WO1999057251A2 - Thrombolytic agents derived from streptokinase - Google Patents
Thrombolytic agents derived from streptokinase Download PDFInfo
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- WO1999057251A2 WO1999057251A2 PCT/US1999/010086 US9910086W WO9957251A2 WO 1999057251 A2 WO1999057251 A2 WO 1999057251A2 US 9910086 W US9910086 W US 9910086W WO 9957251 A2 WO9957251 A2 WO 9957251A2
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- streptokinase
- plasminogen
- nonessential
- complex
- domain
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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
- A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
- A61K38/164—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
- A61K38/166—Streptokinase
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P7/00—Drugs for disorders of the blood or the extracellular fluid
- A61P7/02—Antithrombotic agents; Anticoagulants; Platelet aggregation inhibitors
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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
- C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
- C07K14/315—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Streptococcus (G), e.g. Enterococci
- C07K14/3153—Streptokinase
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- C—CHEMISTRY; METALLURGY
- C07—ORGANIC CHEMISTRY
- C07K—PEPTIDES
- C07K2319/00—Fusion polypeptide
Definitions
- the present invention is generally in the field of thrombolytic agents and more particularly directed to thrombolytic agents derived from streptokinase.
- Plasminogen (SEQ LD NO: 1) is the principal serine protease zymogen in the extracellular fluids of vertebrates, and its active form, plasmin, is implicated in pericellular proteolysis associated with a wide range of physiological and pathological processes, including the hydrolysis of fibrin into soluble degradation products and the suppression of tumors by angiogenesis inhibition (Gately, Proceedings of the National Academy of Sciences, USA 1997; 94: 10868-10872). In general, plasminogen expression is fairly stable and the regulation of the activity of the fibrinolytic system occurs mainly via up- and down- regulation of the expression of plasminogen activators and the inhibitors of these activators.
- plasminogen Activation of plasminogen is a consequence of cleavage of the Arg 561 -Val 562 bond, to form a two-chain, disulfide linked plasmin.
- the two known physiological plasminogen activators are the serine proteases tissue-type plasminogen activator (t-PA) (SEQ ID NO:2) and urokinase (u-PA or UK) (SEQ ID NO:3), both of which directly catalyze the hydrolysis of the activation bond.
- t-PA tissue-type plasminogen activator
- u-PA or UK urokinase
- plasminogen can also be activated by another completely different mechanism, which requires formation of an activator complex with a molecule such as streptokinase.
- plasminogen When streptokinase is complexed with plasminogen, plasminogen spontaneously converts into plasmin. This complexed plasrnin is then able to activate free plasminogen. Plasmin on its own cannot activate plasminogen.
- Streptokinase (SEQ LD NO:4) is a single-peptide secretory protein of 414 amino acid residues produced by various strains of hemolytic Streptococcus (Jackson and Tang, Biochemistry 1982; 21: 6620-6625; Malke et al., Gene 1985; 34: 357-361). SK does not contain cysteine or carbohydrate.
- SK is a flexible multi-domain protein (Conejero-Lara et al., Protein Science 1996; 5: 2583-2591; Medved et al., European Journal of Biochemistry 1996; 239: 333-339; Parrado et al., Protein Science 1996; 5: 693-704; Rodriguez et al., European Journal of Biochemistry 1995; 229: 83-90).
- SK and human plasminogen can form an equimolar activator complex that catalyzes the conversion of plasminogen from different mammalian species to plasmin.
- SK-Plg streptokinase-plasminogen
- Both the SK-Plg and the SK-Plm complexes catalyze the hydrolysis of the specific activation bond, Arg 561 - Val 562 , of the substrate plasminogen, resulting in the formation of plasmin.
- plasmin alone is not a plasminogen activator.
- a native plasminogen molecule contains at least seven structural domains, including the N-terminal 77-residue pre-activation peptide, five 'kringles' and a C-terminal trypsinogen-like zymogen domain (Sottrup-
- plasmin(ogen) An isolated catalytic domain of plasmin(ogen) is called micro- plasmin(ogen) ( ⁇ Plm/ ⁇ Plg).
- Human plasminogen contains 24 disulfide bonds. Human plasminogen is glycosylated at two positions that are located within the third kringle and between the third and fourth kringles, respectively.
- SK- ⁇ Plg streptokinase-micro plasmin(ogen)
- Such a structure would make it possible to predict the portions of SK that complex with plasminogen and to design modified streptokinases, such as a streptokinase having less antigenicity but which is still able to complex plasminogen and lead to activation of plasminogen.
- Structural information about the streptokinase-micro plasminogen complex has been used to identify the part of the streptokinase structure not involved in plasminogen complexation or activation.
- These nonessential portions can be modified to reduce antigenicity, for example, by changing the nonessential portions of streptokinase to more human-like polypeptide portions ("humanization of streptokinase").
- humanization of streptokinase One way this can be done is to compare the nonessential portion to a structural database of human proteins to find similar structures. Then the streptokinase nonessential structural part is replaced with the human structural part such as by genetic engineering of a mutant encoding the individual streptokinases, which is then expressed in a bacterial host such as E. coli.
- the nonessential portions can be removed or truncated to simplify streptokinase to a smaller molecule which retains plasminogen activation activity. Such smaller proteins should have reduced antigenicity and be cheaper and easier to produce.
- the modified streptokinases are useful in treating clotting disorders. Description of the Drawings
- Figure 1 is a stereo view of the activation pocket of the plasmin catalytic domain.
- a 2.9 A resolution 2LF 0 b s I-IFcaicI electron density map, phased with the final refined model and contoured at 1.0 ⁇ , is superimposed on the refined model.
- Figure 2 is a stereo view of the crystal structure of the complex of human micro plasmin ( ⁇ Plm) and streptokinase.
- the ⁇ Plm molecule is in the middle of the complex.
- the ⁇ -domain of SK is at the top, left side of the complex.
- the ⁇ -domain of SK is to the right side of the complex.
- the ⁇ - domain of SK is at the bottom of the complex. Only the C ⁇ traces are shown.
- Figures 3(a)- (c) illustrate ribbon diagrams of the three domains of streptokinase.
- Figure 3(a) is a ribbon diagram of the ⁇ -domain;
- Figure 3(b) is a ribbon diagram of the ⁇ -domain;
- Figure 3(c) is a ribbon diagram of the ⁇ -domain.
- the domains are oriented to illustrate the similarity in their overall ⁇ -grasp folding.
- Figure 4(a) is a stereo view of the interaction between human micro plasmin and the ⁇ -domain of streptokinase.
- the micro plasmin molecule is at the bottom of the complex.
- Figure 4(b) is a stereo view of the interaction between human micro plasmin and the ⁇ -domain of streptokinase.
- the micro plasmin molecule is at the top of the complex.
- the side chains which are involved in the interaction are displayed along with the C ⁇ backbones.
- Figure 5 is a stereo view of the superposition of the catalytic domains of human plasmin and human two-chain tissue-type plasminogen activator (t- PA) (Lamba et al., Journal of Molecular Biology 1996; 258: 117-135).
- t- PA tissue-type plasminogen activator
- Figure 6(a) is modeled view of the substrate binding site of the micro plasminogen- streptokinase complex showing the molecular surface of the complex.
- the orientation of the complex is similar to the orientation of the complex in Figure 1.
- Figure 6(b) is a stereo view illustrating docking of a substrate micro-plasminogen into the substrate binding site.
- the enzyme micro-plasmin is to the left of the complex.
- the streptokinase molecule is in the center of the complex, from top to bottom.
- the substrate micro- plasminogen is to the right of the complex.
- Figure 7 is a stereo view illustrating a putative active-zymogen form of plasminogen, compared with plasmin.
- the cleaved activation loop of plasmin shown in a thicker tube, is at the center of the complex, as is the side chain of Lys 698 in plasmin.
- the corresponding parts of the active- zymogen are towards the right.
- the rest of plasmin(ogen) is towards the top of the complex and possesses an active conformation around the active site, particularly the peptide segment (shown in a thicker tube) upstream of the nucleophile Ser 741 .
- ⁇ -strands in the surrounding region are shown as arrows.
- the salt bridge distance between the tips of Lys 698 and Asp 740 in the active- zymogen form is approximately the same as that between the free amino group of Val 562 and Asp 740 in plasmin.
- Upstream of Lys 698 is the binding site to the ⁇ -domain of streptokinase.
- Figure 8 is a stereo view of the ⁇ -domain of streptokinase (SK) superimposed on staphylokinase (SAK) (SEQ LD NO:5) (Rabijns, et al., Nature Structural Biology 1997; 4: 357-360).
- SAK staphylokinase
- FIG. 8 the side chains of SK Val 19 (SAK Met 26 ) and SK Glu 39 (SAK Glu 46 ) are plotted.
- streptokinase- microplasminogen (SK- ⁇ Plg) complex spontaneously, but slowly, converts to a streptokinase-microplasmin (SK- ⁇ Plm) complex. However, it does crystallize and the crystal diffracts to atomic resolution.
- the three- dimensional structure of the SK- ⁇ Plm complex is disclosed herein.
- Streptokinase Portions Complexed With Plasmin(ogen) Streptokinase complexation portions refers to single amino acid residues or polyp eptides of streptokinase required for the complexation of plasminogen and plasmin to streptokinase and for the activation of plasminogen to plasmin.
- Streptokinase substrate specificity portions refers to single amino acid residues or polypeptides required to impart substrate specificity upon plasmin complexed to streptokinase as compared to plasmin alone.
- Nonessential Portions of Streptokinase refers to those portions of streptokinase that can be modified, such as by being removed or replaced, without destroying the ability of the streptokinase to complex with plasminogen and without destroying the ability of the SK-Plm complex to activate plasminogen.
- the nonessential portions include portions that can be modified, such as by being removed or replaced, or by substituting or deleting one or more of the amino acids, without destroying the ability of streptokinase to impart substrate specificity to plasmin when complexed as SK-Plm compared to plasmin alone.
- the modified streptokinase proteins disclosed and claimed can have one or more of these nonessential portions removed or replaced.
- Native streptokinase can induce formation of anti- streptokinase antibodies following administration of a single dose. Subsequent doses are then attacked by these anti-streptokinase antibodies, making subsequent doses ineffective.
- the nonessential portions are compared against a database of human proteins to identify human proteins or portions thereof which are structurally similar to the nonessential streptokinase portions.
- a chimeric humanized streptokinase mutant can then be made in which the nonessential portion(s) are replaced with the human protein portions.
- a truncated protein can be made in which one or more nonessential portions, or one or more amino acids therein, have been removed.
- the human protein or portion thereof has a high degree of structural similarity to the streptokinase portion.
- the human portion does not have to be structurally identical to the streptokinase portion.
- the human portion does not retain any of the function of the native human protein from which it is derived.
- the humanized or truncated protein should retain substantially all or a substantial fraction of its ability to complex and activate plasminogen.
- the humanized or truncated proteins may be made using methods known to those of skill in the art. These include chemical synthesis, modifications of existing proteins, and expression of humanized proteins or truncated proteins using recombinant DNA methodology.
- the humanized protein can be made as a single polypeptide or the human protein portion can be attached to the base streptokinase polypeptide after separate synthesis of the two component polypeptides. Where the protein is relatively short (i.e. less than about 50 amino acids) the protein may be synthesized using standard chemical peptide synthesis techniques. Solid phase synthesis in which the C-terminal amino acid of the sequence is attached to an insoluble support followed by sequential additional of the remaining amino acids in the sequence is the preferred method for the chemical synthesis of the proteins described herein.
- Chemical synthesis produces a single stranded oligonucleotide. This may be converted into a double stranded DNA by hybridization with a complementary sequence, or by polymerization with a DNA polymerase using the single strand as a template.
- a complementary sequence or by polymerization with a DNA polymerase using the single strand as a template.
- Techniques for solid phase synthesis are described by Barany and Merrifield, Solid-Phase Peptide Synthesis; pp. 3- 284 in The Peptides; Analysis, Synthesis, Biology Vol. 2. Special Methods in Peptide Synthesis, Part A, Merrifield, et al., J. Am. Chem. Soc. 1963; 85: 2149-2156, and Stewart et al., Solid Phase Peptide Synthesis. 2nd ed. Pierce Chem. Co. : Rockford, 111., 1984.
- the protein may be made by chemically modifying a native protein. Generally, this requires cleaving the native protein at one or more sites and then annealing desired polypeptides onto the newly formed termini.
- the desired cleaved peptides can be isolated by any protein purification technique that purifies on the basis of size (e.g. by size exclusion chromatography or electrophoresis).
- various sites in the protein may be protected from hydrolysis by chemical modification of the amino acid side chains which may interfere with enzyme binding, or by chemical blocking of the vulnerable groups participating in the peptide bond.
- the humanized or truncated proteins will be synthesized using recombinant methodology.
- DNA encoding the protein can be prepared by any suitable method, including, for example, cloning and restriction of appropriate sequences or direct chemical synthesis by methods such as the phosphotriester method of Narang et al., Meth. En ⁇ ymol. 1979; 68: 90-99; the phosphodiester method of Brown et al., Meth. Enzymol. 1979; 68: 109-151; the diethylphosphoramidite method of Beaucage et al., Tetra. Lett. 1981; 22: 1859-1862; and the solid support method of U.S. Patent No. 4,458,066.
- partial length sequences may be cloned and the appropriate partial length sequences cleaved using appropriate restriction enzymes. The fragments may then be ligated to produce the desired DNA sequence.
- DNA encoding the protein will be produced using DNA amplification methods, for example polymerase chain reaction (PCR).
- PCR polymerase chain reaction
- the proteins may be expressed in a variety of host cells, including E. coli or other bacterial hosts, yeast, and various higher eukaryotic cells, such as the COS, CHO and HeLa cells lines, insect cells, and myeloma cell lines.
- the recombinant protein gene is operably linked to appropriate expression control sequences for each host.
- the plasmids encoding the protein can be transferred into the chosen host cell by well-known methods such as calcium chloride transformation for E. coli and calcium phosphate treatment or electroporation for mammalian cells. Cells transformed by the plasmids can be selected by resistance to antibiotics conferred by genes contained on the plasmids, such as the amp, gpt, neo and hyg genes.
- the protein can be purified according to standard procedures such as ammonium sulfate precipitation, affinity columns, column chromatography, or gel electrophoresis. Substantially pure compositions of at least about 90 to 95% homogeneity are preferred, and 98 to 99% or more homogeneity are most preferred for pharmaceutical uses.
- the protein may possess a conformation substantially different than the native protein. In this case, it may be necessary to denature and reduce the protein and then to cause the protein to re-fold into the preferred conformation. Methods of reducing and denaturing the protein and inducing re-folding are well known to those of skill in the art.
- the expressed, purified protein may be denatured in urea or guanidium chloride and renatured by slow dialysis.
- proteins should be assayed for biological activity.
- assays well known to those of skill in the art, generally fall into two categories; those that measure the binding affinity of the protein to a particular target, and those that measure the biological activity of the protein.
- modified streptokinase molecules can be administered for treatment of blood clot disorders, such as in heart attacks, as known in the art for administration of native streptokinase and tissue-type plasminogen activator (t-PA) and urokinase (u-PA or UK).
- t-PA tissue-type plasminogen activator
- u-PA urokinase
- the compounds are preferably administered intravenously in appropriate carriers.
- the appropriate dosages will depend upon the route of administration and the treatment indicated, and can be readily determined by one skilled in the art. Dosages are generally initiated at lower levels and increased until desired effects are achieved.
- Recombinant streptokinase and S741 A mutant of human ⁇ Plg were constructed.
- the proteins were expressed in E. coli as inclusion bodies which were washed, dissolved in 8 M urea and combined to be refolded together by rapid dilution.
- the 1 : 1 complex between SK and ⁇ Plg was purified further using S300-chromatography.
- the protein sample was stored at 0°C for more than two months before being used for a successful crystallization.
- the initial crystallization condition was determined by the use of sparse-matrix screens from Hampton Research. Crystals were grown at 20°C from sitting drops with wells containing 1.0 M sodium citrate, 0.2 M HEPES (pH 8.0), 1 mM magnesium chloride.
- Example 2 Crystallographic methods and data processing
- the initial MLR phases at 3.0 A resolution were confirmed by the MR solution of the ⁇ Plm part of the complex.
- the phases were further improved by electron density averaging over two-fold non-crystallographic symmetry and solvent flatting.
- the initial mask for the electron density averaging was derived from the MR solution.
- the electron density improvement was carried out with the program DM (Cowtan and Main, Ada. Crystallographica 1996; D52: 43- 48).
- the SK molecule was seen in three distinct domains adjacent to the region of the ⁇ Plm molecule.
- the initial model of ⁇ Plm was built using the crystal structure of chymotrypsinogen (Wang et al., Journal of Molecular Biology 1985; 185: 595-624) as a template.
- the structure of SK was built directly from the electron density map.
- Model building was performed with the program O (Jones et al., Ada. Crystallographica 1991; A47: 110-119). Iterative refinement and model building were used to improve the model gradually.
- SigmaA-weighted maps were calculated with the program SIGMAA (Read, Ada. Crystallographica 1986; A42: 140-149) and used in the initial model building.
- the final R factor is 20.3% over the 8.0-2.9 A resolution shell (28,600 reflections), and the free R (Brunger, Nature 1992; 355: 472-474) is 30% (3,150 reflections). Bond and angle deviations are 0.01 A and 1.8°, respectively, as determined by XPLOR using Engh and Huber parameters (Engh and Huber, Ada. Crystallographica 1991; A47: 392-400). Structural superposition and solvent accessible surface calculation were carried out with EDPDB (Zhang and Matthews, Journal of Applied Crystallography 1995; 28: 624-630). Figures were created by using OJSCRZPJ (Kraulis, J Appl. Cryst.
- the crystal structure of SK- ⁇ Plm complex was determined at 2.9 A resolution using X-ray crystallography.
- Figure 2 shows the C ⁇ trace of one SK- ⁇ Plm complex.
- the ⁇ Plm component of the complex contains the region from residue Ala 542 to the C- terminal residue Asn 791 of plasmin.
- the dimensions of the ⁇ Plm molecule are about 40 x 45 x 50 A.
- Resembling the architecture of many other trypsin-like serine proteases, ⁇ Plm consists of two domains, each of a six-stranded ⁇ -barrel.
- the C-terminus of ⁇ Plm ends with an ⁇ -helix packing against the N-terminal ⁇ - barrel.
- the catalytic residues, His 603 , Asp 646 , and Ser 741 position confirmed the Ser to Ala
- the coordinate root mean square deviation (rmsd) between ⁇ Plm and chymotrypsin is 0.7 A for 193 C ⁇ atoms, using a 1.5 A cutoff.
- rmsd coordinate root mean square deviation
- the activation bond, Arg 561 -Val 562 has been cleaved as indicated by SDS PAGE and N- terminal sequencing of the crystal contents (data not shown).
- the new C- terminus of the cleaved loop, containing Pro 559 , Gly 560 , and Arg 561 is mobile in the crystal and can be seen in the electron density only at a low contour level.
- the newly liberated N-terminus (WGG) (amino acids 562-565 of SEQ LD NO: 1) enters the activation pocket that is designed precisely to fit both the main- chain atoms and the divaline side chains. Its stability and proper positioning is reinforced by the solvent inaccessible salt bridge linking the terminal amino group to the carboxylate group of Asp 740 . This salt bridge ensures that the loop immediately upstream of nucleophile Ser 741 changes its conformation to an active form. Consequently, the oxyanion hole is formed by the amide groups of residues 738-740, and the SI specificity pocket is properly formed.
- Cys 588 -Cys 604 Three of them, Cys 588 -Cys 604 , Cys 680 -Cys 747 , and Cys 737 -Cys 765 , are within six-residue ranges of the catalytic triad residues and function to maintain the platform of the catalytic triad.
- Cys 558 -Cys 566 which is absent in many other typsin-like proteases, flanks the activation cleavage site.
- this disulfide bond likely constrains the conformation of the short activation loop such that the Arg 561 -Val 562 bond is confined to be readily cleaved by plasminogen activators.
- the two new termini liberated by the activation cleavage are also constrained by the disulfide bond.
- SK appears as a three domain protein with several segments in the primary sequence disordered in the crystal lattice.
- the three domains are linked with each other by coiled coil peptides and are likely to fold independently in solution. They are denoted as ⁇ - ⁇ -, and ⁇ -domains hereafter along the peptide chain from the N-terminus to the C-terminus (see Figure 2).
- the ⁇ -domain begins at residue Asn 15 and ends at about residue Pro 145 .
- Residues 1-11 and two extra residues (Gly-Ser) adopted from the cloning vector are disordered in the electron density map.
- the region of residues 45- 70 has a lack of interpretable electron density.
- a proteolytic cleavage that occurs at the bond between Lys 59 and Ser 60 is located in this disordered region.
- the ⁇ -domain begins at residue Ala 155 and ends at residue Pro 283 .
- This domain also contains a cleavage site, Lys 257 -Ser 258 , which is cleaved only in a portion of total SK- ⁇ Plm complexes as shown in our SDS PAGE analysis.
- N-terminal 16 residues and the C-terminal 40 residues of SK are functionally dispensable for plasminogen activation (Kim et al., Biochemical and Biophysical Research Communications 1996; 40: 939-945; Young et al., Journal of Biological Chemistry 1995; 270: 29601-29606).
- the N- terminal 16 residues of SK play a role in the secretion of this protein from the host cell (Pratap et al., Biochem. Biophys. Res. Commun. 1996; 227: 303-310).
- residues 45-70 which is disordered in the complex structure, exist in an inherently flexible state (Nihalani et al., Protein Science 1998; 7: 637-648).
- Every one of the three domains of SK belongs to the ⁇ -grasp folding class (Murzin et al., Journal of Molecular Biology 1995; 247: 536-540), but with some noticeable differences (see Figure 3).
- the SK ⁇ -domain contains a single ⁇ -helix packing against a mixed five-stranded ⁇ -sheet.
- the ⁇ -strands forming the major ⁇ -sheet are ⁇ ⁇ 2 , ⁇ ⁇ ,, ⁇ ⁇ 7 , ⁇ ⁇ 4 , and ⁇ ⁇ 5 .
- the topology of this ⁇ -sheet (Richardson et al., Journal of Molecular Biology 1976; 102: 221-235) is (+1,- 3x,-l,2x).
- the hydrogen bond network of the major ⁇ -sheet is disrupted at the middle of the ⁇ ⁇ 2 strand by a bulge at position 36.
- the ⁇ -helix is located between ⁇ ⁇ 3 and ⁇ ⁇ 4 and is thus named ⁇ ⁇ 3 , 4 .
- Between the major ⁇ -sheet and the ⁇ -helix is the hydrophobic core of the ⁇ -domain.
- the SK ⁇ -domain shares the same overall folding with the SK ⁇ - domain.
- the coordinate rmsd between the two domains is 1.7 A for 81 residues, using a 4.0 A cutoff. Some corresponding loops between the two domains, however, have different lengths.
- the SK ⁇ -domain contains a four-stranded major ⁇ -sheet and a short two-stranded ⁇ -sheet.
- the major ⁇ -sheet has a topology similar to that of the major ⁇ -sheet of the ⁇ -domain without ⁇ 5 . Between ⁇ ⁇ 2 and ⁇ ⁇ 3 are some coiled coil loops. The qualities of the electron density in the ⁇ - and ⁇ -domains of SK are significantly better than that of the ⁇ - domain region. Correspondingly, the average temperature factors of the ⁇ -, ⁇ -, and ⁇ -domains are 43, 80, and 39 A 2 , respectively. These differences appear correlated with the interactions of each domain of SK with the ⁇ Plm molecule in the complex.
- the SK molecule has extensive interactions with the ⁇ Plm molecule, mostly through the SK ⁇ - and ⁇ -domains.
- the values of buried molecular surface area are 1,650 A 2 , 950 A 2 and 1,500 A 2 between ⁇ Plm and the ⁇ , ⁇ and ⁇ -domains of SK, respectively.
- the SK ⁇ -domain is located near the catalytic triad of ⁇ Plm.
- There are three major contact regions between the SK ⁇ -domain and ⁇ Plm (see Figure 4a).
- the first region contains the interaction between the major ⁇ -sheet, particularly the strands of " ⁇ ] and ⁇ ⁇ 2 , of SK and the loop region of residues 713-721 of ⁇ Plm.
- Arg 719 of plasmin (SEQ ID NO: 1) forms salt bridges with both Glu 39 and Glu 134 of SK (SEQ LD NO:4), and it also has van de Waals interaction with SK Val 19 .
- the uncharged alkyl group side-chain of residue 19 of SK has been shown to be important for plasminogen activation (Lee et al., Biochemistry and Molecular Biology International 1997; 41 : 199- 207). Arg 719 of plasminogen has also been identified as an important residue involved in the SK-Plg complex formation (Dawson and Pontin, Biochemistry 1994; 33: 12042-12047).
- the second contact region contains the interaction between the bulge region in the ⁇ ⁇ 2 strand of SK and the 643-645 region of ⁇ Plg, which is the upstream region of the catalytic residue Asp 646 .
- the positively charged side chain of ⁇ Plm Lys 644 also protrudes towards the C- terminus of the ⁇ -helix, ⁇ ⁇ 3j4 , of SK, presuming a helix dipole-charge interaction.
- the third contact region is between the loop following the ⁇ -helix, ⁇ ⁇ 3 , 4 , of the SK ⁇ -domain and the 606-609 region of ⁇ Plm. The latter is the down stream region of the catalytic residue His 603 .
- Ras-binding protein C-rafl
- Rap la target protein
- the SK ⁇ -domain binds to ⁇ Plm near the activation cleavage site of plasmin (see Figure 4b).
- this interaction mainly involves two loop regions: ⁇ Plm(622-628) in the so called calcium-binding loop and ⁇ Plm(692-695) in the so called autolysis loop.
- the interactions include a salt- bridge between SK Lys 332 and ⁇ Plm Glu 623 , hydrogen bonds (e.g. SK Glu 311 and ⁇ Plm Gin 622 ), and hydrophobic interactions.
- region 622-628 in human plasmin(ogen) is "QEVNLEP” (amino acids 622-628 of SEQ LD NO:l), and in bovine ⁇ lasmin(ogen) is "NEKVREQ” (amino acids 643-649 of SEQ LD NO: 6). Since this region of ⁇ Plm is involved in the SK binding, the sequence difference shown above may provide explanation why the catalytic domain of bovine plasminogen binds with SK significantly weaker than human plasminogen does (Young et al., Journal of Biological Chemistry 1998; 273: 3110-3116). On the other hand, the only close interaction of SK with the activation loop region of ⁇ Plm (i.e.
- kringle domains have been shown to be involved in plasminogen activation by SK. Since the N-terminus of the catalytic domain of plasmin(ogen) is on the hemisphere opposite to the SK binding sites, the extension of kringle 5 from the catalytic domain is unlikely to disturb the observed interactions between SK and ⁇ Plm. Also, it has been shown previously (Rodriguez et al.. European Journal of Biochemistry 1995; 229: 83-90) that the complex of plasmin with the fragment SK(143-293) (i.e. the ⁇ -domain) or SK(143-386) (i.e.
- human plasmin(ogen) is four residues shorter around residue 583. Some of these differences, if not all, are likely responsible for the substrate specificity difference between plasmin and t- PA.
- the SK-plasmin complex may change the substrate specificity of plasmin by compensating for some of these differences.
- the crystal structure of the SK- ⁇ Plm complex shows that the complex has an opened cavity (see Figure 6a) compared with the spherical (convex) shape of the catalytic domain of plasmin(ogen). Therefore the SK-Plg complex should provide more substrate binding surface than the plasmin molecule alone can.
- a manual molecular model to dock a model micro plasminogen molecule into the substrate binding site of the SK- ⁇ Plm complex is shown in Figure 6b.
- the activation bond, Arg 561 -Val 562 , of the substrate (micro) plasminogen is positioned into the active site of the catalytic (micro) plasmin; the N-terminus of substrate ⁇ Plg is positioned to be closed to the disordered region of SK(45-70). From the bottom of the substrate binding concave, ⁇ Plm contributes approximately 1,050 A 2 binding area, mostly from the surface of the strand, ⁇ ⁇ 2 , and the ⁇ -helix, ⁇ ⁇ 3;4 .
- the flexible SK(45-70) region may provide extra substrate binding surface; that would explain the observed high affinity of the SK ⁇ -domain with the kringle domains of plasminogen (Young et al., Journal of Biological Chemistry 1998; 273 : 3110-3116) as well as the important role played by residues 45-51 of SK in binding with plasminogen (Nihalani et al., Protein Science 1998; 7: 637-648).
- the major ⁇ -sheet forms part of the wall of substrate binding concave with its helix side facing outside.
- the ⁇ -strand on the rim of the ⁇ -sheet, p ⁇ 2 potentially forms hydrogen bonds with the strand of residues 625-629 of substrate plasminogen.
- the SK ⁇ -domain contributes -550 A 2 binding surface in total.
- the SK ⁇ -domain contributes some coiled coil, around residue 330, to the substrate binding, about 150 A 2 in total.
- Several potential salt bridges can be predicted from this hypothetical model, including Arg of the substrate plasminogen (s-Plg) to Asp 735 of the catalytic plasmin (c-Plm), s-Plg Lys 557 to c- Plm Glu 606 , and s-Plg Lys 750 to SK Asp 78 .
- Lys 557 of plasminogen was found to be important for plasminogen activation by t-PA (Wang and Reich, Protein Science 1995; 4: 1769-1779) and could be explained if similar binding modes were assumed for binding of t-PA to plasminogen.
- the Asp 735 of c-Plm interacting with the side chain of Arg 561 of s-Plg, defines the substrate specificity of the SK-Plm complex at the SI position.
- Example 7 A possible activation mechanism of human plasminogen by SK
- SK One of the functions of SK is to turn the zymogen plasminogen into an active "enzyme" without cleaving the peptide chain. It appears from the crystal structure of the SK- ⁇ Plm complex that it is the interaction between the SK ⁇ - domain and the catalytic domain of plasminogen that creates the enzymatic activity of human plasminogen-SK complex.
- this salt bridge is formed between the carboxylate group of the aspartate residue that is immediately upstream of the catalytic nucleophile serine residue and the liberated amino terminus after the activation cleavage.
- the formation of the salt bridge reorients the aspartate residue relative to the zymogen structure and thus restructures the active site, which includes the oxyanion hole, the catalytic triad and the SI specificity pocket (Freer et al., Biochemistry 1970; 9: 1997-2009).
- t-PA vampire-bat plasminogen activator
- v-PA vampire-bat plasminogen activator
- SK or SK(16-414) can convert plasminogen to plasmin; however, plasmin alone can not convert other plasminogen to plasmin.
- the additional SK( 16-251) peptides form complexes with the newly formed plasmin molecules and modulate their substrate specificity such that new plasminogen activators are formed.
- Example 8 Structure comparison between the ⁇ -domain of SK and staphylokinase
- staphylokinase is another bacterial source plasminogen activator, whose crystal structure has been determined recently (Murzin et al., Journal of Molecular Biology 1995; 247: 536-540).
- SAK staphylokinase activates human plasminogen by forming a zymogen-activator complex (Lijnen et al., Journal of Biological Chemistry 1991; 266: 11826- 11832).
- SK and staphylokinase do not share detectable sequence homology.
- staphylokinase The size of staphylokinase is only one third that of streptokinase, and its binding mode and activation mechanism to human plasminogen are unknown. It is particularly interesting to find that staphylokinase shares a three- dimensional folding with the SK ⁇ -domain (see Figure 8). The coordinate rmsd between staphylokinase and the SK ⁇ -domain is 1.8 A for 91 C a atoms, using a 4.0 A cutoff.
- staphylokinase binds to plasminogen in the same mode as the SK ⁇ -domain.
- SAK Glu 46 which corresponds to SK Glu 39 , was found to be important for the formation of the SAK-Plg complex (Silence et al., Journal of Biological Chemistry 1995; 270: 27192-27198). This residue would be located on the ⁇ 2 strand and form a salt-bridge with Arg 719 of plasmin(ogen).
- SAK Met 26 which corresponds to SK Val 19 , was also found to be of crucial importance for the activation of plasminogen by staphylokinase (Schlott et al., Biochemical and Biophysical Ada. 1994; 1204: 235-242). Since the side chain at this position has van de Waals contact with the hydrophobic portion of the Arg 719 side chain, disturbing such a contact would result in disturbing the complex contact through both van de Waals and electrostatic interactions.
- staphylokinase A few more residues of staphylokinase that were found important for the activity of the complex of SAK-Plg, including Lys 50 , Glu 65 , and Asp 69 , all would be located on the substrate binding surface that is similar to that we have proposed for the SK- ⁇ Plm complex.
- the N-terminal fragment of staphylokinase i.e. residues 1-20
- residues 1-20 most of which are disordered in the crystal structure, would be located at a position that potentially could affect the conformation of the active site by allosteric binding. Therefore, a one domain protein like staphylokinase would perform multiple functions that are accomplished by two/three domains in SK.
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Application Number | Priority Date | Filing Date | Title |
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JP2000547207A JP2002513810A (en) | 1998-05-06 | 1999-05-06 | Thrombolytic agent derived from streptokinase |
EP99924154A EP1078044A2 (en) | 1998-05-06 | 1999-05-06 | Thrombolytic agents derived from streptokinase |
AU40723/99A AU4072399A (en) | 1998-05-06 | 1999-05-06 | Thrombolytic agents derived from streptokinase |
CA002327526A CA2327526A1 (en) | 1998-05-06 | 1999-05-06 | Thrombolytic agents derived from streptokinase |
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US8439298P | 1998-05-06 | 1998-05-06 | |
US60/084,392 | 1998-05-06 |
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JP (1) | JP2002513810A (en) |
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Citations (5)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP0397366A1 (en) * | 1989-05-09 | 1990-11-14 | The Board Of Regents Of The University Of Oklahoma | Hybrid streptokinases with fibrin binding domains and methods for the synthesis of same |
EP0407942A2 (en) * | 1989-07-11 | 1991-01-16 | Otsuka Pharmaceutical Factory, Inc. | Streptokinase proteins, corresponding genes, corresponding plasmid recombinants, corresponding transformants and processes for preparing same |
WO1994007992A1 (en) * | 1992-10-05 | 1994-04-14 | The General Hospital Corporation | Peptides specifically binding to plasminogen and the dna encoding such peptides |
WO1996041883A1 (en) * | 1995-06-09 | 1996-12-27 | President And Fellows Of Harvard College | Plasmin-resistant streptokinase |
WO1999031247A1 (en) * | 1997-12-15 | 1999-06-24 | The Presidents And Fellows Of Harvard College | Bacterial fibrin-dependent plasminogen activator |
-
1999
- 1999-05-06 JP JP2000547207A patent/JP2002513810A/en not_active Withdrawn
- 1999-05-06 WO PCT/US1999/010086 patent/WO1999057251A2/en not_active Application Discontinuation
- 1999-05-06 AU AU40723/99A patent/AU4072399A/en not_active Abandoned
- 1999-05-06 EP EP99924154A patent/EP1078044A2/en not_active Withdrawn
- 1999-05-06 CA CA002327526A patent/CA2327526A1/en not_active Abandoned
Patent Citations (5)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
EP0397366A1 (en) * | 1989-05-09 | 1990-11-14 | The Board Of Regents Of The University Of Oklahoma | Hybrid streptokinases with fibrin binding domains and methods for the synthesis of same |
EP0407942A2 (en) * | 1989-07-11 | 1991-01-16 | Otsuka Pharmaceutical Factory, Inc. | Streptokinase proteins, corresponding genes, corresponding plasmid recombinants, corresponding transformants and processes for preparing same |
WO1994007992A1 (en) * | 1992-10-05 | 1994-04-14 | The General Hospital Corporation | Peptides specifically binding to plasminogen and the dna encoding such peptides |
WO1996041883A1 (en) * | 1995-06-09 | 1996-12-27 | President And Fellows Of Harvard College | Plasmin-resistant streptokinase |
WO1999031247A1 (en) * | 1997-12-15 | 1999-06-24 | The Presidents And Fellows Of Harvard College | Bacterial fibrin-dependent plasminogen activator |
Non-Patent Citations (8)
Title |
---|
FAY, W.P. ET AL.: "Functional analysis of the amino- and carboxyl-termini of streptokinase" THROMBOSIS AND HAEMOSTATIS, vol. 79, no. 5, May 1998 (1998-05), pages 985-991, XP002115947 * |
JACKSON, K.W. ET AL.: "Active streptokinase from the cloned gene in Streptococcus sanguis is without the carboxy-terminal 32 residues" BIOCHEMISTRY, vol. 25, 1986, page 108-114 XP002115945 * |
NIHALANI, D. ET AL.: "Mapping the plaminogen binding site of streptokinase with short synthetic peptides" PROTEIN SCIENCE, vol. 6, no. 6, June 1997 (1997-06), pages 1284-1292, XP002115949 * |
PARRADO, J. ET AL.: "The domain organization of streptokinase: nuclear magnetic resonance, circular dichroism, and functional characterization of proteolytic fragments " PROTEIN SCIENCE, vol. 5, no. 4, April 1996 (1996-04), pages 693-704, XP002116207 cited in the application * |
REED G L ET AL: "Identification of a plasminogen binding region in streptokinase that is necessary for the creation of a functional streptokinase -plasminogen activator complex" BIOCHEMISTRY, vol. 34, 15 August 1995 (1995-08-15), pages 10266-10271, XP002101129 ISSN: 0006-2960 * |
RODRIGUEZ, P.: "The streptokinase domain responsible for plasminogen binding" FIBRINOLYSIS, vol. 8, no. 5, September 1994 (1994-09), pages 276-285, XP002115946 cited in the application * |
SHI G Y ET AL: "Function of streptokinase fragments in plasminogen activation" BIOCHEMICAL JOURNAL, vol. 304, 15 November 1994 (1994-11-15), pages 235-241, XP002101128 ISSN: 0264-6021 * |
YOUNG, K.C.: "Interaction of streptokinase and plasminogen" THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 270, no. 40, 1995, pages 29601-29606, XP002115948 cited in the application * |
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CA2327526A1 (en) | 1999-11-11 |
JP2002513810A (en) | 2002-05-14 |
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