteomic, Site Mapping and Glycopeptide analyses. [0134] All reagents were purchased from Sigma AldrichTM unless otherwise mentioned. Sequencing-grade modified trypsin was purchased from PromegaTM. Mass spectrometric data acquisition was performed on a Thermo ScientificTM LTQ Orbitrap Fusion Tribrid mass spectrometer attached with a DionexTM nano-LC system and on AB SCIEX MALDI
Attorney Docket No.: 15024-372PC0 Patent TOF/TOF 5800 (Applied BiosystemTM MDS Analytical Technologies) mass spectrometer. Data analysis was performed by using Data Explorer V4.5, Xcalibur 3.0, ByonicTM software and Glycoworkbench 1.1. [0135] Trypsin digestion and extraction of peptides from SDS-PAGE was performed as follows. SDS-PAGE bands from TE sample were cut into 1 mm2 pieces and destained by adding 100 µL acetonitrile: NH4HCO3 (1:1) (ACN:50mM AMBIC BUFFER) and incubated at room temperature (RT) for 30 minutes. Tubes were centrifuged at 14,000 rpm, the supernatant was discarded, and gel pieces were resuspended in 100 µL of ACN. Tubes were incubated for another 20-30 minutes and centrifuged. This process was repeated three times. The proteins in gels then were reduced by adding 50 µL of DTT solution (25 mM), carbamidomethylated by adding 50 µL of iodoacetamide solution (25 mM) and finally washed with 200 µL acetonitrile. Fifty microliters of digestion buffer was added to the gel pieces and proteins were digested by adding 5 µL of sequencing-grade trypsin and/or chymotrypsin (PromegaTM) and incubated at 37 ºC for 12 hours. The digested peptides were extracted in 5% formic acid in 1:2 water-acetonitrile. The digests were dried, the peptides and glycopeptides were subsequently re-dissolved in solvent A (0.1% formic acid in water) and stored at -30 ºC until analysis by nano-LC-MS/MS. [0136] Data acquisition of protein digest samples was performed using nano-LC-MS/MS. Desalted digests of glycoproteins were analyzed on an OrbitrapTM Fusion mass spectrometer equipped with a nanospray ion source and connected to a DionexTM binary solvent system. Pre-packed nano-LC columns of 15 cm length with 75 µm internal diameter (id), filled with 2 µm C18 material (reverse phase) were used for chromatographic separation of samples. The precursor ion scan was acquired at 120000 resolution in an OrbitrapTM analyzer and precursors at a time frame of 3 seconds were selected for subsequent fragmentation using either an HCD product triggered CID program. The threshold for triggering an MS/MS event on an ion-trap was set to 500 counts. Charge state screening was enabled, and precursors with unknown charge state or a charge state of +1 were excluded (positive ion mode). Dynamic exclusion was enabled (exclusion duration of 30 seconds). The fragment ions were analyzed on the OrbitrapTM equipments for HCD and CID at 30000 resolution. [0137] Analysis of proteins and glycoproteins was performed as follows. The LC-MS/MS spectra of tryptic digest of proteins from TE sample were searched against the fasta sequences from the UniProtTM database for Colocasia esculenta using ByonicTM software and
Attorney Docket No.: 15024-372PC0 Patent manually with trypsin and/or chymotrypsin as digestion enzyme with specific cleavage option enabled. Carbamidomethylation as fixed modification, oxidation of methionine as variable modification, was used as search parameters. Table 1: list of peptides identified when searched against the fasta sequences from UniProt database using ByonicTM software and manually with trypsin and/or chymotrypsin as digestion enzyme with specific cleavage option enabled. [0138] The LC-MS/MS spectra of tryptic digest of proteins from TE sample were searched against the fasta FASTA sequences from UniProt database for Colocasia esculenta using ByonicTM software and manually with trypsin and/or chymotrypsin as digestion enzyme with specific cleavage option enabled. These data provided possible proteins based on sequences of the digested proteins and the proteins identified were based on coverage listed in Table 2, which is a list of amino acid sequences identified in TE sample analyzed by LC- MS/MS. Residues colored in gray indicate signal peptides. Residues LRFR (gray) corresponds to a common cleavage site. Peptides in green color font are detected after trypsin digest, and peptides in blue color font are detected after trypsin & chymotrypsin digests. Overlapped of these two peptides is possible and is colored in blue also. Underlined peptides highlight unique peptides to each protein. [0139] Other known data for the sequences derived from ByonicTM and manual inspection are also presented. Carbamidomethylation as fixed modification, oxidation of methionine as variable modification, was used as search parameters. The LC-MS/MS spectra were also analyzed manually for the glycopeptides with the support of XcaliburTM software. The HCD and CID MS2 spectra of glycopeptides were evaluated for the glycan neutral loss pattern, oxonium ions and the glycopeptide fragmentations to assign the sequence and the presence of glycans in the glycopeptides. Table 1. List of peptides identified by searched against the fasta sequences from UniProt database using ByonicTM software and manually with trypsin and/or chymotrypsin as digestion enzyme with specific cleavage option enabled. 12 kDa band 23 kDa band 50 kDa band MSL1 Q 4 7 M ifi l i 1 Al i 12kD S
Attorney Docket No.: 15024-372PC0 Patent 3 NNGDGSTVWR 4 GDYAAVVHPEGR 5 NIPFTNNLLF NIPFTNNLLFSGQVLYGDGR NIPFTNNLLFSGQVLYGDGR N R
Attorney Docket No.: 15024-372PC0 Patent 54 GELIIKDDDFK GELIIKDDDFK GELIIKDDDFK 55 TIWSSSSSSK TIWSSSSSSK 56 HGDYVLILR R R 6]
Attorney Docket No.: 15024-372PC0 Patent 101 DYQIEVCPC
Residues colored in gray indicate signal peptides. Residues LRFR (gray) corresponds to a common cleavage site. Peptides in green color font are detected after trypsin digest, and peptides in blue color font are detected after trypsin & chymotrypsin digests. Overlapped of these two peptides is possible and is colored in blue also. Underlined peptides highlight unique peptides to each protein. Name of UniProt Sequence Sequence ID MSL1 Q39487 Mannose-s ecific lectin 1/ Alternative name: 12kD Stora e G F N A VF N VF N A G F N A V N A n
Attorney Docket No.: 15024-372PC0 Patent LGTNYLLSGQTLDREGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANK GRDCKLTLTDYGELVIKNGDGSTVWRSRAQSVKGNYAAVVHPDGRLVV FGPSVFKIDPWVPGLNS N A V T L A ET L S R )
[0140] The LC-MS/MS spectra were also analyzed manually for the glycopeptides with the support of XcaliburTM software. The HCD and CID MS2 spectra of glycopeptides were evaluated for the glycan neutral loss pattern, oxonium ions and the glycopeptide fragmentations to assign the sequence and the presence of glycans in the glycopeptides. The glycans were dried with nitrogen gas and profiled by MALDI-TOF and ESI-MS.Enzymatic Release of N-glycans. The extracted glycopeptides of each TE band (12 kDa, 23 kDa, and 52 kDa) sample were taken for N-linked glycan profiling. The treatment of PNGase F and/or PNGAse A at 37ºC for 16 hours was used to cleave the N-glycans. The glycans were purified with a C18 cartridge, permethylated, and then analyzed with MALDI-TOF-MS.
Attorney Docket No.: 15024-372PC0 Patent [0141] Chemical Release of N-glycans (hydrazinolysis) was performed as follows. One milligram glycoprotein samples were treated with 200 µL of anhydrous hydrazine and incubated at 85°C for 16 hours, a condition that customarily removes N-glycans from the sample. Hydrazine then then was removed by drying with a steam of nitrogen gas. Five hundred microliters of toluene was added to the tube and the drying procedure repeated. Two more times 500 µL of toluene was added and dried to ensure complete removal of hydrazine from the sample. [0142] A solution of 200 µL of sodium bicarbonate (1 M) was added to the dried sample kept at 0 °C. Fifty microliters of acetic anhydride was added to the sample at 0 °C and kept for 10 minutes. Then another crop of 50 µL of acetic anhydride was added to the reaction mixture and incubated for 50 minutes. This procedure Re-N-acetylate the glycans. Ten microliters of 100 mM Cu (II) acetate in 100 mM acetic acid was added to the Re-N- acetylated sample directly and incubated for 1 hour at room temperature. This step removes a fraction of the hydrazine reagent which reacts with the reducing end of glycans (β- acetohydrazide derivatives). The reaction mixture was loaded to a column of 1 mL DowexTM (H+) (50 W x 8, Sigma AldrichTM) form for desalting and eluted with 3 mL of 5 % acetic acid (collected flow through). The sample in 5 % acetic acid (~ 3 mL) was passed through a C18 cartridge and collected the flow through containing released glycans. The cartridge is washed with 2 mL of 5 % acetic acid and the collected fractions were dried by lyophilization. The released N-linked glycans were permethylated for the structural characterization by mass spectrometry. [0143] Permethylation of glycans was performed as follows. The glycans were permethylated for structural characterization by mass spectrometry using previously reported protocol. Briefly, the dried eluate was dissolved with dimethyl sulfoxide and methylated by using methyl iodide on DMSO/NaOH mixture. The reaction was quenched with nanopure H2O and the permethylated N-glycans were extracted with methylene chloride. The permethylated glycans were dissolved in methanol and crystallized with α-dihydroxybenzoic acid (DHBA) matrix for MALDI analysis. Assignment of glycan structures was done manually and by using GlycoWorkbenchTM software, based on full mass. [0144] C. Glycan microarray of Assay Fluorescent Labeled Samples. [0145] The carbohydrate-binding specificity of TE and rEMSL1 was determined by glycan microarray analysis on printed glycan array slides at ZBiotechTM (Zbiotech.com). More than
Attorney Docket No.: 15024-372PC0 Patent 500 glycans classified in different microarray slides (N-glycan array, O-glycan array, HMO glycan array, blood group glycan array, catch-all glycan array) were screened. In the binding assay, microarray slides were incubated with NHS-Alexa555 fluorescently labeled TE or rEMSL1 proteins. Protein samples were labelled with NHS-Alexa555 in 150 mM sodium bicarbonate buffer (pH 8.3), 1 mM CaCl2 and 1 mM MgCl2 (BCM buffer) with a 4:1 molar excess of the dye. Unreacted dye was removed by Slide-A-LyzerTM MINI Dialysis Device (3K MWCO). Fluorescent intensities were detected by Innopsys InnoscanTM 710. The results were represented as average relative fluorescence units (RFU) for each glycan structure identified with standard deviation of the mean indicated in error bars. Alternatively, biotinylated TE was incubated on the glycan arrays in BCM buffer under a cover slip for 1 hour at room temperature. After washing, TE and rEMSL1 was detected by incubation with cyanine3-labeled streptavidin at 0.5 mg/ml under a cover slip in the same buffer for 1 hour at room temperature. After washing, the slide was analyzed in a fluorescence scanner and the data reported as relative fluorescence units (RFU), corrected by RFU of negative control, for each glycan structure identified by a number on the x-axis. The samples were analyzed on the glycan arrays provided by Z BiotechTM at indicated concentrations. The assay arrays were read out by a microarray scanner (Innopsys InnoscanTM 710). Symbolic glycan structures were drawn using DrawGlycan-SNFG which uses Symbol Nomenclature for Glycans (SNFG). Analysis of the relationship of glycan motifs and the amount of TE binding was performed using MotifFinderTM program. [0146] D. Purification of rEMSL1 and Crystallization. [0147] Recombinant EMSL1 (rMSL1) was codon optimized for the expression in E. coli and subcloned into pSUMO expression vectors. Protein rEMSL1 overexpression was performed after induction with 1.0 mM IPTG (A600 = 0.6 - 0.8) at 20℃ over 16 hours and at 37°C for 3.5 hours (see FIG.1). Bacterial lysates were prepared in buffer containing 50 mM Tris-HCl (pH 8), 500 mM NaCl, 8 M Urea, 5 mM beta-mercaptoethanol (BME), 0.5 mM AEBSF, DNase solution, 10 mM MgCl2, 10 mM EDTA and sonicated. Cell debris were removed by centrifugation at 15000 xg for 45 minutes at 4 °C. The sample was filtered and loaded onto a previously equilibrated HiPrepTM 16/60 IMAC column with buffer A (15 mM Tris-HCl (pH8), 500 mM NaCl, 8 M Urea, 5 mM BME) and B (buffer A plus 1 M imidazol). Sumo-fused EMSL1 was eluted at 200 ± 20 mM imidazole and analyzed by SDS-PAGE. Sumo-fused EMSL1 eluted fractions (molecular weight ~45kDa) were pooled and refolded
Attorney Docket No.: 15024-372PC0 Patent on column decreasing urea concentration step-wise using buffer (15 mM Tris-HCl (pH 8), 500 mM NaCl, 5 mM BME, 1% Glycerol). [0148] Cleavage of the Sumo fusion protein was performed at 4 °C by addition of 150 µL of 1mM Ulp1 protease to refolded Sumo- EMSL1 protein. The completion of the cleavage reaction was checked by SDS-PAGE. A second HiPrepTM 16/60 IMAC column was performed to remove the His-tagged Sumo protein and the His-tagged Ulp1 protease. EMSL1 was collected in the flowthrough (>95% purity) as it was expected and verified by SDS-PAGE. As a final purification step, EMSL1 was concentrated and injected onto a SuperdexTM S200-PG size exclusion column previously equilibrated with buffer 10 mM Tris- HCl, pH 7.0, 150 mM NaCl, 1 mM TCEP. Fractions containing EMSL1 (>99% pure) were eluted from the S200 column (fractions 13-15) and identified using SDS-PAGE. Yield of MSL1purification was typically 7.5-10 mg of purified protein per liter of bacterial cell culture. The identity and purity of rEMSL1 was confirmed by electrospray mass spectrometry (MW=29931.959) and native-PAGE. Size exclusion column S200 was calibrated with a gel filtration standard kit (Biorad #1511901, Hercules, CA), containing thyroglobulin, bovine γ-globulin, chicken ovalbumin, equine myoglobin, and vitamin B12, with M.W.670,000; 158,000; 44,000; 17,000, and 1,350 g/mol, respectively. [0149] E. Crystallization, Data collection, Xray structure solution and refinement. [0150] Crystals were obtained in 0.1M MES pH 5.0, 10% PEG 6000 and diffracted at 3.7 Å resolution at a synchrotron radiation source. The structure was solved using standard methods and refined with a Space group: P6522, 75x75x490; 3 copies in the a.s.u. Rf=0.243. Superposition of rEMSL1 with Tarin shows very small domain movement (RMSD=0.8 Å). Superposition with tarin lectin (PDB ID 5T20) shows very little domain movement, suggesting that proteolytic activation is not required for proper domain arrangement. [0151] Biotinylated proteins were incubated on the glycan arrays in BCM buffer under a cover slip for 1 hour at room temperature. After washing, TE and rEMSL1 were detected by incubation with cyanine3-labeled streptavidin at 0.5 mg/ml under a cover slip in the same buffer for 1 hour at room temperature. After washing, the slide was analyzed in a fluorescence scanner and the data reported as relative fluorescence units (RFU), corrected by RFU of negative control, for each glycan structure identified by a number on the x-axis. The samples were analyzed on the glycan arrays provided by Z BiotechTM at the indicated
Attorney Docket No.: 15024-372PC0 Patent concentrations. The assay arrays were read out by a microarray scanner (Innopsys InnoscanTM 710). Analysis of binding data was performed by PrismTM. [0152] F. Mice. [0153] Syngeneic Balb/cByJ or Balb/c/SCID female mice were purchased from Jackson LaboratoriesTM. All mice were housed in microisolator cages, fed conventional, autoclaved chow and provided drinking water ad libitum. [0154] G. Taro Extract. [0155] Taro extract (TE) was prepared as previously described in United States Patent No. 8,865,642, Example 1, which is hereby incorporated by reference, from peeled, homogenized corm of Colocasia esculenta. Briefly, commercially obtained Taro corm was peeled, combined with PBS in a weight:volume ratio of 1:3, and blended at low speed, followed by high speed to liquefy. After centrifugation at 1200 rpm for 15 minutes at 4℃, the supernatant was subjected to high speed centrifugation (15,000 rpm for 20 minutes at 4℃) and filter sterilized. The protein concentration of the stock taro extract (TE) was determined from multiple preparations of the extract using Coomassie Plus Protein Assay Reagent (PierceTM) and diluted as appropriate to prepare a solution containing about 1.2 mg/mL protein for use. [0156] H. Tumor cell lines. [0157] Human breast cancer cell line MDA-MB-231, immortalized normal mammary epithelial cells (MCF10A, EpH4), and murine metastatic cell lines (410.4, 66.1) were employed. All cell lines were authenticated using short tandem repeat profiling with ATCC markers. For human cell lines, the cultures were monitored for mouse gene contamination. The cultures were screened on a regular basis for mycoplasma and viral contaminants. [0158] Murine mammary tumor cell lines (66.1, 66.1-luciferase and 410.4) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) (Gemini Bio-ProductsTM, Inc.), 2 mM glutamine, penicillin (100 units/ml), streptomycin (100 µg/ml) and 0.1 mM nonessential amino acids in a 10% and 5% CO2 humidified atmosphere, respectively. Human breast cancer cell line MDA-MB-231 was maintained in DMEM supplemented with 10% FBS, 2mM glutamine, penicillin, streptomycin in a 10% CO2 humidified atmosphere. Murine cell lines have been maintained in the laboratory for more than 30 years. The human cell line was acquired from collaborators and all cell lines have been verified within the last 5 years. For cell viability assays, cells were seeded in 24-well plates and PBS, rEMSL1 or TE
Attorney Docket No.: 15024-372PC0 Patent was added at time 0. Seventy-two hours later, cell metabolic activity, as an indicator of cell growth, was determined by MTT assay following the manufacturer’s instructions (SigmaTM Chem. Co.). [0159] I. GFP-rMSL1 binding assay. [0160] Tumor cell lines were incubated with recombinant eGFP-EMSL1, unlabeled rEMSL1, rEMSL1-Y64A or rEMSL1-5xAla. After incubation, cells were centrifuged and washed two times and fluorescence intensity was analyzed by FACSCanto II cytometer and data analyzed with FlowJo software. [0161] J. Metastasis assay. [0162] The metastasis assay was conducted according to known methods. Briefly, PBS, TE or rEMSL1 was injected intraperitoneally in a volume of 200 µL, into syngeneic Balb/cByJ female mice on days 1-4. On day 4, 1-2 x 105 line 66.1 or 410.4 tumor cells were injected into the lateral tail vein. Treatment continued daily for an additional 6 days. Between days 14 -21 post tumor cell injection, when control animals became moribund, mice were euthanized, and surface lung tumor colonies were counted under a dissecting microscope. [0163] K. Migration assay. [0164] Tumor cells were suspended in OPTI-MEM medium and placed in the upper well of MillicellTM tissue culture (24 well) plate well inserts, 8 or 12 µm (MilliporeTM). Fetal bovine serum (FBS, 2%) in OPTI-MEM containing no TE or rEMSL1 (control) or T or rEMSL1 E at 1-50 µg/ml final concentration, was placed in the bottom chamber. Non-migrated cells were removed under vacuum. Migration was assessed at 16-18 hours, as known in the art. Results were expressed as mean ± SE of triplicate wells. [0165] L. Tumorsphere assay. [0166] Tumorsphere assays were performed as previously described in serum-free MammoCultTM medium (StemCell TechnologiesTM). Briefly, line 410.4 or 66.1 cells were plated in 24-well ultra-low attachment plates in triplicate (CorningTM). PBS, rEMSL1 or TE was added at the time of plating. Eight-ten days later, sphere counts were taken from each well. Spheres were dissociated using trypsin and cell number/sphere was calculated. [0167] M. Breast cancer stem cell phenotyping. [0168] The AldefluorTM assay was performed using AldefluorTM kit (StemCell TechnologiesTM) following the company protocol. Fluorescence intensity was analyzed by FACSCantoTM II cytometer and data were analyzed with FlowJoTM software.
Attorney Docket No.: 15024-372PC0 Patent [0169] N. Sequences [0170] Certain relevant sequences pertaining to embodiments of the invention (Engineered Mannose Specific Lectin (EMSL) Families) are presented in Table 3, below. These sequences are the EMSL1, EMSL2, EMSL3, EMSL4 , EMSL5 , EMSL6, EMSL7, EMSL8, EMSL9, ETCI1, ETCI2, and ETCI3 families of proteins, and can be used for the production and manufacturing of this product with existing technologies that are standards of the trade. Each component can be engineered to have optimal stability and then the specific activity of combination of them can be determined. Table 3. Engineered Mannose Specific Lectin (EMSL) Families. Scaffold Scaffold Derivative Sequence D G R S G L S G L Q K G D F A R
Attorney Docket No.: 15024-372PC0 Patent [Methionine is adde D3 rEMSL1D13 d to EMSL1 when subcloned into pET24] MNIPFTNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGW QSNTHGNGEHCFLRLNHKGELIIEDDDFKTIWSSSYSSKQGDYVLILRD A R H F ) T S Y L L K V L T T S Y L M R T S Y L K T S Y L M R N
Attorney Docket No.: 15024-372PC0 Patent GEHCFLRLNHKGELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIY GPAIWETSPQ (SEQ ID NO:30) N D T K D V N D T N D S G N D T P T A V W T G Y N L S G
Attorney Docket No.: 15024-372PC0 Patent rEMSL2D4 LGTNYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTAN NGRDCKLTLTDYGELVIKNGDGSTVWRSRAKSVKGNYAAVLHPDGRL VVFGPSVFKIDPWVPGLNSLRFRNIPFTDNLLFSGQVLYGDGRLTAKNH F V W T G Y A R A R N 1) T S Y L Y C P Q T S Y L W 3) T S
Attorney Docket No.: 15024-372PC0 Patent AMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDG NILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHY QQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITL R T S Y L W T G Y N D T R F V I N D D T N D N 8) N D D T I N
Attorney Docket No.: 15024-372PC0 Patent rEMSL2- (N+1) L V S G V W N N P W T G Y W T G Y V P T V W T G Y V W F H N L
Attorney Docket No.: 15024-372PC0 Patent rEMSL8D3 NIPFTDNLLFSPQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQS NTHGNGEHCFLRLNHKGELIIKDDDFKTIWSSSSSSKQGDYVL (SEQ ID NO:52) N L V W F H A R Q A R N T S Y L Y C P M T S Y L W
Attorney Docket No.: 15024-372PC0 Patent [His-eGFPb D3 rEMSL2D23 ac-EMSL2 ] MGHHHHHHGVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDAT YGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKS Y L L T T S Y L W F H N D T R F T N D D T N D N N D D T S D
Attorney Docket No.: 15024-372PC0 Patent rEMSL8 D(N+1) V W T G Y E L C P Q S E L K G L I S L P E R P A S
[0171] O. Statistical analysis.
Attorney Docket No.: 15024-372PC0 Patent [0172] Data were summarized using descriptive statistics, means and standard errors, medians and ranges. Depending on the data distribution, the Student’s t-test, or its non- parametric alternative, the Wilcoxon test, were used to compare distribution of metastases between treatment groups. All statistical tests were exact and done at the two-sided 0.05 level of significance. [0173] Example 2: Size exclusion Chromatography and Mass Spectroscopy. [0174] TE was subjected to size exclusion chromatography Superdex S200 prior to the LC- MS/MS analysis as described in the methods below. See FIG.2A and FIG.2B, which show TE proteins resolved in SDS-PAGE (4-20%) on mainly 3 bands corresponding to 12, 23 and 52 kDa. Ten microliters of whole TE sample (1mg/ml) was aliquoted, evaporated to 2 µL under stream of nitrogen and added to a matrix of sinapinic acid (SA, 20 mg/mL in 50% v/v methanol:water). BSA (1 mg/ml) was used as positive control for MALDI-TOF analysis. The extrapolation of the molecular weight under the peak is provided and calculated after calibration of the S200 column with standards. [0175] See also the lists below, which show the proteomic analysis of TE 12 kDa, 23 kDa, and 52 kDa bands (FIG.2B) revealing the presence of the peptides listed in Table 1. Characters in underlined illustrate the peptides that were found uniquely in this sequence. The term “coverage” below refers to the percentage of amino acid sequences or peptides identified in TE sample analyzed by LC-MS/MS methods. The sequences of the proteins not identified by LC-MS/MS can be subjected to protein engineering considerations for practical and/or therapeutic purposes including solubility, stability (i.e., pH, temperature, salts, etc), and specific activity relative to binding glycans and/or antimetastatic activity. 1. MSL1 Coverage by MS analysis. The analysis covered 60% of Q39487 sequence. LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTA NKGRDCKLTLTDHGELVINNGDGSTVWRSGAQSVKGDYAAVVHPE GRLVVFSPSVFKIDPSVPGLNSNIPFTNNLLFSGQVLYGDGRLTAKNH QLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIEDD DFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETSPQAK (SEQ ID NO:9) Total: 225; MS:134; MS Coverage: 60%. 2. MSL2 Coverage by MS analysis. The analysis covered 89% of A5HMM7 sequence.
Attorney Docket No.: 15024-372PC0 Patent LGTNYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTA NNGRDCKLTLTDYGELVIKNGDGSTVWRSRAKSVKGNYAAVLHPDG RLVVFGPSVFKIDPWVPGLNSNIPFTDNLLFSGQVLYGDGRLTAKNHQ LVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDDDF RPSGAAVPAPSR (SEQ ID NO:11) Total:
5T20_Lectin|Colocasia esculenta (4460) LGTNYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTANNGRD CKLTLTDYGELVIKNGDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFGPSVF KIDPWVPGLNIPFTDNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGK YGWQSNTHGNGEHCFLRLNHKGELIIKDDDFKTIWSSNSSSKQGDYVLILRD DGFAVIYGPAIWETSA Total:220; Identified (red):204; Coverage:93% 4. MSL4 Coverage by MS analysis. The analysis covered 60% of 5J76 sequence . LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRD CKLTLTDYGELVINNGDGSTVWRSKAQSVKGDYAAVDHPEGRLVVFGPSVF KIDPWVPGNIPFTNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKY GWQSNTHGNGEHCFLRLNHKGELIIKDDDFKTIWSSSSSSKQGDYVLILRDDG FAVIYGPAIWETSPQ Total:225; Red:134; Coverage: 60% 5. MSL5 Coverage by MS analysis. The analysis covered 81% of R9RL27 sequence . LGTNYLLSGQTLDREGHLKNGDFDLVMQDDCNLVLYNGNWQSNTA NKGRDCKLTLTDYGELVIKNGDGSTVWRSRAQSVKGNYAAVVHPDG RLVVFGPSVFKIDPWVPGLNSNIPFTNNLLFSGQVLYGDGRLTAKSHQ LVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDDDF KTIWSSSSSSKHGDYVLILRDDGFAVIYGPAIWETSPQAK (SEQ ID NO:13) Total: 225; Red: 181; Coverage: 81%. 6. MSL6 Coverage by MS analysis. The analysis covered 69% of MQM11449.1 sequence. MAKLLLFLLPAILGLLVPRSAVALGTNYLLSGQTLDREGHLKNGDFDLVMQD DCNLVLYNGNWQSNTANKGRDCKLTLTDYGELVIKNGDGSTVWRSRAQSV KGNYAAVVHPDGRLVVFGPSVFKIDPWVPGLNSLRFR NIPFTNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTH GNGEHCFLRLNHKGELIIKEDDFKTIWRSSSSSKHGDYVLILRDDGFAVIYGPA IWETSPQAKEKMIGMVTAGKL Total: 264; Red: 183; Coverage: 69%. 7. ETCI1 Coverage by MS analysis. The analysis covered 49% of Q39488 sequence. Q39488_25kD Storage. ASNPVLDVDGNELRRGNRYYAISLRSPNSGLTLAVRSNAPCPLNVDQA
Attorney Docket No.: 15024-372PC0 Patent VGSLGLTEDEANLLLNINNE RPHTVRFVKVKEELAASRR (SEQ ID NO:71) Total: 186; Red: 91; Coverage: 49%. 8. ETCI2 Coverage by MS analysis. The analysis covered 74% of Q39489 sequence. ASNPILDVDGDELRRGHRYYAISERRPVSGLTLAARSNAPCPLNVAQT SSNDYGRPLAFFPENAEDDTVQEGNTLNIMFPEPTECRASTVWTLDRE
Total: 9. MSL9 Coverage by MS analysis. The analysis covered 57% of B5LYJ9 variant L119F/R131P sequence . LGTNYLLSGQTLDTEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTAN NGRDCKLTLTDYGELVIKNGDGSTVWKSGAQSVKGNYAAVVHPDGR LVVFGPSVFKIDPWVRGNIPFTNNLLFSGQVLYGDGRLTAKNHQLVM QGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKGELIIKDDDFKTIW SSRSSSKQGEYVLILQDDGFGVIYGPAIFETSS (SEQ ID NO:17) Total: 219; Red: 124; Coverage: 57%. 10. TAR1 Coverage by MS analysis. The analysis covered 45% of Q43418 sequence. LGTNYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTA NNGRDCKLTLTDYGDLVIKNRDGSTVWRSRAKSVKGNYAAVLHPDG RLVVFGPSVFKNDPWVPGLNSNIPSPTTCSSPQVLYGDGRLTAKNHQL GHAGRLQPGPIRLVKYGWQSNTHGNGEHCFLRLNHKGELIIRTTTSRP SGAAVPAPSRVTTFSTSRHVRRALRPAIWRPARSAPLLT (SEQ ID NO:16) Total: 226; Red: 102; Coverage: 45%. [0176] Sequence Alignments are provided below, showing EMSL1(1-268) alignment to its homologous sequences. Conserved residues are underlined. Mutations in lectin variants are highlighted bold italics. [0177] #1 EMSL1(1-268) pairwise alignment to Q39487 LEC1 COLES Mannose-specific lectin 1 Colocasia esculenta (Length = 267; Score = 503 bits (1294); Expect = 4e-180; Identities = 241/241 (100%), Positives = 241/241 (100%), Gaps = 0/241 (0%). See (SEQ ID NO:9), below, showing 100% identity. EMSL1 28 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 87 Q39487 27 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 86 EMSL1 88 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 147 Q39487 87 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 146 EMSL1 148 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 207 Q39487 147 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 206
Attorney Docket No.: 15024-372PC0 Patent EMSL1 208 ELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETSPQAKEKMIGMVTAGKL 268 Q39487 207 ELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETSPQAKEKMIGMVTAGKL 267 [0178] #2 EMSL1(1-268) pairwise alignment to A5HMM7 LEC2 COLES Mannose-specific lectin 2, Agglutinin; Colocasia esculenta (Length=261; Score = 436 bits (1122); Expect = 6e- 154; Identities = 207/234 (89%); Positives = 220/234 (94%); Gaps = 0/234 (0%). See (SEQ ID NO:9 and SEQ ID NO:10), below. EMSL1 28 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 87 A5HMM724 LGTNYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTANNGRDCKLTLTDYGE 83 EMSL1 88 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 147 A5HMM784 LVIKNGDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFGPSVFKIDPWVPGLNSLRFRNIPF 143 EMSL1 148 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 207 A5HMM7144 TDNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 203 EMSL1 208 ELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETSPQAKEKMIG 268 A5HMM7204 ELIIKDDDFRTIWSSSSSSKQGDYVLILQDDGFAVIYGPAIWETSSKRSIADVG 257 [0179] #3 EMSL1(1-268) pairwise alignment to 5T20.pdb (MSL2 (24-134)- R213K/S219N/Q232R -MSL1 (144-253)-N145D/E208K/S219N/Y220S/V236F-D(S249:L268) Lectin Colocasia esculenta, Agglutinin. Gene: Gene: Taro_044356; Length=249; X-ray structure: Chain 1 (PDB ID: 5T1X, 5T20) and Chain 2 (PDB ID:5J76); Identity = 92%. See (SEQ ID NO:9 and SEQ ID NO:10), below. EMSL1 28 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 87 A5HMM7v 24 LGTNYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTANNGRDCKLTLTDYGE 83 EMSL1 88 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 147 A5HMM7v 84 LVIKNGDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFGPSVFKIDPWVPGL------NIPF 143 EMSL1 148 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 207 A5HMM7v 144 TDNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 203 EMSL1 208 ELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETSPQAKEKMIGMVTAGKL 268 A5HMM7v 204 ELIIKDDDFKTIWSSNSSSKQGDYVLILRDDGFAVIYGPAIWETSA------------- 249 [0180] #4 EMSL1(1-268) pairwise alignment 5J76.pdb (EMSL4) X-ray structure: PDB ID:5J76 Mannose-specific lectin Colocasia esculenta. Length=250; Identities = 94%. See (SEQ ID NO:9 and SEQ ID NO:13), below.
Attorney Docket No.: 15024-372PC0 Patent MSL1 28 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 87 5J76 24 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDYGE 83 MSL1 88 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 147 5J76 84 LVINNGDGSTVWRSKAQSVKGDYAAVDHPEGRLVVFGPSVFKIDPWVPG-------NIPF 143 MSL1148 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 207 5J76144 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 203 MSL1 208 ELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETSPQAKEKMIGMVTAGKL 268 5J76 204 ELIIKDDDFKTIWSSSSSSKQGDYVLILRDDGFAVIYGPAIWETSPQ-------------- 250 [0181] #5 EMSL1(1-268) pairwise alignment to R9RL27 CEA COLES Mannose-specific lectin, Agglutinin CEA Colocasia esculenta. Length=264; X-ray structure: PDB ID: 5D5G, 5D9Z; Score = 473 bits (1218); Expect = 1e-168; Identities = 227/241 (94%); Positives = 233/241 (97%); Gaps = 0/241 (0%). See (SEQ ID NO:9 and SEQ ID NO:69), below. EMSL1 28 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 87 R9RL2724 LGTNYLLSGQTLDREGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDYGE 83 EMSL1 88 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 147 R9RL2784 LVIKNGDGSTVWRSRAQSVKGNYAAVVHPDGRLVVFGPSVFKIDPWVPGLNSLRFRNIPF 143 EMSL1 148 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 207 R9RL27144 TNNLLFSGQVLYGDGRLTAKSHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 203 EMSL1 208 ELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETSPQAKEKMIGMVTAGKL 268 R9RL27204 ELIIKDDDFKTIWSSSSSSKHGDYVLILRDDGFAVIYGPAIWETSPQAKEKMIGMVTAGKL 264 [0182] #6 EMSL1(1-268) pairwise alignment to R9RL27 variant S164N/D209E/S209E/K219S A0A843WNH9 COLES Lectin, Colocasia esculenta. Gene: Taro:044356; Length=264; Score = 478 bits (1230); Expect = 1e-169; Identities = 230/245 (94%); Positives = 236/245 (96%); Gaps = 0/245 (0%). See (SEQ ID NO:9 and SEQ ID NO:70), below. EMSL1 28 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 87 R9RL27v 24 LGTNYLLSGQTLDREGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDYGE 83 EMSL1 88 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 147 R9RL27v 84 LVIKNGDGSTVWRSRAQSVKGNYAAVVHPDGRLVVFGPSVFKIDPWVPGLNSLRFRNIPF 143 EMSL1 148 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 207 R9RL27v 144 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 203
Attorney Docket No.: 15024-372PC0 Patent EMSL1 208 ELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETSPQAKEKMIGMVTAGKL 268 R9RL27v 204 ELIIKEDDFKTIWRSSSSSKHGDYVLILRDDGFAVIYGPAIWETSPQAKEKMIGMVTAGKL 264 [0183] #7 A0A843WNH9 COLES Lectin aligned to A0A843UTK6_COLES Lectin See (SEQ ID NO:115 and SEQ ID NO:116), below. tr|A0A843WNH9|A0A843WNH9_COLES MAKLLLFLLPAILGLLVPRSAVALGTNYLLSGQTLDREGHLKNGDFDLVMQDDCNLVLYN 60 tr|A0A843UTK6|A0A843UTK6_COLES MAKLLLFLLPAILGLLIPRSAVALGTNYLLSGQTLDTDGHLKNGDFDLVMQNDCNLVLYN 60 *:* :*:** tr|A0A843WNH9|A0A843WNH9_COLES GNWQSNTANKGRDCKLTLTDYGELVIKNGDGSTVWRSRAQSVKGNYAAVVHPDGRLVVFG 120 tr|A0A843UTK6|A0A843UTK6_COLES GNWQSNTANNGRDCKLTLTDYGELVIKNGDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFG 120 :**::* tr|A0A843WNH9|A0A843WNH9_COLES PSVFKIDPWVPGLNSLRFRNIPFTNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGG 180 tr|A0A843UTK6|A0A843UTK6_COLES PSVFKIDPWVPGLNSLRFRNIPFTNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGG 180 tr|A0A843WNH9|A0A843WNH9_COLES KYGWQSNTHGNGEHCFLRLNHKGELIIKEDDFKTIWRSSSSSKHGDYVLILRDDGFAVIY 240 tr|A0A843UTK6|A0A843UTK6_COLES KYGWQSNTHGNGEHCFLRLNHKGELIIKDDDFKTIWSSNSSSKQGDYVLILRDDGFAVIY 240 *:* *.*:* tr|A0A843WNH9|A0A843WNH9_COLES GPAIWETSPQAKEKMIGMVTAGKL 264 tr|A0A843UTK6|A0A843UTK6_COLES GPAIWETSPQAKEKMIGMVTAGKL 264 [0184] #8 EMSL1(1-268) pairwise alignment to Q43418 Mannose-specific lectin TAR1 COLES Colocasia esculenta; Gene: TAR1; Length=229; Score = 396 bits (1017); Expect = 1e-137; Identities = 189/210 (90%); Positives = 199/210 (95%); Gaps = 0/210 (0%). See (SEQ ID NO:9 and SEQ ID NO:16), below. EMSL1 28 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 87 TARIN 24 LGTNYLLSGQTLNTDGHLKNGDFDLVMQNDCNLVLYNGNWQSNTANNGRDCKLTLTDYGD 83 EMSL1 88 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 147 TARIN 84 LVIKNRDGSTVWRSRAKSVKGNYAAVLHPDGRLVVFGPSVFKNDPWVPGLNSLAFRNIPF 143 EMSL1 148 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 207 TARIN 144 TDNLLFSPQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 203 EMSL1 208 ELIIEDDDFKTIWSSSYSSKQGDYVL 233 TARIN 204 ELIIKDDDFKTIWSSSSSSKQGDYVL 229 [0185] #10 EMSL1(1-268) pairwise alignment to B5LYJ9 Mannose-specific lectin 1 EC1_REMVI Remusatia vivipara. Gene: L1, RVL; Length=256; Score = 439 bits (1129); Expect = 3e-154; Identities = 210/229 (92%); Positives = 219/229 (96%); Gaps = 0/229 (0%). See (SEQ ID NO:9 and SEQ ID NO:), below.
Attorney Docket No.: 15024-372PC0 Patent EMSL1 28 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 87 B5LYJ924 LGTNYLLSGQTLDTEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANNGRDCKLTLTDYGE 83 EMSL1 88 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 147 B5LYJ984 LVIKNGDGSTVWKSGAQSVKGNYAAVVHPDGRLVVLGPSVFKIDPWVRGLNSLRFRNIPF 143 EMSL1 148 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 207 B5LYJ9144 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 203 EMSL1 208 ELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETS 252 B5LYJ9204 ELIIKDDDFKTIWSSRSSSKQGEYVLILQDDGFGVIYGPAIFETS 248 [0186] #10 EMSL1(1-268) pairwise alignment to B5LYJ9-L119F/R131P Mannose- specific lectin 1 LEC1_REMVI Remusatia vivipara. Gene: L1, RVL; Length=256; X-ray structure: PDB ID: 3R0L.pdb; Score = 439 bits (1129); Expect = 3e-154; Identities = 212/229 (93%); Positives = 221/229 (96%); Gaps = 0/229 (0%). See (SEQ ID NO:9 and SEQ ID NO:17), below. EMSL1 28 LGTNYLLSGQTLETEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANKGRDCKLTLTDHGE 87 B5LYJ924 LGTNYLLSGQTLDTEGHLKNGDFDLVMQDDCNLVLYNGNWQSNTANNGRDCKLTLTDYGE 83 EMSL1 88 LVINNGDGSTVWRSGAQSVKGDYAAVVHPEGRLVVFSPSVFKIDPSVPGLNSLRFRNIPF 147 B5LYJ984 LVIKNGDGSTVWKSGAQSVKGNYAAVVHPDGRLVVFGPSVFKIDPWVPGLNSLRFRNIPF 143 EMSL1 148 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 207 B5LYJ9144 TNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKYGWQSNTHGNGEHCFLRLNHKG 203 EMSL1 208 ELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGPAIWETS 252 B5LYJ9204 ELIIKDDDFKTIWSSRSSSKQGEYVLILQDDGFGVIYGPAIFETS 248 [0187] #10 EMSL(1-268) pairwise alignment. See (SEQ ID NOs:1, SEQ ID NO:12, SEQ ID NO:10 and SEQ ID NO:11), below. SEQ MRHIPHGQASPLPP-----PGHPRPPRSWSAVALGTNYLLSGQTLETEGHLKNGDFDLVM 55 SEQ --------------------TNPVLDVDGNELQRGQLYYATSVM------RPGGGLTLAA 34 SEQ MEFVLLLVSSLLLTARAAVASNPVLDVDGNELRRGNRYYAISLR------SPNSGLTLAV 54 SEQ MEFILLLVSSLLLTARAAAASNPILDVDGDELRRGHRYYAISER------RPVSGLTLAA 54 :* . . : * * . ..: *. SEQ --QDDCN---------------LVLYNGNWQSNTANKGRDCKLTLTDHGELVINNGDGST 98 SEQ P-KGSCPLNVAQAPFDEYSGRPLAFFPENADDDTVQEGSTLYIMFPEP-----TRCPQST 88 SEQ RSNAPCPLNVDQAPSKDY-GRPLAFFPENVDDDTVQEGSTLYIMFPEP-----SECREST 108 SEQ RSNAPCPLNVAQTSSNDY-GRPLAFFPENAEDDTVQEGNTLNIMFPEP-----TECRAST 108 : * *.:: * :.:*.::* : : : .. ** SEQ VWRSGAQ-----------------------------SV—KGDYAAVVHPEGRLVVFSPS 127 SEQ VWTFDREAGFVTTGGTTSKAIGPHNSRFAIRKAGDASSQ-PRDYQIEVCPCST------- 140 SEQ VWTLGRETDVVTTGGTSSSAIGPRNSRFTIRRTGDASSK--GEYQIEVCPCSI------- 159 SEQ VWTLDRERGVVTTGGTSSSAIGPHNSRFSIRRAGDASSERERKYQIEVCPCSN------- 161 ** . : * .* * * .
Attorney Docket No.: 15024-372PC0 Patent SEQ VFKIDPSVPGLNSLRFRNIPFTNNLLFSGQVLYGDGRLTAKNHQLVMQGDCNLVLYGGKY 187 SEQ ---------GV-----------------------------------ERPSCRMGCLG-TL 155 SEQ ---------GV-----------------------------------SRAPCRLACVG-S 174
SEQ GWQSNTHGNGEHCFLRLNHKGELIIEDDDFKTIWSSSYSSKQGDYVLILRDDGVAVIYGP 247 SEQ GLA----EGGKNVLLNINNESPHTIRFVKVKEG--------------------------- 184 SEQ GLT----EDEANLLLNINNERPHTVRFVKVKEELAA---SRR------------------ 209 SEQ GLT----EDEGNLLLNINNERPHAIRFVKVKEELPA---SRR------------------ 211 * . : :*.:*:: :. ..* SEQ AIWETSPQAKEKMIGMVTAGKL269 SEQ ----------------------184 SEQ ----------------------209 SEQ ---------------------- 211 [0188] FIG.2C contains an intact mass spectrum of a TE sample by MS-ESI. [0189] Example 3: MALDI-TOF-MS. [0190] Extracted glycopeptides of TE bands (12kD, 23kD, and 52 kD) were obtained by extraction of the TE resolved band in SDS-PAGE (FIG.2B). Samples were taken for N- linked glycan profiling. Treatment with PNGase F and/or PNGAse A at 37ºC for 16 hours was used to cleave the N-glycans. The glycans were purified with a C18 cartridge, permethylated, and then analyzed with MALDI-TOF-MS. See also the results in FIG.3. [0191] Example 4: Protein Sequences. [0192] Protein sequences identified by LC-MS/MS proteomic analysis are shown in FIG. 3A through FIG.3C. FIG.4A presents a multiple sequence alignment of EMSL1 (Q39487), EMSL2 (A5HMM7), EMSL3 (PDBID 5T20), EMSL5D1 and EMSL5D10 (R9RL27), EMSL8 (Q43418) obtained using MUSCLE. [0193] FIG.4B is a ECTI1 [Q39488], and ECTI2 [Q39489] pairwise alignment, separated to illustrate the similarities between the two clusters of proteins. [0194] FIG.4C shows a Neighbor Joining tree calculated from the multiple sequence alignment of EMSL1 (Q39487), EMSL2 (A5HMM70), EMSL3 (PDBID 5T20), ECEA1 and ECEA2 (R9RL27), EMSL8 (Q43418), ETCI1 (Q39488), and ETCI2 (Q39489) proteins. Engineering of these sequences can focus on amino acid residues (<10%) that are outside of the carbohydrate binding sequences (CBSs) or other regions of the protein that are known to contribute to one or more activities. The tree was calculated based on the average distance of all seven identified protein sequences using Blosum62 matrices.
Attorney Docket No.: 15024-372PC0 Patent [0195] FIG.4D shows the structure of rEMSL11-268 in its apo state as a green ribbon representation with the disulfide bond in yellow aligned with TAR1 (PDB ID: 5T20). Crystals were obtained in 0.1M MES pH 5.0, 10% PEG 6000 and diffracted at 3.7 Å resolution. Space group: P6522, 75x75x490; 3 copies in the a.s.u. Rf=0.243. Superposition of rEMSL1 with Tarin shows very small domain movement (RMSD=0.8 Å). Carbohydrate binding sites (CRS-1 and -2) and the conserved motif (CXLXL, SEQ ID NO:1) are highlighted in red in both structures. [0196] Example 5: Active components of TE, isolated, identified and produced by Recombinant Methods. [0197] The active components contained in a gel permeation chromatography purified fraction of TE were isolated and identified for first time as three taro proteins from the GNA- related superfamily were found by N-terminal sequencing: taro 12 kDa storage protein (GenBank accession: BAA03722), the tarin protein (GenBank accession: CAA53717), and the lectin protein (GenBank accession: ABQ32294). The isolated lectins were all that co- eluted with the anti-metastatic activity and together provided a specific activity >20-fold higher than TE. [0198] We now report, upon next-step LC-MS/MS analysis of TE, the existance of unique peptides corresponding to six more isomeric lectins from the GNA-related superfamily. These were identified with high accuracy and sequence coverage. In addition to confirming the N-terminal sequencing data, LC-MS/MS revealed that they all undergo identical processing to give two protein fragments of approximately 12-13 kDa per taro protein. [0199] First, a signal peptide was removed at the N-terminus by cleavage at the SAVA- LGTN sequence followed by a second cleavage step at the FR-NIP sequence, near the middle of the full-length gene product. Importantly, the lectin proteins all harbor a consensus carbohydrate recognition sequence (CRS) in each of the processed fragments (two CRS domains/full-length protein). This sequence is QXDXNXVXY- (SEQ ID NO:2), found in Q39487, A5HMM7, R9RL27, Q43418, and B5LYJ9 var. L119F/R131P). Bold letters highlight site amino acid conservation and X can be any residue. These lectins were highly pH stable and bound complex N-glycans (FIG.3A through FIG.3C). Many lectins are expressed on hematopoietic and CSCs, which may underlie the immune modulatory and direct anti-tumor effects, respectively.
Attorney Docket No.: 15024-372PC0 Patent [0200] Of these ten isolectins, the 12kDa Taro Storage Protein (GenBank accession: BAA03722) was found to have the most promising biophysical properties, including high solubility, high stability, and anti-metastatic activity when prepared recombinantly (i.e. termed rEMSL1). For these reasons, this compound, rEMSL1, was used for subsequent studies. [0201] Example 6: Proteomic analysis of TE by LC-MS/MS. [0202] A total of 135 peptides were identified from TE trypsin/chymotrypsin cleavage using ByonicTM software and manual spectra validation. The analysis allowed unique assignment of the peptides to at least ten isolectins, complementing previous results reported for TE by N-terminus amino acid analysis. TE was determined to be highly represented (>90% amino acid coverage) by lectin or more recently named mannose specific lectin MSL 2 (A5HMM7, GenBank Accession: EF541132.1) and by taro storage protein EMSL1 (aka 12kDa storage), also named mannose specific lectin 1 EMSL1 (Q39487, GenBank accession: D16173.1) from C. esculenta, with 60% amino acid coverage. [0203] Surprisingly, the proteomic analysis revealed that tuber agglutinin CEA (R9RL27, GenBank Accession: JX435122.1) from C. esculenta was also identified in TE with a very high sequence coverage (>80%). Peptides corresponding to a composition of these two lectins, previously denominated as tarin lectin (PDB ID 5T20, 5J76) was recognized with the identification of the unique peptide TIWSSNSSSK (SEQ ID NO:3; A5HM7 variant). For consistency, this lectin is referred to here as mannose specific lectin 3 (formed by EMSL2 (24-234)- EMSL1 (144-253)-E212K/S223N/Y224S/V240F/P25A). Two variants of tuber agglutinin CEA from C. esculenta were found with >80% of amino acid coverage. They were assigned as EMSL5D1 (R9RL27, NCBI accession: JX435122.1) and EMSL5D10, also called as hypothetical taro protein (NCBI accession: MQM11449.1) from C. esculenta. See FIG.21 which is a table showing a list of protein sequences engineered EMSL1-EMSL9 and ETCI1-ETCI3 based on proteomic analysis performed on TE samples and similarity searches using UniProtTM database (uniprot.org). From further analysis, other engineered proteins, can be added. [0204] Pairwise alignment of EMSL5D10 to EMSL5D1 showed that EMSL5D10 was composed by EMSL5D1 (24-252)-S164N/D209E/S217R. Despite the close sequence similarity, these two lectins contain unique peptides that can be uniquely assigned to each one
Attorney Docket No.: 15024-372PC0 Patent of them, i.e. TIWSSSSSSK (from CEA1; SEQ ID NO:13; (R9RL27) and GELIIKEDDFK (from CEA2; SEQ ID NO:50; R9RL27 – K208E Variant) peptides. Tarin or TAR1 (Q39418, GenBank accession: D16173.1) from C. esculenta was identified with 45% amino acid sequence coverage. Sequence alignments of G1 and G2 globulin amino acid sequences and the ten proteins identified in TE sample were performed by LC-MS/MS data analysis. See FIG.4A. [0205] Aside from G1d (AAB24691.1), which aligns perfectly to lectin (A5HMM7), the rest of them, G1a (AAB24694.1), G1c (AAB24693.1), and G1b (AAB24692.1), are close homologues to lectin (5HMM7), 12 kDa storage (Q39487) and tarin (Q43418) sequences, respectively. Globulins G2a and G2b are 89% and 96% similar to 25 kDa storage proteins Q39489 and Q39488, respectively. Analyses of LC-MS/MS data identified three new peptides that exclusively belong to G1a, G1b, and G2b globulins. This finding suggested the presence of three additional isolectins in taro extract. [0206] We determined the presence of two peptides never before identified from a Taro plant (LVVLGPSVFK and VLILQDDGF) but are reported as a mannose-binding lectin from Remusatia vivipara (RVL) or EMSL9 a close homologue of mannose-specific lectin EMSL2 (93% identity) and tuber agglutinin CEA1 (94% identity) from C. esculenta. Mannose- binding lectin from Remusatia vivipara is a well characterized beta-prism II lectin (B5LYJ9, GenBank Accession: EU924066.1) and close homologue to EMSL2 (A5HMM7, GenBank Accession: EF541132.1) from C. esculenta (93% identity) and tuber agglutinin CEA (R9RL27, GenBank Accession: JX435122.1) from C. esculenta (94% identity). This peptide, like mannose-specific lectins from C. esculenta, undergo an identical two-step maturation process as TE proteins. [0207] The peptide search analysis revealed the existence of two unique peptides in the RVL sequence (LVVLGPSVFK (SEQ ID NO:7; from B5LYJ9 var. L11F/R131P) and VLILQDDGF (SEQ ID NO:8; from B5LYJ9 var. L11F/R131P)) that were not present in C. esculenta sequences. These results suggested that a lectin containing these two peptides also could be present in TE as well. See FIG.5. All the recognized isolectins, were previously characterized to undergo an identical two-step processing as TE proteins. Importantly, the isolectins proteins (MSL1, EMSL2, EMSL3 , EMSL5D1, EMSL5D10, EMSL8, and EMSL9) harbor a consensus carbohydrate recognition sequence (CRS: -QXDXNXVXY, SEQ ID NO:2) in each of the processed fragments (or two CBS domains/full-length protein). Many
Attorney Docket No.: 15024-372PC0 Patent of these N-glycan structures are expressed on hematopoietic and CSCs which may underlie the immune modulatory and direct anti-tumor effects, respectively. [0208] An extended peptide search was also performed against TE homologue lectins with similar biophysical properties, i.e., curculin, miraculin, sporamin, and Kunitz trypsin inhibitors. There was no evidence of peptides belonging to any of these lectins, however two 25 kDa storage proteins named as inhibitors of trypsin/chymotrypsin ECTI1 (GenBank accession: D16174.1) and ECTI2 (GenBank accession: D16175.1), with 80% and 70% amino acid coverage, respectively, were assigned with high certainty. [0209] PBS, TE (400 μg/animal/day) or rEMSL1 (SEQ ID NO:9; #001) (40 μg/animal/day) was injected i.p. into syngeneic BALBc/ByJ female mice on days 1-4. On day 4, 3 x 105 line 410.4 tumor cells were injected into the lateral tail vein. Treatments continued daily for an additional 6 days. On day 17 post tumor cell injection, when control animals became moribund, mice were euthanized, and surface lung tumor colonies were counted under a dissecting microscope. P value TE vs PBS = 0.00001; rEMSL1D1 vs PBS = 0.0001. See FIG.6. All together, these data indicate, for the first time, the novel composition of the GNA-related lectin superfamily lectins existing in TE from C. esculenta. [0210] Table 4. TE lectin composition by LC-MS/MS analysis. # Protein Name Organism UniProt GenBank EMBL PDB ID Re Engineered EMSL1 (alternative names) ference Sequence Identity
Attorney Docket No.: 15024-372PC0 Patent [0211] Example 7: Isolation, Identification, and Production of Taro Extract Products. [0212] Taro extract (TE) was prepared by known methods as provided in United States Patent No. 8,865,642. See also, Example 1, above. [0213] Active components of the TE were produced by recombinant methods. Recombinant Mannose Specific Lectin (MSLs) genes, codon optimized for the expression in E. coli and subcloned into pSUMO expression vectors. Protein recombinant Sumo-MSL protein overexpression was performed after induction with 1.0 mM IPTG (A600 = 0.6 - 0.8) at 20°C over 16 hours and at 37 °C for 3.5 hours (FIG.1). Bacterial lysates were prepared in buffer containing 50 mM Tris-HCl (pH 8), 500 mM NaCl, 8 M Urea, 5 mM beta-mercaptoethanol (BME), 0.5 mM AEBSF, DNase solution, 10 mM MgCl2, 10 mM EDTA and sonicated. Cell debris were removed by centrifugation at 15,000 x g for 45 minutes at 4 °C. The sample was filtered and loaded onto a previously equilibrated HiPrep 16/60 IMAC column with buffer A (15 mM Tris-HCl (pH8), 500 mM NaCl, 8 M Urea, 5 mM BME) and B (buffer A plus 1 M Imidazol). Sumo-MSL protein was eluted at 200 ± 20 mM imidazole and analyzed by SDS- PAGE. Sumo-fused rMSL protein eluted fractions (molecular weight ~45kDa) were pooled and refolded on column decreasing urea concentration step-wise using buffer 15 mM Tris- HCl (pH 8), 500 mM NaCl, 5 mM BME, 1% Glycerol. Cleavage of the Sumo fusion protein was performed at 4 °C by addition of 150 μL of 1mM Ulp1 protease to refolded Sumo-MSL protein. The totality of the cleavage reaction was checked by SDS-PAGE. [0214] A second HiPrep 16/60 IMAC column was performed to remove the His-tagged Sumo protein and the His-tagged Ulp1 protease. TSP was collected in the flowthrough (>95% purity) as it was expected and verified by SDS-PAGE. As a final purification step, rMSL protein was concentrated and injected onto a Superdex S200-PG size exclusion column previously equilibrated with buffer 10 mM Tris-HCl, pH 7.0, 150 mM NaCl, 1 mM TCEP. Fractions containing rMSL protein (>99% pure) were eluted from the S200 column (fractions 13-15) and identified using SDS-PAGE. The identity and purity of rMSL was confirmed by electrospray mass spectrometry (MW=29,931.959 Da) and native-PAGE. A size exclusion column S200 was calibrated with a gel filtration standard kit (BioradTM), containing thyroglobulin, bovine γ-globulin, chicken ovalbumin, equine myoglobin, and vitamin B12, with molecular weights 670,000; 158,000; 44,000; 17,000, and 1,350 g/mol, respectively. [0215] Previously, the active components had been isolated from a gel permeation chromatography purified fraction of TE. Three taro proteins from the GNA-related
Attorney Docket No.: 15024-372PC0 Patent superfamily: taro storage protein (GenBank accession: BAA03722), the tarin protein (GenBank accession: CAA53717), and the lectin protein (GenBank accession: ABQ32294) were found via N-terminal sequencing. These isolated lectins were all that co-eluted with the anti-metastatic activity and together provided a specific activity >20-fold higher than TE. FIG.2A illustrates TE chromatographic profile corresponding to the elution from Superdex S200 size exclusion column. The TE sample used was previously purified as described (by methodology in United States Patent, 8,865,642). This chromatography was performed to compare TE and EMSL1D1 elution chromatographic profiles (see FIG.1E). FIG.2B illustrates how TE samples (previously prepared as described in US patent 8,865,642) resolves mainly in 3 bands when it is run on an 4-20% denaturing SDS-PAGE. [0216] In the present work extensive characterization studies of TE have been carried out. These resulted in the identification of additional components of TE. By LC-MS/MS analysis of TE, nine isomeric lectins from the GNA-related superfamily were identified with high accuracy and sequence coverage. In addition to confirming the N-terminal sequencing data, LC-MS/MS revealed that all of the nine undergo identical processing to give two protein fragments of approximately 12-13 kDa per taro protein. [0217] First, a signal peptide was removed at the N-terminus by cleavage at the SAVA- LGTN sequence followed by a second cleavage step at the FR-NIP sequence, near the middle of the full-length gene product. Importantly, the lectin proteins SEQ ID NO:12 (Q39487); SEQ ID NO:10 (A5HMM7); SEQ ID NO:13 (R9RL27); SEQ ID NO:16 (Q43418); and SEQ ID NO:17 (B5LYJ9 var. L11F/R131P) all harbor a consensus Carbohydrate Recognition Sequence (CRS: QXDXNXVXY; SEQ ID NO:2) in each of the processed fragments (or two CRS domains/full-length protein), where bold letters highlight site amino acid conservation and X can be any residue. These lectins were highly pH stable and bind complex N-glycans (see FIG.7 and FIG.8, discussed below). Many are expressed on hematopoietic and cancer cells with stem cell properties (CSCs), which may underlie the immune modulatory and direct anti-tumor effects, respectively. [0218] Example 8: Analysis of Labeled TE Binding on the 100 Glycan Microarray and Top 15 ranked glycan structures TE N-glycan microarray analysis. [0219] Fluorescently labeled TE (NHS-Alexa555) was incubated on the glycan array for 1 hour at room temperature. After washing, the slide was analyzed and fluorescence was
Attorney Docket No.: 15024-372PC0 Patent detected (Innopsys InnoscanTM 710 ). Data is reported in FIG.7A as the average relative fluorescence units (RFU) for each glycan structure identified, with standard deviation of the mean indicated in error bars, by a number on the x-axis. Glycan structures are drawn using DrawGlycanTM-SNFG. FIG.7D illustrates fluorescence of high-mannose glycans (green labels) on the printed 100-glycan microarray during the process of fluorescence detection. [0220] FIG.7B shows the optimization of glycan array conditions at different TE concentrations (red labels). The data plotted in FIG.7A corresponds to 1.9 mg/mL of TE on the 100-Glycan microarray. RFU values at different TE concentrations are in red. FIG.7C shows the calculation of apparent KD for Man-5 and Man-6 data. Glycans are rendered using the Symbolic Nomenclature for Glycans [SNFG]. [0221] AF555-TE, at concentration of 0.4 µg/mL was assessed for N-glycan recognition pattern which consists of 100-N glycans in replicates of 8. For FIG.8, fluorescently labeled TE (NHS-Alexa555) was incubated on the glycan array for 1 hour at room temperature. After washing, the slide was analyzed and fluorescence was detected (Innopsys InnoscanTM 710 ). The results are expressed by the average relative fluorescence units (RFU) for each glycan structure identified with standard deviation of the mean indicated in error bars and top 15 ranked glycan structures are illustrated with its respective glycan number. Glycans structures are drawn using DrawGlycan-SNFG. See FIG.8A, FIG.8B, FIG.8C, and FIG. 8D for results. Classification: (A) Symmetric biantennary Complex N-glycans; (B) Asymmetric biantennary Complex N-glycans; (C) Asymmetric biantennary Complex N- glycans with terminal fucosylation; (D) Asymmetric biantennary Complex N-glycans with core fucosylation. Glycans are rendered using the Symbolic Nomenclature for Glycans (SNFG). FIG.8B illustrates fluorescence of N-glycans on the printed 100 N-glycan microarray during the process of fluorescence detection. FIG.8C shows glycan classification analyzed by MotifFinder. Glycans are grouped by motif and motif families. Individual glycans are given as points on the plot. A-section corresponds to terminal mannose and terminal beta-galactose; B-section includes terminal type-2 LacNAc and sialyl terminated N- glycans; C-section corresponds to mannose N-glycans; and last, section labeled 0, are all the glycans that do not show binding. [0222] FIG.5 provides a list of TE motifs. See Symbol Nomenclature for Glycans (SNFG) for complete key at ncbi.nlm.nih.gov/glycans/snfg. *Motif indicates the remaining glycans not matched by motifs which are a subset. The motif definition needs to be taken in the
Attorney Docket No.: 15024-372PC0 Patent context of the model. Accuracy describes the consistency between common-name definition of the motif and the formal, text-based definition of the motif, in terms of percent agreement in the glycans containing the two motifs. The Common Name label definitions can be seen at carbogrove.org/MotifLabels.php. P-Value refers to difference from Non-Binders with multiple testing correction (TukeysHSD). [0223] Example 9: Taro extract (TE) potently inhibits tumor metastasis in Two TNBC Models. [0224] The ability of a water-soluble extract of taro (TE) to inhibit metastasis in two syngeneic, highly metastatic models of TNBC (66.1 and 410.4) was examined. The initial studies involved an intraperitoneal injection of 150 μL PBS or TE (400 µg total protein) into syngeneic Balb/cByJ female mice on days 1-10. On day 4, either 66.1 or 410.4 tumor cells were injected into the lateral tail vein and, on day +16-21, mice were euthanized, and lung tumor colonies were counted. [0225] FIG.9 relates to TE inhibits experimental and spontaneous metastasis in two TNBC models. In four independent experiments, TE profoundly prevented (98-99%) lung tumor colonization. 150 uL PBS or TE (400 μg total protein) was injected i.p. daily for 10 days. On day 4, 1 x 105 of line 66i.1 or 410.4 tumor cells were injected i.v. On day 21, mice were euthanized, and surface lung tumor colonies counted. See FIG.9A and FIG.9B. [0226] Subsequent studies demonstrated efficacy of TE in a therapeutic model of spontaneous metastasis from established tumors. 5 x 105 of 410.4 tumor cells were injected into mammary gland and on day +5 when tumors were palpable, PBS or TE was injected i.p. daily for the next 18 days. When tumors measured 18 mm average diameter, mice were euthanized, and extent of metastatic disease was assessed. Mice were transplanted with 500,000410.4 tumor cells in the right inguinal mammary gland on day zero. TE treatment reduced spontaneous lung metastases from mammary-gland implanted tumors by 85% (see FIG.9C) in spite of the minimal impact on the overall size of primary tumors. See FIG.9D, which shows primary tumor growth in mice from treatment in FIG.9C (P values are from a Wilcoxon exact two-sided test at 0.05 level of significance). [0227] In an independent experiment, survival time (after i.v. tumor cell injection) was extended significantly by TE. FIG.9E, a Kaplan-Meier survival plot of mice injected i.v.
Attorney Docket No.: 15024-372PC0 Patent with 66.1 cells and treated with TE or PBS. Lung metastases were enumerated at necropsy (TE=10+0.2 mets; PBS=207+0.12 mets). [0228] Thus, in pre-existing disease, TE specifically targets a process relevant to metastasis, but it does not affect primary tumor size, suggesting that it is CSC that are targeted. TE also profoundly inhibited metastasis to the brain, liver and bone (not shown). Due to the pH stability of TE, it is fully active when given by oral gavage, which can facilitate clinical trials. [0229] Example 10: Method of Making Recombinant EMSL1. [0230] Recombinant Mannose Specific Lectin 1 (rEMSL1), previously known as Taro storage protein (rTSP) was codon optimized for expression in E. coli and subcloned into pSUMO expression vectors. Protein recombinant Sumo-MSL1 overexpression was performed after induction with 1.0 mM IPTG (A600 = 0.6 - 0.8) at 20°C over 16 hours and at 37°C for 3.5 hours (see FIG.1). Bacterial lysates were prepared in buffer containing 50 mM Tris-HCl (pH 8), 500 mM NaCl, 8 M urea, 5 mM beta-mercaptoethanol (BME), 0.5 mM AEBSF, DNase solution, 10 mM MgCl2, 10 mM EDTA and sonicated. Cell debris were removed by centrifugation at 15,000 x g for 45 minutes at 4 °C. The sample was filtered and loaded onto a previously equilibrated HiPrep 16/60 IMAC column with buffer A (15 mM Tris-HCl (pH8), 500 mM NaCl, 8 M Urea, 5 mM BME) and B (buffer A plus 1 M Imidazol). Sumo-MSL1 was eluted at 200 ± 20 mM Imidazole and analyzed by SDS-PAGE. [0231] Sumo-fused rEMSL1 eluted fractions (molecular weight ~45kDa) were pooled and refolded on column decreasing urea concentration step-wise using buffer 15 mM Tris-HCl (pH 8), 500 mM NaCl, 5 mM BME, 1% Glycerol. Cleavage of the Sumo fusion protein was performed at 4 °C by addiction of 150 μL of 1mM Ulp1 protease to refolded Sumo-MSL1 protein. The totality of the cleavage reaction was checked by SDS-PAGE. A second HiPrep 16/60 IMAC column was performed to remove the His-tagged Sumo protein and the His- tagged Ulp1 protease. EMSL1 was collected in the flowthrough (>95% purity) as it was expected and verified by SDS-PAGE. [0232] As a final purification step, rEMSL1 was concentrated and injected onto a SuperdexTM S200-PG size exclusion column previously equilibrated with buffer 10 mM Tris- HCl, pH 7.0, 150 mM NaCl, 1 mM TCEP. Fractions containing EMSL1 (>99% pure) were eluted from the S200 column (fractions 13-15) and identified using SDS-PAGE. The yield of rEMSL1 purification was typically 7.5-10 mg of purified protein per liter of bacterial cell
Attorney Docket No.: 15024-372PC0 Patent culture. The identity and purity of rEMSL1 was confirmed by electrospray mass spectrometry (MW=29,931.959 Da) and native-PAGE. Size exclusion column S200 was calibrated with a gel filtration standard kit (BioradTM), containing thyroglobulin, bovine γ- globulin, chicken ovalbumin, equine myoglobin, and vitamin B12, with M.W.670,000; 158,000; 44,000; 17,000, and 1,350 g/mol, respectively. [0233] Example 11: Recombinant EMSL1 inhibits metastasis. [0234] The ability of rEMSL1 to inhibit metastasis was determined in two syngeneic, highly metastatic models of Triple Negative Breast Cancer (66.1; 410.4). The choice of bacteria to produce recombinant rEMSL1 was based on the fact that, by mass spectroscopy, HCD and CID MS2 spectra of glycopeptides (evaluated for the glycan neutral loss pattern) showed that the glycosylation level of TE was very low (1% or lower). See FIG.10A, which shows the relative fluorescence units (y-axis) of TE (blue bar) and MSL1D34 (residues 28-253; red bar) on the 100 N-glycans array (x-axis). Complex-type N-glycans were observed, but there was no evidence of O-glycosylations. See FIG.10, which is a comparison of 100 N-Glycan microarray analyses obtained for TE and EMSL128-253. Relative Fluorescence Units (RFU) (on y-axis) of TE (blue bar) and EMSL1D34 (28-253) (red bar) (SEQ ID#034) on the 100 N- glycans array (x-axis). The data is presented as normalized mean + s.d. of three replicates corrected by background fluorescence reading. FIG.10B and FIG.10C illustrate fluorescence of symmetric biantennary, asymmetric biantennary, and high-mannose N- glycans for TE (FIG.10B) and EMSL1D34 (residues, 28-253) (FIG.10C) on the printed 100 N-glycan microarray library (ZBiotech 100N-glycan) during the process of fluorescence detection. [0235] PBS, TE (200 µg/animal/day) or rEMSL1 (40 µg/animal/day) was injected intraperitoneally into syngenic Balb/cByJ female mice on days 1-4. On day 4, 3 x 105 line 410.4 tumor cells were injected into the lateral tail vein. Treatments continued daily for an additional 6 days. On day 17 post tumor cell injection, when control (PBS)-treated animals became moribund, mice were euthanized and surface lung tumor colonies were counted under a dissecting microscope. As reported previously and confirmed here, treatment with TE led to 99% inhibition of tumor colonization of the lungs (see FIG.6). Treatment of mice with rEMSL1 resulted in 69% inhibition of lung colonization. TE vs PBS; p<0.00001;
Attorney Docket No.: 15024-372PC0 Patent rEMSL1 vs PBS, p<0.0001. In all four independent experiments, rEMSL1 inhibited metastasis by 50%, 55%, 69% and 78% relative to control-treated mice. [0236] The Y64A mutant did not compete with recombinant eGFP-EMSL1 for binding to mammary tumor cells by flow cytometry or in glycan binding assays (FIG.11). [0237] Eliminating the ability of rEMSL1 to bind glycans should abolish the anti-metastatic activity. To test this, two rEMSL1 constructs were engineered with a mutated CBS domain; (1) rEMLS1-Y64A and (2) rEMSL1- Q56A/D58A/N60A/V62A/Y64A. The latter contains five residues in the CBS domain mutated to Ala (Q→A; D→A; N→A; V→A; Y→A). Balb/cByJ female mice treated daily with rEMSL1D1 (50 μg protein) (SEQ ID:9; #001) or mutant rEMSL1D1 Y64A protein for 10 days. Mice injected with 1 x 10566.1-luciferase cells and bioluminescent imaging conducted on days +1, +7, +10, +14, +17 relative to tumor cell injection, p=0.018. The experimental results are shown in FIG.12, which shows only the results with the Y64A mutant. The data were reported as photons in lungs FIG.12A. Surface lung tumor colonies at necropsy are shown in FIG.12B. Treatment of mice with endotoxin-free rEMSL11-268 resulted in significant reduction in lung metastases compared to mice treated with mutant protein Y64A (FIG.12A, p=0.018) and 55% fewer lung metastases (FIG.12B, p=0.009). [0238] Example 12: Recombinant EMSL1 and TE thermal denaturation. [0239] To determine whether TE and rEMSL1 bind complex fucosylated and sialylated N- glycans, the following studies were undertaken. Expression of recombinant EMSL1 (GenBank accession: BAA03722) has promising biophysical properties for therapeutic development including high solubility and high stability when prepared recombinantly. See FIG.1. Therefore, the next studies focused on rEMSL1, however, other promising TE lectins examined thus far were pursued with similar approaches. Tarin lectin (EMSL3), a taro- derived lectin previously identified, as well as TE and rEMSL1, bind to high mannose N- glycans. See FIG.7 and FIG.8. [0240] TE and rEMSL1 bind to Lewisx type carbohydrate structures that are frequently overexpressed on cancer cells. See FIG.10D and FIG.13C. There is literature describing the unique glycan patterns in malignant versus normal cells, but very limited information regarding the expression of these ligands on cancer stem cells (CSC). Increased core fucosylated N-glycans in the ovarian CSC population has been reported.
Attorney Docket No.: 15024-372PC0 Patent [0241] Glycan binding profiles of TE and rEMSL1 were compared. See FIG.13, blue bars and red bars, respectively. The results show that the glycan binding profiles were remarkably similar. TE exhibited excellent binding to a pentasaccharide with a chitobiose core (GlcNAc2) as Man-5 and extension to Man-6. Further extensions with extra mannose units, however, weakened the interaction (i.e. Man-7, Man-8 or Man-9). Additionally, TE proteins displayed high affinity to complex biantennary N-glycans with both symmetric (N001 to N004) or asymmetric (i.e. N031, N051, N211) branches. N-glycan fucosylation of the terminal antennae (i.e. Lewis X), resulted in increased binding affinity (i.e. N004, N054, N214) compared to non-fucosylated counterparts (i.e. N001, N051, N211). Sialylation or addition of N-acetylneuraminic acid (Neu5Ac) to terminal glycoprotein (i.e. sialyl Lewis X) also bind TE with high affinity. Like TE, rEMSL1 bound to complex symmetrical and asymmetrical biantennary N-glycans with similar intensity, but rEMSL1 binding to high- mannose N-glycans was limited as compared to lectins reported by other groups. Importantly, the two CBS binding mutants rEMSL1-Y64A and rEMSL1-5xAla did not exhibit any specific binding to any glycan on the array. See FIG.13B. Taken together, the TE and rEMSL1 glycan microarray analysis revealed the high specificity and selectivity that TE lectins exhibit towards complex fucosylated and sialylated N-glycans, important biosignatures of TNBC and HER-2+ human breast cancers. Remarkably, a single lectin from TE, rEMSL1, could mimic this glycan-binding profile as well as the anti-metastatic activity (see FIG.8, FIG.13, and FIG.6). [0242] Example 13: Engineered rEMSL1 Characteristics. [0243] The engineered rEMSL1 can be produced in large quantities with improved bioavailability and superior anti-metastatic activity when benchmarked versus wild type (wt) rEMSL1. Wild type rEMSL1 has been structured by X-ray crystallography, and some dynamic features have been determined by NMR. See FIG.1H; sharp contours in 8.0 to 8.5 (1H region). Importantly, rEMSL1 also has significant anti-metastatic activity in vivo that is not observed in constructs mutated on the glycan binding region (see FIG.12). Thus, it is hypothesized that the glycan binding region of rEMSL1 generates anti-metastatic activity via binding to complex biantennary N-glycans, including glycoproteins such as PD-L1. [0244] The crystal structure of rEMSL1 has been solved. FIG.4D, shows stable structural domains, but some regions of dynamic character were observed by NMR (see FIG.1H, an
Attorney Docket No.: 15024-372PC0 Patent 15N-TROSY NMR spectrum of rEMSL128-253 in solution showing good dispersion of NMR resonances is observed). The glycan binding motifs that most readily interact with rEMSL1 have been characterized (see FIG.10 or FIG.13). FIG.4D shows the X-ray structure of rEMSL1 in ribbon (green) highlighting the disulfide bond (yellow) and the carbohydrate binding sites (CRS#1 and #2) in red. The rEMSL1 structure is aligned with tarin lectin MSL3 (5T20.pdb in gray) to illustrate similarity (RMSD = 0.8 Å). Glycan binding to rEMSL1 as grouped by structurally similar motifs (A, B, C, 0) is shown in FIG.8C. Motif A (red) represents N-glycans having terminal type-2 lactosamines (LacNAc), terminal N-Acetyl glucosamines (GlcNAc) Motif B (green) represents Lewis X type N-glycans; and Motif C (cyan) represents N-glycans having terminal mannose; and motif 0 (purple) represents glycans that do not bind rEMSL1. [0245] Thus, any further optimization of rEMSL1 should focus on stabilizing flexible regions of rEMSL1 while maintaining and/or improving structured regions important for glycan binding and anti-metastatic activity. Thus, while keeping functional regions of rEMSL1 intact, protein-engineering changes of amino sequence in these flexible regions are genereated and screened to find constructs with improved biophysical properties of rEMSL1 as judged via stability measurements. The stability of rEMSL1 is already reasonably high (Tm=65.0+0.5 ºC). [0246] Example 14: Recombinant EMSL1 Xray Structure and Comparison with Tarin Lectin 5T20.pdb. [0247] The crystal structure of rEMSL1 (SEQ ID#001) was solved showing stable structural domains. See FIG.4D. This crystal structure plus the identification of some regions of dynamic character observed by NMR will facilitate engineering an EMSL1 molecule with improved stability while retaining biological activity as a means to improve its therapeutic efficacy and PK/PD properties. [0248] Example 15: 100 N-Glycan Microarray Binding Assays (TE). [0249] In addition, the CBS domain is critical to the anti-cancer and glycan-binding activities, consistent with results known from the prior art. FIG.10 shows 100 N-Glycan microarray binding assays for TE and rEMSL128-253. See FIG.10A, which presents the relative fluorescence units (RFU) (y-axis) of TE (blue bars) and rEMSL1 (red bars) on the
Attorney Docket No.: 15024-372PC0 Patent 100 N-glycans array (x-axis). The data is presented as the normalized mean + s.d. of three replicates corrected by background fluorescence reading. FIG.10B illustrates fluorescence of symmetric biantennary, asymmetric biantennary, and high-mannoe N-glycans binding to TE (FIG.10B) and EMSL1 D34 (residues 28-253) (FIG.10C) on the printed 100 N-glyan microarray (ZBiotechTM 100 N-glycan) during the process of fluorescene detection FIG.10C. Representative N-glycan motifs were analyzed by MotifFinderTM. The red shadowed fucosylated antenna, also known as Lewis X carbohydrate, is a characteristic biomarker in cancer. [0250] Example 16: 100 N-Glycan Microarray Binding Assays (rMSL1). [0251] FIG.13A presents a 100 N-Glycan microarray binding assay for rEMSL1(28-253) (blue bar) and FIG.13B illustrates rEMSL1 mutant proteins rEMSL1-Y64A (orange bar) and rEMSL1-5xAla (green bar). Bar charts show Relative Fluorescence Units (RFU) (on y-axis) for selected N-glycans by their order of glycan ID (on x-axis). The data are presented as normalized mean+standard deviation of three replicates corrected by background fluorescence reading. Each experiment was repeated three times. [0252] FIG.13C shows representative N-glycan structures showing binding to rEMSL1: Complex type biantennary N-linked glycans as N001; Lewis X type N-glycans as in N224 (circled in red); Terminal Type 2 N-acetyllactosamine (LacNAc) as in N6030 (circled in blue). In addition, TE binds to high-mannose type N-glycans as Man-5. Automated analysis of glycan array data was performed using MotifFinderTM. [0253] The red shadowed fucosylated antenna is a characteristic biomarker in cancer, also known as Lewis X carbohydrate. Predominantly complex-type glycans with Man3GlcNAc2 as a predominant structure were discovered, however due to the low level of glycosylation it was not possible to determine the glycosylation sites. [0254] Example 17: Binding and Competition Studies. [0255] FIG.14 presents competitive binding studies with line 66.1 cells and recombinant eGFP-fused-EMSL1 in the presence or absence of increasing concentrations of unlabeled rEMSL1. This experiment examines binding of recombinant eGFP-EMSL1 in presence of unlabeled rEMSL1, rEMSL1-Y64A or rEMSL1-5xAla. Line 66.1 tumor cells were incubated
Attorney Docket No.: 15024-372PC0 Patent with recombinant eGFP-EMSL1 or unlabled rEMSL1. After incubation, cells were washed and fluorescence intensity analyzed by FACSCanto II cytometer and data analyzed with FlowJo software. Unlabeled rEMSL1 (400, 400 ug) was able to compete with recombinant eGFP-MSL1 (40 ug) for binding to live cells. rEMSL1D1 is able to compete with labeled rEMSL1D21 (eGFP-EMSL1D1) for binding to live murine 66.1 cells. The figure shows binding of rEMSL1D21 (eGFPbac-EMSL1D1) (geometric mean=876) is competed off by rEMSL1D1 (SEQ ID NO:9; #001) (400 μg, mean=488) but weakly by rEMSL1D1 - Y64A (SEQ ID#1001) (mean=722) or rEMSL1D1- 5xAla (mean=726). [0256] FIG.11 examines binding of recombinant eGFP-rEMSL1 in presence of unlabeled rEMSL1, rEMSL1-Y64A or rEMSL1-5xAla. Binding of recombinant eGFP-EMSL1 (Geometric mean=876) is competed off by unlabeled rEMSL1 (400ug, mean = 488) but weakly by Y64A (mean=722) or 5xAla (mean=726). [0257] Example 18: TE and rEMSL1 Inhibit Proliferation in vitro. [0258] It has been reported previously that TE inhibits the proliferation of murine and human breast cancer cell lines as well as human prostate and ovarian cancer cell lines. [0259] In our work, it was determined whether rEMSL1 could inhibit proliferation of murine 66.1 cells as follows. See FIG.15A. One hundred thousand line 66.1 cells were seeded in 24-well plates and either PBS or rEMSL1 added at the time of seeding. Seventy- two hours later, cell counts were determined by trypan blue staining. rEMSL1 was able to inhibit proliferation in a dose-dependent manner rMSL125 µg/ml vs PBS, p<0.006; rEMSL1 50 µg/ml, p<0.002; rEMSL175 µg/ml, p<0.0004. [0260] One x 105 of human line MDA-MB-231 cells were seeded and PBS, TE or rEMSL1D1 (SEQ ID NO:9; #001) was added. Seventy-two hours later, cell metabolic activity, as an indicator of cell growth, was determined by MTT assay. See FIG.15B. P values comparing TE vs PBS at 25 μg/ml=0.001; 50 μg/ml=0.000004; 75 μg/ml=0.00003. P values comparing EMSL1D1 vs PBS at 25 μg/ml=0.001; 50 μg/ml=0.004; 75 μg/ml=0.0005. Like murine breast tumor cells, human breast cancer cell line MDA-MB-231 is inhibited by rEMSL1 and TE. In replicate experiments, independent isolations of rEMSL1 were always able to inhibit cell growth, but not always as effectively as TE. [0261] The capacity of rEMSL1 and TE to inhibit proliferation then was compared. In a side-by-side comparison, rEMSL1 was comparable to TE in the ability to inhibit 66.1 cells.
Attorney Docket No.: 15024-372PC0 Patent PBS, TE, rEMSL1, Y64A or 5xAla were added to cells at final protein concentrations as indicated. At 48 hours, cell number was determined. **p<0.002. See FIG.16. Neither Y64A nor 5xAla mutant proteins led to statistically significant inhibition supporting the functional importance of the CRS. [0262] Example 19: rEMSL1 Inhibits Tumor Cell Migration. [0263] The ability of cells to migrate across a membrane in response to serum was used to model one step in the metastatic process. We determined the ability of rEMSL1 to inhibit the migration of murine tumor cell lines. Line 66.1 cells were placed in the upper well of a migration plate containing PBS or rEMSL1D1 (SEQ ID NO:9; #001) in both upper and lower chamber. FBS was added as chemoattractant. Plate well inserts: fetal bovine serum (FBS, 2%) in OPTI-MEMTM containing no rEMSL1 (control) or rEMSL1 at 1-25 µg/ml at final concentration was placed in the bottom chamber and also corresponding upper wells with the cells. After a 16-18 hour incubation, non-migrated cells were removed from the upper chamber under vacuum and migrated cells in the lower chamber were labeled with Calcein AM for 45 minutes and detected at EX-485 and Emi-520. Cells from the bottom of the inserts were dislodged using 1% colorless trypsin. Readings were taken at Ex-485 and Emi- 520 and expressed as OD. P values for rEMSL1D1 vs PBS; 1 µg/ml=n.s.; 6.25 µg/ml=0.17; 12.5 µg/ml=0.16; 25 µg/ml=0.03. [0264] The results are shown in FIG.17. The migration of line 66.1 cells was inhibited in the presence of rEMSL1 in a dose-dependent manner, achieving statistical significance at the highest concentration. Migration of 410.4 cells was also inhibited by rEMSL1. [0265] Example 20: TE and rEMSL1 inhibit cancer cells with stem-like properties. [0266] There is evidence for a breast cancer stem cell (CSC) population that is resistant to conventional therapies and is responsible for relapse and tumor progression. The potent anti- metastatic activity of TE and rEMSL1 could be related, in part, to direct inhibition of CSC. [0267] See FIG.18. Therefore, the ability of rEMSL1 to inhibit tumorsphere formation under low attachment conditions (a measure of CSC function) was examined. TumorsphereTM assays were performed in serum-free MammoCultTM medium. lIne 66.1 cells plated in ultra-low attachment plate and PBS, TE or rEMSL1D1 (SEQ ID NO:9; 1) added at time of plating. Eight days later, spheres were collected, dissociated using trypsin and cell
Attorney Docket No.: 15024-372PC0 Patent number/well calculated using trypan blue. P values for TE vs PBS; 6.25 µg/ml=0.000001; 12.5 µg/ml=0.0000007; 25 µg/ml=0.00000005; P values for rEMSL1 vs PBS; 6.25 µg/ml=n.s.; 12.5 µg/ml=0.3; 25 µg/ml=0.00004. [0268] See FIG.18, which shows that rEMSL1 was able to inhibit the ability of 66.1 cells to form primary tumorspheres but to a lesser degree than the same protein concentration of TE. Likewise, rEMSL1 or TE were able to inhibit secondary tumorspheres formed by 410.4 cells. [0269] In a separate study, Line 66.1 cells grown as tertiary tumorspheres in the presence of rEMSL1D1 (SEQ ID NO:9; #001) or PBS and on day +8, the percent of ALDH1+ cancer stem cells determined. ** P<0.0001. Some breast CSC are characterized by high aldehyde dehydrogenase activity. Aldefluor assay, ALDH1+ 66.1 CSC in tertiary tumorspheres were reduced in the presence of rEMSL1. See FIG.19. [0270] Example 21: Fluorescence microarray: rEMSL1 and TE binding to PD-L1/PD-1. [0271] PD-L1 and PD-1 represent an immune checkpoint pair that can lead to inhibition of potential anti-cancer immune responses. See FIG.20. We determined the ability of rEMSL1 (A) or TE (B) to bind to either PD-L1 or PD-1. Change of relative Fluorescence Units (RFU) (on y-axis) indicates complex formation at nM concentrations (TE KD, app =170±20 nM (mPD-1), 110±10 nM (mPD-L1), 110±20 nM (hPD-1) and 6±10 nM (hPD-L1); rEMSL1 KD, app = 210±20 nM (mPD-L1) and 250±50 nM (hPD-L1). The data are presented as normalized mean + s.d. of five replicates corrected by background fluorescence reading. Example 22: Sequences SEQ ID NO identification(s) 1 motif CXLXL 2 consensus QXDXNXVXY 3 unique TIWSSNSSSK 4. unique TIWSSSSSSK 5. unique TIWSSYSSSK 6 unique GELIIKEDDFK 7. unique LVVLGPSVFK 8 unique VLILQDDGF 9 MSL1, EMSL1 and rEMSL1D1 (UniProt:Q39487; #001) 10 MSL2, EMSL2 and rEMSL2 D1 (UniProt:A5HMM7; #201) 11 MSL3, EMSL3 and rEMSL3 D1 (PDB ID:5T20; #301) 12 MSL4, EMSL4 and rEMSL4 D1 (PDB ID:5J76; UniProt: Q39487- variant H81Y/G98K/V110D/S120D/S129G/Y210K/Y220S/V236F) 13 MSL5, EMSL5 and rEMSL5 D1 (UniProt:R9RL27; #501)
Attorney Docket No.: 15024-372PC0 Patent 14 MSL6, EMSL6 and rEMSL6 D1 (UniProt: A0A843WNH9) 15 MSL7, EMSL7 and rEMSL7 D1 (UniProt: A0A843UTK6) 16 MSL8, EMSL8 and rEMSL8 D1 (UniProt:Q43418; #801) 17 MSl9, EMSL9 and rEMSL9 D1 (TAR1; UniProt: B5LYJ9 variant L119F/R131P; #901) 18 MSL11, EMSL11 and rEMSL11 D1 19 MSL12, EMSL12 and rEMSL12 D1 20 rEMSL1D2 21 rEMSL1D3 22 rEMSL1D4 23 rEMSL1D11 24 rEMSL1D12 25 rEMSL1D13 26 rEMSL1D14 27 rEMSL1D21 28 rEMSL1D22 29 rEMSL1D23 30 rEMSL1D24 31 rEMSL1D31 32 rEMSL1D32 33 rEMSL1D33 34 rEMSL1D34 35 rEMSL2D2 36 rEMSL2D3 37 rEMSL2D4 38 rEMSL2D11 39 rEMSL2D12 40 rEMSL2D13 41 rEMSL2D14 42 rEMSL2D21 43 rEMSL2D22 44 rEMSL2D23 45 rEMSL2D24 46 rEMSL2D31 47 rEMSL2D32 48 rEMSL2D33 49 rEMSL2D34 50 rEMSL5D10 rMSL5, EMSL5 and rEMSL5 D10 (UniProt:R9RL27-K208E variant; #510) 51 rEMSL8D2 52 rEMSL8D3 53 rEMSL8D4 54 rEMSL8D11 55 rEMSL8D12 56 rEMSL8D13 57 rEMSL8D14 58 rEMSL8D21 59 rEMSL8D22
Attorney Docket No.: 15024-372PC0 Patent 60 rEMSL8D23 61 rEMSL8D24 62 rEMSL8D31 63 rEMSL8D32 64 rEMSL8D33 65 rEMSL8D34 66 rEMSL1000D1 67 rEMSL1000D2 68 rEMSL2-EMSL1 (MSL3, EMSL3 and rEMSL3 D1 (PDB ID:5T20; #301)) 69 CEA1, ECEA1, rECEA1D1 (UniProt:R9RL27) 70 CEA2, ECEA2, rECEA2D1 (UniProt:R9RL27; UniProt:R9RL27-K208E variant) 71 TCI1, ETCI1 (UniProt: Q39488; #1101) 72 TCI2, ETCI2 (UniProt: Q39489; #1201) 73 TCI3, ETCI3 (UniProt: P35812; #1301) 74-114 Fusion constructs 115-116 COLES lectin alignment (Bulb-type lectin domain-containing protein; UniProt:A0A843WNH9 - A0A843UTK6) REFERENCES [0272] All references listed below and throughout the specification are hereby incorporated by reference in their entirety. 1. Van Damme et al., The Major Tuber Storage Protein of Araceae Species 1s a Lectin. Plant Physiology 1995, 107, 1147-1158. 2. Kreike et al., Genetic diversity of taro, Colocasia esculenta (L.) Schott, in Southeast Asia and the Pacific. Theor Appl Genet 2004, 109 (4), 761-8. 3. Nunes et al., DNA barcoding assessment of the genetic diversity of varieties of taro, Colocasia esculenta (L.) Schott in Brazil. In Breeding and Genetic Engineering - The Biology and Biotechnology Research, Ltd, i. P., Ed. iConcept Press Ltd: 2015. 4. Chair et al., Genetic Diversification and Dispersal of Taro (Colocasia esculenta (L.) Schott). PLoS One 2016, 11 (6), e0157712. 5. Brown et al., anti-cancer effects of poi (Colocasia esculenta) on colonic adenocarcinoma cells In vitro. Phytother Res 2005, 19 (9), 767-71. 6. Sakano et al., Inhibition of human lanosterol synthase by the constituents of Colocasia esculenta (taro). Biol Pharm Bull 2005, 28 (2), 299-304.
Attorney Docket No.: 15024-372PC0 Patent 7. Kalariya et al., Neuropharmacological activity of hydroalcoholic extract of leaves of Colocasia esculenta. Pharm Biol 2010, 48 (11), 1207-12. 8. Goncalves et al., Influence of taro (Colocasia esculenta L. Shott) growth conditions on the phenolic composition and biological properties. Food Chem 2013, 141 (4), 3480-5. 9. Kim et al., Lignans from the tuber-barks of Colocasia antiquorum var. esculenta and their antimelanogenic Activity. J Agric Food Chem 2010, 58 (8), 4779-85. 10. Biren et al., The anti-inflammatory activity of Colocasia esculenta. Saudi Pharmaceutical Journal 2007, 15, 228-32. 11. Brown and Valiere, The medicinal uses of poi. Nutr Clin Care 2004, 7 (2), 69-74. 12. Vasant et al., Antihypertensive and Diuretic Effects of the Aqueous Extract of Colocasia esculenta Linn. Leaves in Experimental Paradigms. Iran J Pharm Res 2012, 11 (2), 621-34. 13. Eleazu et al., Ameliorative potentials of cocoyam (Colocasia esculenta L.) and unripe plantain (Musa paradisiaca L.) on the relative tissue weights of streptozotocin-induced diabetic rats. J Diabetes Res 2013, 2013, 160964. 14. Kumawat et al., Antidiabetic activity of ethanol extract of Colocasia esculenta leaves in alloxan induced diabetic rats. International Journal of PharmTech Research 2010, 2, 1246- 1249. 15. Li et al., Inhibitory effects of Colocasia esculenta (L.) Schott constituents on aldose reductase. Molecules 2014, 19 (9), 13212-24. 16. Wei et al., Characterization of anticancer, antimicrobial, antioxidant properties and chemical compositions of Peperomia pellucida leaf extract. Acta Med Iran 2011, 49 (10), 670-4. 17. Dhanraj et al., Phytochemical screening and antibacterial activity of Western region wild leaf Colocasia esculenta. J Biol Sci 2013, 2, 18-23. 18. Pereira et al., Purification and characterization of the lectin from taro (Colocasia esculenta) and its effect on mouse splenocyte proliferation in vitro and in vivo. Protein J 2014, 33 (1), 92-9. 19. Boban et al., Hypolipidaemic effect of chemically different mucilages in rats: a comparative study. Br J Nutr 2006, 96 (6), 1021-9. 20. Kaur et al., Studies on physicochemical and pasting properties of Taro (Colocasia esculenta L.) flour in comparison with a cereal, tuber and legume flour. J Food Sci Technol 2013, 50 (1), 94-100.
Attorney Docket No.: 15024-372PC0 Patent 21. Du Thanh et al., H.; Oxalate Content of Taro Leaves Grown in Central Vietnam. Foods 2017, 6 (1). 22. Kumoro et al., Kinetics of Calcium Oxalate Reduction in Taro (Colocasia esculenta) Corm Chips during Treatments Using Baking Soda Solution. Procedia Chemistry 2014, 9, 102-112. 23. Kundu et al., Antimetastatic activity isolated from Colocasia esculenta (taro). Anticancer Drugs 2012, 23 (2), 200-11. 24. Kundu et al., An Extract of Taro (Colocasia esculenta) Mediates Potent Inhibitory Actions on Metastatic and Cancer Stem Cells by Tumor Cell-Autonomous and Immune- Dependent Mechanisms. Breast Cancer (Auckl) 2021, 15, 11782234211034937. 25. Hirai et al., cDNAs encoding for storage proteins in the tubers of taro (Colocasia esculenta Schott). Jpn J Genet 1993, 68 (3), 229-36. 26. Pereira et al., Structural analysis and binding properties of isoforms of tarin, the GNA- related lectin from Colocasia esculenta. Biochim Biophys Acta 2015, 1854 (1), 20-30. 27. Pereira et al., Crude extract from taro (Colocasia esculenta) as a natural source of bioactive proteins able to stimulate haematopoietic cells in two murine models. Journal of Functional Foods 2015, 18, 333-343. 28. Pereira et al., High-resolution crystal structures of Colocasia esculenta tarin lectin. Glycobiology 2017, 27 (1), 50-56. 29. Hart and Copeland, Glycomics hits the big time. Cell 2010, 143 (5), 672-6. 30. Hauselmann and Borsig, Altered tumor-cell glycosylation promotes metastasis. Front Oncol 2014, 4, 28. 31. Fuster and Esko, The sweet and sour of cancer: glycans as novel therapeutic targets. Nat Rev Cancer 2005, 5 (7), 526-42. 32. Shajahan et al., Glycomic and glycoproteomic analysis of glycoproteins-a tutorial. Anal Bioanal Chem 2017, 409 (19), 4483-4505. 33. Shajahan et al., Tool for Rapid Analysis of Glycopeptide by Permethylation via One-Pot Site Mapping and Glycan Analysis. Anal Chem 2017, 89 (20), 10734-10743. 34. Cheng et al., DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information. Glycobiology 2017, 27 (3), 200-205. 35. Haab and Klamer, Advances in Tools to Determine the Glycan-Binding Specificities of Lectins and Antibodies. Mol Cell Proteomics 2020, 19 (2), 224-232.
Attorney Docket No.: 15024-372PC0 Patent 36. Carneiro et al., Isolation and characterization of the major albumin from Colocasia esculenta corms. Plant Science 1990, 67, 39-46. 37. De Castro et al., Spatial and Temporal Gene Expression Patterns Occur during Corm Development. The Plant Cell 1992, 4, 1549-1559. 38. Bezerra et al., A corm-specific gene encodes tarin, a major globulin of taro (Colocasia esculenta L. Schott). Plant Mol. Biol.1995, 28, 137-144. 39. Monte-Neshich et al., Characterization and spatial localization of the major globulin families of taro (Colocasia esculenta L. Schott) tubers. Plant Science 1995, 112, 149-159. 40. Van Damme et al., A comparative study of mannose-binding lectins from the Amaryllidaceae and Alliaceae. Phytochemistry 1991, 30, 509-514. 41. Van Damme et al., Phylogenetic and specificity studies of two-domain GNA-related lectins: generation of multispecificity through domain duplication and divergent evolution. Biochem J 2007, 404 (1), 51-61. 42. Shewry, Tuber storage proteins. Ann Bot 2003, 91 (7), 755-69. 43. Das et al., Characterization of a Highly Potent Insecticidal Lectin from <i>Colocasia esculenta</i> Tuber and Cloning of Its Coding Sequence. American Journal of Plant Sciences 2013, 04 (02), 408-416. 44. Sindhura et al., High mannose N-glycan binding lectin from Remusatia vivipara (RVL) limits cell growth, motility and invasiveness of human breast cancer cells. Biomed Pharmacother 2017, 93, 654-665. 45. Shetty et al., structure of a beta-prism II lectin from Remusatia vivipara. Glycobiology 2012, 22 (1), 56-69. 46. Vajravijayan et al., Structural analysis of beta-prism lectin from Colocasia esculenta (L.) S chott. Int J Biol Macromol 2016, 91, 518-23. 47. Chattopadhyaya et al., Crystal Structure of Colocasia esculenta Tuber Agglutinin at 1.74 Å Resolution and Its Quaternary Interactions. Journal of Glycobiology 2017, 06 (02). 48. Mathews et al., Isolation and characterization of full-length cDNA clones of the giant taro (Alocasia macrorrhiza) trypsin/chymotrypsin inhibitor. Plant Mol Biol 1996, 30 (5), 1035-9. 49. Pereira et al., Tarin, a Potential Immunomodulator and COX-Inhibitor Lectin Found in Taro (Colocasia esculenta). Compr Rev Food Sci Food Saf 2018, 17 (4), 878-891.
Attorney Docket No.: 15024-372PC0 Patent 50. Scott et al., Increases in Tumor N-Glycan Polylactosamines Associated with Advanced HER2-Positive and Triple-Negative Breast Cancer Tissues. Proteomics Clin Appl 2019, 13 (1), e1800014. 51. Scott and Drake, Glycosylation and its implications in breast cancer. Expert Rev Proteomics 2019, 16 (8), 665-680. 52. Scott et al., Specific N-Linked Glycosylation Patterns in Areas of Necrosis in Tumor Tissues. Int J Mass Spectrom 2019, 437, 69-76. 53. Lin et al., Evaluation of STAT3 signaling in ALDH+ and ALDH+/CD44+/CD24- subpopulations of breast cancer cells. PLoS One 2013, 8 (12), e82821. 54. Kundu et al., Prostaglandin E receptor EP4 is a therapeutic target in breast cancer cells with stem-like properties. Breast Cancer Res Treat 2014, 143 (1), 19-31. 55. United States Patent No.8,865,642. 56. Van Damme, Isolation and characterization of a lectin with exclusive specificity towards mannose from snowdrop (Galanthus nivalis) bulbs. FEBS Lett 1987;215(1):140-4.
Claims
Attorney Docket No.: 15024-372PC0 Patent CLAIMS 1. An isolated recombinant taro protein selected from the group consisting of SEQ ID NOs: 9, 10, 12, 13, 14, 15, 16, 17, 50, 71, 72, 73. 2. The isolated recombinant protein of claim 1 selected from the group consisting of SEQ ID NOs: SEQ ID NOs: 9, 10, 12, 13, 14, 15, 16, 17, 50, 71, 72, 73. 3. The isolated recombinant protein rEMSL1 (SEQ ID NO:9). 4. A pharmaceutical composition comprising a pharmaceutically acceptable carrier or vehicle and an isolated recombinant protein selected from the group consisting of SEQ ID NOs: 9 - 116. 5. A pharmaceutical composition comprising a pharmaceutically acceptable carrier or vehicle and the isolated recombinant protein of claim 1, claim 2, or claim 3. 6. A DNA expression vector that expresses one or more of the peptides of claim 1, claim 2, or claim 3. 7. The DNA expression vector of claim 5 which is codon optimized for expression in E. coli. 8. A pharmaceutical composition comprising a pharmaceutically acceptable carrier or vehicle and the DNA expression vector of claim 6 or claim 7. 9. A method of treating cancer in a subject in need thereof, comprising administering the pharmaceutical composition of claim 5 or claim 8 to the subject. 10. The compounds EMSL1, EMSL2, EMSL3, EMSL4 , EMSL5 , EMSL6, EMSL7, EMSL8, EMSL9, ETCI1, ETCI2, and ETCI3.
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| WO2024249713A3 (en) | 2025-02-27 |
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