Patent BR-112014022624-A2 (BR)
Title: métodos e materiais para tratamento de doença de pompe
Inventor: GWENDA NOELLA PYNAERT
IPC: A61K38/47
Filed: 2013-03-14
Abstract: methods and materials for treatment of pompe's disease cross-reference to related applications this application claims the benefit of u.s. provisional application serial no. 61/611,485, filed march 15, 2012. the disclosure of the prior application is considered part of (and is incorporated by reference in) the disclosure of this application. technical field this invention relates to isolated molecular complexes having acid alpha glucosidase activity, and more particularly to molecular complexes comprising at least two polypeptides derived by proteolysis from a precursor molecule, wherein the molecular complex includes at least one modification that results in enhanced ability of the molecular complex to be transported to the interior of a mammalian cell. background pompe's disease (also referred to as glycogen-storage disease type ii or acid-maltase deficiency) is a rare autosomal recessive disorder that results in an accumulation of glycogen in the lysosome due to a deficiency of acid alpha glucosidase (gaa). the build-up of glycogen causes progressive muscle weakness (myopathy) throughout the body and affects various body tissues, including the heart, skeletal muscles, live, and nervous system. pompe's disease is broadly classified into infantile and late onset forms. in the infantile-onset form, infants typically present during early infancy (4-8 months of age) with weakness and floppiness, and are unable to hold up their heads and cannot do other motor tasks common for their age, such as rolling over. without treatment, infants with pompe's disease usually die before 12 months of age due to heart failure and respiratory weakness. see, united pompe foundation. late onset forms (including juvenile and adult forms), have a later onset and progress more slowly than the infantile form. recombinant human gaa (myozyme(r) or lumizyme(r)) is used to treat pompe's disease. however, myozyme(r) or lumizyme(r) are both very expensive, with costs well over $300,000 per year. as such, there is a need for improved treatments for pompe's disease. summary in one aspect, this document features an isolated molecular complex having acid alpha glucosidase (gaa) activity and that includes at least two polypeptides (e.g., at least three or at least four polypeptides), each polypeptide having at least 85% (e.g., at least 90%, 95%, 99%, or 100%) sequence identity to a segment of the amino acid sequence set forth in seq id no: 1, each segment being derived by proteolysis of the amino acid sequence set forth in seq id no: 1 at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65). the molecular complex includes at least one modification that results in enhanced ability of the molecular complex to be transported to the interior of a mammalian cell. proteolysis of the amino acid sequence set forth in seq id no:1 further can include cleavage at one or more sites between amino acid 719 and amino acid 746 or cleavage at one or more sites between amino acid 137 and amino acid 151 of the amino acid sequence set forth in seq id no:1. proteolysis further can include cleavage at one or more sites between amino acid 719 and amino acid 746 of the amino acid sequence set forth in seq id no:1 and cleavage at one or more sites between amino acid 137 and amino acid 151 of the amino acid sequence set forth in seq id no:1. in any of the molecular complexes described herein, at least one of the polypeptides can include one or more phosphorylated n-glycans and the modification can include uncapping and demannosylation of at least one phosphorylated n-glycan. at least 40% (e.g., at least 60%, 80%, 90%, 95%, or 99%) of the n-glycans on at least one of the polypeptides can be uncapped and demannosylated. in any of the molecular complexes described herein, for one of the at least two polypeptides, the segment includes amino acids 22 to 57 of seq id no:1, and wherein for one of the at least two polypeptides, the segment includes amino acids 66 to 896 of seq id no:1. in any of the molecular complexes described herein containing at least three polypeptides, for one of the at least three polypeptides, the segment includes amino acids 22 to 57 of seq id no:1, wherein for one of the at least three polypeptides, the segment includes amino acids 66 to 726 of seq id no:1, and wherein for one of the at least three polypeptides, the segment includes amino acids 736 to 896 of seq id no:1. in any of the molecular complexes described herein containing at least four polypeptides, for one of the at least four polypeptides, the segment includes amino acids 22 to 57 of seq id no:1, wherein for one of the at least four polypeptides, the segment includes amino acids 66 to 143 of seq id no:1, wherein for one of the at least four polypeptides, the segment includes amino acids 158 to 726 of seq id no:1, and wherein for one of the at least four polypeptides, the segment includes amino acids 736 to 896 of seq id no:1. in any of the molecular complexes described herein, the at least one modification can include any one of the following fused to at least one polypeptide in the molecular complex: a ligand for an extracellular receptor, a targeting domain that binds an extracellular domain of a receptor on the surface of a target cell, a urokinase-type plasminogen receptor, or the recognition domain of human insulin-like growth factor ii. this document also features compositions that include any of the molecular complexes described herein, wherein the molecular complex is lyophilized. the composition can be packaged as a single use vial. this document also features a pharmaceutical composition that includes any of the molecular complexes described herein and a pharmaceutically acceptable carrier. the composition can be formulated for intravenous or subcutaneous administration. the composition can be formulated for intravenous infusion. in another aspect, this document features a method of treating pompe's disease. the method includes administering any of the compositions described herein to a patient diagnosed with pompe's disease. the patient can be diagnosed with infantile onset pompe's disease or late onset pompe's disease. this document also features a method for making a molecular complex. the method includes contacting a polypeptide having at least 85% sequence identity to the amino acid sequence set forth in seq id no:1 with a protease having at least 85% (e.g., at least 90%, at least 95%, at least 99%, or 100%) sequence identity to the amino acid sequence set forth in seq id no:8, wherein the protease cleaves the polypeptide at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65). the contacting step can be performed in vitro. this document also features a method for making a molecular complex that includes uncapped and demannosylated phosphorylated n-glycans. the method includes contacting a molecular complex with a mannosidase capable of (i) hydrolyzing a mannose-1-phospho-6-mannose moiety to mannose-6-phosphate and (ii) hydrolyzing terminal alpha-1,2 mannose, alpha-1,3 mannose and/or alpha-1,6 mannose linkages, the molecular complex having gaa activity and including at least two polypeptides, each polypeptide having at least 85% sequence identity to a segment of the amino acid sequence set forth in seq id no: 1, each segment being derived by proteolysis of the amino acid sequence set forth in seq id no: 1 at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65), wherein before the contacting, at least one of the polypeptides includes phosphorylated n-glycans containing one or more mannose-1-phospho-6-mannose moieties. the mannosidase can be a family 38 glycosyl hydrolase (e.g., a canavalia ensiformis mannosidase or a yarrowia lipolytica mannosidase). the contacting can occur in a recombinant fungal cell expressing the mannosidase. this document also features a method of making a molecular complex that includes uncapped and demannosylated phosphorylated n-glycans. the method includes contacting a molecular complex with a mannosidase capable of hydrolyzing terminal alpha-1,2 mannose, alpha-1,3 mannose and/or alpha-1,6 mannose linkages, the molecular complex having gaa activity and comprising at least two polypeptides, each polypeptide having at least 85% sequence identity to a segment of the amino acid sequence set forth in seq id no: 1, each segment being derived by proteolysis of the amino acid sequence set forth in seq id no: 1 at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65), wherein at least one of the polypeptides includes prior to contacting, phosphorylated n-glycans comprising uncapped mannose-6-phosphate moieties. the mannosidase can be a family 47 glycosyl hydrolase (e.g., an aspergillus satoi mannosidase), a family 92 glycosyl hydrolase (e.g., a cellulosimicrobium cellulans mannosidase), or a family 38 glycosyl hydrolase (e.g., a canavalia ensiformis mannosidase). the contacting can occur in a recombinant fungal cell expressing the mannosidase. this document also features a method of making a molecular complex that includes uncapped and demannosylated phosphorylated n-glycans. the method includes contacting a molecular complex with a mannosidase capable of hydrolyzing a mannose-1-phospho-6-mannose moiety to mannose-6-phosphate, the molecular complex having gaa activity and including at least two polypeptides, each polypeptide having at least 85% sequence identity to a segment of the amino acid sequence set forth in seq id no: 1, each segment being derived by proteolysis of the amino acid sequence set forth in seq id no: 1 at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65), wherein at least one of the polypeptides includes, before the contacting, one or more mannose-1-phospho-6-mannose moieties. the mannosidase can be a family 38 glycosyl hydrolase (e.g., a canavalia ensiformis mannosidase or a yarrowia lipolytica mannosidase). in another aspect, this document features a method of making a molecular complex that includes uncapped and demannosylated phosphorylated n-glycans. the method includes a) contacting a molecular complex with a mannosidase capable of hydrolyzing a mannose-1-phospho-6-mannose moiety to mannose-6-phosphate to uncap mannose-6-phosphate moieties on at least one polypeptide in the molecular complex, the molecular complex having gaa activity and comprising at least two polypeptides, each polypeptide having at least 85% sequence identity to a segment of the amino acid sequence set forth in seq id no: 1, each segment being derived by proteolysis of the amino acid sequence set forth in seq id no: 1 at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65); and b) contacting the molecular complex with a mannosidase capable of hydrolyzing terminal alpha-1,2 mannose, alpha-1,3 mannose and/or alpha-1,6 mannose linkages. step (a) and step (b) can be catalyzed by two different enzymes or catalyzed by a single enzyme. the contacting steps can be performed together or separately, and in either order. the contacting can occur in a recombinant fungal host cell, the fungal host cell expressing a mannosidase capable of catalyzing step (a) and a mannosidase capable of catalyzing step (b). the contacting can occur in a recombinant fungal host cell, the fungal host expressing a mannosidase capable of catalyzing steps (a) and (b). any of the molecular complexes described herein that include at least one uncapped and demannosylated n-glycan can be used to contact a mammalian cell, wherein, after the contacting, the molecular complex is transported to the interior of the mammalian cell with enhanced efficiency. the mammalian cell can be a human cell. this document also features a method of transporting a molecular complex having gaa activity to the interior of a cell. the method includes contacting a mammalian cell with the molecular complex, the molecular complex including at least two polypeptides, each polypeptide having at least 85% sequence identity to a segment of the amino acid sequence set forth in seq id no: 1, each segment being derived by proteolysis of the amino acid sequence set forth in seq id no: 1 at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65); wherein phosphorylated n-glycans on at least one of the polypeptides have been uncapped and demannosylated as set forth in the methods described herein. the mammalian cell can be in vitro or in a mammalian subject. the mammalian cell can be a human cell. in another aspect, this document features a method of transporting a molecular complex having gaa activity to the interior of a cell. the method includes contacting a mammalian cell with the molecular complex that includes at least two polypeptides, each polypeptide having at least 85% sequence identity to a segment of the amino acid sequence set forth in seq id no: 1, each segment being derived by proteolysis of the amino acid sequence set forth in seq id no: 1 at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65), the molecular complex comprising at least one modification that results in enhanced ability of the molecular complex to be transported to the interior of a mammalian cell. the mammalian cell can be in vitro or in a mammalian subject. the mammalian cell can be a human cell. the modification can include any one of the following fused to at least one polypeptide in the molecular complex: a ligand for an extracellular receptor, a targeting domain that binds an extracellular domain of a receptor on the surface of a target cell, a urokinase-type plasminogen receptor, or the recognition domain of human insulin-like growth factor ii. in another aspect, this document features an isolated fungal cell that includes an exogenous nucleic acid encoding an alkaline protease having at least 85% sequence identity to the amino acid sequence set forth in seq id no:8. this document also features an isolated fungal cell comprising a nucleic acid encoding the gaa amino acid sequence set forth in seq id no:1 and a nucleic acid encoding an alkaline protease having at least 85% sequence identity to the amino acid sequence set forth in seq id no:8. the fungal cell produces a molecular complex having gaa activity and comprising at least two polypeptides, each polypeptide having at least 85% sequence identity to a segment of the amino acid sequence set forth in seq id no: 1, each segment being derived by proteolysis of the amino acid sequence set forth in seq id no: 1 at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65) by the alkaline protease. in some embodiments, the fungal cell further comprises a nucleic acid encoding a mannosidase, the mannosidase being capable of hydrolyzing a mannose-1-phospho-6-mannose moiety to mannose-6-phosphate. in some embodiments, the fungal cell further includes a nucleic acid encoding a mannosidase, the mannosidase being capable of hydrolyzing a terminal alpha-1,2 mannose, alpha-1,3 mannose and/or alpha-1,6 mannose linkage. in some embodiments, the fungal cell further can include a nucleic acid encoding a mannosidase, the mannosidase being capable of (i) hydrolyzing a mannose-1-phospho-6-mannose moiety to mannose-6-phosphate and (ii) hydrolyzing a terminal alpha-1,2 mannose, alpha-1,3 mannose and/or alpha-1,6 mannose linkage. any of such fungal cells further can include a nucleic acid encoding a polypeptide capable of promoting mannosyl phosphorylation and/or be genetically engineered to be deficient in och1 activity. unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the exemplary methods and materials are described below. all publications, patent applications, patents, genbank(r) accession nos, and other references mentioned herein are incorporated by reference in their entirety. in case of conflict, the present application, including definitions, will control. the materials, methods, and examples are illustrative only and not intended to be limiting. other features and advantages of the invention will be apparent from the following detailed description, and from the claims. description of drawings fig. 1 is a depiction of the amino acid sequence (seq id no:1) of human acid alpha glucosidase (gaa) after cleavage of the signal sequence. fig. 2a is a depiction of the nucleotide sequence of the open reading frame (orf) of dsba-cellulosimicrobium cellulans mannosidase 5 (ccman5) (seq id no:2). fig. 2b is a depiction of the amino acid sequence of the ccman5 polypeptide with the signal sequence in bold (seq id no: 3). fig. 2c is a depiction of the amino acid sequence of the ccman5 polypeptide without signal sequence (seq id no:4). the predicted molecular weight of the ccman5 polypeptide without the signal sequence is 173 kda. fig. 3a and 3b are a series of electropherograms depicting the n-glycan analysis of rhgaa treated with ccman5 and jbman. analysis was performed using dna sequencer-assisted, fluorophore-assisted carbohydrate electrophoresis (dsa-face). the y-axis represents the relative fluorescence units as an indication of the amount of each n-glycan structure. the x-axis represents the relative mobility of each n-glycan structure through a capillary. in both fig. 3a and fig. 3b, panel a is a reference sample containing the n-glycans released from rnaseb with pngasef. in fig. 3a, panels b and c contain the n-glycan analysis from hugaa (76 kd variant) before and after treatment, respectively, with ccman5 and jbman. in fig. 3b, panels b, c, and d contain the n-glycan analysis from hugaa 76 kd form, 95 kd form, and 110 kd form, respectively. fig. 4 is a line graph of the amount of glucose formed per minute with myozyme (), 76 kda gaa (?), 95 kda gaa (?), and 110 kda gaa (?) using rabbit liver glycogen as substrate. fig. 5a contains two depictions of the glycogen levels (µg/mg protein) of individual mice in heart. fig. 5b contains two depictions of the glycogen levels (µg/mg protein) of individual mice in skeletal muscle. red dots are females, black dots are males. line represents the median of each group. fig. 6 contains a depiction of the amino acid sequence of the yarrowia lipolytica ams1 mannosidase (seq id no: 5). fig. 7 contains a depiction of the amino acid sequence of the aspergillus satoi mannosidase (seq id no:6). fig. 8 contains a depiction of the amino acid sequence of the cellulosimicrobium cellulans mannosidase 4 (ccman4, seq id no:7), with signal sequence in bold. the predicted molecular weight of the ccman4 polypeptide without the signal sequence is 184 kda. fig. 9 contains a depiction of the amino acid sequence of the aspergillus oryzae alkaline protease including the signal peptide (21 amino acids), pro-peptide (100 amino acids) and mature protein (282 amino acids) (seq id no:9). fig. 10 contains a depiction of the nucleotide sequence of the fusion construct containing the y. lipolytica codon optimized sequence encoding the a.oryzae alkaline protease (seq id no:10). restriction sites used for cloning are underlined. the nucleotide sequence encoding the linker is in bold and the nucleotide sequence encoding the his tag (10 his residues) is italicized. detailed description in general, this document provides isolated molecular complexes having acid alpha-glucosidase (gaa) activity and at least one modification that results in an enhanced ability to be transported to the interior of a mammalian cell. gaa is synthesized as a 110 kda precursor containing n-linked glycans. the precursor is proteolytically processed to remove the signal sequence and then further proteolytically processed to major species of 95 kda, 76 kda, and 70 kda. however, at least some of the peptides that are released from the precursor remain associated with the major species. see, for example, moreland et al., j. biol. chem., 280:6780-6791 (2005). thus, the molecular complexes having gaa activity described herein include at least two polypeptides (at least two, three, or four polypeptides) that are derived from proteolytic cleavage of the precursor molecule at one or more sites. at least two polypeptides in the molecular complex result from proteolytic cleavage at one or more sites in the precursor. for example, proteolysis of the amino acid sequence set forth in seq id no:1 can be between amino acid 50 and amino acid 74, e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65, to produce at least two polypeptides. a molecular complex containing two polypeptides is referred to as the 95 kda form herein. in some embodiments, at least three polypeptides in the molecular complex result from proteolytic cleavage at two or more sites in the precursor. for example, proteolysis of the amino acid sequence set forth in seq id no:1 can include, in addition to cleavage between amino acid 50 and amino acid 74 (e.g., between amino acid 50 and amino acid 74 or between amino acid 60 and amino acid 65), cleavage at one or more sites between amino acid 719 and amino acid 746 or cleavage at one or more sites between amino acid 137 and amino acid 151 of the amino acid sequence set forth in seq id no:1. a molecular complex containing three polypeptides is referred to as the 76 kda form herein. in some embodiments, at least four polypeptides in the molecular complex result from proteolytic cleavage at three or more sites in the precursor. for example, proteolysis of the amino acid sequence set forth in seq id no:1 can include, in addition to the cleavage between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65), cleavage at one or more sites between amino acid 719 and amino acid 746 of the amino acid sequence set forth in seq id no:1 and cleavage at one or more sites between amino acid 137 and amino acid 151 of the amino acid sequence set forth in seq id no:1. a molecular complex containing four polypeptides is referred to as the 70 kda form herein. it will be appreciated that cleavage can occur at one or more sites in one molecule, and that the site of cleavage can be different in different molecules. a commercially available protease mix containing proteases from aspergillus oryzae (e.g., from sigma or novozymescorp) can be used to cleave the amino acid sequence set forth in seq id no:1 between amino acids 50 and 74, e.g., between amino acids 56 and 68 or between amino acids 60 and 65. alternatively, an alkaline protease having at least 85% (e.g., at least 90%, 95%, 97%, 98%, 99%, or 100%) sequence identity to the alkaline protease from aspergillus oryzae (seq id no:8) can be used. for example, as described herein, a gaa polypeptide having the amino acid sequence set forth in seq id no:1 can be contacted with a protease having at least 85% sequence identity to the amino acid sequence set forth in seq id no:8 or seq id no: 9. seq id no: 8 is the amino acid sequence of the mature aspergillus oryzae alkaline protease. seq id no: 9 is the amino acid sequence of the aspergillus oryzae protease including the signal peptide, pro-peptide, and mature protein. the contacting can occur in vitro using protease that has been isolated from aspergillus oryzae or that has been recombinantly produced. alternatively, a fungal host can be engineered such that the gaa polypeptide and alkaline protease are both secreted into the culture medium, where the alkaline protease can cleave the amino acid sequence set forth in seq id no:1 between amino acid 50 and amino acid 74 (e.g., between amino acids 56 and 68 or between amino acid 60 and amino acid 65). the isolated molecular complexes described herein have at least one modification that results in an enhanced ability to be transported to the interior of a mammalian cell. non-limiting examples of modifications that enhance the ability of the complex of being transported to the interior of a mammalian cell include uncapping and demannosylation of phosphorylated n-glycans or peptide tags that facilitate transport. methods and materials are described herein for preparing molecular complexes containing tags or uncapped and demannosylated n-glycans. the isolated molecular complexes described herein are particularly useful for treating patients with pompe disease, including a patient diagnosed with pompe's disease, both infantile onset pompe's disease and late onset pompe's disease. pompe's disease results in an accumulation of glycogen in the lysosome due to a deficiency of gaa. the build-up of glycogen causes progressive muscle weakness (myopathy) throughout the body and affects various body tissues, including the heart, skeletal muscles, live, and nervous system. each of the polypeptide in the molecular complex have at least 85% sequence identity (e.g., at least 90%, 95%, 97%, 98%, 99%, or 100%) to a segment of the amino acid sequence set forth in seq id no: 1, each segment being derived by proteolysis of the amino acid sequence set forth in seq id no: 1 at one or more sites between amino acid 50 and amino acid 74 (e.g., between amino acid 56 and amino acid 68 or between amino acid 60 and amino acid 65). the percent identity between a particular amino acid sequence and the amino acid sequence set forth in seq id no: 1 can be determined as follows. first, the amino acid sequences are aligned using the blast 2 sequences (bl2seq) program from the stand-alone version of blastz containing blastp version 2.0.14. this stand-alone version of blastz can be obtained from fish & richardson's web site (e.g., www.fr.com/blast/) or the u.s. government's national center for biotechnology information web site (www.ncbi.nlm.nih.gov). instructions explaining how to use the bl2seq program can be found in the readme file accompanying blastz. bl2seq performs a comparison between two amino acid sequences using the blastp algorithm. to compare two amino acid sequences, the options of bl2seq are set as follows: -i is set to a file containing the first amino acid sequence to be compared (e.g., c:\seq1.txt); -j is set to a file containing the second amino acid sequence to be compared (e.g., c:\seq2.txt); -p is set to blastp; -o is set to any desired file name (e.g., c:\output.txt); and all other options are left at their default setting. for example, the following command can be used to generate an output file containing a comparison between two amino acid sequences: c:\bl2seq -i c:\seq1.txt -j c:\seq2.txt -p blastp -o c:\output.txt. if the two compared sequences share homology, then the designated output file will present those regions of homology as aligned sequences. if the two compared sequences do not share homology, then the designated output file will not present aligned sequences. similar procedures can be following for nucleic acid sequences except that blastn is used. once aligned, the number of matches is determined by counting the number of positions where an identical amino acid residue is presented in both sequences. the percent identity is determined by dividing the number of matches by the length of the full-length polypeptide amino acid sequence followed by multiplying the resulting value by 100. it is noted that the percent identity value is rounded to the nearest tenth. for example, 78.11, 78.12, 78.13, and 78.14 is rounded down to 78.1, while 78.15, 78.16, 78.17, 78.18, and 78.19 is rounded up to 78.2. it also is noted that the length value will always be an integer. it will be appreciated that a number of nucleic acids can encode a polypeptide having a particular amino acid sequence. the degeneracy of the genetic code is well known to the art; i.e., for many amino acids, there is more than one nucleotide triplet that serves as the codon for the amino acid. for example, codons in the coding sequence for a given gaa polypeptide can be modified such that optimal expression in a particular species (e.g., bacteria or fungus) is obtained, using appropriate codon bias tables for that species. in one embodiment, a molecular complex can include at lea