# Patent

## Title
Polypeptides derived from vitamin D nuclear receptor, and their uses in particular for screening vitamin D analogues

## Abstract

Polypeptides derived from vitamin D nuclear receptor, which nuclear receptor comprises a ligand-binding domain, or LBD, which contains a flexible insertion domain. The polypeptides are charactarised in that the LBD flexible insertion domain is modified by substituting or suppressing at least 30 acids. The invention also concerns the use of the polypeptides in particular for screening synthetic vitamin D analogues or for producing tests (double or triple hybrid) for identifying other proteins (activator, repressor, . . . ) interacting with the vitamin D receptor using constructs containing the polypeptide used with Gal4 for example, or for analyzing three dimensional structures of complexes formed between the polypeptides and a particular molecule by crystallography or NMR.

## Background
The invention concerns polypeptides derived from vitamin D nuclear receptor, the nucleotide sequences coding for these polypeptides, and the use of these polypeptides in particular for screening synthetic vitamin D analogues, or for producing tests (e.g. double or triple hybrid etc.) for identifying other proteins (activator, repressor etc.) interacting with the vitamin D receptor using constructs containing the polypeptide fused with Gal4 for example, or for analysing the three-dimensional structure of complexes formed between said polypeptides and a particular molecule by crystallography or NMR techniques.
The vitamin D receptor (VDR) is a ligand-dependent transcriptional regulator belonging to the superfamily of nuclear receptors (NRs) (Mangelsdorf et al., 1995).
The members of this family possess the same modular structure with a highly conserved DNA-binding domain (DBD) and a more variable ligand-binding domain (LBD) (Mangelsdorf et al., 1995; Wurtz et al., 1996).
The VDR binds to the corresponding response element, of type DR3, in the promoter region of the target genes, in heterodimer form with retinoic acid X receptor (RXR), which leads to the activation or repression of the transcription via an interaction with the transcriptional co-factors and the basal transcriptional machinery (Deluca & Zierold, 1998).
Vitamin D metabolites are used, or can be used, in various treatments for osteodystrophy, osteoporosis, psoriasis, cancer and auto-immune diseases (Bouillon et al., 1995).
Hypercalcaemia caused by vitamin D (or 1α,25-dihydroxyvitamin D3, or 1,25(OH)2 D3) limits the use of the natural ligand in these clinical applications, which has led to the development of analogues which may have reduced secondary effects.
The LBD sequence of hVDR is poorly conserved in comparison with the human γ retinoic acid receptor (hRARγ) and of the human α retinoic acid X receptor (hRXRα) (25% and 17% identical with hVDR respectively).
The presence of an insertion domain in the LBD of the VDRs connecting the helices H1 and H3 represents a characteristic typical of the VDRs. The size of this connection region varies between 72 and 81 residues in the family of VDRs, whilst it varies between 15 and 25 residues in other nuclear receptors.
It should be stressed that, in the following, the amino acid numbering system used for the peptide sequences of the different VDRs corresponds to the amino acid numbering of human VDR. This numbering system can be extended to sequences other than that of human VDR without ambiguity based on the alignment shown in FIG. 1a below.
The sequence conservation rate of this insertion domain is very low (9% identity between amino acids 157–215 of hVDR). This region is accessible to the proteases, and contains a phosphorylation site at the level of the serine in position 208, for which it has not been possible to define any functional role.
The presence of this domain could explain the difficulties hitherto encountered in crystallising the LBDs of the VDRs. In fact, this domain is poorly structured, as shown by the secondary structure analyses which predict only a few short strands with fairly low statistics, and contain a very high percentage of negatively charged residues. These two factors could increase the number of conformers in this loop, thus affecting the stability of the protein, and encouraging non-specific contacts which interfere with the crystallisation processes.
The present invention aims to provide polypeptides derived from vitamin D nuclear receptors in soluble form, and capable of being crystallised.
The invention also aims to provide nucleotide sequences coding for these derived polypeptides, and processes for the preparation of said polypeptides derived by transformation of appropriate cells with said nucleotide sequences.
The invention also aims to provide new methods of screening vitamin D analogue compounds and/or analysis of the three-dimensional structure of the complexes formed between these polypeptides and a particular molecule, said methods being effected by means of the above-mentioned derived polypeptides.
The invention also aims to provide kits for implementation of the above-mentioned methods.



The invention will be illustrated by means of the following figures:
FIG. 1: a) alignment of the peptide sequences of the VDRs of different species (hVDR: VDR of homo sapiens [human]; bVDR: VDR of bos taurus [bovine]; gVDR: VDR of gallus gallus [chicken]; rVDR: VDR of ratus norvegicus [rat]; mVDR: VDR of mus musculus [mouse]; cVDR: VDR of cotumic japonica [Japanese quail]; xVDR: VDR of xenopus laevi [African frog] with human RXRα [hRXRα] and human RARγ (hRARγ) sequences. The insertion domains of the VDRs which have been suppressed are those in boxes.
b) general conformation of the domain of the ligand-binding domain of hVDR; the helices are represented by cylinders and the β sheets by arrows.
FIG. 2: a) Scatchard analysis of the binding of 1,25(OH)2 D3 to the LBD of the wild-type hVDR (118–427; dotted curve indicated by triangles) and to the LBD of the mutant derived from the hVDR (118–427 Δ165–215; complete curve indicated by diamond-shapes); the quantity of bound marked 1,25(OH)2 D3 is indicated on the abscissa in nM and the B/U ratio between the bound (B) or unbound (U) wild-type LBDs is indicated on the ordinate.
b) CAT activities of the wild-type hVDR and of the mutant hVDR; these activities are indicated on the ordinate as a percentage; column 1 corresponds to the CAT activity measured in the absence of vitamin D (VD), of wild-type (wild-type) hVDR and of mutant (truncated) hVDR; column 2 corresponds to CAT activity measured in the presence of VD and in the absence of wild-type hVDR and of mutant hVDR; column 3 corresponds to CAT activity measured in the presence of wild-type hVDR and in the absence of VD and of mutant hVDR; column 4 corresponds to CAT activity measured in the presence of VD and of wild-type hVDR and in the absence of mutant hVDR; column 5 corresponds to CAT activity measured in the presence of mutant hVDR, and in the absence of VD and of wild-type hVDR; column 6 corresponds to CAT activity measured in the presence of mutant hVDR and of VD and in the absence of wild-type hVDR.
FIG. 3: a) representation of the β sheet region of RARγ,
b) representation of the β sheet region of the VDR in the same orientation as that of the above RARγ,
c) representation of the intramolecular interactions of the helix H12 in the VDR,
d) interface between the LBD of the VDR and the helix H3n of a symmetrically bound molecule.
FIG. 4: a) diagram of 1,25(OH)2 D3,
b) diagrammatic representation of the hVDR ligand binding pocket,
c) vitamin D in its electronic density contoured at 1 σ,
d) cavity of the ligand.



The invention concerns polypeptides derived from vitamin D nuclear receptor in humans or different animal species possessing such a receptor, said nuclear receptor comprising a ligand-binding domain, or LBD, this LBD containing a flexible insertion domain, said derived polypeptides being characterised in that they comprise:

    
    
        the peptide sequences of said nuclear receptors in which:
        
            the flexible insertion domain of the LBD is modified by substitution or suppression of at least approximately 30 amino acids, and preferably of at least approximately 40 amino acids, or of all the amino acids comprising this insertion domain (i.e. approximately 50±10 amino acids),
            and, where appropriate, one or more, or all of the amino acids situated in positions 1 to approximately 125, in particular in positions 1 to 117 or 123, of the peptide sequences of said VDRs, are modified by substitution or suppression, said derived polypeptides having the following characteristics:
            the ligand-binding and LBD-transactivation properties of the vitamin D receptor are conserved,
            they are stable, i.e. they can be conserved, in particular in NaCl 100 mM at pH 7 for at least approximately one week, without the above-mentioned properties of the LBD being affected, in contrast to the non-modified LBD which is unstable under the above-mentioned conditions,
            they can be crystallised in aqueous solvents, in particular at 4° C. by the suspended droplet vapour diffusion method,
            and they are soluble in aqueous solvents,
        
        
        or the peptide sequences derived from the peptide sequences defined above, in particular by suppression, addition or substitution of one or more amino acids, said derived sequences having the above-mentioned characteristics of said derived polypeptides.
    
    


The invention concerns more particularly polypeptides derived from VDRs of human or animal origin as defined above, said derived polypeptides being characterised in that they comprise the peptide sequences of said nuclear receptors in which the delimited peptide fragment is suppressed:

    
    
        on the one hand, by an amino acid situated approximately at one of the positions 155 to 175 of the peptide sequences of the vitamin D nuclear receptors of human or animal origin, in particular of the peptide sequences of the VDRs represented in FIG. 1a, and more particularly by the amino acid situated at one of the positions 159 to 168 of these sequences.
        and, on the other hand, by an amino acid situated approximately at one of the positions 204 to 225 of the peptide sequences of the vitamin D nuclear receptors of human or animal origin, in particular of the peptide sequences of the VDRs represented in FIG. 1a. 
    
    


The invention concerns more particularly derived polypeptides such as those defined above, said derived polypeptides being chosen from those comprising:

    
    
        the amino acid sequence delimited by the amino acids situated at positions 118 and 427, or at positions 124 and 427 of the peptide sequences of the VDRs of human or animal origin, in particular of the peptide sequences of the VDRs represented in FIG. 1a, and in which the residues situated at positions 165 to 215 of said peptide sequences of the VDRs are suppressed,
        or a peptide sequence derived from the above-mentioned amino acid sequence, in particular by suppression, addition or substitution of one or more amino acids, said derived sequence having the above-mentioned characteristics of said derived polypeptide.
    
    


The invention concerns more particularly derived polypeptides such as those defined above, chosen from the following:

    
    
        the SEQ ID NO: 4 polypeptide derived from VDR of human origin in which the peptide fragment delimited by the amino acids situated at positions 165 and 215 is suppressed,
        the SEQ ID NO: 6 polypeptide [still designated hVDR (118–427 Δ165–215)] derived from VDR of human origin in which the peptide fragment delimited by the amino acids situated at positions 1 and 117, and the peptide fragment delimited by the amino acids situated at positions 165 and 215 are suppressed,
        the SEQ ID NO: 8 polypeptide [still designated hVDR (124–427 Δ165–215)] derived from VDR of human origin in which the peptide fragment delimited by the amino acids situated at positions 1 and 123, and the peptide fragment delimited by the amino acids situated at positions 165 and 215 are suppressed.
    
    


The invention also concerns the nucleotide sequences coding for a polypeptide derived as defined above.
The invention on this basis concerns more particularly nucleotide sequences chosen from:

    
    
        the sequences SEQ ID NO: 3, SEQ ID NO: 5 and SEQ ID NO: 7 represented by FIGS. 6, 7 and 8 respectively,
        or a nucleotide sequence derived by degenerescence of the genetic code of the above-mentioned nucleotide sequences, and coding for a polypeptide derived from hVDR as defined above,
        or a nucleotide sequence derived from the above-mentioned nucleotide sequences, in particular by substitution, suppression or addition of one or more nucleotides, and coding for a peptide sequence derived from the polypeptides derived from the hVDR defined above, and having the above-mentioned characteristics of said derived polypeptides.
    
    


The invention also concerns the recombinant nucleotide sequences comprising a nucleotide sequence as defined above in association with the elements necessary for transcription of the latter sequence, in particular with a transcription promoter and terminator.
The invention also concerns vectors, in particular plasmids or viruses such as the baculoviruses, containing a nucleotide sequence as defined above.
The invention also concerns host cells transformed by an above-mentioned vector, said cells being chosen in particular from bacteria such as E. Coli, or insect cells which can be infected by a baculovirus.
The invention also concerns a process for preparation of a polypeptide derived as defined above, said process comprising the following steps:

    
    
        transformation of cells by means of a recombinant vector as defined above,
        culturing of the cells thus transformed and recovery of said polypeptide produced by said cells, optionally after purification.
    
    


The invention also concerns polypeptides derived from vitamin D nuclear receptor as defined above, bound to vitamin D or to a vitamin D analogue, in particular to any ligand capable of binding to said polypeptides with a high affinity, i.e. an affinity above approximately 10−6M.
The invention also concerns polypeptides derived from the vitamin D nuclear receptor as defined above, optionally bound to vitamin D or to a vitamin D analogue, or presenting themselves in the form of crystals.
Advantageously, the above-mentioned crystals of the present invention are obtained by vapour diffusion in particular in the presence of ammonium sulphate as a precipitant, or of another precipitant agent.
Still advantageously, the crystals of the invention can be used in X-ray crystallography techniques.
The above-mentioned crystals can attain a resolution determined by X-ray crystallography below 25 Å, which provides information at atomic level of the interaction between a target molecule and the receptor.
The invention concerns more particularly the crystals of hVDR (118–427 Δ165–215) complexed with 1,25(OH)2 D3, characterised in that they belong to the orthorhombic space group (P212121) with a=45.193 Å, b=52.443 Å, c=133.286 Å, α=β=γ=90°.
The invention also concerns the use of a polypeptide as defined above, optionally in the form of above-mentioned crystals, for the implementation of a method for screening synthetic vitamin D analogues.
The invention concerns more particularly the above-mentioned use of a polypeptide as defined above, optionally in the form of above-mentioned crystals, for the implementation of a method for screening agonistic or antagonistic vitamin D analogues which can be used in pharmaceutical compositions, in particular in the treatment of cancerous pathologies, osteodystrophy, osteoporosis, psoriasis and auto-immune diseases.
The invention also concerns processes for screening vitamin D analogues or co-factors, comprising the following steps:

    
    
        introduction of a polypeptide derived as defined above, optionally in the form of above-mentioned crystals, advantageously bound to a solid support, with the analogue or co-factor tested, the one said derived polypeptide or vitamin D analogue being advantageously marked, in particular by means of a fluorescent, radioactive or enzymatic marker,
        detection of any bond between said derived polypeptide and tested analogue by measuring the marker used, in particular after rinsing of the support used during the previous step.
    
    


The invention also concerns the use of a polypeptide derived as defined above, optionally in the form of above-mentioned crystals, for implementation of a method of analysis of the three-dimensional structure of the complexes formed between said polypeptide and a specific molecule.
On this basis, the invention concerns more particularly, a method for analysis of the three-dimensional structure of the complexes formed between a polypeptide derived as defined above, optionally in the form of above-mentioned crystals, and a specific molecule, said process comprising the following steps:

    
    
        introduction of a polypeptide derived as defined above, optionally in the form of above-mentioned crystals, with the specific molecule,
        crystallisation of the complex formed between said derived polypeptide and the specific molecule, in particular by vapour diffusion, and three-dimensional analysis of said complex, in particular by molecular replacement,
        or three-dimensional analysis of said complex in solution, in particular by NMR.
    
    


The invention also concerns application of the above-mentioned analysis method to the design of vitamin D compounds capable of being agonistic or antagonistic, as defined above.
The invention concerns more particularly agonistic or antagonistic vitamin D analogues as obtained by implementation of above-mentioned screening process, as well as pharmaceutical compositions comprising these analogues in association with an acceptable pharmaceutical vehicle.
The invention also concerns kits (or packages) for the implementation of an above-mentioned process of screening or method of analysis, said kits comprising a polypeptide derived as defined above, optionally in the form of above-mentioned crystals, in association with one or more reagents for the implementation of the above-mentioned process or method.
The invention will be further illustrated by means of the following detailed description of the hVDR derived polypeptide (118–427 Δ165–215), and of the analysis of the crystalline structure and of the properties of the derived polypeptide thus obtained.
The derived polypeptide represented in FIG. 7 (still designated VDR LBD mutant (residues 118–427 Δ165–215)) was prepared in its flexible insertion domain by suppressing the hVDR residues 165 to 215 (FIG. 1a) and leaving some thirty residues to connect the helices H1 and H3.
The VDR LBD mutant (residues 118–427 Δ165–215) was overexpressed in E. coli and purified by affinity and ion-exchange chromatography, and by gel filtration, according to the method described below.
A) Expression and Purification of the VDR LBD Mutant 118–427 Δ165–215
The mutated VDR receptor (residues 118–427 Δ165–215) was overproduced in the form of peptide with a hexahistidine tag. The cDNA amplified by PCR was sub-cloned into the NdeI-BamHI sites of the vector pET15b (Novagen). The plasmid was then amplified in the XL-1 Blue E. coli bacteria to check the sequence, and was introduced into BL21DE3 E. coli bacteria for overexpression. A pre-culture of 200 ml of LB with 200 μg ampicillin/ml was used to inoculate 6×11 LB containing 200 μg ampicillin/ml. Cells are cultivated at 37° C. up to an absorbency of 0.6, then the expression of the protein is induced by the addition of 1 mM IPTG to the culture medium for 6 hours at 20° C. The cells are separated by ultracentrifugation and kept at −80° C.
The cellular residue representing 11 of culture is placed in 25 ml of buffer containing 20 mM Tris pH 8.0, 250 mM NaCl, 5 mM Imidazole, 5% glycerol, 0.5 μg/ml protease inhibitor cocktail, 1 mM β-mercaptoethanol and 1 mM PMSF. Lysis of the cells is carried out by sonication and the raw extract is obtained by ultracentrifugation at 45 K for 1 hour and 30 minutes. Purification is carried out in three steps. Initially the raw extract is packed into a metal affinity column (Talon, Clonetech). After washing, the protein is eluted with a buffer containing 20 mM Tris pH 8.0, 250 mM NaCl, 150 mM Imidazole and 5% glycerol. The protein is then concentrated on Centiprep 30 and diluted with 4 volumes of buffer 20 mM Tris pH 7.5, NaCl 50 mM and DTT 5 mM. The sample is then packed into an anionic exchange column Q15 (Sartorius) and eluted by an NaCl gradient (0→1M). To cut the hexahistidine tag, the protein is digested by thrombin (1 unit per mg of protein) at 4° C. for 12 hours in the presence of CaCl2 5 mM. Finally the protein is applied to Superdex 75 16/60 filtration gel (Pharmacia) equilibrated with 10 mM Tris pH 7.0, 100 mM NaCl, 10 mM DTT and eluted with this same buffer. The ligand is then added in excess, and incubated with the protein at 4° C. for 1,2 hours. The complex is then concentrated on Centricon 30 for crystallisation.
The quantity of purified protein is 2 mg/l of culture. The quality and homogeneity of the protein are analysed by electrophoresis in denaturing and native condition. The protein is pure at more than 95% and a single band is observed on native gel. The protein is monomeric depending on elution of the gel filtration and light diffusion measures. The protein concentration is measured by the Bradford method and by spectrophotometry. The sample is monodisperse depending on the light diffusion measures.
B) Analysis and Properties of the VDR 118–427 Δ165–215.
The capacity of the mutant protein to bind to 1,25(OH)2 D3 has been determined by the Scatchard method, using raw extracts of the recombinant protein (FIG. 2a: the Scatchard analyses were carried out on Dextran/carbon; the raw extracts of BL21 E. coli (DE3) expressing wild-type or mutant hVDR/pET 15b, were diluted 1000 times and incubated with increasing quantities of (3H-26,27, Amersham) 1,25(OH)2 D3 in Tris 20 mM, NaCl 250 mM, dithiothreitol (DTT) 5 mM, glycerol 10% for 16 hours at 4° C.; after incubation, 25 μl of Dextran/carbon (1.5%) were added to 25 μl of the mixture of proteins; after 5 min the tubes were centrifuged at 13,000 rpm for 5 min; the concentrations of bound ligand (B) were determined by liquid scintillation counting on the surnatant; the total ligand concentrations were measured by liquid scintillation counting on 15 μl of the mixture of proteins before addition of Dextran/carbon; U represents the unbound ligand; each point represents the average of three values: the results were analysed by the least-square non-linear method according to the method described by Claire et al., 1978; the unbroken curve and the dotted curve correspond respectively to the experimental results obtained with the derived mutant polypeptide and the wild-type protein with the parameters N=0.073±0.006 nM, Kd=0.37±0.05 nM, β=0.058±0,002 for the derived mutant polypeptide and N=0.10±0.01 nM, Kd=0.55±0.08 nM, β=0.051±0.003 for the wild-type protein, with N=number of sites, Kd=dissociation constant and β=non-specific bond; the experiments were repeated twice.
No significant change was observed between the dissociation constants of the wild-type and mutant VDRs was observed, the values being similar to that described previously for the whole receptor (Bouillon et al., 1995). In order to compare the transactivation properties of the two proteins, the wild-type and mutant LBDs were fused at the GAL4 yeast activator DNA binding domain. The chimeric proteins were expressed by transfection into Cos cells, and the transactivation was measured with an appropriate reporter responding to GAL4. The two proteins have comparable transactivation properties in this system (FIG. 2b: the LBDs of wild-type or mutant VDR were fused at the Gal4 (1–147) yeast activator DNA binding domain by cloning of the cDNA into the XhoI-BamHI sites of the vector PXJ440 (Xiao et al., 1991); the Cos cells were transfected according to the method described by Xiao et al., 1991, with the vectors (250 ng) containing the wild-type or mutant LBDs of hVDR with 2 μg of 17 m5-TATA-CAT reporter gene and 2 μg of an internal control recombinant pCH110lacZ (Pharmacia) expressing β-galactosidase made up to 20 μg with a DNA support; the cells were treated with EtOH or 1,25(OH)2 D3 10−7M; the CAT activities, standardised in equal units of β-galactosidase are expressed in relation to CAT activity (100%) induced by the wild-type VDR in the presence of 1,25(OH)2 D3).
Consequently the deletion of the insertion domain has no major effect on the ligand bond, the transactivation or dimerisation with the LBD of RXRα.
Suppression of the flexible insertion domain in the VDR LBD has led to a more soluble protein, which can be crystallised in the form of a complex with 1,25(OH)2 D3. It has been possible to obtain crystals by vapour diffusion techniques using ammonium sulphate as a precipitant. The crystal structure was resolved by a combination of molecular replacement, using a partial RARγ model (Renaud et al. 1995; Klaholz et al., 1998) and isomorphic replacement with a mercury derivative. The results obtained are summarised in Table 1 below.










TABLE 1









Natural
Thiomersal



compound
Derivative











group of data









source of X rays
Hamburg BW7B
Laboratory


wave length
  0.8345 Å
  1.5418 Å


resolution
20.0-1.8 Å
20.0-2.9 Å


single reflections
29434
6404


completeness
  97.4%
 84.9%


multiplicity
  4.1
  2.8


Rsyma
  6.1%
  9.8%


last resolution section
24%, 5.06%, 93.3%
20.6%, 3.2, 71.4%


number of sites

  4


phasing power (c/a)

1.33/1.72


R centric factor

 53%











Refinement



free R factor (10% of reflections)b
 21.4%


R factor
 19.1%


number of non-hydrogen atoms


protein
1994


ligand
 30


water molecules
 166


Rmsd on bond length (Å)
  0.004


Rmsd on bond angles (Å)
  1.083


average of B factors for non-hydrogen atoms (Å2)


protein
 31.0


ligand
 22.3


water
 45.6









Table 1: Crystallisation experiments were carried out at 4° C. using the suspended droplet vapour diffusion method; the protein was concentrated from 4 to 10 mg/ml; hVDR crystals (118–427 Δ165–215) complexed with 1,25(OH)2 D3 were obtained in 4 days from a solution containing ammonium sulphate 0.7 M, buffer Mes 50 mM pH 6.0. Tris 5 mM, DTT 5 mM equilibrated against a reservoir containing ammonium sulphate 1.4 M, Mes 0.1 M pH=6.0; the crystals belong to the orthorhombic space group (P212121) with a=45.193 Å, b=52.433 Å, c=133.286 Å, α=β=γ=90°; the asymmetric unit contains one monomer; the solvent content of the crystals is 48%; the B-factor estimated using the Wilson method is 29. The heavy-atom derivative was obtained by soaking the crystals in Thiormesal (ethyl mercurylthiosalicylate) for 4 days; the results of X-ray diffusion of the natural crystals were measured at 4° C. on the Hamburg synchrotron beamline BW7B; the results were processed using DENZO and SCALEPACK software (Otwinoswski et al., 1997); the intial phases were obtained by molecular replacement with AMORE (Navaza et al., 1994), using the RARγ as an initial model; this model contains the conserved helices H1, H3–H5, H7–H10 (FIG. 1a); the solution has a 31% correlation and an R factor of 53.6% after AMORE rigid-body replacement; completed by the phases obtained using the mercurial derivative whose diffraction data were registered on a Mar Research bidimensional image detector in the laboratory at 4° C.; the derived sites were found and refined using SOLVE software (Tervilliger et al., 1987).
The map obtained by the combined phases was calculated at a resolution of 3 Å using a solvent correction. The refinement was carried out using CNS software (Brünger et al., 1998). Model construction cycles with O software (Jones et al., 1991) and a least-square minimisation, followed by an individual B-factor anisotropic refinement led to the final model. All the results between 20 and 1.8 Å were included in the refinement without cut-off thresholds. The solvent molecules in the first hydration layer were located using CNS software on a Fo-Fc map at 3 sigma. The maximum B-factor values (40–50) correspond to the residues in the loop before H1, the junction and the loops H9–H10 and H11–H12. The quality of the final model was analysed using PROCHECK software (Laskowski et al., 1993). The Ramachadran angle distribution indicates 92.4% of the most favourable conformations, and 7.6% of authorised conformations.
The final model contains 250 residues, 166 water molecules and one ligand molecule. No clear density was observed for the first two N-terminal residues and the last four C-terminal residues. Three additional residues, 375 to 377 in the H9–H10 loop were not included in the refinement due to the moderate quality of the electronic density map in this region.
The global topology of the VDR LBD (FIG. 1b) is similar to that of the other LBDs of nuclear receptors, with 13 helices sandwiched in 3 layers and a β sheet with three strands. The nomenclature is based on the structure of HRXRα (Bourguet et al., 1995). The domain binding the helices H1 and H3 contains two small helices H2 and H3n. The new helix H3n forms the base of the structure and replaces the Ω loop in the structure of RARγ. The intrinsic flexibility of the three glycine residues (162–164) situated at the junction favours a mild adaptation.
This fragment of three residues is rather distant from the ligand, and it is consequently unlikely that it plays a role in the ligand binding. The VDR structure is closer to that of the RARγ complexed with agonists. The proteins are superposed with an rmsd of 1.2 Å on 179 residues (cut-off threshold of 2.5 Å on Cα), the excluded regions being the peptide connecting H1 to H3, the β2 strand, the H6 helix and some connection loops.
The most notable difference is to be found at the level of the connection between the helices H1 and H3, which in the RARγ surrounds the β sheet, and in the VDR follows a path between H3 and the end of the β sheet, identical to that of ERα (Brzozowski et al., 1997). Consequently, the end of the β sheet is displaced towards the outside and enlarges the vitamin D binding cavity (FIGS. 3a and 3b). All the β strands have residues in contact with the ligand. In the β1 strand, Trp 286, specific to the VDR receptors, plays an important role in the positioning of the ligand. It forms part of a network of hydrogen bonds involving Ser 275 which is itself bound by hydrogen bond to Gln 317 and to the carbonyl of Met 272. The end of the β sheet is thus stabilised by hydrogen bonds between the carbonyl groups of Glu 292 and Lys 294, and Arg 158 of the connection loop between the helices H2 and H3n.
The helix H12, whose positioning is important for the coactivation and transactivation bond is in the agonist position (FIG. 3c). The helix is stabilised in this orientation by hydrophobic contacts (Ile 268 of H5 and Phe 422 of H12) and polar interactions. These last interactions involve the conserved Lys 264-Glu 420 bridge and a hydrogen bond between Ser 235 of H3 and Thr 415. Moreover, the carbonyl groups of Met 412 and Leu 414 of the H11–H12 loop are bound by H bond to Arg 154 (end of H12) which itself forms H bonds with Asp 232 (H3). All these residues are conserved in the VDR receptors. The guided mutagenesis of the residues Lys 264 and Glu 420 which establish the saline bridge has shown that these mutations suppress the transactivation dependent on the ligand, but have no effect on the ligand bond, heterodimerisation with RXR or DNA binding (Nakajima et al., 1998).
A strong crystalline contact is observed between the helix H3n and the helices H3, H4 and H12 of a symmetrically bound molecule (FIG. 3d). H3n mimics the contacts of the peptide SRCl observed in the ternary complex of PPAR (Nolte et al., 1998), although it does not contain the motif LXXLL found in most coactivators. This helix is anchored by polar contacts across the H bonds between the N-terminal region of H3n (Ser 216, Val 217 and Thr 218) and Glu 420 (H12). At the C-terminal region of the helix H3n, Ser 222 is bound by hydrogen bond to Lys 246 (end of the helix H3). The functional importance of this lysin has been demonstrated by mutation into glycin which strongly affects transactivation (Whitfield et al., 1995). Between the residues Lys 246 and Glu 420, a hydrophobic cavity is formed by the helices H3, H4 and H12. The residues of the helix H3n (Val 217, Thr 218, Leu 219, Leu 221, and Ser 222) are in contact by van der Waals bond with Ile 242 (H3), Ile 260 (H4), Leu 417 and Val 421 (H12). This observation shows that sequences other than LXXLL must be taken into consideration in the nuclear receptor recognition process.
The structure of the VDR bound to its natural ligand has made it possible to resolve a number of ambiguities and questions concerning the conformation of active vitamin D. Comparison with the crystallographic structure of the free molecule of vitamin D (Suwinska et al., 1996) shows that the two ligands have an identical conformation for the nuclei A, C and D (FIG. 4a). The most appreciable difference is the non-planar geometry of the conjugated triene in the complex, which results from the curved shape of the ligand necessary for its fixation to the receptor. The ligand binding pocket is bordered by predominant hydrophobic residues (FIGS. 4b and 4c). The extended ligand includes the helix H3 with its nucleus A (FIGS. 3b and 3c) oriented towards the C-terminal ends of the helix H5 and the hydroxyl-25 group close to the helices H7 and H11. The methyl 27 group forms a weak interaction with the helix H12 (Val 418). The distances separating the hydroxyl-25 parts of the hydroxyl groups of the nucleus A, 1-OH and 3-OH are 13 Å and 15.4 Å respectively.
In the complex, the nucleus A adopts a conformation B bracketed with the groups 1-OH and 3-OH respectively in equatorial and axial orientations. The hydroxyl part in position 1 forms two H bonds with Ser 237 (H3) and Arg 274 whilst the group 3-OH forms two H bonds with Ser 278 (H5) and Tyr 143 which is conserved only in mammals. Arg 274 is contained in a tight network of H bonds with water molecules and the carbonyl of Thr 142 at the end of H1 (FIG. 4c).
The conjugated triene (FIG. 4a) connecting the nuclei A and C is situated in a hydrophobic canal sandwiched between Ser 275 (H5-β loop) and Trp 286 (β1) on one side and Leu 233 (H3) on the other side. The single bond C6–C7 has a trans conformation which deviates 30% from the planar geometry. This deviation explains the lack of biological activity of the analogues having a trans or cis conformation of the bond C6–C7 (Norman et al., 1997). In an exclusive manner, hydrophobic residues surround this chain. The hydroxyl-25 group is bound by H bond to His 305 (H6–H7 loop) and His 397 (H11) (FIG. 4). An H bond network around the histidine residues indicates that His 305 and His 397 are H bond acceptors and givers respectively. All the residues involved in the H bond network with the exception of Ser 306 are conserved among the VDRs. The natural mutants found in vitamin D-resistant rachitism, Arg274Leu and His305Gln (Kristjansson et al., 1993), confirm the critical role for the bond to the ligand of Arg 274 and His 305, involved in the anchoring of 1-OH and 25-OH respectively.
In accordance with the fact that the ligand 1,25(OH)2 D3 is greater than oestradiol, progesterone and all trans retinoic acid, the VDR ligand binding pocket is greater (697 Å3) (FIG. 4d) than that of the ER (369 Å3), the PR (427 Å3) and of the RARγ (421 Å3). However, the increase in size is not proportional, as 1,25(OH)2 D3 only occupies 56% of the VDR ligand bond, in comparison with 63%, 67% and 66% respectively in the case of oestradiol, progesterone and all trans retinoic acid.
The accessible volume of the VDR cavity shows an expansion of the pocket in proximity to position 2 of the nucleus A, which is occupied by two water molecules and represents 40 Å3. This additional space could receive the massive methyl group of the synthetic ligand 2 α-methyl 1,25(OH)2 D3 which actually has a binding affinity 4 times greater than the natural ligand (Fujishima et al., 1998). Moreover, the additional space around the aliphatic chain could allow the accommodation of different chain lengths.
Several vitamin D analogues have been shown to behave differently from the natural ligand with regard to transactivation and recruitment of coactivator (Takeyama et al., 1999; Rachez et al., 1998). In order to understand this specificity, preliminary ligand modelling studies have been carried out. Synthetic ligands having a rather rigid aliphatic chain in position 17, such as MC 903 (22ene-26, 27-cyclopropyl-1α, 24S (OH)2 D3 or EB 1089 (22,24 diene-24, 26, 27 tri-homo 1α, 25 (OH)2 D3) (one or two double bonds respectively), can be accommodated in the binding pocket with only a few minor adjustments to the geometry of 1,25(OH)2 D3. The nuclei C and D must only be displaced to accommodate the methyl groups in positions 26 and 27 of EB 1089 or the cyclopropyl nucleus of MC 903. For the analogues 20-epi-1,25(OH)2 D3 and KH 1060, only the low-energy conformers, with a left anti conformation around C20 can be accommodated. With such a geometry, the methyl group in C21 points into the same cavity as the natural ligand, whilst the rest of the chain, due to the combination of the anti conformation of C20–C22 and the epimerisation of C20, borders the opposite side of the binding cavity. This path variation leads to different contacts for the two epimers. The distance from the 1-hydroxyl part to the 25-hydroxyl part is shorter in the 20-epi analogue, so that long chains, as in the case of KH1060, can be accommodated. Ligands with a longer aliphatic chain adopt a more compact conformation and form additional van der Waal contacts with the binding cavity which can then stabilise the helix in position H12 and/or affect less rigid regions of the binding pocket like the H6–H7 loop.
These different contacts with a rather rigid binding cavity may explain the differences in the half-lives and transcriptional activities.
The structure of vitamin D has been the subject of numerous studies during the last ten years. The present invention for the first time provides an image of 1,25(OH)2 D3 in its active conformation. Up to now, the natural lateral chain of 1,25(OH)2 D3 has been the main target of chemical modifications with a view to discovering new, more specific agonistic ligands.
It has not been possible to modify the skeleton made up of the nuclei A to D without loss of ligand binding capacity. Analogues lacking entire C and/or D nuclei but having normal spacing of the hydroxyl groups may form normal points of contact inside the binding pocket, explaining their normal biological potential (Verstuyf et al., 1998).
The complex according to the invention discloses the three-dimensional arrangement of the binding pocket around 1,25(OH)2 D3 and provides new perspectives for the design of original skeletons.
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## Claims

1. A polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 4, SEQ ID NO: 6, and SEQ ID NO: 8.

2. The polypeptide according to claim 1, wherein the polypeptide comprises SEQ ID NO: 4.

3. The polypeptide according to claim 1, wherein the polypeptide comprises SEQ ID NO: 6.

4. The polypeptide according to claim 1, wherein the polypeptide comprises SEQ ID NO: 8.