Classifications

• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
  • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16B20/30—Detection of binding sites or motifs
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
  • C12N9/14—Hydrolases (3)
  • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
  • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
  • C12N9/64—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
  • C12N9/6421—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue from mammals
  • C12N9/6424—Serine endopeptidases (3.4.21)
• • 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
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
  • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
  • G16B15/20—Protein or domain folding
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2299/00—Coordinates from 3D structures of peptides, e.g. proteins or enzymes
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
  • G16B15/00—ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• • G—PHYSICS
  • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
  • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
  • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

Definitions

• the present invention relates to crystals of a polypeptide comprising the catalytic domain of MASP-2. Furthermore the invention relates to uses of said crystal for in silico screening methods to identify compound capable of interacting with MASP-2 and/or compound capable of modulating the activity of MASP-2.
• the complement system is a key element of innate immunity in vertebrates. It is capable of recognizing and eliminating invading pathogen microorganisms and altered host cells through opsonization and lysis. Complement is a sophisticated cascade system, where serine protease enzymes activate each other in a strictly ordered manner. According to our present knowledge the activation of the complement system can be initiated by three independent pathways: the classical, the lectin, and the alternative pathways.
• the first components of the classical and lectin pathways are supramolecular enzyme complexes consisting of a recognition subunit and associated serine proteases (Gal and Ambrus, 2001).
• the recognition subunit of the classical pathway is C1q, which resembles to a bunch of six tulips consisting of N-terminal collagen-like arms and C- terminal globular heads.
• the globular heads bind to the activator structures, which results in the activation of the serine protease zymogens (C1r and C1s) associated with the collagen-like region.
• C1r and C1s serine protease zymogens
• One C1q together with a heterotetramer of C1r and C1s proteases (C1s-C1 r-C1r-C1s) form the C1 complex (Arlaud et al., 1987; Schu aker et al., 1987).
• the first enzymatic event in the classical pathway is the autoactivation of C1r zymogen.
• Activated C1 r then cleaves zymogen C1s, which in turn cleaves and activates C2 and C4, the components of the C3-convertase enzyme complex.
• the initiation complex of the lectin activation pathway resembles superficially the C1 complex.
• the recognition subunit of the lectin pathway, the mannose-binding lectin (MBL) has C-terminal globular C-type lectin domains and N-terminal collagen-like stalks (Turner, 1996). MBL is capable of binding to carbohydrate arrays on the surface of pathogens and trigger the activation of the complement cascade through associated serine proteases.
• MASP-1/-2/-3 mannose-binding lectin-associated serine protease-1 , -2 and -3
• MAp-19 small non enzymatic protein MAp-19
• MBL-MASP complexes exist with respect to the oligomer status of the MBL (ranging from two trimeric subunits to six) and the number and type of MASPs that associate with it (Dahl et al., 2001 ; Thielens et al., 2001).
• MASP-1 and MASP-2 can act independently, they do not form hetero oligomers and do not require each other in order to become activated. Both MASP-1 and MASP-2 can autoactivate, and the activated serine proteases show significant activity towards different substrates (Ambrus et al., 2003).
• MASP-2 is a C1s- like enzyme, cleaving C4 and C2 (Thiel et al., 1997; Rossi et al., 2001). Unlike C1s however, MASP-2 can autoactivate and therefore trigger the complement cascade without the contribution of any other protease (Vorup-Jensen et al., 2000). It has been shown that a complex consisting of two MBL subunits and two MASP-2 molecules represents the minimal complement-fixing unit (Chen and Wallis, 2001). Consequently a MASP-2 dimer is able to perform all functions mediated by the C1r 2 C1s 2 tetramer in the C1 complex.
• the C1r, C1s, MASP-1/-2/-3 enzymes form a family of proteases with common modular organization (Sim and Laich, 2000; Volanakis and Arlaud, 1998; Schwaeble et al., 2002).
• the N-terminal interacting region of these enzymes contains an EGF-like domain surrounded by two CUB domains.
• the C-terminal catalytic region contains the serine protease (SP) domain preceded by two complement control protein (CCP) (also referred to as SCR or sushi) modules.
• SP serine protease
• CCP complement control protein
• the SP domain is sufficient for autoactivation and can cleave the C2 substrate as efficiently as the intact molecule.
• the presence of the CCP2 module is essential.
• the CCP2 module may contain additional substrate binding sites for the C4 molecule.
• the CCP2-SP fragment can therefore be considered as the catalytic domain of MASP-2.
• Information about the 3D structure of the catalytic domain of MASP proteins would facilitate identification of useful compounds capable of interacting with MASP proteins. For example information about the 3D structure of the catalytic domain of active and non- active MASP may be useful. In particular, modulators of MASP proteins, such as inhibitors may be designed using information of the 3D structure of the catalytic domain of MASP proteins.
• polypeptide comprising at least 150 consecutive amino acids from the serine protease domain of MASP-2.
• Said polypeptide may be catalytically active, or said polypeptide may be catalytically inactive.
• Information of the 3D structure of MASP-2 may be used to identify compounds, capable of interacting with MASP-2.
• in silico screening methods may be employed to identify compounds, which with high probability can interact with MASP-2.
• the method may be repeated with another data set comprising the structure coordinates of another polypeptide comprising at least 150 consecutive amino acids from the serine protease domain of MASP-2.
• the method may in particular be repeated using one catalytically active MASP-2 polypeptide and one MASP-2 polypeptide, which lacks catalytic activity, for example one MASP-2 polypeptide in the two-chain form and one MASP-2 polypeptide in the one chain form.
• the method may comprise selecting compounds capable of interacting only with a catalytically active MASP-2 polypeptide, or compound capable of interacting only with MASP-2 lacking catalytic activity or compounds capable of interacting with both catalytically active MASP-2 and MASP-2 lacking catalytic activity.
• the methods of the invention furthermore comprise the steps of vii) Providing at least one selected compound; viii) Providing a polypeptide comprising at least 150 consecutive amino acids from the serine protease domain of MASP-2; ix) Contacting said polypeptide with said selected compound under conditions for interaction; x) Detecting interaction between said polypeptide and said selected compound, thereby identifying compounds capable of interacting with said polypeptide
• the polypeptide used for the in vitro methods may be the same polypeptide, which co- ordinates were used for establishing the 3D model or it may be a different polypeptide also comprising at least 150 consecutive amino acids from the serine protease domain of MASP-2.
• the polypeptide used for the in vitro methods may be a full length MASP-2 polypeptide, whereas the polypeptide used for establishing the 3D model may be a polypeptide merely comprising the CCP-2 and serine protease domains of MASP-2.
• Information of the 3D structure of MASP-2 may also be used to identify compounds, capable of inhibiting MASP-2 activity.
• compounds capable of interacting with a site required for MASP-2 activity may be useful inhibitors of MASP-2 activity.
• compounds capable of interacting with the C4 binding pocket of MASP-2 may be useful inhibitors of MASP-2.
• a method for identifying a compound capable of inhibiting MASP-2 activity comprises the steps of i) providing a computer system for producing a three-dimensional representation of a molecule or molecular complex, wherein said computer system comprises: a machine-readable data storage medium comprising a data storage material encoded with machine-readable data, wherein said data comprises the structure co-ordinates of a polypeptide comprising the CCP- 2 and the serine protease domain of MASP-2; a working memory for storing instruction for processing said machine- readable data; a central-processing unit coupled to said working memory and to said machine-readable data storage medium for processing said machine- readable data into said three-dimensional representation; and a display coupled to said central-processing unit for displaying said three- dimensional representation; and ii) executing instructions on the computer for generating a three dimensional representation of a substrate binding site on said polypeptide from structural co-ordinates of a crystal of said polypeptide, such
• an inhibitor could for example be a compound that interacts with the active site. If the MASP-2 polypeptide is zymogen MASP-2, then an inhibitor could for example be a compound that interacts with the MASP-2 auto-cleavage site. Such a compound could then inhibit activation of MASP- 2.
• the methods of the invention may furthermore comprise the steps of vii) Providing at least one selected compound; viii) Providing MASP-2; ix) Determining MASP-2 activity in the presence and absence of said compound; x) Identifying compounds in the presence of which MASP-2 activity is lower than in the absence of said compound
• Fig. 1 Overall structure of the MASP-2 CCP2-SP fragment.
• A Stereo ribbon diagram of molecule A (dark grey) and molecule B (light grey) of the crystal structure, with the SP domains superimposed. The ⁇ -strands of the CCP2 module and the C-terminus are labelled. Residues of the catalytic triad are shown as sticks and are labelled 'a.s.'
• B Superimposition of the CCP module of molecule A onto that of C1 s (light blue) and C1 r (green), with the ⁇ -strands labelledf.
• C Superimposition of the active SP domain of molecule A onto that of C1s and C1r with the active site residues shown as sticks. The loops are labelled according to Perona and Craik (1997).
• FIG. 2 The CCP2/SP interface region.
• A Backbone conformations of MASP-2 molecule A (red), molecule B (yellow), C1s (light blue), and C1r (CCP2-SP active form: light green) are shown with the CCP2 module superimposed. Due to differences in the topology of the interface contacts, the active site of MASP-2 (serine c195 side chain shown as space filling representation; also shown for CCP2-SP zymogen in medium green and CCP1- CCP2-SP zymogen in dark green) is shifted significantly compared to that of C1 r and C1s. B-D represent a 90° rotated view (side view) from that of A.
• MASP-2 The CCP2/SP interface region of MASP-2 molecule A (B), molecule B (C), and C1s (D) is shown.
• Residues forming interdomain contacts in MASP-2 are shown as balls and sticks, as well as the corresponding residues of C1s.
• these residues form a hydrogen bond network (shown as green dotted lines), which is not established in C1s.
• green dotted lines For the sake of clarity, some side chain atoms are not shown, the carbon atoms and the ribbon representation of SP domains are shown in blue, while those of the interdomain linkers are in yellow, the N- terminal loop and B1 are in rose and the rest of CCP2 module is in orange, respectively.
• Fig. 3 Substrate binding subsites of MASP-2.
• A Sequences of the P4-P4' segments are shown for the natural substrates: MASP-2, C2 and C4, as well as for the pseudosubstrate C1 inhibitor.
• B Stereo view of the molecular surface of MASP-2 substrate binding subsites region is colored by residue type (acidic: red, basic: blue, polar: yellow, hydrophobic: grey). A model peptide (drawn as sticks) representing the P4-P2' residues of C2 is shown superimposed over the MASP-2 structure.
• C4d Molecular surface representation of C4d is colored for electrostatic potential (red: negative, blue: positive), with its residues possibly forming electrostatic interactions with the MASP-2/C1s CCP2 module labelled in italics. Conformations of side chains C1s E356 / MASP-2 E378 were adjusted.
• D Side view of the superimposed structures. Ribbon representation of C4d is shown in light purple, with its C- and N-termini and thioester region labelled, while MASP-2 and C1s are shown in magenta and light blue, respectively.
• Fig.6 Alignment of the human MASP-1 , MASP-2, C1 r and C1 s sequences indicating the presence of the individual domains is MASP-2. Amino acids conserved in the four proteins are furthermore indicated by asterisk.
• Fig. 7 illustrates the IC 50 determination of PMSF and MASP2 ⁇ B.
• Fig. 8 illustrates the IC 50 determination of Pefablock and MASP2 ⁇ B.
• Fig. 9 illustrates the IC 50 determination of Benzamidin and MASP2 ⁇ B.
• Fig. 10 illustrates the IC 50 determination of NPGB and MASP2 ⁇ B.
• Fig. 11 illustrates the IC 50 determination of APMSF and MASP2 ⁇ B.
• Fig. 12 illustrates the IC 50 determination of Leupeptine and MASP2 ⁇ B.
• Fig. 13 illustrates the IC 50 determination of E64 and MASP2 ⁇ B.
• Fig. 14 illustrates the structure of benzamidine
• Fig. 15 illustrates the structure of leupeptin
• Fig. 16 illustrates the structure of NPGB
• Fig. 17A shows a superimposed view of the 200 docked conformations of benzamidine in the substrate binding pocket of MASP-2. There are two closely spaced separate clusters
• Fig. 17B illustrates the structure of benzamidine in the substrate binding pocket of MASP- 2.
• the protein is shown in surface, the benzamidine is shown in ball and sticks representation.
• Fig. 18A shows a superimposed view of 200 docketed conformations of leupeptin in the substrate binding pocket of MASP-2.
• Fig. 18B illustrates the minimum energy conformation of leupeptin in the substrate binding pocket of the MASP2.
• the protein is shown in surface, leupeptin is shown in ball and sticks representation.
• Fig. 19A shows a superimposed view of the 200 docked conformations of NPGB in the substrate binding pocket of MASP-2. Two close clusters are well visible.
• Fig. 19B illustrates the minimum energy conformation of the NPGB in the substrate binding pocket of the MASP2.
• the protein is shown in surface, NPGB is shown in ball and sticks representation.
• the MASP-2 protein comprises of a number of domains namely the CUB1 , EGF, CUB2, CCP1 , CCP2 and serine protease domains.
• a schematic presentation of MASP-2 is given in figure 5. Position of the individual domains within human MASP-2 is indicated in figure 2.
• a catalytic domain of MASP-2 is any domain of MASP-2 comprising catalytic activity. In general the catalytic domain comprises at least the serine protease domain of MASP-2.
• Catalytic activity of MASP-2 is preferably serine protease activity towards a suitable substrate, such as zymogen MASP-2, C2 and/or C4. Catalytic activity may be determined using any of the methods described herein below in the section "MASP-2 activity".
• polypeptides comprising at least 150, for example at least 175, such as at least 200 consecutive amino acids from the serine protease domain of MASP-2.
• polypeptides of MASP-2 are designated "polypeptides of MASP-2" herein.
• Polypeptides of MASP-2 preferably comprise the serine protease domain of MASP-2.
• polypeptides of MASP-2 may also comprise one or more further domains of MASP-2, such as the CCP-2 domain.
• said polypeptides comprises the CCP-2 domain and the serine protease domain of MASP-2.
• MASP-2 any MASP-2 molecule known to the person skilled in the art and functional homologues thereof.
• Said MASP-2 may for example be derived from a mammal, for example MASP-2 may be derived from a human being.
• MASP-2 is human MASP-2 as identified by SEQ ID 1 or a functional homologue thereof sharing at least 50%, preferably at least 60%, more preferably at least 70%, even more preferably at least 80%, yet more preferably at least 90%, yet even more preferably at least 95% homology or more preferably identity with SEQ ID 1.
• polypeptide comprising the serine protease domain of MASP-2 comprises aa 363 to 686 of SEQ ID 1.
• polypeptide comprising the serine protease domain of MASP-2 comprises aa 299 to 686 of SEQ ID 1.
• polypeptide may comprise other sequences, for example an extra peptide sequence comprising at least one amino acid, preferably in the range of 1 to 500, such as 1 to 250, for example 1 to 100, such as 1 to 75, for example 1 to 50, such as 1 to 25, for example 1 to 10 amino acids not derived from MASP-2.
• said extra peptide sequence consists of at the most 20, such as at the most 10, for example at the most 5, for example around 4 amino acids.
• the extra peptide sequence may be situated at the N-terminus or at the C-terminus or internally in the MASP-2 fragment.
• the fragment is situated at the N-terminus of the C- terminus of the MASP-2 derived fragment.
• the polypeptide comprise an extra peptide of the sequence ALA SER MET THR.
• said sequence is positioned N-terminally.
• the polypeptide consists of the sequence ALA SER MET THR coupled N-terminally to aa 363 to 686 of SEQ ID1.
• the polypeptide consists of the sequence ALA SER MET THR coupled N-terminally to aa 299 to 686 of SEQ ID 1.
• the polypeptide of MASP-2 is in an enzymatically active form (herein also designated catalytically active form).
• the polypeptide preferably has at least 20%, such as at least 30%, for example at least 40%, such as at least 50%, for example at least 60%, such as at least 70%, for example at least
• MASP-2 activity may be determined as described herein elsewhere. It is thus preferred that the polypeptide is in the enzymatically active, two-chain form.
• polypeptides of MASP-2 as used herein is meant to cover both the one-chain and two-chain form of MASP-2. '
• MASP-2 is in the one-chain form.
• the one-chain form is also referred to as zymogen MASP-2.
• MASP-2 may comprise one or more mutations, preferably one or more mutations within the cleavage site.
• the MASP-2 polypeptide may in one embodiment of the invention comprise at least 150 consecutive amino acids of MASP-2 of SEQ ID 1 , wherein one or more amino acids have been mutated. In particular, it is preferred that at least one of the amino acids 443 to 445 of SEQ ID 1 are mutated.
• the MASP-2 polypeptide may comprise or consist of amino acid 296 to 686 of SEQ ID 1 , wherein aa 444 is mutated, preferably aa 444 is mutated from R to Q.
• Functional equivalents or functional homologues of polypeptides of MASP-2 or polypeptides comprising the serine protease domain of MASP-2 are polypeptides which share at least some sequence identity with the predetermined amino acid sequence of said polypeptides (for example a fragment of the amino acid sequence outlined in SEQ ID 1).
• Functional equivalents should furthermore retain at least 30%, such as at least 40%, for example at least 50%, such as at least 60%, for example at least 70%, such as at least 80%, for example at least 90%, such as at least 95% MASP-2 activity. Methods of determining MASP-2 activity are described herein below.
• the terms "functional equivalent” and “functional homologue” are used interchangeably herein.
• Functional homologues comprise polypeptides with an amino acid sequence, which are sharing a homology with the predetermined MASP-2 polypeptide sequences as outlined herein above.
• polypeptides are at least about 40 percent, such as at least about 50 percent homologous, for example at least about 60 percent homologous, such as at least about 70 percent homologous, for example at least about 75 percent homologous, such as at least about 80 percent homologous, for example at least about 85 percent homologous, such as at least about 90 percent homologous, for example at least 92 percent homologous, such as at least 94 percent homologous, for example at least 95 percent homologous, such as at least 96 percent homologous, for example at least 97 percent homologous, such as at least 98 percent homologous, for example at least 99 percent homologous with the predetermined polypeptide sequences as outlined herein above.
• Homology may preferably be calculated by any suitable algorithm or by computerised implementations of such algorithms for example CLUSTAL in the PC/Gene program by Intelligenetics or GAP, BESTFIT, BLAST, FASTA and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG).
• the homology between amino acid sequences may furthermore be calculated with the aid of well known matrices such as for example any one of BLOSUM 30, BLOSUM 40, BLOSUM 45, BLOSUM 50, BLOSUM 55, BLOSUM 60, BLOSUM 62, BLOSUM 65, BLOSUM 70, BLOSUM 75, BLOSUM 80, BLOSUM 85, and BLOSUM 90.
• Functional homologues according to the present invention are preferably polypeptides with an amino acid sequence, which is at least about 50 percent, preferably at least about 60 percent, more preferably at least about 70 percent, even more preferably at least about 75 percent, yet more preferably at least about 80 percent, even more preferably at least about 85 percent, yet more preferably at least about 90 percent, even more preferably at least 95 percent homologous, most preferably at least 98 percent identical with the predetermined MASP-2 polypeptide sequences as outlined herein above.
• Functional homologues may comprise an amino acid sequence that comprises at least one substitution of one amino acid for any other amino acid.
• a substitution may be a conservative amino acid substitution or it may be a non- conservative substitution.
• said substitutions are conservative substitution.
• a conservative amino acid substitution is a substitution of one amino acid within a predetermined group of amino acids for another amino acid within the same group, wherein the amino acids within a predetermined groups exhibit -similar or substantially similar characteristics.
• conservative amino acid substitution is a substitution of one amino acid within a predetermined group of amino acids for another amino acid within the same group, wherein the amino acids within a predetermined groups exhibit -similar or substantially similar characteristics.
• one amino acid may be substituted for another within groups of amino acids characterised by having
• polar side chains (Asp, Glu, Lys, Arg, His, Asn, Gin, Ser, Thr, Tyr, and Cys,)
• non-polar side chains (Gly, Ala, Val, Leu, lie, Phe, Trp, Pro, and Met)
• amino acids being monoamino-dicarboxylic acids or monoamino-monocarboxylic- monoamidocarboxylic acids (Asp, Glu, Asn, Gin).
• the addition or deletion of an amino acid may be an addition or deletion of from 2 to 5 amino acids, such as from 5 to 10 amino acids, for example from 10 to 20 amino acids, such as from 20 to 50 amino acids.
• additions or deletions of more than 50 amino acids, such as additions from 50 to 200 amino acids are also comprised within the present invention.
• sterically similar compounds may be formulated to mimic the key portions of the peptide structure and that such compounds may also be used in the same manner as the peptides of the invention. This may be achieved by techniques of modelling and chemical designing known to those of skill in the art. For example, esterification and other alkylations may be employed to modify the amino terminus of, e.g., a di-arginine peptide backbone, to mimic a tetra peptide structure. It will be understood that all such sterically similar constructs fall within the scope of the present invention.
• Functional equivalents also comprise glycosylated and covalent or aggregative conjugates, including dimers or unrelated chemical moieties. Such functional equivalents are prepared by linkage of functionalities to groups which are found in fragment including at any one or both of the N- and C-termini, by means known in the art.
• Functional equivalents may thus comprise fragments conjugated to aliphatic or acyl esters or amides of the carboxyl terminus, alkylamines or residues containing carboxyl side chains, e.g., conjugates to alkylamines at aspartic acid residues; O-acyl derivatives of hydroxyl group-containing residues and N-acyl derivatives of the amino terminal amino acid or amino-group containing residues, e.g. conjugates with Met-Leu-Phe.
• Derivatives of the acyl groups are selected from the group of alkyl-moieties (including C3 to C10 normal alkyl), thereby forming alkanoyl species, and carbocyclic or heterocyclic compounds, thereby forming aroyl species.
• the reactive groups preferably are difunctional compounds known per se for use in cross-linking proteins to insoluble matrices through reactive side groups.
• Functional homologues may furthermore be polypeptide encoded by a nucleic acid which is able to hybridise to the complementary strand of a nucleic acid sequence encoding the predetermined MASP-2 polypeptide sequences as outlined herein above under stringent conditions.
• Stringent conditions as used herein shall denote stringency as normally applied in connection with Southern blotting and hybridisation as described e.g. by Southern E. M., 1975, J. Mol. Biol. 98:503-517. For such purposes it is routine practise to include steps of prehybridization and hybridization.
• Such steps are normally performed using solutions containing 6x SSPE, 5% Denhardt's, 0.5% SDS, 50% formamide, 100 ⁇ g/ml denaturated salmon testis DNA (incubation for 18 hrs at 42°C), followed by washings with 2x SSC and 0.5% SDS (at room temperature and at 37°C), and a washing with 0.1 x SSC and 0.5% SDS (incubation at 68°C for 30 min), as described by Sambrook et al., 1989, in "Molecular Cloning/A Laboratory Manual", Cold Spring Harbor), which is incorporated herein by reference.
• a crystal of a polypeptide of MASP-2 according to the present invention should preferably be useful for determining the structure of said crystal using X-ray diffraction.
• the crystal is a crystal of a polypeptide comprising the CCP-2 and serine protease domain of MASP-2.
• the crystal may comprise more than one peptide, for example 2.
• the crystal comprises the CCP-2 and serine protease domain of MASP-2 in the active two chain form.
• the crystal diffracts X-rays for determination of atomic coordinates to a resolution of at least 5 A, preferably at least 4 A, more preferably at least 3 A, even more preferably at least 2.5 A, most preferably at least 2.25 A.
• the crystal comprises atoms arranged in a spatial relationship represented by the structure co-ordinates of table 3, or by co-ordinates having a root mean square deviation therefrom of not more than 2.5 A, preferably not more than 2.25 A, more preferably not more than 2.0 A, even more preferably not more than 1.75 A, yet more preferably not more than 1.5 A, for example not more than 1.25 A, such as not more than 1.0 A.
• the co-ordinates has a root mean square deviation therefrom, of not more than 2.5 A, preferably not more than 2.25 A, more preferably not more than 2.0 A, even more preferably not more than 1.75 A, yet more preferably not more than 1.5 A, for example not more than 1.25 A, such as not more than 1.0 A.
• the crystal comprises or more preferably consists of the structure as deposited to the PDB with id 1q3x.
• the crystal may also comprise the CCP-2 and the serine protease domain of MASP-2 in the one chain form, preferably such MASP-2 comprises at least one mutation within the cleavage site (see details regarding zymogen MASP-2 herein above).
• the crystal comprises atoms arranged in a spatial relationship represented by the structure co-ordinates of table 4, or by co-ordinates having a root mean square deviation therefrom of not more than 2.5 A, preferably not more than 2.25 A, more preferably not more than 2.0 A, even more preferably not more than 1.75 A, yet more preferably not more than 1.5 A, for example not more than 1.25 A, such as not more than 1.0 A.
• the co-ordinates has a root mean square deviation therefrom, of not more than 2.5 A, preferably not more than 2.25 A, more preferably not more than 2.0 A, even more preferably not more than 1.75 A, yet more preferably not more than 1.5 A, for example not more than 1.25 A, such as not more than 1.0 A.
• the crystal may comprise more than one polypeptide of MASP-2 per asymmetric unit, in a preferred embodiment of the invention the crystal comprises polypeptides of MASP-2 per asymmetric unit.
• crystal has the following data:
• MASP-2 activity may be determined by any suitable assay.
• Useful assays include assays, wherein serine protease activities of MASP-2/MBL complexes are tested.
• Preferred assays are assays determining cleavage of C2 and/or C4 and/or MASP-2. Most preferably assays determining cleavage of C2 or C4.
• Inhibitors of MASP-2 activity may be tested for inhibition of C2 and/or C4 deposition, i.e. inhibition of C2 and/or C4 cleavage.
• the assays may involve the steps of preparing a solid surface on which an MBL associating agent is immobilised, binding MBL/MASP-2 complexes to said MBL associating agent and screening for inhibition of MASP-2 catalysed reactions.
• the solid surface may be any useful solid surface, for example microtiter wells.
• the MBL associating agent may be any compound to which MBL binds with high affinity, for example MBL antibodies, mannan or mannose, preferably however it is mannan.
• the MBL/MASP-2 complexes may be derived from any suitable source, it may for example be recombinant MBL, recombinant MASP-2 or MBL and/or MASP-2 purified from serum. Recombinant MBL/MASP-2 may be full length MBL/MASP-2 or functional fragments thereof. Furthermore, recombinant MBL/MASP-2 may be attached to one or more other compounds, such as genetic tags.
• MBL and/or MASP-2 may be derived from any suitable species for example it may be human MBL/MASP-2.
• the MBL/MASP-2 complexes are found in full serum and are not purified prior to performing the assay. Said assays then test inhibition of deposition of substrate, i.e. C4 in full serum.
• the MASP-2 catalysed reaction is preferably deposition of C2 and/or C4.
• the compound to be screened for inhibition activity is added to the bound MBL/MASP-2. Controls without added compound are preferably also performed.
• the compound may be added in any suitable concentration depending on the nature of the specific compound. For example in concentrations in the range of 1 ⁇ (g/ml to 10,000 ⁇ g/ml, such as in the range of 5 ⁇ (g/ml to 1000 ⁇ g/ml, for example in the range of 10 ⁇ (g/ml to 300 ⁇ g/ml, such as in the range of 15 ⁇ (g/ml to 200 ⁇ g/ml, for example in the range of 20 to 100 ⁇ (g/ml.
• a MASP-2 substrate is added to the MBL/MASP-2 complexes.
• said substrate is either C2 or C4 or a mixture of both or an artificial MASP-2 substrate.
• the substrate is C4.
• the substrate may be recombinantly produced or a serum derived substrate.
• the substrate may or may not have been purified prior to use, but preferably it is purified.
• the substrate may be labelled with a detectable label, for example with an enzyme, a radioactive compound, a fluorescent compound, a dye, a heavy metal, a chemilumniscent compound or the like.
• deposition is detected using specific binding agent, such as an antibody, specifically recognising digested substrate.
• specific binding agent such as an antibody, specifically recognising digested substrate.
• antibodies recognising human complement C4c may be used.
• Said antibodies may be labelled, by a directly or indirectly detectable label.
• an enzyme a radioactive compound, a fluorescent compound, a dye, a heavy metal, a chemilumniscent compound or an affinity compound.
• Affinity compounds include for example other antibodies or biotin, streptavidin.
• MBL/MASP-2 complexes may be mixed with the substrate for example 5 min. to 2 hours.
• MBL/MASP-2, substrate and antibody is premixed, when MBL/MASP-2 complexes are present in serum and have not previously been purified from serum.
• the activity of MASP-2 is determined using any of the methods described in examples 2, 3 and 6 herein below.
• compounds capable of inhibiting C4 deposition should preferably be able to inhibit C4 deposition in at least one, preferably both of the methods described in example 2 or 3.
• Compounds capable of inhibiting C4 deposition should more preferably at least be able to inhibit C4 deposition according to the methods described in example 2, whereas compounds capable of inhibiting C4 deposition in full serum should be capable of inhibiting C4 deposition in full serum as described in example 3.
• co-crystals of said polypeptide and a compound capable of interacting with said polypeptide are prepared.
• Said compound may have been identified by any of the methods outlined herein below.
• the compound may in one aspect of the invention be a modulator, such as an inhibitor of MASP-2 activity.
• the co-crystals are useful for designing optimised compounds, with enhanced binding properties.
• the co-crystals may be useful for designing better inhibitors of MASP-2.
• the buffer preferably comprises in the range of 5 to 25% polyethylene glycol, more preferably in the range of 10 to 20%, even more preferably in the range of 12 to 18%, yet more preferably in the range of 14 to 16 %, most preferably around 15% polyethylene glycol.
• Polyethylene glycol (PEG) may be any suitable PEG for example a PEG selected from the group consisting of PEG 4000, PEG 6000 and PEG 8000, preferably polyethylene glycol is PEG 6000.
• the buffer preferably comprises in the range of 0.01 M to 0.5 M salt, more preferably in the range of 0.02 to 0.4 M, even more preferably in the range of 0.05 to 0.3 M, yet more preferably in the range of 0.08 to 0.2 M, most preferably around 0.12 M salt.
• the salt may be any useful salt, preferably the salt is NaCl.
• the buffer preferably comprises in the range of 1 to 10% an alcohol selected from the group consisting of glycerol and 2-methyl-2,4-penthanediol, more preferably in the range of 2 to 9%, even more preferably in the range of 3 to 8%, yet more preferably in the range of 4 to 6%, most preferably around 5% an alcohol selected from the group consisting of glycerol and 2-methyl-2,4-penthanediol.
• said alcohol is glycerol.
• the buffer preferably has a pH in the range of 6 to 9, more preferably in the range of 6.5 to 8.5, even more preferably in the range of 7 to 8, yet more preferably in the range of 7.4 to 7.5.
• Incubation should be performed at a suitable temperature, preferably at a temperature in the range of 5 to 25°(C, more preferably in the range of 10 to 25°C, even more preferably in the range of 15 to 25°C, even more preferably in the range of 18 to 22°C, yet more preferably around 20°C.
• the crystals may be grown by any suitable method, for example by the hanging drop method. Determination of structure
• the structure of crystals may be determined by any method known to the person skilled in the art, for example using X-ray diffraction. Once a structure has been identified, said structure may be refined using suitable software.
• a molecular replacement technique may be used. Such techniques involves that the structure is determined by obtaining x-ray diffraction data for crystals of the polypeptide or complex for which one wishes to determine the three dimensional structure. Then, one determines the three-dimensional structure of that polypeptide or complex by analysing the x-ray diffraction data using molecular replacement techniques with reference to known structural co-ordinates of a structurally similar protein. In the case of polypeptides comprising domains of MASP-2, structural coordinates of similar domains in C1 r or C1 s may be used. As described in U.S. Pat. No.
• molecular replacement uses a molecule having a known structure as a starting point to model the structure of an unknown crystalline sample. This technique is based on the principle that two molecules which have similar structures, orientations and positions in the unit cell diffract similarly.
• Molecular replacement involves positioning the known structure in the unit cell in the same location and orientation as the unknown structure. Once positioned, the atoms of the known structure in the unit cell are used to calculate the structure factors that would result from a hypothetical diffraction experiment. This involves rotating the known structure in the six dimensions (three angular and three spatial dimensions) until alignment of the known structure with the experimental data is achieved. This approximate structure can be fine-tuned to yield a more accurate and often higher resolution structure using various refinement techniques.
• the resultant model for the structure defined by the experimental data may be subjected to rigid body refinement in which the model is subjected to limited additional rotation in the six dimensions yielding positioning shifts of under about 5%.
• the refined model may then be further refined using other known refinement methods.
• Homology modelling involves constructing a model of an unknown structure using structural co-ordinates of one or more related proteins, protein domains and/or subdomains. Homology modelling may be conducted by fitting common or homologous portions of the protein or peptide whose three dimensional structure is to be solved to the three dimensional structure of homologous structural elements. Homology modelling can include rebuilding part or all of a three dimensional structure with replacement of amino acids (or other components) by those of the related structure to be solved.
• Structural coordinates of a crystalline polypeptide of this invention may be stored in a machine-readable form on a machine-readable storage medium, e.g. a computer hard drive, diskette, DATA tape, CD-ROM etc., for display as a three-dimensional shape or for other uses involving computer-assisted manipulation of, or computation based on, the structural coordinates or the three-dimensional structures they define.
• a machine-readable storage medium e.g. a computer hard drive, diskette, DATA tape, CD-ROM etc.
• data defining the three dimensional structure of a polypeptide of MASP-2 may be stored in a machine-readable storage medium, and may be displayed as a graphical three- dimensional representation of the protein structure, typically using a computer capable of reading the data from said storage medium and programmed with instructions for creating the representation from such data.
• This invention thus encompasses a machine, such as a computer, having a memory which contains data representing the structural coordinates of a crystalline composition of this invention, e.g. the coordinates set forth in table 3 or the coordinates set forth in table 4, together with additional optional data and instructions for manipulating such data.
• data may be used for a variety of purposes, such as the elucidation of other related structures and drug discovery.
• a first set of such machine readable data may be combined with a second set of machine- readable data using a machine programmed with instructions for using the first data set and the second data set to determine at least a portion of the coordinates corresponding to the second set of machine-readable data.
• the first set of data may comprise a Fourier transform of at least a portion of the coordinates for the complex set forth in table 3 or the coordinates set forth in table 4, while the second data set may comprise X-ray diffraction data of a molecule or molecular complex.
• one of the objects of this invention is to provide three-dimensional structural information of co-complexes comprising the catalytic domain of MASP-2.
• a 3D representation of the polypeptides described in the present invention may be useful for several purposes, for example for determining the structure of similar proteins or polypeptides (see also herein above) or for designing compounds capable of interacting with said polypeptides.
• the three dimensional structure defined by the machine readable data for the polypeptide of MASP-2 may be computationally evaluated for its ability to associate with various chemical entities or test compounds.
• chemical entity refers to chemical compounds, complexes of at least two chemical compounds, and fragments of such compounds or complexes.
• a first set of machine-readable data defining the 3-D structure of polypeptide of MASP-2 or complex thereof is combined with a second set of machine-readable data defining the structure of a chemical entity or test compound of interest using a machine programmed with instructions for evaluating the ability of the chemical entity or compound to associate with the polypeptide of MASP-2 or complex thereof and/or the location and/or orientation of such association.
• Such methods provide insight into the location, orientation and energetic of association of protein surfaces with such chemical entities.
• the three dimensional structure defined by the data may be displayed in a graphical format permitting visual inspection of the structure, as well as visual inspection of the association of the polypeptide component(s) with an interacting compound. Alternatively, more quantitative or computational methods may be used.
• one method of this invention for evaluating the ability of a chemical entity to associate with any of the molecules or molecular complexes set forth herein comprises the steps of: (a) employing computational means to perform a fitting operation between the chemical entity and a binding site or other surface feature of the molecule or molecular complex; and (b) analyzing the results of said fitting operation to quantify the association between the chemical entity and the binding site.
• This invention further provides for the use of the structural coordinates of a crystalline composition of this invention, or portions thereof, to identify reactive amino acids, such as cysteine residues, within the three-dimensional structure, preferably within or adjacent to a binding site; to generate and visualise a molecular surface, such as a water-accessible surface or a surface comprising the space-filling van der Waals surface of all atoms; to calculate and visualise the size and shape of surface features of the protein or complex, e.g., substrate binding sites; to locate potential H-bond donors and acceptors within the three-dimensional structure, preferably within or adjacent to a ligand binding site; to calculate regions of hydrophobicity and hydrophilicity within the three-dimensional structure, preferably within or adjacent to a ligand binding site; and to calculate and visualize regions on or adjacent to the protein surface of favorable interaction energies with respect to selected functional groups of interest (e.g.
• reactive amino acids e.g., cysteine
• complementary characteristics e.g., size, shape, charge, hydrophobicity/hydrophilicity, ability to participate in hydrogen bonding, etc.
• the structural coordinates of the polypeptide of MASP-2, or portion or complex thereof are entered in machine readable form into a machine programmed with instructions for carrying out the desired operation and containing any necessary additional data, e.g. data defining structural and/or functional characteristics of a potential interacting compound or moiety thereof, defining molecular characteristics of the various amino acids, etc.
• One method of this invention provides for selecting from a database of chemical structures a compound capable of binding to a polypeptide of MASP-2.
• the method starts with structural co-ordinates of a crystalline composition of the invention, e.g., co-ordinates defining_the_three dimensional structure of polypeptide of MASP-2 or a portion thereof or a complex thereof. Points associated with that three dimensional structure are characterised with respect to the favourability of interactions with one or more functional groups.
• a database of chemical structures is then searched for candidate compounds containing one or more functional groups disposed for favorable interaction with the protein based on the prior characterisation. Compounds having structures which best fit the points of favourable interaction with the three dimensional structure are thus identified.
• a first set of machine-readable data defining the 3D structure of a polypeptide of MASP-2, or a portion or polypeptide/interacting compound complex thereof is combined with a second set of machine readable data defining one or more moieties or functional groups of interest, using a machine programmed with instructions for identifying preferred locations for favourable interaction between the functional group(s) and atoms of the polypeptide.
• a third set of data, i.e. data defining the location(s) of favourable interaction between polypeptide and functional group(s) is so generated.
• That third set of data is then combined with a fourth set of data defining the 3D structures of one or more chemical entities using a machine programmed with instructions for identifying chemical entities containing functional groups so disposed as to best fit the locations of their respective favourable interaction with the polypeptide.
• Compounds having the structures selected or designed by any of the foregoing means may be tested for their ability to bind to a polypeptide of MASP-2.
• the compound is preferably a modulator of MASP-2 activity.
• a compound capable of interacting with a substrate binding site of MASP-2 may be a good inhibitor of MASP-2 activity.
• compounds having the structures selected or designed by any of the foregoing means may be tested for their ability to modulate MASP-2 activity, such as for inhibition of MASP-2 activity (see herein above).
• the Molecular Similarity application permits comparisons between different structures, different conformations of the same structure, and different parts of the same structure.
• the procedure used in Molecular Similarity to compare structures is divided into four steps: (1) load the structures to be compared; (2) define the atom equivalences in these structures; (3) perform a fitting operation; and (4) analyse the results.
• Each structure is identified by a name.
• One structure is identified as the target (i.e., the fixed structure); all remaining structures are working structures (i.e., moving structures). Since atom equivalency within QUANTA is defined by user input, for the purpose of this invention we define equivalent atoms as protein backbone atoms (N, C ⁇ ,(, C and O) for all conserved residues between the two structures being compared and consider only rigid fitting operations.
• the working structure is translated and rotated to obtain an optimum fit with the target structure.
• the fitting operation uses a least squares fitting algorithm that computes the optimum translation and rotation to be applied to the moving structure, such that the root mean square difference of the fit over the specified pairs of equivalent atom is an absolute minimum. This number, given in angstroms, is reported by QUANTA.
• root mean square deviation means the square root of the arithmetic mean of the squares of the deviations from the mean. It is a way to express the deviation or variation from a trend or object.
• the "root mean square deviation” defines the variation in the backbone of a protein from the backbone of a protein of this invention, such as the CCP-2/serine protease domain of MASP-2 as defined by the structural coordinates of table 3 or the zymogen CCP-2/serine protease domain of MASP-2 as defined by the structural coordinates of table 4 and described herein.
• least squares refers to a method based on the principle that the best estimate of a value is that in which the sum of the squares of the deviations of observed values is a minimum.
• the structural co-ordinates generated for a crystalline substance of this invention e.g. the structural co-ordinates set forth in table 3 or the structural coordinates set forth in table 4, it is often necessary or desirable to display them as, or convert them to, a three-dimensional shape, or to otherwise manipulate them. This is typically accomplished by the use of commercially available software such as a program, which is capable of generating three-dimensional graphical representations of molecules or portions thereof from a set of structural co-ordinates.
• Midas (Univ. of California, San Francisco) MidasPlus (Univ. of Cal., San Francisco) MOIL (Univeristy of Illinois) Yummie (Yale University)
• a machine-readable storage medium comprising a data storage material encoded with machine readable data which, when using a machine programmed with instructions for using said data, e.g. a computer loaded with one or more programs of the sort identified above, is capable of displaying a graphical three- dimensional representation of any of the molecules or molecular complexes described herein.
• Machine-readable storage media comprising a data storage material include conventional computer hard drives, floppy disks, DAT tape, CD-ROM, and other magnetic, magneto-optical, optical, floptical and other media which may be adapted for use with a computer.
• a machine-readable data storage medium that is capable of displaying a graphical three-dimensional representation of a molecule or molecular complex that is defined by the structural co-ordinates of a polypeptide of MASP-2, such as the co-ordinates set forth in table 3+/- a root mean square deviation from the conserved backbone atoms of the amino acids thereof of not more than 1.5 A.
• An illustrative embodiment of this aspect of the invention is a conventional 3.5" diskette, DAT tape or hard drive encoded with a data set, preferably in PDB format, comprising the co-ordinates of table 3.
• FIG. 1 illustrates a print-out of a graphical three-dimensional representation of such a polypeptide.
• the machine-readable data storage medium comprises a data storage material encoded with a first set of machine readable data which comprises the Fourier transform of the structural coordinates set forth in table 3 or table 4 (or again, a derivative thereof), and which, when using a machine programmed with instructions for using said data, can be combined with a second set of machine readable data comprising the X-ray diffraction pattern of a molecule or molecular complex to determine at least a portion of the structural co-ordinates corresponding to the second set of machine readable data.
• Such a system may for example include a computer comprising a central processing unit (“CPU"), a working memory which may be, e.g., RAM (random-access memory) or “core” memory, mass storage memory (such as one or more disk drives or CD-ROM drives), one or more cathode-ray tube (“CRT”) display terminals, one or more keyboards, one or more input lines (IP), and one or more output lines (OP), all of which are interconnected by a conventional bidirectional system bus.
• CPU central processing unit
• working memory which may be, e.g., RAM (random-access memory) or “core” memory
• mass storage memory such as one or more disk drives or CD-ROM drives
• CRT cathode-ray tube
• keyboards such as one or more keyboards
• IP input lines
• OP output lines
• Input hardware coupled to the computer by input lines, may be implemented in a variety of ways.
• Machine-readable data of this invention may be inputted via the use of a modem or modems connected by a telephone line or dedicated data line.
• the input hardware may comprise CD-ROM drives or disk drives.
• a keyboard may also be used as an input device.
• Output hardware coupled to the computer by output lines, may similarly be implemented by conventional devices.
• output hardware may include a CRT display terminal for displaying a graphical representation of a protein of this invention (or portion thereof) using a program such as QUANTA as described herein.
• Output hardware might also include a printer, so that hard copy output may be produced, or a disk drive, to store system output for later use.
• the CPU coordinates the use of the various input and output devices, coordinates data accesses from mass storage and accesses to and from working memory, and determines the sequence of data processing steps.
• a number of programs may be used to process the machine-readable data of this invention. Examples of such programs are discussed herein above. Algorithms suitable for this purpose are also implemented in programs such as Cast-3D (Chemical Abstracts Service), 3DB Unity (Tripos, Inc.), Quest- 3D (Cambridge Crystallographic Data Center), and MACCS/ISIS-3D (Molecular Design Limited). These geometric searches can be augmented by steric searching, in which the size and shape requirements of the binding site are used to weed out hits that have prohibitive dimensions.
• Programs that may be used to synchronize the geometric and steric requirements in a search applied to the FRB of FRAP include CAVEAT (P. Bartlett, University of California, Berkeley), HOOK (MSI), ALADDIN (Daylight Software) and DOCK (http://www.cmpharm.ucsf.edu/kuntz-/kuntz.html and references cited therein). All of these searching protocols may be used in conjunction with existing corporate databases, the Cambridge Structural Database, or available chemical databases from chemical suppliers.
• the methods involve identifying a number of compounds potentially capable of interacting with MASP-2 or a fragment thereof, for example the methods may involve identification of a sub-library of compounds potentially interacting with MASP-2 or fragments thereof. This may be accomplished using any conventional method. For example, alLthe.possible members of a combinatorial library may first be enumerated, according to the available reagents and the established synthetic chemistries. Individual members may then separately be docked into a binding site of a polypeptide of MASP-2. Finally, an optimal sub-library may be selected for synthesis, based on the ranking of their docking scores and/or diversity measures.
• QuaSAR-CombiDesign is another combinatorial library design tool available in MOE that provides a non-enumerative method for combinatorial library generation, and can, e.g. test against rule of five filters using statistical sampling techniques during library creation, creating smaller sub-libraries with user-defined property ranges.
• the docking step that follows library creation can be conducted using any of the available docking programs like DOCK or FlexX ⁇ , while the diversity selection for example may be performed using software available from Daylight, Tripos (diverse solutions), or BCI or by high throughput docking as for example described by Diller and Merz. In another example a 'divide-and-conquer' approach may be used.
• the methods of invention comprise application of pharmacophores obtained using active site maps.
• active site is meant to describe a site responsible of interaction with a compound and not a catalytically active site.
• the method may for example be a computational approach comprising the generation of multiple, promising, structurally diverse test compounds.
• the search for multiple structural series may be accomplished by coupling protein structural information with combinatorial library design using any suitable method. For example the "design in receptor” method (Murrary et al., 1999) or the method outlined herein below may be used.
• Methods to account for multiple protein conformations for example as described by Mason et al., 2000 may also be used, including the creation of a dynamic pharmacophore model (as for example described by Carlson et al., 2000) from molecular dynamics simulations.
• experimental and computational needle screening approaches for mapping active sites with molecular fragments may be used for example as described in Boehm et al., 2000.
• Any suitable software tools for mapping site points e.g. GRID and SITEPOINT
• MCSS techniques for generating site maps may be used.
• Suitable methods may for example comprise generation of active site maps from protein structures. Then all possible 2-, 3- and 4-point pharmacophores can be enumerated from the site map and encoded as a bit string (signature) these pharmacophores define a space to be probed by compounds that are selected using the informative library design tool.
• the metric used to evaluate the success of the approach is the number of active scaffolds selected in the library design, with the number of active compounds as a secondary measure.
• Any suitable algorithm for site map generation may be used, for example algorithms generating between 10 and 80 feature positions for each active site. An example of such a method is outlined in example 4.
• the method comprises preparing a 3D structure of a MASP-2 in pdbqs (protein data bank) format with partial charges and salvation parameters.
• the partial charges may be assigned to a MASP-2 polypeptide X-ray crystal structure using a suitable computer program such as SYBYL 6.3 and for example the Mulliken population analysis method.
• the structure thus prepared may be converted to pdbq format using a suitable script such as mol2topdbq.
• Solvation parameters may be assigned to a MASP-2 using any suitable computer program such as ADDSOL.
• the method furthermore comprises preparing structures in pdbq format of compounds potentially capable of interacting with and/or inhibiting MASP-2 in pdbqs format.
• Charges may be assigned using for example Mulliken population analysis method.
• any suitable algorithm may be used, such as the Lamarckian Genetic Algorithm.
• a person skilled in the art will readily be able to set suitable parameters for use with the algorithm.
• Based on the docking file several properties may be calculated. It is preferred that at least one of the following properties is determined: estimated free energy binding, estimated Ki or final docking energy. In general a compound interacting with and/or inhibiting MASP-2 has a low estimated free energy.
• the estimated K is preferably less than 2.0x10 "6 M, more preferably less than I .OxlO "6 M, even more preferably less than 5x10 "7 M, more preferably less than 1.0x10 "7 M, even more preferably less than 5x10 "8 M, more preferably less than I .OxlO "8 , even more preferably less than 5x10 "9 , such as less than 3.0x10 "9 M, for example less than 2x10 "9 M.
• an inhibitor of MASP-2 should have an estimated K, which is preferably less than 2.0x10 "6 M, more preferably less than I .OxlO "6 M, even more preferably less than 5x10 "7 M, more preferably less than 1.0x10 "7 M, even more preferably less than 5x10 "8 more preferably less than 1.0x10 "8 , even more preferably less than 5x10 "9 M, such as less than 3.0x10 "9 M, for example less than 2x10 "9 M.
• K is preferably less than 2.0x10 "6 M, more preferably less than I .OxlO "6 M, even more preferably less than 5x10 "7 M, more preferably less than 1.0x10 "7 M, even more preferably less than 5x10 "8 more preferably less than 1.0x10 "8 , even more preferably less than 5x10 "9 M, such as less than 3.0x10 "9 M, for example less than 2x10 "9 M.
• the invention relates to methods of identifying inhibitors of MASP-2 activity.
• Compounds capable of interacting with a specific substrate binding site of MASP-2 are potential inhibitors of MASP-2 activity. Therefore, it is an object of the invention to identify compounds capable of interacting with a substrate binding site of MASP-2. This may for example be done using any of the methods outlined herein above.
• Natural substrates of MASP-2 include MASP-2 itself (autoactivation), C2 and C4.
• Pseudosubstrates include C1 inhibitor.
• the substrate binding site may be selected from the group consisting of the C4 binding site, the C2_binding site, a MASP-2 binding site and the C1 inhibitor binding site.
• the substrate binding site is selected from the group consisting of the C4 binding site, the C2 binding site and MASP-2 binding sites. More preferably, the substrate binding site is selected from the group consisting of the C4 binding site and the C2 binding site.
• MASP-2 activity is C2 cleavage.
• MASP-2 activity is C4 cleavage.
• MASP-2 activity is MASP-2 autoactivation.
• the invention relates to identification of compounds specifically interacting with MASP-2.
• the invention relates to identification of specific modulators of MASP-2 activity.
• the compounds are specific inhibitors of MASP-2 activity.
• the compounds may inhibit the protease activity of MASP-2, but not the protease activity of other serine proteases.
• the compound may inhibit the protease activity of MASP-2, but not the activity of the related serine proteases Cl r and C1s.
• the methods of the invention may therefore comprise calculating using computer aided means, whether a compound may interact with C1r and/or C1s. This may be done as described herein above in relation to compounds capable of interacting with MASP-2 fragments. Compounds identified by in silico methods as being capable of interacting with MASP-2 or fragments thereof, but not with C1 r and/or C1 s may then be selected.
• the specificity may be confirmed using for example in vitro methods, such as binding assays, competition assay or inhibition/activation assays.
• the invention thus relates to methods, which also comprise the steps of i) executing instructions on the computer for generating a three dimensional representation of a second polypeptide from structural coordinates of a crystal of said second polypeptide, such that the computer loads into memory thereof computer-readable data comprising structural coordinates of a molecular model of said second polypeptide; iii) calculating, from said molecular models, one or more possible molecular complexes which could be formed by association of said second polypeptide with one or more selected test compounds; iv) generating output data indicative of the degree of interaction; v) selecting compounds not capable of interacting with said second polypeptide
• said second polypeptide comprises C1 r, C1s, MASP-1 or a fragments thereof, wherein said fragments preferably comprises the serine protease domain.
• said fragments preferably comprises the serine protease domain.
• a compound capable of interacting with MASP-2 may be redesigned for enhanced interaction.
• the compound is an inhibitor of MASP-2 activity, then a more efficient or a more specific inhibitors may be designed using said compound as starting point.
• a co-crystal between a polypeptide of MASP-2 and said compound may be prepared.
• Said co-crystal may for example be prepared by any of the methods of preparing crystals outlined herein above.
• the structure of said crystal may then be determined, for example using any of the methods described above for determining the structure of a polypeptide of MASP-2.
• a new compound capable of interacting with said polypeptide may be designed using information derived from said structure.
• the compounds that may interact with MASP-2 or fragments thereof and optionally modulate the activity of MASP-2 may be any useful chemical entity.
• the compounds may be small organic molecules, peptides, peptidomimetics, nucleic acids or the like.
• the compounds may be a component of a combinatorial library, such as a combinatorial library of small organic molecules. It is also possible, that the compound is a component of a virtual combinatorial library.
• Compounds designed, selected and/or optimised by methods described above may be evaluated for interacting activity with respect to polypeptides of MASP-2 using various approaches, a number of which are well known in the art. For instance, compounds may be evaluated for activity as competitive inhibitors of the binding of a natural substrate, such as C2, C4 or MASP-2. Competitive inhibition may be determined using any of the numerous available technologies known in the art.
• the compounds may also be evaluated for interaction with MASP-2 polypeptides or fragments thereof using conventional binding assays.
• assays may for example involve immobilisation of the compound on a solid support, incubation in the presence of MASP-2, washing and detection the presence/absence of immobilised MASP-2 using for example specific antibodies to MASP-2.
• any other suitable method may also be employed.
• the compounds may be further evaluated for modulation of MASP-2 activity. Assays for MASP-2 activity are described herein above.
• Modulators of MASP-2 activity may for example be used in the treatment of clinical conditions characterised by aberrant activity of the MBLectin pathway.
• inhibitors of MASP-2 activity may be used in the treatment of chronic inflammatory diseases or in clinical conditions characterised by massive cell loss, for example due to apoptosis or necrosis.
• Non-limiting examples of inhibitors of MASP-2 includes NPGB, Leupeptin, APMSF, PMSF, Pefabloc-SC or Benzamidine.
• the recombinant construct (328 amino acids) contains an Ala-Ser-Met-Thr extra tetrapeptide at the N-terminus, which is followed by the Ile363 residue of MASP-2. The purification and functional characterization of this fragment is described elsewhere (Ambrus et al., 2003). Since human MASP-2 does not contain glycosylated side chains, the recombinant protein produced in E.coli cells is identical to that isolated from natural sources. The structure was solved by molecular replacement, and refined to 2.25 A resolution (Table I). At the end of refinement the R work and R free factors were 0.174 and 0.224, respectively.
• the asymmetric unit contains two molecules (denoted molecules A and B) with somewhat different conformations (Figure 1A). 97% of the residues could be built in the electron density maps. All residues are in the most favored (458) and additionally favored (67) regions of the Ramachandran plot, except for residue 405 of molecule A and residue 389 of molecule B, which are in the generously allowed region.
• the conformations of the SP domains of the two molecules are very similar, except for the 439-441 region and some surface side chains. Non-crystallographic restraints were applied to the rest of the SP domain. There are small differences in the loop conformations of CCP2 modules, as well as in the interdomain linkers of both molecules.
• the overall conformation of the CCP2 module with six ⁇ -strands (B1-B6, Figure 1 B) is very similar to that of CCP2 found in the C1s (Gaboriaud et al., 2000) and C1 r (Budayova- Spano et al., 2002a, b) catalytic fragment structures.
• the highest B-factors of the CCP2 modules are those farthest from the interdomain linker.
• the N-terminal segment and loop B4-B5 of molecule B are disordered.
• the overall difference of the C ⁇ atoms of CCP2 for molecule A and B (r.m.s.d.
• Figure 1B shows the CCP2 modules of molecule A, C1s and C1r active forms with the ⁇ -strands B1 , B2 and B4 superimposed.
• the N-terminal end of the MASP-2 protein chain of molecule A is part of the CCP1-CCP2 linker. It has similar conformation to that detected in the C1r CCP1-CCP2-SP fragment structures (Budayova-Spano et al., 2002a), supporting the previous assumption (Feinberg et al., 2003) that the configuration around CCP1-CCP2 junction is similar to that of C1 r.
• Comparison of the structure of the CCP2 module with those of C1r and C1s highlights three regions of major differences.
• loop B1-B2 (residues 379-385), [MASP-2 numbering is used for the CCP2 module] C1s has a deletion. The conformation of this loop is similar in MASP-2 and C1r. Loop B3-B4 (residues 404-409) is disordered both in C1 r and C1s. In MASP-2 it is shorter and its conformation is stabilized by a hydrogen bond between the side chains of Asn406 and Glu424. The third region of major differences is loop B4-B5 (region 420-424), which is of the same length in the three molecules.
• MASP-2 molecule A and B correspond to slight twists of the two end of the CCP2 module: the region far form the CCP2/SP interface (loops B1-B2, B3-B4 and B5-B6) is twisted about the long axis of the CCP2 module, while the region closer to the interface (loops B2-B3 and B3-B4) is twisted about an axis perpendicular to that.
• the maximal C ⁇ atom shifts for B1-B2, B2-B3, B3-B4 and B5-B6 loops are of 1.7 A, 1.4 A 1.3 A and 2.3 A, respectively.
• the C1r CCP2-SP zymogen form can be considered as an intermediate conformation between that of C1s and MASP-2 structures, possessing some of hydrogen bonds and contacts of both type, but with elongated interatomic distances. It should be noted, that the existence of two conformational variants of MASP-2 can not be an artefact caused by differences in the crystallization medium, since they are present in the same crystal structure. The domain orientations in the MASP-2 molecules are possibly not biased by crystal contacts either, because the CCP2 modules are loosely bound in the crystal network. It suggests a possibly emerged interdomain flexibility in solution, as well which can correspond to fulfilling different functions.
• the Tyr401 hydroxyl group of molecule B is connected to Val542 (c112) carbonyl oxygen through a water molecule (W325), while that of molecule A is rotated further away and is stabilized by a hydrogen bond with the Asp475 (c49) side chain.
• an interdomain hydrogen bond is formed by Lys541 (d 11) and Ser374 sidechains, which is not found in the C1s and C1 r structures.
• a hydrogen-bonded network of water molecules stabilizes the interface.
• a glycerol molecule is bound in a cavity formed by side chains of Leu473 (c47), Tyr474 (c48), residues Glu431 , Pro432, Cys434 (d) and backbone atoms of 550 (c120) - 552 (c122).
• This cavity is more open and it has a more hydrophobic character in C1r and C1s, because Tyr474 is replaced by a shorter side chain and Glu431 by a hydrophobic residue.
• Lys541 c111
• Ser546 c1 16
• Thr399 in the case of C1r only one is different).
• the lower proline content of this region can also contribute to the higher flexibility detected in MASP-2.
• the relatively high flexibility observed for the CCP2/SP interface of MASP-2 may have important functional implications.
• MASP-2 forms homodimers through its N-terminal CUB-EGF-CUB region (Thielens et al., 2001).
• MASP-2 and MASP-1 do not form hetero-oligomers and the MASP-2 dimer can bind directly to MBL.
• MASP-2 the functional unit of MASP-2 is the homodimer form. It is remarkable that the MASP-2 homodimer can perform all those functions (e.g. binding to MBL, autoactivation, cleaving C4 and C2) that are mediated by the C1s-C1 r-C1r-C1s tetramer in the C1 complex.
• the C1r 2 C1s 2 tetramer has a high degree of flexibility, which is required for its function (Arlaud et al., 1987; Tseng et al., 1 997; L ⁇ rinczLQLincz et al., 2000).
• the MASP-2 homodimer should be at least as flexible as the C1 r 2 C1s 2 tetramer. Nevertheless, the C1 r 2 C1s 2 tetramer has twice as many hinge points as the MASP-2 dimer, to produce the same level of flexibility.
• the hinge regions of MASP-2 should allow greater conformational movements than the corresponding regions of C1r and C1s.
• the hinge bending between the CCP2 and SP domains can contribute to the correct positioning of the SP domains of the MASP-2 dimer during autoactivation, when the active site of one SP domain should contact with the activation site (Arg444-lle445 bond) of the other SP domain. After autoactivation the SP domains should turn outside of the dimer to access the large protein substrates: C2 and C4.
• the SP domain consists of two six-stranded ⁇ -barrel domains packed against each other, with the catalytic residues Ser633 (c195), His483 (c57) and Asp532 (c102) located at the junction of the two barrels ( Figure 1C).
• the structure shows the elements of the catalytic apparatus in active conformation 1 .
• the SP domains of the two molecules of MASP-2 are in virtually equivalent conformations, except for 440 and 441 (c10, d 1) residues of the activation peptide and some surface side chains. Only the C-terminal residues of the cleaved activation peptide are disordered, which is typical for the activated SP structures.
• MASP-2 has similar functions to C1r (autoactivation upon recognition of target surface by MBL/C1q) and C1s (C2 and C4 cleavage) conformation most of the surface loops is different from both of those.
• Loop A [we use the loop nomenclature proposed by Perona and Craik (1997)] of MASP-2, C1r and C1s are similar in position, but their conformations are different, in spite of the fact, that loop A of MASP-2 and C1r are of same length. Only MASP-2 shows the extension of the preceding helix to residues 485-490 (c59-c60d) of loop B (residues 485- 496). The conformation of this segment is stabilized by sandwiching the His490 (c60e) ring with Tyr486 (c60) and Lys489 (c60c) side chain carbon atoms.
• Loop B stabilizes loop A by the Gln488 N ⁇ 2 (c60b) Leu463 (c34) carbonyl oxygen hydrogen bond, as well as loop C by the stacking interaction established between the Tyr486 (c60) and His525 (c96) side chains.
• Loop D and E of MASP-2 have deletions. Loop D MASP-2 and C1r possess similar positions, but different conformations. In C1s loop C is significantly longer than in C1r or MASP-2 and restricts the access to the active site. In MASP-2 it is loop 2 that has an insertion making the substrate binding site narrower, but from the other side. Loop 1 and 2 form the bottom and one side of the substrate specificity pocket, and they have very similar conformation to that of trypsin.
• Loop 3 closes the substrate binding groove from the N-terminal end with Pro 605 (c170B) and Pro606 (c170C). In contrast to that, loop 3 of C1r and C1s is longer (the one of C1s shows disorder) and both leave the substrate binging groove more open than that of MASP-2. In the case of the C1r CCP1-CCP2-SP dimer structure, some residues of loop regions B and E are involved in intermolecular contacts in the CCP1-SP interactions.
• MASP-2 The corresponding loops of MASP-2 are different in length and also in conformation, indicating that in contrast to a recent model of MBL-MASP-2 complex (Feinberg et al., 2003), the interactions and the way of dimer formation observed for the zymogen form of C1 r can not be directly transferred to MASP-2.
• Substrate specificity of MASP-2 MASP-2 has only few natural substrates: zymogen MASP-2, C2, C4, and the pseudo-substrate C1 inhibitor, suggesting that the access to the substrate binding subsites is restricted.
• the S2' and S3_subsit.es may establish more contacts with the substrate, while the S2 and S1' subsites are more exposed than those of C1 r and C1s.
• MASP-2 shares substrates with C1s, most of its substrate binding subsites show differences.
• the conformations of loops 1 and 2 are similar to those of trypsin forming an S1 pocket deeper than that of C1 r and C1s.
• the access to the substrate binding pocket is not affected by any disordered side chains, as Arg630 (c192) side chain carbon atoms are stabilized by hydrophobic contacts with Leu575 (c143).
• a glycerol molecule is bound at the entrance of the S1 pocket, and a sodium ion at the bottom of the pocket connected via a water molecule and Ser657 (c217) O ⁇ to the nearby acidic side chains of Asp627 (c189) and Glu662 (c221), respectively.
• the sodium ion is bound in a pocket formed by the 657-662 (c217-c222) segment of loop 2, which includes a one residue insertion in this region and possesses a similar conformation to that of chymotrypsin.
• the sodium ion as well, as the glycerol molecule must be dissociated from the S1 site upon substrate binding, since the glycerol and water molecules coordinated to the sodium ion overlap with the P1 arginine residue.
• Asp627 (c189) the primary determinant of the S1 specificity is in a canonical conformation in the MASP-2 crystal structure.
• the groove that binds the N-terminal part of the bound peptide is shallow compared to that of C1 r and C1s.
• the S2 subsite is shallow, Phe529 (c99) is in a similar position to that of C1r and C1s.
• the side chain of the P2 residue is partially solvent exposed, while this site is buried by loop C in C1s.
• Water mediated hydrogen bonds may be established by a P2 Gin side chain and Tyr523 (c94) and Gln526 (c96a) side chains of loop C.
• hydrophobic interactions can be established by Met658 (c218) of loop 2 with the apolar P3 side chain of the substrate.
• P3 and residue Gly656 c216 stabilizing the backbone of the bound peptide.
• the S1' site is open, like in C1r and C1s.
• the small P1' side chains of C4 and C1 inhibitor can contact Thr466 (c37), while the P1' Lys side chain of C2 may form a salt bridge with Glu487 (c60a) of loop B.
• P2' side chains are hydrophobic or aromatic, and are bound in a hydrophobic pocket formed by Gly631 (c193) and side chain carbon atoms of Arg630 (c192), Leu581 (c148), Leu575 (c143) and Thr467 (c41). This subsite is a hydrophobic pocket also in C1r and C1s, although it is built up by different residues among the three enzymes.
• MASP-2 is a further example of an enzyme with Tyr in position c225. Its loop 2 region has a one residue insertion. Our in vitro experiments demonstrated that MASP-2 is not a Na + -activated enzyme (data not shown).
• the structure of MASP-2 is in accordance with the experimental data, since it shows a closed S1 site, and the backbone conformation of the 661-667 (c221 A-c226) segment of loop 2 is virtually identical to that of trypsin.
• the carbonyl oxygen of Gln665 (c224) is also in a position similar to that of trypsin, and different from those of enzymes with tyrosine c225 including C1r and C1s.
• the trypsin-like conformation of the 665-666 (c224-c225) peptide bond can be explained by the fact that loop 1 is of equal length in MASP-2 and trypsin and similar backbone-backbone interactions are formed between loop 1 and 2 in MASP-2 and trypsin.
• the 620-664 (c185-c223) and 623-662 (c188-c221) hydrogen bonds keep close the carbonyl group of residue Gln665 (c224) to that of Leu621 (c185), and force it to keep a position found previously in c225 proline containing enzymes of the family. This suggests, that the length of not only loop 2, but also loop 1 is more important, than the nature of the c225 residue in forming the Na + binding site.
• CCP modules are widely spread in the complement system having an important role in modulating and regulating the action of the complement components. However there is little known of their binding sites and the structural details of the way of their action. For C4 the binding sites of CCP modules of other proteins are not known. Considering the high homology between C4 and C3 there is a likely CCP-module binding site on C4d, which is similar to C3d.
• the structure of C3d with the CCP1 module of complement receptor 2 (CR2) bound on its surface, as well as the structure of C4d have been published (Szakonyi et al., 2001 , van den Elsen et al., 2002).
• the C3d-CR2 complex can serve as a starting point for modeling the binding of CCP2 module of MASP-2/C1s by C4d.
• the N- and C-terminal ends of the C3d chain are opposite to the CCP-binding surface of C3d.
• CCP binding on the corresponding surface of C4d allows complex formation between C4 and MASP-2/C1s without steric conflicts of the other domains of these molecules.
• MASP-2 plays a central role in the initiation of the lectin pathway of complement, since it is capable of autoactivating and cleaving C4 and C2 - the components of the C3 convertase enzyme complex.
• these proteolytic activities are mediated by two distinct proteases: C1r and C1s.
• the structure described in this study provides the first insight into the catalytic machinery of a protease of the lectin pathway, a constituent of innate immunity.
• the MASP-2 dimer binds to the collagen-like stalks of MBL, like the C1 r 2 C1s 2 tetramer binds to C1q in the C1 complex.
• the CCP2 module In the case of C1s the CCP2 module is fixed tightly at the surface of the SP module through a proline- and tyrosine-rich hydrophobic framework of side chains. In the case of C1 r the corresponding interaction is weaker and flexibility is detected. In the case of MASP-2, the CCP2/SP interface is not only flexible, but the different conformers are stabilized by different interactions. During autoactivation precise positioning of the interacting SP domains is required for efficient cleavage. The fact that both C1r and MASP-2 show flexibility at the CCP2/SP interface indicates that changes in the relative positions of CCP2 and SP domains could be an important factor in the autoactivation process.
• the C1r molecules are linked together through the catalytic CCP1-CCP2-SP regions. This means that the SP domains of the two C1r monomers are relatively close in the resting state of the C1 complex.
• the MASP-2 molecules form dimers via interactions of the N-terminal CUB1-EGF-CUB2 region, so the SP domains of the MASP-2 monomers are at the opposite ends of the dimer. It is likely, therefore, that significant flexibility is needed to place the distal SP domains of MASP-2 in the correct position during autoactivation.
• the subsequent cleavage of C2 and C4 substrates also requires significant conformational movements of the MASP-2 dimer, and especially the SP domains.
• the SP domains which are in close vicinity during autoactivation, should be separated in order to access the large protein substrates.
• the closed circular conformation of the MASP-2 dimer should be converted into an open form.
• Similar conformational changes should take place in the C1 complex, where C1s is responsible for the C4 and C2 cleavage.
• the SP domains of C1s are in the two opposite ends of the C1r 2 C1s 2 tetramer.
• the tetramer is about twice as long as the dimer, and a restricted flexibility at the hinge points can result in a significant conformational change.
• the other potential hinge points of MASP-2 e.g.
• the CCP1-CCP2 and the CUB2-CCP1 junctions are more flexible than the corresponding regions of C1s and possibly even those of C1r.
• the substrate specificity of MASP-2 is determined by the CCP2 and SP domains (Ambrus et al., 2003).
• the SP domain of MASP-2 and C1s contains all necessary contact sites for efficient C2 binding and cleavage and it forms a covalent complex with C1 -inhibitor. It is surprising, therefore, that most of the surface loops, which determine S1 and subsite preferences, exhibit different conformations in the two, functionally closely related, highly specific SP domains. It is likely that the same substrate specificity can be realized through different enzyme-substrate interactions.
• variable Clr digestive, coagulation enzymes
• the different conditions including testing PEG 6000 and PEG 3500 in different concentrations (from 10% to 30%), different temperatures (20°(C and 4°(C), at different pH values (from pH7 to pH8.5 using 0.2 increment). Other factors such as NaCl and glycerol were also varied. Furthermore the protein concentration and the volume of the hanging drop was optimised.
• Crystals were grown by the hanging drop method at 20°C. Crystals were obtained by mixing 2 ⁇ (l reservoir solution and 2 ⁇ (l protein solution.
• the reservoir solution contained 30% PEG 6000, 0.1 M NaCl, 10% glycerol and 0.1 M Tris-HCI pH 7.5.
• the protein solution contained 0.8 mg/ml of the active form of MASP2 CCP2-SP (Ambrus et al., 2003), 140mM NaCl and 20mM Tris/HCI pH 7.4. Synchrotron data were collected at LURE on the DW32 beamline, and at SPring-8 on the BL41XU beamline. Due to scaling problems, the former dataset was used for structure determination.
• the final model contains residues 362-440 and 445-686 of molecule A, and 366-412, 416-441 and 445-686 of molecule B.
• the stereochemistry of the structure was assessed with PROCHECK (Laskowski et al 1993). Refinement statistics are shown in Table I.
• the atomic coordinates and structure factors were deposited in the Protein Data Bank with accession code 1q3x. Figures were generated using the programs MOLSCRIPT (Kraulis, 1991),
• Raster3D (Merritt and Bacon, 1997)
• Swiss-PDBViewer (Guex and Peitsch, 1997).
• Structural alignments were carried out using O program and Swiss-PDBViewer. Surface areas were calculated using the program SURFACE (Lee and Richards, 1971).
• the assay is composed of three steps 1) preparation of mannan coated microtiter wells 2) binding of rMBL and rMASP-2 to mannan coated wells 3) screening for inhibition of MASP-2 catalysed C4 deposition.
• 96 wells microtiter plates (FluroNunc, Nalgene Nunc Int., Denmark) are coated with mannan (10 mg/L, Sigma Chemical Co., St. Louis, USA) in a coating buffer r (Na 2 C0 3 : 3.18 g/L; NaHC0 3 : 5.86g/L; pH adjusted to 9.6 using HCl) over night at 4 ° C.
• Wells are washed twice in TBS (10mM Tris, 150mM NaCl,, pH adjusted to 7.4 using HCl). Wells are then blocked by incubation for 1 hr at room temperature in a buffer as above except that 1 mg/mL of human albumin is added (State Serum Institute, Copenhagen Denmark).
• 0.8ng/well of recombinant purified human His-tagged MASP-2 and 1 ng/well of recombinant purified human MBL are bound to mannan coated microtiter wells by in cubation over night at 4 ° C in the above washing buffer except that 1 mg/mL of human albumin is added (State Serum Institute, Copenhagen Denmark). Wells are then washed 3 timers in washing buffer and are ready for use.
• the compound to be screened for inhibition activity is added to rMBL/rMASP-2 bound to mannan coated microtiter wells in the above washing buffer except that 1 mg/mL of human albumin is added (State Serum Institute, Copenhagen Denmark) and incubated for 1 hr at room temperature. Wells are washed 3 times in washing buffer and incubated 1.5 hr at 37 ° C with purified human complement component C4 (approx. 1.5-2 ng/mL) in a buffer of barbital sodium (5 mM), NaCl (181 mM), CaCI2 (2.5mM), MgCI2 (1.25 mM), pH 7.4, 1 mg/mL of human albumin (State Serum Institute, Copenhagen Denmark) is added before use.
• Wells are washed 3 times in washing buffer and 0.89 mg/L biotinylated rabbit anti- human complement component C4c is added (Dako, Denmark, biotinylated according to standard procedures). Wells are incubated for 1 hr at room temperature and washed 3 times in washing buffer. Europium labelled streptavidin (Wallac, Turku, Finland) is added at a concentration of 0.1 mg/L in the above washing buffer except that calcium is omitted and 50 ⁇ M EDTA is included. Wells are incubated 1 hr at room temperature and washed 3 times in washing buffer.
• Wells are developed by adding 100 ⁇ L of Delfia Enhancement Solution (Perkin Elmer Wallac, Norton, USA) and incubated on an orbital shaker for 5 min. at room temperature. Wells are counted in a Wallac Victor 2 d Multi counter 1420 (Wallac, Turku, Finland).
• Inhibition is seen as decreased counts compared to wells where no inhibiting substance has been added.
• the serum sample to be analysed is diluted 250 times (final concentration) in the above barbital buffer and C4 is added (1.5-2 ng/mL, final concentration).
• the compound to be screened for inhibition activity is added and samples are incubated between 5 min and 2 hours at 37 ° C. Normally incubation is 15 min. 100 ⁇ l is added to mannan coated microtiter wells prepared as described above and incubated VA hr at 37 ° C. Wells are washed 3 times in the above washing buffer and 0.89 mg/L biotinylated rabbit anti-human complement component C4c is added (Dako, Denmark, biotinylated according to standard procedures). Wells are incubated for 1 hr at room temperature and washed 3 times in washing buffer.
• Europium labelled streptavidin (Wallac, Turku, Finland) is added at a concentration of 0.1 mg/L in the above washing buffer except that calcium is omitted and 50 ⁇ M EDTA is included.
• Wells are incubated 1 hr at room temperature and washed 3 times in washing buffer.
• Wells are developed by adding 100 ⁇ L of Delfia Enhancement Solution (Perkin Elmer Wallac, Norton, USA) and incubated on an orbital shaker for 5 min. at room temperature. Wells are counted in a Wallac Victor 2 d Multi counter 1420 (Wallac, Turku, Finland).
• Generating a site map Feature points complementary to the active site are computed using an internally developed software tool. For ex-ample, a hydrogen bond donor feature is mapped in the proximity of a hydrogen bond acceptor in the protein active site.
• the collection of 3D coordinates and labels (acceptors, donors, negatives, positives, hydrophobes and aromatics) is called a site map.
• the site map is the union of three separately computed maps, ESMap which contains the electrostatic feature points (P, N, and H)
• the electrostatic feature map, ESMap is computed by first using the sphere placement algorithm employed in the program PASS (Brady et al., 2000). It generates an evenly- distributed setof points (ProbeMap) in regions of buried volume along the protein surface.
• a subset of points in the ProbeMap comprises the P, N, and H feature points depending upon the local electrostatic character of the protein.
• the CVFF molecular mechanics force field is used to compute the electrostatic potential, ⁇ i , at each point /of ProbeMap, along with the mean potential ⁇ and mean magnitude
• ⁇ (X) denotes the standard deviation about the mean of quantity X. This normalizes the point assignments relative to the overall electrostatic environment of the active site. This presents non charge-neutral protein structures (which may result from counter ions not being resolved or present in the crystal structures) from skewing feature point assignments unreasonably.
• the hydrogen-bonding feature map, HBMap is determined by projecting complementary points outward from known hydrogen-bonding atoms of the protein. The resulting superset of points is filtered on the basis of steric clash, insufficient burial and minimal proximity of alike feature points. Ideal hydrogen-bonding points are positioned on the basis of the mean angle and distance as observed in the PDB (see for example table 3). Points that clash with the protein are removed. However, for robustness, small positional perturbations are applied to retain potentially important hydrogen-bonding positions. Bifurcated hydrogen-bonding points are computed heuristically by investigating full rings of points equally bifurcated between protein atoms_that_are considered moderate or strong hydrogen bond participants.
• the AroMap set of aromatic feature points is computed by repeatedly docking a benzene ring into the protein active site and retaining the centroids of the top-scoring configurations.
• the protein is represented using a polar-hydrogen CVFF force field.
• the docking is performed using internal code in local optimization mode. One hundred separate local docking trials with different starting positions are performed. Any of the docked configurations whose score lies within an energy window of 5 kcal/mol of the minimum-energy configuration is included in AroMap. Again points are subjected to filtration on the basis of burial and mutual proximity.
• Pharmacophores are generated on the basis of feature points in the active site by exhaustive enumeration of all 2-,3-, and 4-point subsets of the feature points. For all pairs of feature points their distance in 3D-space is precomputed. In order to arrive at a discrete representation of a pharmacophore, the distances are binned, applying a user-defined binning scheme. Chirality is denoted by encoding the handedness of 4- point pharmacophores. Each pharmacophore is mapped onto a unique address, such that any possible combination of up to four features and distances is represented. The address is taken for a binary representation of the pharmacophores, called a signature.
• the length of the signature is the highest possible address for an encoding of a 4-point pharmacophore. All bits in the signature are initially set to 0. In order to represent a pharmacophore the bit at the respective address in the signature is turned on (set to 1). For the representation of the active site all pharmacophores are exhaustively enumerated and the respective bits are turned on.
• Multiple signatures may be combined.
• the binary union of multiple signatures yields a single bit string representing all pharmacophores present in any structure.
• Any consensus threshold c can be used to define the consensus representation of multiple active sites.
• a pharmacophore is present in at least c of active site conformations. Note that this way of handling multiple active site snapshots is quite expedient.
• Test compounds are encoded as follows. First, conformers are generated for each compound using an internal tool, that generates a fairly complete conformational model of the molecule. Features are assigned using a substructure-based set of rules. Pharmacophores are enumerated from these three-dimensional feature positions following the same protocol as for the active site, thus ensuring compatibility of the binary encodings. However, multiple conformers need to be represented simultaneously here. This is done by wrapping the exhaustive enumeration of pharmacophores for a single conformer into an extra loop over all the conformers of a compound. That is, any pharmacophore on any conformer of a compound is represented by turning the respective bit in the signature on.
• the meaning of a bit at a certain address is the same (the same pharmacophore, within the tolerances of the distance binning). Therefore, representing a design space amounts to masking all molecule signatures by the active site signature.
• Masking a signature means taking the logical anc of the bits of the site signature and the molecule signature. For a given molecule, bits representing pharmacophores not present in the active site are turned off, whereas the bits of the pharmacophores in the active site can be either on or off, depending on their presence or absence in the molecules. This way only the pharmacophore space defined by the active site is taken into account.
• Informative library design is a molecule selection strategy that optimizes information return for a given virtual library. The goal is to detect a set of features (pharmacophores) that determine activity against a particular test compound. Informative design aims at selecting a set of compounds such that the resulting subset will interrogate the test compound in different, but overlapping ways. Molecules are selected for synthesis and screening such that each pharmacophore in the design space has a unique pattern of occurrence in the molecules of the set. This unique 'code' enables the identification and retention of the important pharmacophores when the set of compounds is assayed, regardless of the actual experimental outcome. This is in contrast to diversity methods that seek to produce a unique pattern of pharmacophore occurrences in each molecule.
• a pharmacophore class refers to the subset of pharmacophores that all have the same code or pattern. Note that the optimum solution is a set of compounds that enables decoding each individual pharmacophore. However, this may not be possible due either to the source pool, bit correlation or to limited size of selection.
• the cost function for an unconstrained optimization in terms of molecule selection is the entropy of the class distribution. The entropy is given by
• H is the entropy of the feature classes
• C the number of distinct classes
• f the number of features in the design space
• is the size of class i.
• molecules are selected, such as to maximize H.
• Example 5 A three dimensional model of the CCP-2 and serine protease domain of MASP-2 can be constructed based on the crystallographic co-ordinates of table 3 (see also example 1).
• the molecular modeling is done achieved with commercially available Insightll 2000 20 and SYBYL 6.2 21 software packages.
• the quantum chemistry calculation is carried out using Gaussian 98. 22 All of the computational work is performed on Silicon Graphics workstations (Indigo II and 02).
• the size and spatial orientation of the active site are identified by the grid analysis implemented in the Binding Site Analysis module within Insightll.
• the grid size for searching the polypeptides is set to 1 A x 1 A x 1 A.
• MCSS multiple copy simultaneous search
• the functional groups chosen for the MCSS calculation are benzene, propane, cyclohexane, phenol, methanol, ether, and water, representing a hydrophobic functional group, a polar functional group, and solvent. Replicas of a given functional group are randomly distributed inside the binding site and then simultaneously and independently energy- minimized.
• Pairs of molecules are considered to be identical if the root-mean-square deviation (rmsd) between them is less than 0.2 A, and in such cases, one of the pairs is eliminated.
• the above protocol may be repeated, for example 10 times for each of the functional groups to allow complete searching of the active site. All calculations may be performed using the CHARMM 22 force field and MCSS 2.1 program.24
• the de novo design program LUDI may be employed to further explore the important regions in the active site for compound binding.
• the grid points produced by the Insightll/Binding Site Analysis module are divided into four subsites. The residues inside a 6 A radius sphere, which is centered on the centroid of each subsite, are used to generate the interaction site.
• Three different types of interaction sites are defined in the program: lipophilic, hydrogen bond donor, and hydrogen bond acceptor.
• the standard default parameter and a fragment library supplied with the program are used during the LUDI search.
• the best test compounds, i.e. lead molecules may be constructed by manually linking some of the MCSS minima. The new bond is constructed so that there is no introduction of significant internal strain in the candidate ligand.
• the synthetic accessibility of the generated structures is taken into account during the fragment connection step.
• the newly formed ligand molecules are subsequently energy-minimized in the rigid protein to regularize the internal coordinates using the CVFF force field in the Discover 95.0 program within Insightll.
• the flexible ligand docking procedure in the Affinity module within In-sightll is then used to define the lowest energy position for the generated molecules by using a Monte Carlo docking protocol. All of the atoms within a defined radius (6 A) of the lead molecules are allowed to move.
• the solvation grid supplied with the Affinity program is jsed. If the resulting compound/polypeptide of MASP-2 system is within a predefined energy tolerance of the previous structure, the system is subjected to minimization.
• the resulting structure is accepted on the basis of an energy check, which used the Metropolis criterion, and also a check of the rms distance of the new structure versus the structure found so far.
• the final conformations are obtained through a simulation annealing procedure from 500 to 300 K, and then 5000 rounds of energy minimization are performed to reach a convergence, where the resulting interaction energy values are used to define a rank order.
• Each energy-minimized final docking position of the lead molecules is evaluated using the interaction score function in the LUDI
• said molecule may be synthesised and interaction may be confirmed in vitro.
• MASP-2 CCP1-CCP2-SP fragment also designated MASP2 ⁇ B herein.
• the minimal catalytic unit of MASP-2 is the CCP2-SP fragment. It can cleave the protein substrates (C2 and C4) as efficiently as the entire molecule.
• C2 and C4 protein substrates
• small molecular weight synthetic substrates and inhibitors which interact with the active site of the protease domain.
• the CCP modules stabilize the structure of the serine protease domain and make the fragment more suitable for experimental handling.
• MASP-2 is a trypsin-like serine protease, it cleaves the polypeptide chain after Lys and Arg.
• C1 r and C1s, related complement proteases can be measured as esterases using Lys-O-R or Arg-O-R synthetic substrates, while their amidolytic activity is hardly measurable.
• Our preliminary experiments showed that the synthetic thiolester Z-Lys-S-Bzl (Sigma) substrate is readily cleaved by the recombinant MASP-2.
• the kcat/KM value was 3X104M-1s-1 for the MASP-2 CCP1-CCP2-SP.
• the leaving group reacts with the chromophore helper substrate DTDP (4,4'-dithiodipiridine), and the resulting complex can ⁇ be detected spectrophotometrically at 324 nm.
• concentrations of the stock solutions were as follows: Z-Lys-S-Bzl ⁇ 10mM in H20 stored at -20°C DTDP 20mM in DMF stored at -20°C
• Pefabloc-SC 4-(2-aminoethyl)-benzenesulfonyl fluoride
• Chymostatin N-(N ⁇ -carbonyl-([S,S]- ⁇ -(2-iminohaxahydro-4-pyrimidyl)-glycine)-X-Phe-al)- Phe X Leu/Val/lle
• E-64 trans-epoxylsuccinyl-L-leucilamido(4-guanidino)-butane
• PMSF phenylmethyl sulfonyl fluoride Leupeptin acetyl-Leu-Leu-Arg-al NPGB p-nitrophenyl p
• Table 6 summarizes several important features of the nine selected inhibitors, including suggested working concentrations.
• the inhibitor stock solutions were stored in aliquots at -20°C to prevent excessive freeze- thaw cycle.
• MASP-2 were incubated with the inhibitors for 30min at 37°C before the activity measurements, as stated in the protocol. All data points are the average of three independent measurements.
• IC50 value was calculated by means of nonlinear curve fitting using the Grafit 5 program.
• the data set for IC50 determination is shown in table 7 and in figure 7.
• the ICso of PMSF is 16.4 ⁇ M
• the IC 50 of Pefabloc-SC is 221.7 ⁇ M.
• the IC50 of benzamidine is 0.688mM.
• Data set for IC 50 determination is shown in table 10 and in figure 1.0.
• the IC50 of NPGB is 229.6 nM.
• the IC50 of APMSF is 11.0 ⁇ M.
• the IC50 of leupeptin is 7.7 ⁇ M. 2.7 E64
• E64 is a very weak inhibitor of MASP-2, it causes a low effect at relatively high inhibitor concentration.
• the program calculates an IC 50 value (0.87 mM).
• Table 16 summarizes the results of our measurements with nine different inhibitors. The inhibitors are ranked according to their IC 50 values (#1 has the smallest IC50 value, therefore it is the best inhibitor).
• NPGB is the best inhibitor having an IC 0 value in the nanomolar range.
• Leupeptin has an IC 50 value one order of magnitude higher than NPGB has, but it is still a very potent inhibitor.
• PMSP and APMSF the two related inhibitors shows practically the same inhibitory effect.
• Pefabloc-SC which is a newly developed very potent inhibitor of serine proteases (IC 50 values for trypsin and chymotrypsin are 81 ⁇ M and 44 ⁇ M, respectively) is an average inhibitor of MASP-2.
• Benzamidine is a small but not very specific inhibitor of serine proteases. Three inhibitors showed essentially no inhibitory effect.
• E64 is an inhibitor of cysteine protesases, it does not usually inhibit serine proteases.
• Chymostatin and ⁇ ACA are serine protease inhibitors, but their inhibitory effect on the activity of recombinant MASP-2 is negligible.
• the 3D structure of the enzyme was in pdbqs (protein data bank) format with partial charges, and solvation parameters.
• pdbqs protein data bank
• the total charge on the enzyme is -11 e.
• the structure was saved as mol2 file format (/m-kollnolp.mol2), and then converted to pdbq format by the awk script mol2topdbq and saved as /m-kollnolp.pdbq.
• the inhibitors structures were also in pdbq file format.
• SYBYL 6.3 was used to develop the 3D structures of the inhibitors with AM1 semi-empirical calculations, and the charges were assigned by Mulliken population analysis method (log files: /ligands/chymostatinaml .out, /ligands/npgbgaussian.out). Since the inhibitors were treated flexible, we defined active torsions of the molecule, which were done by Autotors (Autodock 3.0 package). The following coordinate files were used for the inhibitors:
• the benzamidine have +1 e total charge, and 2 active ratable bounds between atoms: C7_7, N1_8 and between A1_1 and C7_7.
• the leupeptin also have +1 e total charge and have 19 active torsion angles.
• Leupeptin The structure of Leupeptin is given in figure 15.
• NPGB p-Nitrophenyl-p-guanidinobenzoate
• Mw 336,74 Da NPGB has +1 e total charge and seven active torsions.
• the structure of the NPGB is given in figure 16.
• ATOM 12 A2 ⁇ 1> 0 -2.813 -1.271 -0.189 1. .00 0. .00 0 .013
• the main parameters were: population size 100 max. number of energy evaluations 25000000 max. number of generations 27000 run number 200
• the time needed for docking reflects the degree of freedom of the inhibitors.
• Table 17 summarizes the time coast of the docking.
• the Autodock calculates a free energy function, and based on it an estimated inhibition constant (Ki).
• Ki estimated inhibition constant
• the most likely docked conformation is the RUN 100.
• the coordinates of the 3D structure is the RUN 100.
• ATOM 8 HN LEU A 1 -12. .503 17, .581 72. .254 +0, .10 -0, .10 +0, .319 69 .370
• the inhibitors can be ranked.
• the strength of inhibitors are inversely proportional to free energy of binding, therefore the strongest inhibitor belongs to the lowest binding energy.
• MASP-2 is a highly specific serine protease of the lectin pathway of the complement, that cleaves C2 andC4 protein substrates.
• the present invention described resolution of the 3D structure of the catalytic region (CCP2-SP) of MASP-2 by means of X-ray crystallography (see example 1 above).
• CCP2-SP catalytic region
• X-ray crystallography see example 1 above.
• the inhibitors were ranked according to their experimentally determined IC 50 values, and three inhibitors were selected for in silico docking studies.
• NPGB very strong inhibitor
• IC 50 229 nM
• Table 4 comprises the structure coordinates of a zymogen MASP-2 with the primary sequence aa 296 to 686 of SEQ ID 1 , wherein aa R444 has been mutated to Q.
• LamzinN.S. and Wilson, K.S. (1997) Automated refinement for protein crystallography. Methods Enzymol. , 277, 269-305.
• MASPs mannan- binding lectin-associated serine proteases
• MAp19 four components of the lectin pathway activation complex encoded by two genes. Immunbioi, 205, 455- 466.

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