Patent Application
20200325217
This application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Mar. 9, 2020, is named ENZ-93-D1-D1-Application-SL.txt and is 4,096 bytes in size.
This invention relates to the field of immunotherapy, the discovery and application of pharmacological agents, and to the diagnosis and treatment of Sclerostin-related disorders.
All patents, patent applications, patent publications, scientific articles and the like, cited or identified in this application, are hereby incorporated by reference in their entirety in order to describe more fully the state of the art to which the present invention pertains.
Although the nature of a protein is dictated primarily by the particular amino acid sequences derived from transcription of its nucleic acid coding sequence, there are post-transcriptional processes that may also affect its properties. Some of these modifications are large scale rearrangements such as: (a) conversion of an inactive pro-enzyme into an active form by removal of part of an amino acid sequence; (b) protease digestion of a composite protein into individual segments with varied functions as seen in some viral proteins (for instance, the polyprotein of HIV); or (c) removal of an internal amino acid sequence (an intein) by protein splicing. In addition to these cleavage processes, modification of individual amino acids can take place by enzymatic addition of functional groups such as methyl, acetyl, phosphate, glycosyl, palmitoyl, sulfonate and ubiquitin groups.
The difference in functionality caused by these modifications can induce radical differences in properties. For instance, proinsulin is an inactive enzyme that is only found in its active form (insulin) after proteolytic cleavage transforms the protein into separate peptide chains connected by disulfide bonds. In another instance, the addition of a ubiquitin moiety doesn't necessarily affect its enzymatic functions but generates a signal for degradation of the “tagged” protein. Even relatively modest alterations, such as acetylation and phosphorylation of one or more amino acids in a protein, can induce remarkable changes in the properties of a protein target. The importance of both of these processes in controlling levels of activities within cells by such modifications can be seen by the abundance of substrate specific versions of each of these family of proteins (acetylases and kinases) within a cell. Further control is exerted by the action of proteins that reverse these changes, i.e., de-acetylases and phosphatases. These modifications can result in an increase or a decrease in the activity level of the target protein and/or a change in its physical locale.
Although the kinase and acetylase modifications are well known areas of research, the importance of sulfonation is receiving increased attention. For recent reviews see Stone et al., 2009 New Biotechnology 25; 299-317 and Monigatti et al., 2006 Biochim Biophys Acta 1764 1904-1913). Sulfonation of Tyrosines is believed to take place in about 1% of the Tyrosines in proteins and appears to facilitate protein-protein interactions (Baeuerle and Huttner 1985 JBC 260; 6434-6439, Kehoe and Bertozzi 2000 Chem Biol 7; R57-R61). Of special interest the connection between sulfonation with receptors and their ligands, since the enzymes, TPST-1 and TPST-2, responsible for sulfonation are localized in the Golgi apparatus. Although these have been observed to be mostly cytokine receptors and their ligands, it has been recently noted that unsulfonated Wnt does not generate as strong a signal as sulfonated Wnt, presumably due to a differential ability of the unsulfonated ligands to bind the LRP5/6 receptors that are involved in the Wnt signaling system (Cha et al., 2009 Current Biol 19; 1573-1580). In addition to Tyrosine, evidence has become available that Serine and Threonine are also potential sites, although at the present time it is not known if this is carried out by the same enzymes (TPST-1 and TPST-2) that modify Tyrosines or if some enzyme or enzymes are responsible (Medzihradszky et al., 2004 Molec Cell Proteomics 3; 429-440).
Testing for the presence of sulfonation modifications in a protein can be carried out using various methods (for reviews, see Monigatti et al. 2006, Stone et al. 2009 and Seibert and Sakmar 2007 Polymer 90; 459-477). The two most popular methods for this type of analysis is the use of mass spectrometry (MS), or antibodies that are specific for Sulfo-Tyr. With regard, to mass spectrometry, definitive answers on the presence of sulfonated Tyrosines can be achieved, but due to the lability of the bond between the sulfonate group and Tyrosine, special modifications have to be made to the standard mass spectrometry protocols (Drake and Hortin, 2010 Int J Biochem Cell Biol 42; 174-179). In a more biological approach, antibodies have been developed that can detect the presence of sulfonated Tyrosine residues. Antibodies have been developed that can detect the presence of sulfonated Tyrosine's regardless of the particular peptide sequence they are embedded within (Kehoe et al., 2006 Molec Cell Proteomics 5; 2350-2363; Hoffhines et al., 2006 J. Biol Chem 281; 37,877-37,887). The general nature of their recognition allows a wide variety of different proteins to be recognized as long as they contain a sulfonated Tyrosine. In many cases, proteins have to be isolated or separated for this type of analysis to observe individual effects, since there is no discrimination between the different sulfonated proteins by such antibodies. For instance, the extent of sulfonation can be determined for individual isolated proteins of interest or patterns of a group of proteins can be analyzed. On the other hand, antibodies have been developed for a specific protein with a sulfonated Tyrosine. These antibodies can detect differences between sulfonated and non-sulfonated forms and can identify the presence of the sulfonated protein in a mixture of other proteins (Bundgaard et al., 2008 Methods Mol Bio 446; 47-66). The specificity of the epitope requires that a new antibody has to be developed for each particular protein of interest.
As information has accumulated concerning the amino acid sequences that are used as substrates for sulfonation, it has become clear that there is no simple consistent recognition sequence (see Niehrs et al., 1990 JBC 265; 8525-8532, Bundgaard et al., 1997 JBC 272; 31,700-31,705 for instance). A computer program called “Sulfinator” has been created recently that is capable of analyzing protein sequences and predicting the presence or absence of sulfonation sites (Monigatti et al. 2002 Bioinformatics 18; 769-770). The program achieves its highest accuracy only when proteins are tested that are either receptors, or ligands for receptors, because these are proteins that are processed through the Golgi apparatus where the TPST-1 and TPST-2 enzymes are localized. Proteins that are cytosolic in nature are physiologically irrelevant since even if they have appropriate sequences they would never come into contact with the Tyrosine sulfotransferases. The Sulfinator does not detect the extent of sulfonation.
In detecting the extent of sulfonation, experiments have shown that even proteins that are substrates for sulfonation do not always represent a homogeneous population with complete sulfonation. For instance, gastrin peptides which are easily sulfonated show a mixed population of both sulfonated and unsulfonated forms in roughly equal proportions (Hilsted and Rehnfeld 1987 JBC 262; 16,953-16,957). In another instance, there may be tissue specific differentiation on the extent of Tyrosine sulfonation of Chromogranin A that depends upon whether it is made in parathyroid or adrenal cells (Gorr and Cohn, 1999, JBC 265; 3012-3016). Different effects have also been observed for proteins such as gastrin/cholecystokinin peptides and their precursors where varying degrees of modification are seen during ontogenesis and pathogenesis of certain diseases (Rehfeld et al., 1989 Biochimie 70; 25-31). Furthermore, in certain circumstances, such as in the expression of cloned recombinant proteins, there may be undersulfonation of proteins that would otherwise be completely modified (Seibert and Sakmar 2008 Biopolymers 90; 459-477).
Although extensive efforts have been made in searching for pharmaceutical agents that affect kinase activity, compounds that affect sulfonation modifications have only recently attracted attention (for instance, see Hemmerich et al., 2004 Drug Discovery Today 9; 967-975). The potential utility of influencing sulfonation reactions can be seen, however, by recent discoveries that CCR5, one of the receptors for recognition of HIV, is sulfonated. The importance of this modification can be seen by results with chlorate (an inhibitor of Tyrosine sulfonation), where the presence of this factor decreases the affinity of gp120/CD4 complexes towards the CCR5 receptor (Farzan et al., 1999 Cell 96; 667-676). Although there are instances where the presence of a sulfonation modification may enhance binding, there are also numerous instances where there is actually an absolute requirement for sulfonation to have taken place in order for certain proteins to have biological activity (Farzan et al., 2001 J Exp Med 193; 1059-1065, Costaglia et al. 2002 EMBO J 21; 504-513, Gao et al., 2003 JBC 278; 37902-37908, Gutierrez et al., 2004 JBC 279; 14726-14733, Hirata et al., 2004 JBC 279; 51775-51782, Fieger et al., 2005 FASEB J 19; 1926-1928 and Colvin et al., 2006 Molec Cell Biol 26; 5838-5849).
Furthermore, in vitro studies also show the importance of sulfonation with regard to binding of gp120/CD4 complexes with CCR5 peptides (Cormier et al., 2000 Proc. Nat. Acad. Sci USA 97; 5762-5767). As such, it has been recognized that the disruption of the sulfonation of CCR5 may be a treatment for HIV infection and disease processes. In another example, Liu et al. 2008 (Am J Resp Cell Molec Biol 38; 738-743) hypothesized that sulfonation was a general feature of cytokine receptors and found that at least 10 different cytokine receptors that are involved in asthma and chronic obstructive pulmonary disease (COPD) are sulfonated. On this basis, the authors concluded that incorporation of this discovery into the structural design of receptor antagonists might show value in the development of effective drug therapies for asthma, COPD and similar inflammatory lung diseases.
Changes in sulfonation patterns have also been found for tumour derived enzymes (Itkonen et al., 2007 FEBS Journal 275; 289-301 and a dependency on sulfonation has been shown for binding of P-selectin to cancer cells (Ma and Geng 2002 J Immunol 168; 1690-1696) and tumorigenesis (Feng et al., 2010 J Vir 84; 3351-3361).
The present invention is based upon the discovery that Sclerostin possesses post-translational modifications where at least two amino acids are sulfonated in vivo. It is known that sulfonation modifications are frequently involved in protein-protein interactions and as such, it has been found that Sclerostin exhibits sulfonation-dependent alterations in a variety of biological properties that are likely derived from protein-protein interactions. These include effects on the binding of Sclerostin to the LRP5 receptor as well as differential effects upon Wnt signaling as judged by inhibition of blockage by various amounts of Sclerostin on the induction of alkaline phosphatase by Wnt. The discovery of modifications of these proteins allows recognition of previously unknown epitopes that can be used as the basis for the selection of antibodies against the sulfonated regions of these proteins for diagnostic or therapeutic purposes.
Thus, in one particular embodiment of the present invention, antibodies are isolated or produced that recognize the sulfonated portions of Sclerostin. The antibodies may be specific for epitopes where the amino acid is sulfonated. Alternatively, the antibody may recognize and bind only to epitopes where the amino acid remains unsulfonated.
In another embodiment of the present invention, antibodies are isolated or produced that recognize the sulfonation region of Sclerostin, regardless of whether the amino acid in this target region is sulfonated or not. The antibodies of the present invention may be used alone or in conjunction with other previously described antibodies to Sclerostin that may be specific to regions that do not comprise sulfonation modification sites.
Another embodiment of the present invention is directed towards diagnostic utility, where the potential dependency of biological properties on the presence or absence of sulfonation in these sites would allow evaluation of clinical properties that may depend upon the degree of sulfonation of these proteins. This may be used for the identification of a disease condition or used to monitor the effects of a therapeutic program.
In another embodiment of the present invention, antibodies against the sulfonate modified regions of Sclerostin may be administered to block or interfere with binding of Sclerostin with an interacting protein, thereby reducing the functional activity of Sclerostin in a subject and providing beneficial effects.
Furthermore, in another embodiment of the present invention, the discovery of a linkage between the sulfonation state of Sclerostin and biological activity presents an opportunity to use the sulfonated regions as targets for intervention, where pharmaceutical compounds may be used to affect the degree of sulfonation and thereby modulate the biological activity of Sclerostin.
In another aspect of the present invention, potential differential effects of therapeutic compounds on sulfonated or unsulfonated forms of Sclerostin may now be addressed due to the discovery of sulfonation modifications in Sclerostin. Consequently, virtual screening processes for identification of compounds that bind to selected sites on Sclerostin may now be carried out where the virtual model of the target molecule includes a substitution of the sulfonated amino acid for the unmodified form in Sclerostin, thereby altering projected binding affinities when compounds are screened.
Another embodiment of the present invention makes use of the fact that sulfonation modifications are usually involved in protein-protein interactions, and as such, the identification of sulfonation modification sites in Sclerostin serves as an indication that these regions can be indentified as previously unknown sites that participate in interactions with other protein molecules. Therefore, in another embodiment of the present invention, the synthesis of peptides that comprise the sulfonation region may have utility as modulators, altering the ability of Sclerostin to interact with its binding partners. In carrying out such a role, both sulfonated and unsulfonated forms of such peptides may provide utility.
Lastly, interactions between Sclerostin and a binding partner are usually described in the context of heterodimeric complexes such as Sclerostin/LRP or Sclerostin/BMP receptor. It is a further consideration of the present invention, however, that the discovery of sulfonation modifications may have ramifications with regard to homodimeric complexes that may take place between two Sclerostin monomeric units.
The present invention describes the discovery that Sclerostin, a ligand of various LRP receptors, can be sulfonated in at least two different sites, Tyr43 and Tyr213 (using the UniProtKB Accession No. Q9BQB4 of unprocessed Sclerostin as reference points). A further discovery is that an ex vivo sulfonation treatment of a preparation of recombinant Sclerostin results in an increase in the affinity of the Sclerostin to the LRP5/6 receptor as well as an increase in its ability to suppress Wnt induced expression of Alkaline Phosphatase. Various means may be employed to determine the presence of sulfonation modifications in proteins of interest. As described in Example 2 below, mass spectrometry (mass spec) analysis was carried out using Sclerostin that was expressed in cells capable of carrying out post-synthetic modifications such as sulfonation. It should be noted that the standard conditions that are usually employed in mass spec studies leads to a rapid loss of sulfonate groups. As such, when detection of sulfonated targets is desired, avoidance of acidic conditions and lower energy inputs are required in order to increase the sensitivity of detection of sulfonated Tyrosines in specimens of interest (Drake and Hortin, 2010). This type of analysis may lead to the identification of the presence of sulfonated Tyrosines and in many cases the exact position of the sulfonated amino acid. A caveat to be considered is that the simultaneous presence of both sulfonated and unsulfonated Tyrosines for a given fragment does not give any estimate for their relative proportions prior to analysis since the process is still liable to losses of sulfonate moieties, thereby generating some unsulfonated Tyrosines de novo. Distinguishing between pre-existing and converted unsulfonated Tyrosines is problematic and as such, mass spec serves best as a qualitative tool for whether sulfonation occurs at all at a given site.
Prior to carrying out the mass spec analysis, some of the Sclerostin was used in a reaction with TPST-1 (Example 1) such that if any Tyrosine modification sites were present in the sample they could be converted into a modified from. As described in the mass spec analysis described in Example 2, the presence of sulfonation modifications was found in both the treated and untreated samples of Sclerostin, indicating that the recombinant Sclerostin being tested had undergone sulfonation modifications prior to secretion from the cells used for recombinant expression. As noted above, however, the mass spec analysis can determine the presence of sulfonation modifications, but is unable to provide information on whether there is complete or partial modification on the sulfonation sites. A protein having the appropriate sulfonation sequence may be a candidate for post-synthetic modification as it passes through the Golgi apparatus prior to secretion outside of a cell, but recombinant expression systems are essentially abnormal states and there may be undersulfonation of sites that normally would be fully converted.
As such, treated and untreated Sclerostin has been used in biological assays to investigate whether there were any differences in the properties of Sclerostin after an in vitro treatment. As described in Example 3 and as shown in
A further method of investigation is the use of a software program called Sulfinator that can predict the presence of a sulfonation site with 98% accuracy from the amino acid sequence alone. When the sequences from Sclerostin were analyzed with this program, it successfully identified the amino terminal modification of Sclerostin at Tyr43 detected by MS analysis but missed the carboxy terminal modification at Tyr213. The failure in predictability is likely due to the Tyrosine in Sclerostin that is modified at the carboxy end of Sclerostin being the terminal amino acid itself; since the Sulfinator program uses the neighboring sequences surrounding a Tyrosine for evaluating its likelihood of being sulfonated, by definition, a terminal Tyrosine of Sclerostin would intrinsically lack sequences on one side. It should be pointed out that although the presence of a site predicted to be a sulfonation site is likely dependable, there are incidents where sulfonation modifications were unrecognized by the Sulfinator program but later identified in physical studies (Onnerfjord et al., 2004 JBC 279; 26-33, Hoffhines et al., 2006 JBC 281; 37877-37887). Nonetheless, the recognition of the Tyr43 modification by the Sulfinator program is an independent confirmation of the sulfonation of this particular amino acid in Sclerostin.
It should be understood that although sulfonated Tyrosines have been observed in many secreted ligands and their receptors, their presence is not necessarily required and it is inappropriate to make any predictions about their presence in the absence of any investigational analysis. As noted above, it has been estimated that ˜1% of the Tyrosines in cellular proteins are modified Tyrosines (Huttner 1984 Methods Enzymol 107; 200-223) which in turn has the implication that ˜99% of them would not have this modification.
The discovery that Sclerostin, which participates in the Wnt signaling system, has modified amino acids offers unique methods of analysis as well as therapeutic means. As described in earlier related patent applications (2005/0196349; 2006/0030523; 2008/0119402, hereby incorporated by reference), compounds that block the interaction between LRP5/6 receptors and the Dkk and Sclerostin ligands can offer a variety of useful therapeutic means. Since it has now been discovered that the amino acid sequence of Sclerostin can also comprise a post-synthetic sulfonation modification, compounds that have been previously tested for effects on Sclerostin with regard to Wnt signaling may be retested using separate reaction mixtures or binding assays where either the modified or unmodified versions of these proteins are tested separately. As has been pointed out earlier, some proteins exist as a mixture of sulfonated and unsulfonated forms and previous experiments may have been based upon such a mixture, without recognition that the net effects might be a composite of the individual effects on modified and unmodified Sclerostin. Control over the particular form (sulfonated or unsulfonated) of Sclerostin will now allow investigation into whether compounds are more or less effective with regard to using sulfonated or unsulfonated versions of Sclerostin in assays. The lack of recognition of the potential presence of a mixture of different forms also allows for the possibility that some effective compounds may have been missed due to the use of Sclerostin preparations that had a preponderance of one form over another.
Furthermore, the presence of a site that is involved in protein-protein interactions is in itself a potential therapeutic target. Thus, a series of compounds can be surveyed to see if they specifically interrupt in vitro or in vivo sulfonate modification of the Tyrosines in Sclerostin. Such pharmaceutical agents would have the potential for modifying the level of activity induced by Sclerostin by controlling the degree of sulfonation and thereby their affinity in protein-protein interactions. Pharmaceutical reagents that may be used to disrupt sulfonation processes can include but not be limited to small molecules, peptides, organic molecules, cyclic molecules, heterocyclic molecules, lipids, charged lipids, glycolipids, polar lipids, non-polar lipids and aptamers. The compounds may be ones that have been designed to bind to the surface of Sclerostin through a virtual screening process as described in US Patent Application No. 2005/0196349. Contrariwise, compounds may be tested independently from virtual screening and tested strictly on a random basis or they may be selected to have a physical resemblance to compounds that result from virtual screening processes. In this process, a revised virtual structure of sclerostin may be devised to takes into consideration the presence of the sulfonation of amino acids. Such a process can also include the use of mutational substitutions at the modification sites (see, for instance, Wu et al., 2005/0196349). Thus, a series of (selected or random) compounds may be assayed for an ability to eliminate or reduce sulfonation of Sclerostin, by any means that have previously been described for analysis and/or detection of sulfonation of proteins. As a control, one or more proteins that also have sulfonation sites may be included to insure that the blockage of sulfonation is specific for the target of interest. Any means that have been described in the past for detection of the presence of sulfonated Tyrosines may be used in this aspect of the present invention, thus for example, these means may be as complex as carrying out MS analysis to simpler methods such as incorporation of 35S PAPS by TPST, immunoassays that use antibodies that recognize proteins with sulfonated Tyrosines irrespective of their context (Kehoe et al., 2006 and Hoffhines et al., 2006), or antibodies that are specific for the sulfonated or unsulfonated forms of Sclerostin (as will be discussed in more detail below). If desired, truncated versions of Sclerostin that comprise the target area of interest may also be used as substrates in assays as long as their biological structures/functions are similar to the parent protein. In addition, peptides that may represent the sulfonation site of Sclerostin may also be used for evaluation.
Investigations into compounds that might interrupt sulfonation of proteins has been previously described by Hortin et al., 1988 BBRC 150; 342-348 where compounds were found that were non-specific in that they inhibited sulfonation of proteins, oligosaccharides and proteoglycans (although with varying efficiencies). A similar study has been done more recently by Kehoe et al., 2002 (Bioorg Med Chem Letters 12; 129-132) where two compounds were identified that inhibited sulfonation by TPST-2. Similar to the results published earlier by Hortin et al., further testing showed that the inhibitors affected other sulfotransferases as well. Even if these inhibitors only affected the TPST reaction itself, however, this approach would indiscriminately block sulfonation of a wide variety of different protein targets and thereby lead to potentially toxic effects. It should be noted that knockout mice lacking either TPST-1 (Ouyang et al., 2002 JBC 277; 23,731-23,787) or TPST-2 (Borghei et al., JBC 281; 9423-9431) activity are essentially viable but exhibit a variety of pleiotropic defects. Partial overlap in the functionality of the two TPST enzymes can be seen by experiments with a double knockout that is missing both TPST-1 and TPST-2 where most progeny died soon after birth and any survivors failed to thrive (Westmuckett et al., 2008). These double knockouts exemplify a situation that may be more akin to the presence of a general TPST inhibitor. In addition, as noted previously, there are many proteins involved in protein-protein interactions where sulfonation is obligatory for biological activity and some are involved in inflammatory responses that require sulfonation for functionality; as such, it may be that the double knockouts are phenotypically silent except under certain conditions where such responses would be induced or required. Targeting the modification of a particular sulfonation target as described in the present invention is likely to be superior to efforts to block sulfonation in general since it is likely to have more specific effects than a general blockage that may produce deleterious as well as beneficial effects.
The identification of peptide sequences comprising a modified Tyrosine also allows the use and design of artificial peptides that contain these modifications. Presumably these should have higher binding affinities than their unmodified counterparts. Binding of these peptides to the protein that normally interacts with the complete protein may produce a variety of effects. For instance, some of these peptides could act in a positive fashion by invoking the same response that the intact protein induces. Contrariwise, the peptide could act as a competitive inhibitor and prevent the intact protein from binding. For example, a peptide with sequences from either the carboxy or amino end could reduce the ability of Sclerostin to bind to a LRP receptor. Although the sulfonated peptide would be the basis for the design, it is understood that the actual components can be artificial equivalent of these peptides. Examples of compounds made with such components can comprise but not be limited to the peptide mimetics described in related pending U.S. patent application Ser. No. 11/097,518, as well the substitution of dextro isomers instead of the normal levo forms and peptidomimetics such as those described in Hammond et al., 2006 Chem & Biol 13; 1247-1251. Other examples of analogs that may find use with the present invention are “unnatural amino acids” where in it is understood that in the context of the present invention “unnatural amino acids” refers to amino acids that are not genetically encoded i.e. they are not represented by a nucleotide triple codon. This would include the dextro isomers discussed above as well as other amino acids such as Aib (amino-isobutyric acid), bAib (3-aminoisobutyric acid), Nva (norvaline), β-Ala, Aad (2-amino-adipic acid), bAad (3-aminoadipic acid), Abu (2-aminobutyric acid), Gaba (γ-aminobutyric acid), Acp (6-am inocaproic acid), Dbu (2,4-diaminobutyric acid), TMSA (trimethylsilyl-Ala), aIle (allo-Isoleucine), Nle (Norleucine), tert.Leu, Cit (Citrulline), Orn, Dpm (2,2′-diaminopimelic acid), Dpr (2,3-diaminopropionic acid), α- or β-Nal, Cha (cyclohexyl-Ala), hydroxy-proline, Sar (Sarcosine) etc., cyclic amino acid units and Na-alkylated amino acid units, e.g. MeGly (Nα-Methyl-glycine), EtGly (Nα-ethylglycine) and EtAsn (Nα-ethyl-asparagine). Accordingly, synthetic peptides can be made that include one or more of these unnatural amino acids.
Another series of reagents that may be effective are antibodies directed to the sulfonation site. In the first place, the identification of the sulfonation site offers evidence that the site is likely to be involved in protein-protein interactions. Thus, for instance, the particular portion of the Sclerostin protein involved in interaction with LRPS/6 has not been clearly identified, but the discovery of the sulfonation site of Sclerostin in the amino terminal sequences described in Example 2 provides a novel target for antibody binding that might affect the interaction of Sclerostin with LRPS/6 that is different from the Sclerostin sequences previously postulated by Ververka et al., 2009 JBC 284; 10,890-10,900, Weidauer et al., 2009 BBRC 380; 160-165 and Krumlauf in U.S. Pat. No. 7,585,501. In one embodiment of the present invention, an epitopes is five amino acids or greater. In another embodiment, the epitope encompasses ten or more amino acids. A comparison of the identity and location of potential epitopes of the present invention and sequences used as epitopes in prior art is given in
Development and isolation of antibodies that are targeted to the sulfonation regions discovered and described in the present invention may be carried out by any of the means that have been described previously, including those taught in Bundgaard et al., 2008; Hoffhiner et al., 2006; Kehoe et al. 2006, Craig et al., 2009 Hybridoma 28; 377-381; U.S. Pat. No. 7,585,501, US Patent Application 2004/0009535 and US Patent Application 2009/02130113, all of which are incorporated by reference. One source of antigens that may be used for this purpose can be artificial peptides that represent the sulfonated sequences; these can be obtained from a wide variety of commercial sources that provide custom made peptides. The peptide or peptides used for immunization may be modified or unmodified, depending upon whether the antibody is desired to recognize the modified or unmodified epitope. Post-synthetic modifications can be carried out either chemically or by in vitro modification by TPST-1. Screenings of antibody libraries can then be carried out to determine the nature of the recognition such that it is specific for the sulfonated version of the target protein, the unsulfonated form or is independent of the state of sulfonation. In addition to such custom libraries, pre-existing libraries such as the HuCal phage library is commercially available from AbD Serotec (Raleigh, N.C.) and is advertised as having more than 15 billion functional human antibody specificities. Another commercially available library comprises camelid derived antibodies and is available from Ablynx, Ghent, Belgium. These libraries have the advantage of not requiring any particular immunogen prior to screening. Screenings of this library may also be carried out as discussed above. The antibody of the present invention may take any form that is described for use in immunodetection or immunotherapy. For instance, the antibody may be polyclonal, monoclonal, chimeric, human, humanized, bispecific, multispecific, primatized or an antibody fragment. Antibody fragments that me be of use in the present invention may comprise but not be limited to is Fab, ScFv, Fab′, F(ab′)2, Fv, Fv(ab)2 or aggregates thereof.
The presence of a sulfonation group should in itself be sufficient to define part of an epitope. In an analogous fashion for another post-synthetic modification, the literature is replete with a large number of antibodies that are dependent on targets being either in phosphorylated or unphosphorylated forms and these form the basis of numerous assays for kinase activity. Furthermore, as described previously, the presence or absence of such small chemical moieties as a phosphate or sulfonate group can have profound effects upon activity, thus validating the ability of biological partners to be able to recognize the differences between modified and unmodified forms. Specific examples of the search and identification of antibodies that are specific to epitopes of target proteins comprising a sulfonated Tyrosine have been described by Bundgaard et al., cited above. In a further example, an antibody (Mab15) that was selected for recognizing thyrotrophin receptor (TSHr) was found to have an epitope that was only found in mature forms of its target protein suggesting that some form of processing was required to create the appropriate epitope (Costagliola et al., 2002 EMBO J 21; 504-513). In vivo treatment of cells with chlorate (which as mentioned earlier reduces sulfonation modifications) resulted in production of a mature protein that was now unrecognizable by Mab15 indicating that the antibody was able to distinguish between the sulfonated and unsulfonated forms of its epitope and would only bind to the sulfonated version. Thus, even though it was not originally selected for this feature, the use of sulfonated antigens allowed isolation and identification of an antibody specific for a sulfonate epitope in this target.
Although peptides may be used for the generation of linear epitopes, antibodies can also be found that recognize a three-dimensional set of determinants (sometimes referred to as interrupted epitopes or non-linear epitopes) and development and isolation of these types of antibodies can be carried out by using three-dimensional antigens such as the entire protein of interest or selected fragments as immunogens. Such antibodies may also be realized from screening of pre-formed libraries that are independent of an immunogen. Screening can then be carried out for an ability to distinguish between sulfonated and unsulfonated versions of the protein of interest. For a discussion on the use of conformationally derived epitopes, see Van Regenmortel 1998, J Immunol Methods 216; 37-48, Villen et al., 2001 Biologicals 29; 265-269, Moreau et al., 2006 Bioinformatics 22; 1088-1095 and Huang and Honda 2006 BMC Immunology 7; 7.
In addition to acting as pharmacological agents, the development of antibodies directed against the sulfonation site of Sclerostin, may also find use for analytical or diagnostic purposes for evaluating the presence of sulfonated proteins and/or the extent of sulfonation. As described previously, shifts in the level of sulfonation levels has previously noted to be a feature of gastrin and cholcystokinin in cancer cells (Rehnfeld, 1990). The protein samples may be products that are excreted in the media or they may be derived from cell extracts. By these means, evaluation of physiological levels of sulfonation of Sclerostin can be carried out with biological specimens. These may be used in a variety of ways to compare specimens that differ from each other in terms of origin, treatment or physiological conditions. An antibody specific for a sulfonated form of a target protein may be used alone for this purpose or it may be combined in an assay that further includes an antibody directed towards the unsulfonated form or an antibody that recognizes both sulfonated and unsulfonated forms. In reference to the latter, an ability to recognize both sulfonated and unsulfonated forms may be a property of an antibody that recognizes the epitope where the sulfonation is located but is generically independent of the sulfonation state, or it can an antibody that lacks relevance to the sulfonation state by recognizing an epitope that is located outside of the modification region of Sclerostin.
As discussed above, antibodies of this nature may also be used to evaluate in vitro assays of sulfonation where they may be used to monitor conversion of the unsulfonated form into the modified form. These antibodies may also be used alone or in conjunction with antibodies that recognize an epitope specific for the unsulfonated form and/or for antibodies to an epitope in an amino acid sequence different from the sulfonation sequence. Thus, for instance, an antibody that is specific for the sulfonated form of Sclerostin may be used in conjunction with an antibody that is specific for an unsulfonated region of Sclerostin for normalization purposes. In another example of use, an antibody that is specific for the unsulfonated form can be used in conjunction with an antibody that recognizes the same region but essentially offers no discrimination between the sulfonated and unsulfonated forms of the antigen. Alternatively, two antibodies can be used where one is specific for the sulfonated form and another is for the unsulfonated form.
Furthermore, although the binding of Sclerostin to an LRP receptor is responsible for biological effects, it is also known that Sclerostin interacts with other proteins such as BMPs (Bone Morphogenic Proteins) (Winkler et al., 2003 EMBO J 22; 6267-6276), Noggin (Winkler et al., 2004 J Biol Chem 279; 36293-36298) and “Cysteine-rich protein 61” (Craig et al 2010 (BBRC 392; 36-40). As such, the discovery of the sulfonated amino acids in Sclerostin allows application of the present invention to interactions between Sclerostin and these other proteins as well as the interactions with LRP receptors. Additionally, although the Tyrosine modifications have been discussed in terms of alterations of a Sclerostin's affinity for a binding partner in a heterodimeric interaction, dimerization is also an example of a protein/protein interaction and as such, a homodimeric Sclerostin interaction may also be influenced by sulfonation modifications, and Sclerostin itself, should be included in the potential list of binding partners for Sclerostin. The degree of dimerization may have further effects with regard to binding to other proteins, where the affinity of a dimeric protein may be higher than that of a monomeric form. For instance, see Jekel et al., Biochimica Biophica Acta 1996 1291; 195-198 where the affinity of a dimerized antigenic peptide is higher than the monomeric form with regard to binding to an antibody. In another instance, TNF-α exists in trimeric form and binds to three receptors simultaneously (Banner et al., 1993, Cell, 73:431-445). Since dimerization or multimerization of proteins may be affected by sulfonation processes, the methods above may also be applied to homodimeric interactions when the ability of a compound to affect sulfonation is being analyzed. Assays that measure the ability of sulfonated and unsulfonated Sclerostin to form a complex with a binding partner may also be carried out with another Sclerostin molecule as the intended binding partner. Antibodies may also be developed that are specific to dimers as compared to monomers as previously described by Raven et al., in US Patent application No. 20050163776. Selectivity may be carried out by testing for the ability to react with dimers and then counter-selecting by eliminating antibodies that exhibit cross-reactivity with the monomeric form.
Antibodies directed against sulfonation sites in Sclerostin and pharmaceutical agents that disrupt or inhibit sulfonation of Sclerostin may find theraputic utility with a variety of “Sclerostin-related disorders”. The compositions and methods of the present invention are particularly suitable for treating, preventing or diagnosing Sclerostin-related disorders and/or aberrant bone mineral density disorders, e.g., osteoporosis. Compositions of the present invention may also be useful for improving outcomes in orthopedic procedures, dental procedures, implant surgery, joint replacement, bone grafting, bone cosmetic surgery and bone repair such as fracture healing, nonunion healing, delayed union healing and facial reconstruction. One or more compositions may be administered before, during and/or after the procedure, replacement, graft, surgery or repair.
As used herein, “a Sclerostin-related disorder” includes disorders in which bone mineral density (BMD) is abnormally and/or pathologically low relative to healthy subjects. Disorders characterized by low BMD and/or bone fragility include but are not limited to primary and secondary osteoporosis, osteopenia, osteomalacia, osteogenesis imperfecta (OI), avascular necrosis (osteonecrosis), fractures and implant healing (dental implants and hip implants), bone loss due to other disorders (e.g., associated with HIV infection, cancers, or arthritis). Other “Sclerostin-related disorders” include but are not limited to rheumatoid arthritis, osteoarthritis, arthritis, and the formation and/or presence of osteolytic lesions.
As used herein, “a Sclerostin-related disorder” includes conditions associated with or characterized by aberrant Sclerostin levels. These include cancers and osteoporotic conditions (e.g., osteoporosis or osteopenia), some of which overlap with “Sclerostin-related disorders” as defined herein. Sclerostin-related cancers can include myeloma (e.g., multiple myeloma with osteolytic lesions), breast cancer, colon cancer, melanoma, hepatocellular cancer, epithelial cancer, esophageal cancer, brain cancer, lung cancer, prostate cancer, or pancreatic cancer, as well as any metastases thereof.
A “Sclerostin-related disorder” can also include renal and cardiovascular conditions, due at least to Sclerostin's expression in the kidney and cardiovasculature. Said disorders include but are not limited to such renal disorders as glomerular diseases (e.g., acute and chronic glomerulonephritis, rapidly progressive glomerulonephritis, nephrotic syndrome, focal proliferative glomerulonephritis, glomerular lesions associated with systemic disease, such as systemic lupus erythematosus, Goodpasture's syndrome, multiple myeloma, diabetes, polycystic kidney disease, neoplasia, sickle cell disease, and chronic inflammatory diseases), tubular diseases (e.g., acute tubular necrosis and acute renal failure, polycystic renal diseasemedullary sponge kidney, medullary cystic disease, nephrogenic diabetes, and renal tubular acidosis), tubulointerstitial diseases (e.g., pyelonephritis, drug and toxin induced tubulointerstitial nephritis, hypercalcemic nephropathy, and hypokalemic nephropathy) acute and rapidly progressive renal failure, chronic renal failure, nephrolithiasis, gout, vascular diseases (e.g., hypertension and nephrosclerosis, microangiopathic hemolytic anemia, atheroembolic renal disease, diffuse cortical necrosis, and renal infarcts), or tumors (e.g., renal cell carcinoma and nephroblastoma).
Said disorders also include but are not limited to such cardiovascular disorders as ischemic heart disease (e.g., angina pectoris, myocardial infarction, and chronic ischemic heart disease), hypertensive heart disease, pulmonary heart disease, valvular heart disease (e.g., rheumatic fever and rheumatic heart disease, endocarditis, mitral valve prolapse, and aortic valve stenosis), congenital heart disease (e.g., valvular and vascular obstructive lesions, atrial or ventricular septal defect, and patent ductus arteriosus), or myocardial disease (e.g., myocarditis, congestive cardiomyopathy, and hypertrophic cariomyopathy).
According to a further embodiment of the invention, the antibodies and other pharmacological agents of the present invention may be employed as adjunct or adjuvant to other therapy, e.g. a therapy using a bone resorption inhibitor, for example as in osteoporosis therapy, in particular a therapy employing calcium, a calcitonin or an analogue or derivative thereof, e.g. salmon, eel or human calcitonin, calcilytics, calcimimetics (e.g., cinacalcet), a steroid hormone, e.g. an estrogen, a partial estrogen agonist or estrogen-gestagen combination, a SERM (Selective Estrogen Receptor Modulator) e.g. raloxifene, lasofoxifene, bazedoxifene, arzoxifene, FC1271, Tibolone (Livial®), a SARM (Selective Androgen Receptor Modulator), a RANKL antibody (such as denosumab), a cathepsin K inhibitor, vitamin D or an analogue thereof or PTH, a PTH fragment or a PTH derivative e.g. PTH (1-84) (such as Preos™), PTH (1-34) (such as Forteo™), PTH (1-36), PTH (1-38), PTH (1-31)NH2 or PTS 893. According to another embodiment, the antibodies of the invention may be employed in combination with other current osteoporosis therapy approaches, including bisphosphonates (e.g., Fosamax™ (alendronate), Actonel™ (risedronate sodium), Boniva™ (ibandronic acid), Zometa™ (zoledronic acid), Aclasta™/Reclast™ (zoledronic acid), olpadronate, neridronate, skelid, bonefos), statins, anabolic steroids, lanthanum and strontium salts, and sodium fluoride. When pharmacological agents of antibodies of the present invention are administered together with another agent, the two can be administered in either order (i.e. sequentially) or simultaneously.
The examples which follow are set forth to illustrate various aspects of the present invention but are not intended in any way to limit its scope as more particularly set forth and defined in the claims that follow thereafter.
Human Sclerostin (25 μg R&D Systems, Minneapolis, Minn.)) was reconstituted in 100 □l of 100 mM MES pH=7.0. Sulfonation was carried out by mixing 50 μl (12.5 μg) human Sclerostin and 22.5 μl (10.0 μg) of human TPST1 (R&D Systems) with 125 μL of assay mix [78.87mM MES pH=7.0, 2.5 mM MgCl2, 2.5 mM MnCl12 1.25 mM CaCl2 and 200 μM PAPS (Sigma)]. Incubation was carried out for 1.5 hrs at 37° C. Buffer was then exchanged into 10 mM Tris pH=7.5 using protein desalting spin columns (Pierce Biochemicals, Rockford, Ill.).
Peptides from the Sclerostin from Example 1 as well as untreated Sclerostin was digested with either trypsin or GluC and loaded onto a C18 column followed by injection into a LTQ mass spectrometer. In the first analysis, the mass spectrometer was instructed to make MS/MS of all eluting peptides. The resulting data was analyzed and three peptides from Sclerostin containing tyrosines were identified: LGEYPEPPPELE, YVTDGPCR and ANQAELENAY. In the second analysis, targeted analysis was performed where the mass spectrometer was instructed to only do MS/MS on masses corresponding to the putative sulfonated tyrosine containing peptides. For the GluC sample, the mass spectrometer was set to perform MS/MS at m/z 725.6, the mass of the doubly charged peptide LGEYPEPPPELE plus sulfation, at a normalized collision energy for CID at 2%, 4% or 10% and an MS3 of the highest fragment in each of the three MS/MS. In the tryptic sample, MS/MS was performed at m/z 602.0, the mass of the doubly charged peptide ANQAELENAY plus sulfonation, and at m/z 524.5, the mass of the doubly charged peptide YVTDGPCR plus sulfonation, at a normalized collusion energy for CID at 2%, 4% and 10% and an MS3 of the highest fragment in each of the three MS/MS. Both peptides at m/z 725.6 and 602.0, corresponding to sulfonated peptide LGEYPEPPPELE and ANQAELENAY, respectively, showed a neutral loss of 80Da (40Da for a 2+ ion) at 10% CE which suggests that these peptides were sulfonated, whereas at 2% and 4%, the loss was not very pronounced (see
293T cells were seeded into 9cm dishes. The next day, each dish was transfected with 12 μg of LRP5R1/2AP construct using Lipofactamine Plus (Invitrogen, Carlsbad, Calif.) according to the manufacturer's instructions. LRP5R1/2-AP is a nucleic acid construct that expresses LRPS extracellular domains 1 and 2 fused to alkaline phosphatase. 48 hours after transfection, the supernatant of the culture was collected as LRP5R1/2AP conditioned medium and concentrated 20 times using a Centricon unit (Millipore, Billerica, Mass.) and stored at −80° C.
Various amounts of unmodified Sclerostin or the in vitro treated Sclerostin from Example 1 were diluted into 80 μl of TBST buffer and added to individual wells of 96 well plates. After overnight incubation, unbound proteins were removed after which point the coated plates were blocked with 3% nonfat milk in PBS. The plates were than decanted and 0.5X LRP5R1/2AP conditioned medium was added to the plates. After 2.5 hours, the conditioned medium was removed and the 96 well plates were washed five times for three minutes with TBST. The Alkaline Phosphatase activity in each well was then determined using the Tropix luminescence assay kit (Invitrogen, Carlsbad, Calif.).
As seen in
Growing cultures of 10T1/2 cells were washed with PBS and trypsinized for 5 minutes. Cells were resuspended at a concentration of 6×105 cells/ml and 10 μl were seeded into individual wells of a Costar 96 well plate (Corning, Inc.). Wnt 3a and either the untreated Sclerostin or the Sclerostin from Example 1 were added and the plates were incubated at 37° C. for 24 hours. 50 μl of universal lysis buffer (from the Luciferase Reporter Gene Assay, Roche Applied Science, Indianapolis, Ind.) was added to each well at ambient temperature for 5 minutes. Detection of alkaline phosphatase was measured by the addition of 50 μl of ready-to-use CPSD with Sapphire Enhancer (Applied Biosystems) followed by an incubation at ambient temperature for 25 minutes.
As seen in
It should be noted that the Sclerostin used in these experiments was derived from recombinant clones in mammalian cell lines. Consequently, as seen in the MS results in Example 2, there is a significant population of Sclerostin proteins that already have pre-existing sulfonation modifications. Thus, the positive effects seen in the experiments above is the result of conversion of any remaining unsulfonated forms into the sulfonated version by TSPT-1.
The “Sulfinator” program is an online methodology of predicting the presence of sites in proteins that are substrates for tyrosine sulfonation (Monigatti et al. 2002 Bioinformatics 18; 769-770). It can be accessed at the website http://www.expasy.org/tools/sulfinator/ with documentation available at http://www.expasy.org/tools/sulfinator/sulfinator-doc.html. When this program was applied to the human Sclerostin sequence (UniProtKB Accession No. Q9BQB4), the amino acid sequence ELGEYPEPPPELENNK in the N terminal region of Sclerostin was identified as corresponding to a Tyrosine sulfonation site with sulfonation taking place with Tyr43 in agreement with the MS results from Example 2. The corresponding sequences in the mouse and rat are GLGEYPEPPPENNQTM and GLREYPEPPQELENNQ respectively (UniProtKB Accession No Q99P68 and Q99P67) where differences in the amino sequence are underlined. Evaluation of the mouse and rat Sclerostin sequences by the Sulfinator program revealed that the rat protein should also be sulfonated (and at the corresponding Tyr residue) while the mouse sequence did not show a positive result. It should be noted, however, that part of the criteria used by the Sulfinator program is contextual neighboring amino acid sequences and when the oligopeptide GLGEYPEPPPENNQTM from the mouse Sclerostin sequences was independently tested, it was indicated as being potential site for sulfonation. The loose structure at the amino terminal end of Sclerostin (to be discussed below) is likely responsible for the oligopeptide Sulfinator results of mouse Sclerostin being in agreement with the binding assay results.
The region of Sclerostin involved in binding to LRP5/6 is not precisely known. It has been described as “Finger 2” (˜aa's 115-147) by Weidauer et al., (2009 BBRC 380; 160-165) and “Loop 2” (˜aa's 86-112) by Veverka et al., (2009 JBC 284; 10,890-10,900) where amino assignments are based on the mature protein. It can be seen that neither putative location corresponds to the Tyr43 site. Nonetheless, a visualization of the predicted 3-dimensional structure shows that Tyr43 is part of a loosely organized peptide strand that could located in proximity with the binding site in “loop 2” predicted by Ververka et al. As such, it is possible that the amino terminal portion of Sclerostin also participates in binding of Sclerostin to LRP5/6 and sulfonation may have effects on this particular protein/protein interaction. Further support is from U.S. Pat. No. 7,585,501 where the Tyr43 site is a short distance away from an additional Sclerostin sequence (#15) that was described as participating in binding with LRP5/6. This point is illustrated further in
Peptides from the sulfonation modification sites regions may be useful in modulating protein-protein interactions between a sulfonated protein and a binding partner. Thus, for example, the sequences ELGEYPEPPPELENNK and KANQAELENAY from Sclerostin can be used to artificially synthesize peptides that can be used as therapeutic compounds. Both modified and unmodified versions of these peptides can be made and tested to see which ones are more effective and if they are equivalent in potency.
Antibodies that are specific for Sclerostin can be developed using peptides derived from the recognition sequences described in Examples 2 and 5. In
The discovery of a sequence in Sclerostin that comprises a sulfonate modified Tyrosine provides information concerning previously unknown epitopes in Sclerostin that may be used to generate novel antibodies that target these sites. For this purpose, a peptide can be used that comprises the sequence ELGEYPEPPPELE where the Tyrosine is modified to comprise a sulfonate group in order to generate an antibody that targets the sulfonated Tyrosine site at the amino end of Sclerostin. This modification can be carried out either chemically or by treatment with TPST-1 and PAPS. Another peptide, comprising the sequence KANQAELENAY (where the Tyrosine is also modified by sulfonation) can be used to generate an antibody to the sulfonated Tyrosine site at the carboxyl end of Sclerostin. Generation and isolation of an antibody can then be carried out by the methods described by Bundgaard et al., 2008 in conjunction with the methods taught in U.S. Pat. No. 7,585,501, US Patent Application 20040009535 and US Patent Application 20090130113, all of which are incorporated by reference.
When using a peptide with a sulfonated Tyrosine as the immunogen, resultant antibodies can display a variety of different affinities. For example, in an article giving the protocol for generating antibodies against peptides containing a phosphorylated Tyrosine, the point is made: “Such an immunization will generate an immune response with at least four components: (1) anti-carrier protein reactivity, (2) general antiphosphotyrosine reactivity, (3) phosphorylation-independent anti-peptide reactivity and (4) phosphorylation-dependent anti-peptide reactivity.” (DiGiovanna et al., 2002 Current Protocols in Cell Biology 16.6.1-16.6.18). As such, this article points out that even when using a peptide with the appropriate modification, antibodies can be generated that may only require the appropriate amino acid sequence and ignore the presence or absence of a modified Tyrosine. Consequently, many of the past efforts to isolate an antibody against a phoshphorylated peptide have included a counter-selection step to eliminate antibodies that bind to the unphosphorylated version of the target peptide/protein.
In contrast, although it is a goal of the present invention to generate and isolate antibodies that are specific for a protein that has a sulfonated tyrosine, utility is also found during such a search to identify and isolate antibodies that are specific for the sulfonated Tyrosine site but that are also independent of the sulfonation state of the target protein. Thus in parallel, identification processes can be carried out that initially are identified in terms of an the ability to bind to the region encompassed by the sulfonation modifications and then a secondary screening can be carried out for a) antibodies that have the ability to detect only epitopes that include the sulfonation modification and b) antibodies that are independent of the sulfonation status of the target region.
Many obvious variations will no doubt be suggested to those of ordinary skill in the art in light of the above detailed description and examples of the present invention. All such variations are fully embraced by the scope and spirit of the invention as more particularly defined in the claims that now follow.
This application is a divisional of U.S. application Ser. No. 15/447,496, filed Mar. 2, 2017, which is a divisional of U.S. application Ser. No. 12/802,447, filed Jun. 7, 2010 (now U.S. Pat. No. 9,617,323), which is hereby incorporated by reference in its entirety.
| Number | Date | Country | |
|---|---|---|---|
| Parent | 15447496 | Mar 2017 | US |
| Child | 16830330 | US | |
| Parent | 12802447 | Jun 2010 | US |
| Child | 15447496 | US |
