Patent Application
20050202548
The present invention relates to methods for recombinant expression of mammalian oxidosqualene synthase (OSC), to crystal forms of mammalian OSC and the three-dimensional X-ray crystal structure derived thereof, the modeling of new structures, the binding mode of a OSC ligand, as well as methods for rational drug design based on the use of such data.
2,3-Oxidosqualene:lanosterol cyclase (OSC, E.C.5.4.99.7) is a monotopic integral membrane protein associated with the endoplasmaic reticulum in eucaryotic cells. It catalyzes the key step in the conversion of the linear triterpene (3S)-2,3-oxidosqualene into fused ring compounds such as lanosterol in mammals and fungi or cycloartenol in plants. Lanosterol is the precursor of cholesterol and numerous steriodal hormones. High stereoselectivity and precision of the skeletal rearrangements has aroused the interest of researchers for nearly half a century, and valuable data on studying mechanistic details in the complex enzyme-catalyzed cyclization cascade has been collected (Viola, F., et al. (2000), Rationally designed inhibitors as tools for comparing the mechanism of squalene-hopene cyclase with oxidosqualene cyclase, Lipids 35, 297-303). Today, interest in cyclases is still unbroken, since OSCs became targets for the development of antifungal and hypocholesterolemic drugs (Morand, O. H., et al. (1997), Ro 48-8.071, a new 2,3-oxidosqualene:lanosterol cyclase inhibitor lowering plasma cholesterol in hamsters, squirrel monkeys, and minipigs: comparison to simvastatin, J Lipid Res 38, 373-90). OSC is downstream of farnesyl-pyrophosphate, beyond the synthesis of isoprenoids and coenzyme Q. In hamsters, pharmacologically active doses of an OSC inhibitor showed no adverse side-effects, in contrast to a statin which reduced food-intake and body weight, and increased plasma bilirubin, liver weight and liver triglyceride content (Morand et al., J. Lipid Res. 38, 1997, 373-390). OSC inhibition does not trigger the overexpression of HMGR because of an indirect, negative feed-back regulatory mechanism involving the production of 24(S),25-epoxycholesterol (Peffley et al., Biochem. Pharmacol. 56, 1998, 439-449; Nelson et al., J. Biol. Chem. 256, 1981, 1067-1068; Spencer et al., J. Biol. Chem. 260, 1985, 13391-13394; Panini et al., J. Lipid Res. 27, 1986, 1190-1204; Ness et al., Arch. Biochem. Biophys. 308, 1994, 420-425). This negative feed-back regulatory mechanism is fundamental to the concept of OSC inhibition because (i) it potentiates synergistically the primary inhibitory effect with an indirect down-regulation of HMGR, and (ii) it prevents the massive accumulation of the precursor monooxidosqualene in the liver. In addition, 24(S),25-epoxycholesterol was found to be one of the most potent agonists of the nuclear receptor LXR (Janowski et al., Proc. Natl. Acad. Sci. USA 96, 1999, 266-271). Considering that 24(S),25-epoxycholesterol is a by-product of inhibition of OSC it is hypothesized that the inhibition of OSC could also indirectly activate LXR-dependent pathways such as (i) cholesterol-7alpha-hydroxylase to increase the consumption of cholesterol via the bile acid route, (ii) expression of ABC proteins with the potential to stimulate reverse cholesterol transport and increase plasma HDL-C levels (Venkateswaran et al., J. Biol. Chem. 275, 2000, 14700-14707; Costet et al., J. Biol. Chem. June 2000, in press; Ordovas, Nutr Rev 58, 2000, 76-79; Schmitz and Kaminsky, Front Biosci 6, 2001, D505-D514), and/or inhibit intestinal cholesterol absorption (Mangelsdorf, XIIth International Symposium on Atherosclerosis, Stockholm, June 2000). In addition, possible cross talks between fatty acid and cholesterol metabolism mediated by liver LXR have been hypothesized (Tobin et al., Mol. Endocrinol. 14, 2000, 741-752). Compounds inhibiting OSC therefore also inhibit the biosynthesis of cholesterol, ergosterol and other sterols, and reduce the plasma cholesterol levels. They can therefore be used in the therapy and prophylaxis of hypercholesterolemia, hyperlipemia, arteriosclerosis and vascular diseases in general. Furthermore, they can be used in the therapy and/or prevention of mycoses, parasite infections, gallstones, cholestatic liver disorders, tumors and hyperproliferative disorders, e.g. hyperproliferative skin and vascular disorders. In addition, these compounds can also be of therapeutical use to improve glucose tolerance in order to treat and/or prevent related diseases such as diabetes.
The structure of the bacterial squalene hopene cyclase has been solved in complex with an inhibitor (Lenhart, A., Weihofen, W. A., Pleschke, A. E. and Schulz, G. E., Chemistry & Biology, 2002, Vol. 9, 639-645). However, in contrast to mammalian OSC the bacterial squalene hopene cyclase (SHC) is dimeric (Wendt, K. U., Poralla, K., Schulz, G. E., (1997) Structure and function of a squalene cyclase, Science, 277, 1811-1815) and is catalyzing a reaction with different educts and products as compared to OSC. Therefore, there are marked differences between mammalian OSC and SHC in the active site region and the substrate binding pocket that need to be considered in the design of OSC ligands.
Studies on membrane proteins like the triterpene synthases are often hampered by the generally low amount of protein in cells, difficulties in establishing overexpression system, their limited solubility and crystallizability. Also in the case of OSC only limited amounts of pure protein were available (Cattel, L. & Ceruti M. (1998) Inhibitors of 2,3-oxidosqualene cyclase as tools for studying the mechanism and function of the enzyme. Crit. Rev. Biochem. Mol. Biol. 33, 353-373). In most cases the protein was purified from natural sources as it was done for rat OSC (Kusano, M., Abe, I., Sankawa, U. & Ebizuka, Y. (1991) Purification and some properties of squalene-2,3-epoxide: lanosterol cyclase from rat liver. Chem Pharm Bull (Tokyo) 39, 239-241). Heterologous expression of rat OSC in yeast yielded only small amounts of recombinant protein (Abe, I. & Prestwich, G. D. (1995). Molecular cloning, characterization, and functional expression of rat oxidosqualene cyclase cDNA. Proc. Natl. Acad. Sci. USA 92, 9274-9278).
The present invention provides a solution to the problem of identifying and/or designing inhibitors of OSC activity by providing methods for recombinant expression of sufficient amounts of OSC, crystal forms of OSC and their crystal structure information, methods of preparing such crystals, and methods of identifying and/or designing inhibitors of OSC with these crystals by structure based drug design.
The present invention comprises crystal forms of mammmalian OSC and the crystal structure information obtained from them, methods for recombinant expression of OSC and methods of preparing such crystal forms, and their use for the identification and/or design of inhibitors of OSC activity. A further subject matter of the invention are methods for the identification and/or design of inhibitor compounds of OSC activity, the inhibitor compounds of OSC activity identified by these methods and their use in pharmaceutical compositions for the treatment and/or prevention of diseases which are associated with OSC comprising hypercholesterolemia, hyperlipemia, arteriosclerosis, vascular diseases, mycoses, parasite infections and gallstones, and/or treatment and/or prophylaxis of impaired glucose tolerance, diabetes, tumors and/or hyperproliferative disorders, preferably for the treatment and/or prophylaxis of hypercholesterolemia and/or hyperlipemia.
The present invention provides methods for expressing, purifying and crystallizing mammalian OSC to form a crystal which diffracts x-rays with sufficiently high resolution to allow determination of the three-dimensional structure of the OSC, or a portion or subdomain thereof. The three-dimensional structure is useful for rational design of ligands of OSC. The crystals may be used for determining the binding mode of potential ligands (e.g., inhibitors) by soaking the compounds into the crystals and then determining the structure of the complex.
In one aspect the present invention provides a crystal form of mammalian OSC, preferably having the space group symmetry C2221 (space group No. 20) and one monomer of OSC in the asymmetric unit. Preferably, the crystal includes a unit cell having dimensions a, b, and c; wherein a is from 186 Å to 194 Å, b is from 198 Å to 206 Å, and c is from 58 Å to 66 Å; and α=β=γ=90°. Preferably, the crystal includes atoms arranged in a spatial relationship represented by the atomic structure coordinates as listed in Table 3 and any three-dimensional structure thereof having an overall fold as illustrated in
The crystals of the invention include apo crystals and co-crystals. The apo crystals of the invention refer to crystals of mammalian OSC formed without a bound active site or allosteric ligand but could include bound detergents and/or lipids. The co-crystals generally comprise OSC with a ligand bound to the active site or to an allosteric site. The “active site” refers in general to the site where the enzymatic reaction catalyzed by the enzyme takes place. An active site ligand refers to any compound, which specifically binds to the active site of a mammalian OSC. Some data also give hints to allosteric sites of OSC by showing non-competitive inhibition (Abe, I., Zheng, Y. F. & Prestwich, G. D. (1998) Photoaffinity labeling of oxidosqualene cyclase and squalene cyclase by a benzophenone-containing inhibitor. Biochemistry 37, 5779-5784).
Preferably, the co-crystal form of the present invention is characterized as having a space group of C2221 (space group No. 20) and one monomer of OSC in the asymmetric unit.
More preferably, the co-crystal form has unit cell dimensions of a is from 186 Å to 194 Å, b is from 198 Å to 206 Å, and c is from 58 Å to 66 Å; and α=β=γ=90=and a C222, symmetry.
The co-crystal forms of the invention generally comprise a crystalline OSC polypeptide in association with one or more compounds at an active or allosteric binding site of the polypeptide. The association may be covalent or non-covalent.
The OSC (2,3-Oxidosqualene:lanosterol cyclase (E.C.5.4.99.7)) of the present invention may be a mammalian OSC. Preferably, the OSC of the present invention is a human OSC (hOSC). Preferably, OSC comprises the amino acid sequence as set forth in SEQ. ID NO: 5 as well as shorter variants thereof comprising all amino acids necessary for forming the active site or longer variants comprising C-terminal amino acid additions as set forth in SEQ ID NO: 6.
It is to be understood that the crystal forms of OSC of the invention are not limited to crystal forms of naturally occurring or native OSC including recombinantly produced OSC. Indeed, the crystals of the invention include mutants of the native OSC. Mutants of native OSC are obtained by replacing at least one amino acid residue in the native OSC with a different amino acid residue, or by adding or deleting amino acid residues within the native polypeptide or at the N- or C-terminus of the native polypeptide, and have substantially the same three-dimensional structure as the native OSC from which the mutant is derived.
By having substantially the same three-dimensional structure is meant having a set of atomic structure coordinates from an apo- or co-crystal that have a root mean square deviation of less than or equal to about 1.5 Å when superimposed with the atomic structure coordinates of the native OSC when at least 50% of the alpha carbon atoms of OSC are included in the superposition.
In some instances, it may be particularly advantageous or convenient to substitute, delete and/or add amino acid residues to native OSC in order to provide convenient cloning sites in cDNA encoding the polypeptide, to aid in purification of the polypeptide, etc. Such substitutions, deletions and/or additions which do not substantially alter the three dimensional structure of the native OSC will be apparent to those having skills in the art.
It should be noted that the mutants contemplated herein need not exhibit OSC activity. Indeed, amino acid substitutions, additions or deletions that interfere with the enzymatic activity of the OSC but which do not significantly alter the three-dimensional structure of the domain are specifically contemplated by the invention. Such crystalline polypeptides, or the atomic structure coordinates obtained therefrom, can be used to identify compounds that bind to the native enzyme. These compounds may affect the activity of the native enzyme.
The native and mutated OSC polypeptides described herein may be isolated from natural sources or produced by methods well known to those skilled in the art of molecular biology. Expression vectors to be used may contain a native or mutated OSC polypeptide coding sequence and appropriate transcriptional and/or translational control signals. These methods include in vitro recombinant DNA techniques, synthetic techniques and in vivo recombination/genetic recombination. See, for example, the techniques described in Maniatis et al. (1989) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY and Ausubel et al. (1989) Current Protocols in Molecular Biology, Greene Publishing Associates and Wiley Interscience, NY.
A variety of host-expression vector systems may be utilized to express the OSC coding sequence. These include but are not limited to microorganisms such as bacteria transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing the OSC coding sequence; yeast transformed with recombinant yeast expression vectors containing the OSC coding sequence; insect cell systems infected with recombinant virus expression vectors (e.g. baculovirus) containing the OSC coding sequence; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosiac virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing the OSC coding sequence; or animal cell systems. The expression elements of these systems vary in their strength and specificities. Depending on the host/vector system utilized, any of a number of suitable transcription and translation elements, including constitutive and inducible promoters such as pL of bacteriophage μ, plac, ptrp, ptac (ptrp-lac hybrid promoter) and the like may be used; when cloning in insect cell systems, promoters such as the baculovirus polyhedrin promoter may be used; when cloning in plant cell systems, promoters derived from the genome of plant cells (e.g., heat shock promoters; the promoter for the small subunit of RUBISCO; the promoter for the chlorophyll a/b binding protein) or from plant viruses (e.g., the 35 S RNA promoter of CaMV; the coat protein promoter of TMV) may be used; when cloning in mammalian cell systems, promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter) may be used; when generating cell lines that contain multiple copies of the OSC coding sequence, SV40-, BPV- and EBV-based vectors may be used with an appropriate selectable marker.
In a preferred embodiment of the present invention, an isolated nucleic acid sequence encoding hOSC comprising the nucleotide sequence of SEQ ID NO: 4 is provided.
Additionally, an expression vector containing an isolated nucleic acid sequence encoding hOSC comprising the nucleotide sequence of SEQ ID NO: 4 is provided. Preferably, the expression vector is an expression vector for the expression of proteins in Pichia pastoris. Furthermore, a host cell transformed with the said expression vector is provided. Preferably, the host cell is Pichia pastoris.
A further aspect of the present invention relates to a method of producing the hOSC comprising culturing the host cell with the said expression vector under conditions permitting the expression of hOSC by the host cell. Preferably, the host cell is P. pastoris. The present invention also provides hOSC produced by this method. Preferably, hOSC is produced in amounts sufficient for obtaining crystal forms of OSC in a quality appropriate for high-resolution structure determination.
The apo-, derivative and co-crystals of the invention can be obtained by techniques well-known in the art of protein crystallography, including batch, liquid bridge, free interface diffusion, dialysis, vapor diffusion and hanging drop methods (see e.g. McPherson (1982), Preparation and Analysis of Protein Crystals, John Wiley, NY; McPherson (1990), Eur. J. Biochem. 189:1-23; Webber (1991) Adv. Protein Chem. 41:1-36; Crystallization of Nucleic Acids and Proteins, Edited by Arnaud Ducruix and Richard Giege, Oxford University Press; Protein Crystallization Techniques, Strategies, and Tips, Edited by Terese Bergfors, International University Line, 1999). Generally, the apo- or co-crystals of the invention are grown by placing a soluble and substantially pure OSC polypeptide in an aqueous buffer containing a precipitant at a concentration just below that necessary to precipitate the protein. Water is then removed from the solution by controlled evaporation to produce crystallizing conditions, which are maintained until crystal growth ceases.
Preferably, the crystal forms of OSC are produced by a method for crystallizing mammalian OSC, the method comprising providing a buffered, aqueous solution of pH 7.5 to 9.5 with a concentration of 2 mg/ml to 40 mg/ml of monodisperse mammalian OSC. More preferably, mammalian OSC is provided in micelles of a detergent selected from the group comprising nonionic detergents comprising alkyl glucosides, e.g., n-octyl-β-D-glucopyranoside (β-OG), alkyl maltosides, e.g., DDM (dodecyl maltoside), alkyl oligooxyethylenes, e.g., C8E5, and polydisperse polyoxyethylenes, e.g. Triton, and zwitterionic detergents (amphotheric detergents) comprising sulfobetaines, e.g., zwittergent, and betaines, and cationic detergents comprising alkyldimethylamine oxides, e.g., lauryldimethylamine oxide (LDAO), and the CHAPS series, e.g., CHAPS. Preferably, the detergent is a non-ionic detergent or a cationic detergent. More preferably, the detergent is an alkyl glucoside, e.g., β-OG present in a concentration between 0.3% w/v to 3% w/v. Most preferably, the crystal forms of OSC are produced by a method for crystallizing mammalian OSC comprising (a) providing a buffered, aqueous solution of pH 7.5 to 9.5 with a concentration of 2 mg/ml to 40 mg/ml of mammalian OSC in β-OG micelles and (b) growing crystal forms using a buffered precipitant solution comprising between 2% and 25% of a small organic amphiphilic molecule, and between 10% and 35% of PEG (polyethylene glycol). Preferably, the small organic amphiphilic molecule is selected from the group comprising glycerol, ethylen glycol, butyl ether, benzamidine, dioxane, ethanol, isopropanol, butanol, pentanol, methyl pentanediol, pentanediol, hexanediol, heptanetriol and sucrose. Preferably, mammalian OSC is produced in the yeast Pichia pastoris (P. pastoris).
Preferably, co-crystals are produced by a method for co-crystallizing mammalian OSC and an active site ligand, the method comprising providing a buffered, aqueous solution of pH 7.5 to 9.5 with a concentration of 2 mg/ml to 40 mg/ml of monodisperse mammalian OSC and adding the active site ligand to the aqueous solution of mammalian OSC. More preferably, mammalian OSC is provided in micelles of a detergent selected from the group comprising nonionic detergents comprising alkyl glucosides, e.g., n-octyl-β-D-glucopyranoside (β-OG), alkyl maltosides, e.g., DDM (dodecyl maltoside), alkyl oligooxyethylenes, e.g., C8E5, and polydisperse polyoxyethylenes, e.g. Triton, and zwitterionic detergents (amphotheric detergents) comprising sulfobetaines, e.g., zwittergent, and betaines, and cationic detergents comprising alkyldimethylamine oxides, e.g., lauryldimethylamine oxide (LDAO), and the CHAPS series, e.g., CHAPS. Preferably, the detergent is a non-ionic detergent or a cationic detergent. More preferably, the detergent is an alkyl glucoside, e.g., β-OG present in a concentration of 0.3% w/v to 3% w/v. Most preferably, the crystal forms of OSC are produced by a method for crystallizing mammalian OSC comprising (a) providing a buffered, aqueous solution of pH 7.5 to 9.5 with a concentration of 2 mg/ml to 40 mg/ml of mammalian OSC in β-OG micelles, (b) adding the active site ligand to the aqueous solution of mammalian OSC, and (c) growing crystal forms using a buffered precipitant solution comprising between 2% and 25% of a small organic amphiphilic molecule, and between 10% and 35% of PEG (polyethylene glycol). Preferably, the small organic amphiphilic molecule is selected from the group comprising glycerol, ethylen glycol, butyl ether, benzamidine, dioxane, ethanol, isopropanol, butanol, pentanol, methyl pentanediol, pentanediol, hexanediol, heptanetriol and sucrose. Preferably, mammalian OSC is produced in the yeast Pichia pastoris (P. pastoris). Preferably, the active site ligand is added in a molar excess.
A further aspect of the present invention relates to a crystal or co-crystal form of OSC produced by the methods for crystallizing or co-crystallizing OSC of the present invention.
Furthermore, the present invention provides a crystal form of OSC or a co-crystal form of OSC with a bound ligand for the determination of the three-dimensional structure of mammalian OSC.
Another aspect of the present invention is the use of the crystal form and active site to identify potential OSC ligands. The atomic coordinate/x-ray diffraction data may be used to create a physical model which can then be used to design molecular models of compounds that may interact with the determined active sites, binding sites or other structural or functional domains or subdomains of OSC. Alternatively, the atomic coordinate/x-ray diffraction data of the complex may be represented as atomic model output data on computer readable media which can be used in a computer modeling system to calculate different molecules expected to interact with the determined active sites, binding sites, or other structural or functional domains or subdomains of the OSC. For example, computer analysis of the data allows one to calculate the three-dimensional interaction of the OSC and the ligand to confirm that the ligand binds to, or changes the conformation of, particular domain(s) or subdomain(s) of OSC. Ligands identified from the analysis of the physical or computer model can then be synthesized and tested for biological activity with an appropriate assay.
The atomic coordinate/x-ray diffraction data of the present invention are generally provided on computer readable media. A skilled artisan can then access the data and analyze it for structure determination and/or rational ligand (e.g., inhibitor) design using a computer-based system. A typical computer system includes hardware means, software means, and data storage means. The hardware means typically includes a central processing unit (CPU), input means, output means and data storage means. One skilled in the art will readily appreciate which of the currently available computer-based systems are suitable for use in the practice of the present invention.
A variety of commercially available software programs are available for conducting the analysis and comparison of data in the computer-based system. One skilled in the art will readily recognize which of the available algorithms or implementing software packages for conducting computer analyses can be utilized or adapted for use in the computer-based system. A target structural motif or target motif refers to any rationally selected sequence or combination of sequences in which the sequence(s) are chosen based on a three-dimensional configuration or electron density map which is formed upon the folding of the target motif. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzymatic active sites, structural subdomains, epitopes, functional domains and signal sequences. A variety of structural formats for the input and output means can be used to input and output the information in the computer-based systems of the present invention.
A variety of comparing means can be used to compare a target sequence or target motif with the data storage means to identify structural motifs or interpret electron density maps derived in part from the atomic coordinate/x-ray diffraction data. One skilled in the art can readily recognize any one of the publicly available computer modeling programs that can be used.
Suitable software that can be used to view, analyze, design, and/or model a protein comprise MOLOC (Roche, 1985), FRED, MAIN, FlexX, Gold, XtalView, Alchemy™, LabVision™, Sybyl™, Molcadd™, Leapfrog™, Matchmaker™, Genefold™ and Sitel™ (available from Tripos Inc., St. Louis, Mo.); Quanta™, Cerius2™, X-Plor™, CNS™, Catalyst™, Modeller™, ChemX™, Ludi™, Insight™, Discover™, Cameleon™ and Iditis™ (available from Accelrys Inc., Princeton N.J.); Rasmol™ (available from Glaxo Research and Development, Greenford, Middlesex, U.K.); MOE™ (available from Chemical Computing Group, Montreal, Quebec, Canada); Maestro™ (available from Shrdinger Inc.,); Midas/MidasPlus™ (available from UCSF, San Francisco, Calif.); VRML (webviewer—freeware on the internet); Chime (MDL—freeware on the internet); MOIL (available from University of Illinois, Urbana-Champaign, Ill.); MacroModel™ and GRASP™ (available from Columbia University, New York, N.Y.); Ribbon™ (available from University of Alabama, Tuscaloosa, Ala.); NAOMI™ (available from Oxford University, Oxford, UK); Explorer Eyechem™ (available from Silicon Graphics Inc., Mountain View, Calif.); Univision™ (available from Cray Research Inc., Seattle Wash.); Molscript™ and 0 (available from Uppsala University, Uppsala, Sweden); Chem 3D™ and Protein Expert™ (available from Cambridge Scientific); and upgraded versions thereof.
Crystals may be frozen prior to data collection.
The mosaic spread of the frozen crystals could sometimes be reduced by annealing, wherein the stream of cold nitrogen gas is briefly blocked, allowing the frozen crystal to thaw momentarily before re-freezing in the nitrogen gas stream.
Diffraction data typically extending to 2.2 Å was collected from the frozen crystals at the synchrotron beam line PX6A at the Swiss light source (SLS, Villigen, Switzerland). Under optimum conditions, data extending to 1.8 Å was recorded. Preferably, data is collected to a resolution of 3.5 Å or better. More preferably, data is collected to a resolution of 2.7 Å or better.
Derivative crystals of the invention can be obtained by soaking apo or co-crystals in mother liquor containing salts of heavy metal atoms, according to procedures known to those of skill in the art of X-ray crystallography.
Co-crystals of the invention can be obtained by soaking an apo crystal in mother liquor containing a ligand that binds to the active site, or can be obtained by co-crystallizing the OSC polypeptide in the presence of one or more ligands that bind to the active site or to an allosteric site. Preferably, co-crystals are formed with an active site OSC ligand, which is not converted by the enzyme. One example for such an active site ligand is [4-[6-(allyl-methyl-amino)-hexyloxy]-2-fluoro-phenyl]-(4-bromo-phenyl)-methanone fumarate.
In a further embodiment of the present invention a method for determining the three-dimensional structure of a crystal form of mammalian OSC to a resolution of 3.5 Å or better is provided, the method comprising
The present invention further relates to a machine-readable data storage medium comprising a data storage material encoded with machine readable data which, when using a machine programmed with instructions for using said data, displays a graphical three-dimensional representation of a molecule or molecular complex comprising at least a portion of mammalian OSC comprising the amino acids of SEQ ID NO:5 comprising the ligand binding active site being defined by a set of points having a root mean square deviation of less than about 1.5 Å from points representing the backbone alpha carbon atoms of said amino acids as represented by structure coordinates as listed in Table 3.
The crystals of the invention, and particularly the atomic structure coordinates obtained therefrom, have a wide variety of uses. For example, the crystals and structure coordinates described herein are particularly useful for identifying compounds that interact with OSC as an approach towards developing new therapeutic agents. Pharmaceutical compositions of said compounds can be developed, and said compounds can be used for the manufacture of a medicament comprising said compound for the treatment and/or prevention of diseases which are associated with OSC comprising hypercholesterolemia, hyperlipemia, arteriosclerosis, vascular diseases, mycoses, parasite infections and gallstones, and/or treatment and/or prophylaxis of impaired glucose tolerance, diabetes, tumors and/or hyperproliferative disorders, preferably for the treatment and/or prophylaxis of hypercholesterolemia and/or hyperlipemia. Hyperproliferative skin and vascular disorders particularly come into consideration as hyperproliferative disorders.
Therefore, the present invention also relates to the use of a crystal form or a co-crystal form of the invention for the identification and/or design of inhibitors of OSC activity.
Moreover, the present invention relates to a method for identifying a compound that interacts with OSC, comprising the steps of
In another aspect, the method further comprises the steps of
The compound in these methods may be a compound that interacts with the active site of OSC or may be a compound that interacts with an allosteric site of OSC. Preferred are compounds, which interact with the active site of OSC. Even more preferred are compounds, which show an inhibitory effect on OSC activity in step (d) of the methods of the present invention.
In a further aspect of the present invention the method for identifying a compound that interacts with OSC is a computer-assisted method. Preferably, determining whether the compound is expected to bind to or interfere with the molecule or molecular complex includes performing a fitting operation between the compound and a binding site or substrate binding surface of the molecule or molecular complex, followed by computationally analyzing the results of the fitting operation to quantify the association between, or the interference with, the compound and the binding site. Optionally, the method further includes screening a library of compounds. Optionally, the method further includes supplying or synthesizing the compound, then assaying the compound to determine whether it interacts with and has an effect on mammalian OSC activity.
The present invention also relates to the compounds identified by the said methods for identifying a compound that interacts with OSC.
The structure coordinates described herein can be used as phasing models in determining the crystal structures of additional native or mutated OSC, as well as the structures of co-crystals of such OSC with active site inhibitors or activators bound. The structure coordinates, as well as models of the three-dimensional structures obtained therefrom, can also be used to aid the elucidation of solution-based structures of native or mutated OSCs, such as those obtained via NMR. Thus, the crystals and atomic structure coordinates of the invention provide a convenient means for elucidating the structures and functions of OSC or other cyclases.
For purposes of clarity and discussion, the crystal forms of the invention will be described by reference to specific OSC exemplary apo crystals and co-crystals. Those skilled in the art will appreciate that the principles described herein are generally applicable to crystal forms of any mammalian OSC, including, but not limited to hOSC.
Therefore, in a further aspect of the present invention a pharmaceutical composition comprising the compound identified by the methods of the present invention as having an effect on OSC activity, or pharmaceutically acceptable salts thereof, and a pharmaceutically acceptable carrier is provided.
The phrase “pharmaceutically acceptable” is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
As used herein, “pharmaceutically acceptable salts” refer to derivatives of the disclosed compounds wherein the parent compound is modified by making acid or base salts thereof. Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like. The pharmaceutically acceptable salts include the conventional non-toxic salts or the quaternary ammonium salts of the parent compound formed, for example, from non-toxic inorganic or organic acids. For example, such conventional non-toxic salts include those derived from inorganic acids such as hydrochloric, hydrobromic, sulfuric, sulfamic, phosphoric, nitric and the like; and the salts prepared from organic acids such as acetic, propionic, succinic, glycolic, stearic, lactic, malic, tartaric, citric, ascorbic, pamoic, maleic, hydroxymaleic, phenylacetic, glutamic, benzoic, salicylic, sulfanilic, 2-acetoxybenzoic, fumaric, benzenesulfonic, toluenesulfonic, methanesulfonic, ethane disulfonic, oxalic, isethionic, and the like.
The pharmaceutically acceptable salts of the present invention can be synthesized from the parent compound which contains a basic or acidic moiety by conventional chemical methods. Generally, such salts can be prepared by reacting the free acid or base forms of these compounds with a stoichiometric amount of the appropriate base or acid in water or in an organic solvent, or in a mixture of the two; generally, nonaqueous media like ether, ethyl acetate, ethanol, isopropanol, or acetonitrile are preferred. Lists of suitable salts are found in Remington's Pharmaceutical Sciences, 17th ed., Mack Publishing Company, Easton, Pa., 1985, p. 1418, the disclosure of which is hereby incorporated by reference.
“Stable compound” and “stable structure” are meant to indicate a compound that is sufficiently robust to survive isolation to a useful degree of purity from a reaction mixture, and formulation into an efficacious therapeutic agent.
Furthermore, a compound identified by the methods of the present invention as having an effect on OSC activity for use as a therapeutic active substance, in particular for the treatment and/or prevention of diseases which are associated with OSC comprising hypercholesterolemia, hyperlipemia, arteriosclerosis, vascular diseases, mycoses, parasite infections and gallstones, and/or treatment and/or prophylaxis of impaired glucose tolerance, diabetes, tumors and/or hyperproliferative disorders, preferably for the treatment and/or prophylaxis of hypercholesterolemia and/or hyperlipemia, is provided. Hyperproliferative skin and vascular disorders particularly come into consideration as hyperproliferative disorders.
A further aspect of the present invention relates to the use of a compound identified by the methods of the present invention as having an effect on OSC activity for the manufacture of a medicament for the treatment and/or prevention of diseases which are associated with OSC comprising hypercholesterolemia, hyperlipemia, arteriosclerosis, vascular diseases, mycoses, parasite infections and gallstones, and/or treatment and/or prophylaxis of impaired glucose tolerance, diabetes, tumors and/or hyperproliferative disorders, preferably for the treatment and/or prophylaxis of hypercholesterolemia and/or hyperlipemia. Hyperproliferative skin and vascular disorders particularly come into consideration as hyperproliferative disorders.
Having now generally described this invention, the same will become better understood by reference to the following specific examples and figures, which are included herein for purpose of illustration only and are not intended to be limiting unless otherwise specified.
Commercially available reagents referred to in the examples were used according to manufacturer's instructions unless otherwise indicated.
Abbreviations used comprise β-OG (n-Octyl-β-D-glucopyranoside); DDM (Dodecyl maltopyranoside); C8E5 (n-Octyl-pentaoxyethylene); LDAO (Lauryldimethylamine oxide).
Preparation of DNA probes, digestion with restriction endonucleases, DNA ligation and transformation of E. coli strains were performed as described by Sambrook (Sambrook, J., et al. (1989), Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory Press, 1989). For DNA sequencing, the ABI PRISM BigDye Terminator Cycle Sequencing Ready Reaction Kit and ABI PRISM 310 Genetic analyzer was used. PCR were performed in the T3 Thermocycler (Whatman Biometra), using the Pfu polymerase (Stratagene).
Human OSC (hOSC) was amplified by PCR using a cDNA as a template. The oligonucleotides used for PCR were 5′-GTACCTTTCGAAACAATGACGGAGGGCACGTGTCTGCGG-3′ (SEQ ID NO: 1) with a SfuI site (in bold) and 5′-GCCTCTAGATCAGGGGTGGCCAGCAAGGG-3′ (SEQ ID NO: 2) for hOSC with His-tag or 5′-GGCTCTAGATCAGGGGTGGCCAGCAAGGG-3′ (SEQ ID NO: 3) for wildtype hOSC (SEQ ID NO: 4) both with a XbaI site (in bold). Using the two new restriction sites, both amplified DNA fragment were cloned into pPICZB vector (Invitrogen) leading to a fusion with the myc-epitope and the 6×His-tag at the C-terminus for the construct with tag. The sequence was confirmed by sequencing. pPICZB-hOSC was linearized with PmeI, transformed by electroporation in P. pastoris strain GS115 and the phenotype of the colonies obtained was checked as recommended by the distributor Invitrogen.
The monotopic membrane protein hOSC was cloned into the pPICZB vector resulting in a construct with and without a tag. For the variant with tag due to the cloning the last amino acid, a proline, was changed to a leucine followed by the myc-epitope and the 6×His-tag (EQKLISEEDLNSAVDHHHHHH). Sequencing of the whole gene shows one mutation L642V in comparison to the reported sequence (Sung, C. K., et al. (1995), Molecular cloning of cDNA encoding human lanosterol synthase, Biol Pharm Bull 18, 1459-61 and Young, M., et al., (1996), The human lanosterol synthase gene maps to chromosome 21q22.3, Hum Genet 97, 620-4). This conservative mutation is described in the literature as single nucleotide polymorphism (SNPs) and seems to be very common (Roessler, J., et al. (1989). Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, N.Y., Cold Spring Harbor Laboratory Press 1999).
Expression of Recombinant Human OSC in P. pastoris
Transformation into GS115 with PmeI linearized hOSCtag-pPICZB and hOSC-pPICZB results for both constructs in numerous colonies on the selection plate with 100 μg/ml Zeocin. For each construct eight clones with phenotype MutS plus a control GS115 with pPICZB were tested for hOSC expression. For this small scale expression tests colonies were grown at 30° C. in YPD medium (1% yeast extract, 2% peptone, 2% glucose) with zeocin (100 μg/ml) to an OD600 of 10-12. Cells were collected by centrifugation and resuspended in YP medium supplemented with 2% methanol. The same amount of methanol was added every 24 h. After 48 h cells were harvested, disrupted with glass bead lysis. The supernatant was analyzed by Western blot with a monoclonal antibody against the myc-epitope (Invitrogen) or a polyclonal antibody raised by immunization of rabbits against a synthetic peptide (C471-P-H-V-T-E-H-I-P-R480; SEQ ID NO: 7) was used. Supernatant of the glass beads lysis of P. pastoris cells were separated by SDS-PAGE and immobilized on a PDVF-membrane (Invitrogen) by transfer electrophoresis at 25V for 120 min using as transfer buffer12 mM Tris base, 96 mM Glycine and 10% methanol. For blocking and the detection the Lumi-Lightplus-Kit from Roche Diagnostics was used following the manufacturer's recommendations.
For both constructs only one clone could be identified with a significant signal in the Western blot with the polyclonal hOSC antibody.
For the large scale expression a one liter culture (2×2 L shake flasks with 500 ml medium) of the transformed cell line with the strongest signal in the Western blot has been carried out with the same protocol as described above. The production level was modest with approximately 1-2 mg and 0.5 mg per one gram cell mass for the variant with and without tag, respectively.
Purification of hOSC with 6×His-tag
Cells expressing hOSC 6×His-tag (SEQ ID NO: 6) harvested from one liter culture (40 g) were resuspended in 50 mM Tris-HCl pH 7.5, 5% glycerol, 2 mM TCEP and 2 mM Mg2Cl2 (buffer A) supplemented with 1 mM DNAse (Roche Diagnostics) and two tablets Complete protease inhibitor (Roche Diagnostics) per 50 ml. The cell suspension was disrupted with 1.9 kbar in the Basic Z Model Cell homogenizer (Constant Systems LTD), sonicated for 3 minutes (50%, level 5 and 0° C.) and was passed a second round through the cell homogenizer. Triton X-100 (Fluka) was added to the crude extract with a final concentration of 0.2% and incubated for one hour at 4° C. After centrifugation with 31000×g (JA20, Beckman) for half an hour the supernatant was loaded on a Ni-NTA-agarose column (10×2.5 cm) equilibrated with buffer A plus 0.2% Triton X-100. The column was washed with 1 column volumes (CV) of the same buffer and 5 CV of buffer A plus 0.2% N-Octyl-beta-D-Glucopyranoside (β-OG, Applichem). The His-tag bound protein was then eluted with a linear gradient to 0.5M imidazole in buffer A. Collected fractions were screened on SDS-PAGE. Fractions containing hOSC were pooled and concentrated with a millipore filter device. The concentrated protein solution was loaded on a Fractogel EMD Biosec size exclusion column (1.6 cm×60 cm, Merck), that was equilibrated with buffer A plus 0.8% β-OG. Fractions were analyzed by SDS-PAGE, showing a purity around 95%. For storage the pooled fractions were shock-frozen in liquid nitrogen and stored at −80° C.
For the solubilization two different detergents, —OG (0.8%) and Triton X-100 (0.2%), were tried. Effectiveness was estimated by the yield obtained after Ni-NTA-chelate column. Triton X-100 gave the best results in yield. Also the incubation time was very critical, incubation longer than 1 hour resulted in one major contamination binding to the affinity column. After centrifugation at 31400×g (JA20, Beckman) the supernatant was applied to Ni-NTA-chelate column. Different combinations of β-OG and Triton X-100 both together, alone, above and below the CMC for β-OG were tried for the wash and elution steps. The best results were obtained with 0.2% β-OG in the wash and elution buffer, which is below the CMC (0.6%). The purification with the Ni-chelating column gave two peaks with hOSC one directly after the detergent exchange from Triton X-100 to β-OG and a second one in the normal Imidazol gradient. Two separate pools were made. The largest amount of protein (100 mg) was found in the detergent exchange pool, whereas only a quarter eluted in the imidazol gradient. N-terminal sequencing showed that in both pools the protein lost its N-terminal methionine. Additionally, mass spectroscopy analysis showed clearly a difference in mass, which corresponds to one histidine. Thus, the OSC eluted directly in the detergent exchange has only five histidines at the C-terminus and may bind less tightly as the one with six histidines. The solubilized hOSC was stable enough for one or two days with a detergent concentration under the CMC (0.2% for β-OG). The two pools were worked off separately. After size exclusion chromatography for both pools the protein had a purity to 95% as judged by SDS-PAGE (
Purification of hOSC Wild-Type
Cells expressing hOSC wildtype (SEQ ID NO: 5) harvested from one liter culture (45 g) were resuspended in buffer A and disrupted as described for the variant with 6×His-tag. After centrifugation at 31000×g (JA20, Beckman) for 30 min, the supernatant was further centrifuged at 40000×rpm for 60 min in the ultracentrifuge (Centrikon T-2070, Kontron) to isolate the membrane fraction. The pellet was resuspended in buffer A supplemented with 0.2% Triton X-100 and centrifuged again at 40000×rpm for 60 min. The supernatant was loaded on TMAE-Fractogel (1.6 cm×13 cm, Merck) equilibrated with the resuspension buffer. The column was washed with six column volumes (CV) of buffer A supplemented with 0.2% β-OG and eluted with a linear gradient to 0.5 M sodium chloride in the same buffer. Collected fractions were screened on SDS-PAGE. Fractions containing hOSC were pooled. As a last step a gel filtration run was performed as described for the variant with His-tag.
In the case of hOSC without tag the membrane fraction was isolated containing hOSC as a major component as a first enrichment step. For the selective solubilization process three different detergents were tried β-OG (0.8%), Triton X-100 (0.2%) and Octyl-POE (0.6%). Amount and purity were estimated by SDS-PAGE. The best results in yield and purity were obtained again with Triton X-100. The solubilized protein was bound classically to an anion exchanger, the detergent exchanged to β-OG by washing the column with 5 column volumes and eluted in a single peak at approximately 100 mM sodium chloride. The protein lacked again the N-terminal methionine and had a purity to 90% as judged by SDS-PAGE. In respect to stability and storage conditions it behaved identical to the variant with tag.
Purification of hOSC was followed by electrophoresis on 10-20% Tricine SDS polyacrylamide gradient gels. Protein concentrations were determined according to Bradford (Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal Biochem 72, 248-2541976) or for pure protein by absorption spectroscopy (Pace, C. N., Vajdos, F., Fee, L., Grimsley, G. & Gray, T. (1995). How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411-2423.) using the calculated molecular extinction coefficient at 280 nm of 181240 M−1cm−1.
Activity of OSC
Activity assay and IC50 determination was carried out as described for liver microsomal preparations (Lenhart, A., et al. (2003), Binding structures and potencies of oxidosqualene cyclase inhibitors with the homologous squalene-hopene cyclase, J Med Chem 46, 2083-92, 2003). Only the reaction buffer was modified by adding a detergent. The final conditions for IC50 measurements were 30 μM of [14C] R,S-MOS in reaction buffer (50 mM sodium phosphate buffer (pH 7.4), 1 mM EDTA, 1 mM dithiothreitol and 0.8% β-OG), containing 0.5% albumin, and ethanol <2%, in a total volume of 801 μl. The protein concentration of recombinant hOSC was 0.4 μg/ml. For testing the influence of different detergents on the activity the protein concentration was varied between 0.1 and 10 μg/ml in the presence of 0.2% β-OG, 0.6% C8E5, 0.1% Triton X-100 or 0.016% DDM. As positive control human liver microsomes were used at a final concentration of 0.4 mg/ml without detergent (Lenhart, A., et al. (2003), Binding structures and potencies of oxidosqualene cyclase inhibitors with the homologous squalene-hopene cyclase, J Med Chem 46, 2083-92 2003).
The activity of the recombinant enzyme was tested with different detergents in assay buffer (DDM, C8E5, β-OG or Triton X-100; all above the CMC). The highest activity was observed with Triton X-100, followed by C8E5 and β-OG (
Oligomerisation State of OSC
Sedimentation equilibrium (SE) runs were performed at various speeds at 20° C. with sample volume of 100 μl using an Optima XL-I analytical ultracentrifuge (Beckman-Coulter, Palo Alto). The initial protein concentrations were 0.2-0.6 mg/ml in 20 mM Tris-HCl pH 7.5, 5% glycerol, 1 mM TCEP, 0.8% β-OG and 1 mM MgCl2 (buffer B). The equilibrium absorbance profiles were recorded after 20 hours at 280 nm. A further record taken 2 hours later proved the equilibrium was reached.
Analysis of the profiles was performed with the Beckman software package and the Schuck program DISCREEQ (Schuck P. (1994). Simultaneous radial and wavelength analysis with the Optima XL-A analytical centrifuge, Progr. Colloid Polym. Sci. 94, 1-13). All solvent densities matched to the detergent densities by addition of sucrose, or not matched, were measured with a PAAR density meter, type DMA4500 (Anton Paar, Graz, Austria). They are given in Table 2. The detergent densities were assessed in the buffer without protein from separate SE runs where the interference detection optics was used for the non absorbing detergents. The partial specific volume computed from the amino acids sequence according to Edsall (Edsall J T, in Cohn E J, Edsall J T (eds) (1943) Protein, amino acids and peptides as ions and dipolar ions. Reinhold, N.Y., 370-381) is 0.729 cm3/g. Because of the sucrose addition the hydration state of the protein has to be considered. An estimated value for vbar can be given by the average between a fully hydrated protein vbar=0.787 cm3/g (Rickwood D. and Chambers J. A. A. (1984) in Centrifugation, a practical approach, 2nd Edition, Edited by D. Rickwood, IRL Press, Oxford) and the non-hydrated protein as indicated above. Best fits however were obtained for vbar=0.766 cm3/g. Thus, this value was used. In the case of LDAO the density of 0.914 g/cm3 was not compensated. The profiles were analysed by a model with various numbers of bound micelles. Best fits were obtained with 1 bound micelle. Thus, the analysis was carried out under this assumption providing a vbar value of 0.791 cm3/g. Similarly, the non-density-matched sample with β-OG under the cmc was analysed with vbar=0746 cm3/g. This value corresponds to 10 bound β-OG.
The purified OSC on SDS-PAGE showed a protein band, corresponding to a molecular mass of 80 kDa, which is a little bit lower than the predicted molecular mass of 85'690 Da. Mass spectral analysis of the protein resulted in a mass of 85'700 Da. This result was nearly identical to the theoretical predicted mass for hOSC-tag without the N-terminal methionin indicating that the protein is not glycosylated or posttranlational modified.
The purified hOSC-tag was characterized by a sedimentation equilibrium experiment with the analytical ultracentrifuge. The solvent density was adjusted to the density of the detergent according to the approach established by Lustig et al. (Lustig, A., Engel, A., Tsiotis, G., Landau, E. M. & Baschong, W. (2000). Molecular weight determination of membrane proteins by sedimentation equilibrium at the sucrose or nycodenz-adjusted density of the hydrated detergent micelle. Biochim Biophys Acta 1464, 199-206). At a β-OG concentration of 0.8% the protein was monomeric with a moelcular weight of 86 kDA. The same oligomerisation state was found for the wild-type hOSC. At a concentration of 0.2% large losses for aggregates with molecular mass higher than 400 kDa and a broad distribution between dimers, trimers and tetramers (Table 2) were observed. Since analytical ultracentrifugation allows such a detailed picture on the oligomerisation state this method was used also to test the influence of other detergents on the oligomerisation state. In the presence of 0.2% Triton X-100 in the buffer the protein is also monomeric and monodisperse. The same was found at a C8E5 concentration of 0.6% (CMC 0.2%), but 50% of the protein was lost as large aggregates (>400 kDa). In detergents like LDAO and DDM the protein was polydisperse with a mixture of monomers, dimers and tetramers and more than 50% of the protein was lost as large aggregates. This effect was more pronounced for DDM. The correlation with the activity measurements showed that the detergents with monomeric hOSC have the highest activity (
For crystallization hOSC was concentrated to approximately 10 mg/ml in a buffer containing 0.3% (w/v) β-OG. Detergent was added prior to crystallization to concentrations above the CMC. For inhibitor complex co-crystals the protein was incubated with 5 mM [4-[6-(allyl-methyl-amino)-hexyloxy]-2-fluoro-phenyl]-(4-bromo-phenyl)-methanone fumarate (
Initial hOSC crystals were obtained at room temperature by mixing equal volumes of a reservoir solution containing 30% (w/v) PEG 4000, 0.2M sodium acetate in 0.1M Tris pH 8.5 with the protein solution containing 2.4% (w/v) β-OG. The resulting β-OG concentration is well above the saturation concentration of β-OG at the crystallization conditions and crystals of β-OG grew in the crystallization setups together with the protein crystals (
Crystallization of hOSC can be achieved at numerous conditions, as long as the pH is around pH 8.5 and the precipitant is PEG. hOSC was crystallized at PEG concentrations varying from 20% to 30% (w/v) PEG 3350 and PEG 4000. The addition of 100 mM to 400 mM of a salt, preferably ammonium or sodium acetate, helped in obtaining crystals. But hOSC could be crystallized in the absence of salt and in the presence of all of the following salts: ammonium acetate, sodium acetate, sodium and potassium tartrate, sodium malonate, sodium succinate and sodium citrate, magnesium chloride, ammonium sulfate, sodium chloride, lithium sulfate. Big and untwinned hOSC crystals suitable for structure determination could be grown in the presence of the small amphiphilic organic molecules glycerol, ethylene glycol or sucrose at concentrations ranging from 5% to 15%(w/v). These molecules have an amphiphilic characteristic that influences the phase behavior of β-OG, avoiding phase separation in the crystallization drops. These molecules also increase viscosity of the solution and therefore slow down crystal growth. Moreover they act as cryo protectants.
Well diffracting crystals of membrane proteins often grow at crystallization conditions near the cloud point, when no phase separation is observed (Rosenow, M., et al. (2001), Amphiphiles modify the properties of detergent solutions used in crystallization of membrane proteins, Acta Crystallogr D Biol Crystallogr 57, 925-7 2001). The phase behavior of β-OG was modulated by the variation of acetate concentration and the addition of small amphiphiles in order to avoid phase separation in the crystallization drop. Dynamic light scattering is used to predict the crystallization properties of soluble proteins by assessing the aggregation state. Monodispers proteins are more likely to crystallize. (D'Arcy, A. (1994), Crystallizing Proteins—a Rational Approach?, Acta Cryst D50, 469-471). In the case of the membrane protein hOSC the assessment of protein aggregation by analytical ultra centrifugation proved to be a tool for the prediction of the crystallizability. In agreement with the results on aggregation obtained by analytical ultra centrifugation, it was only possible to crystallize hOSC that was monodispersely solubilized with the detergent β-OG at concentrations above the CMC.
Crystals were mounted in a loop and fast cooled in liquid nitrogen. Diffraction images in several crystal orientations were collected with CuKα radiation at the home source in order to detect crystal disorder that was not readily visible under the microscope alone. Untwinned crystals were selected for the collection of full data sets with synchrotron radiation at the beamline PX6A at the Swiss Light Source (Villigen, Switzerland) at 120K. The crystals diffracted at the beam line X06A up to 1.8 Å resolution. The crystals belong to space group C222, with cell dimensions of about 190 Å, 202 Å and 62 Å. Data was processed with DENZO (Otwinowski, Z. & Minor, W. M. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997)) and XDS (Kabsch, W. (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants J. appl. Cryst. 26, 795-800).
Structure Determination and Refinement
The structure was solved by molecular replacement with the CCP4 (Collaborative Computational Project, Number 4, The CCP4 Suite: Programs for Protein Crystallography Acta Cryst. D 50, 760-763(1994)) program MOLREP (A. Vagin, A. Teplyakov, MOLREP: an automated program for molecular replacement., J. Appl. Cryst. 30, 1022-1025. (1997)) using squalene hopene cyclase (Wendt, K. U., Lenhart A., Schulz, G. E. The structure of the membrane protein squalene hopene cyclase at 2.0 Å resolution, J. Mol. Biol. 286, 175-187, (1999), pdb-entry 2sqc) as search model and was automatically rebuilt and refined using the program ARP/wARP (Morris, Perrakis & Lamzin, Acta Cryst. D58:968-975,2002). After adding the ligands to the model and minor manual rebuilding of the protein with the molecular graphics program MOLOC (Gerber P. R., Müller K., The MOLOC program with the MAB force field, J. Comput. Aided Mol. Design 9, 251-268 (1995)) it was refined with REFMAC (Murshudow, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelyhood method. Acta Cry stallogr. D53, 240-255 (1997)).
Monomeric Structure of hOSC
As a typical membrane protein hOSC is not soluble in the absence of detergents and detergents had to be added to obtain stable and active enzyme. Crystals of hOSC were grown in the presence of β-OG micelles and the structure was solved by molecular replacement. In agreement with our gel filtartion results and the analytical ultra centrifuge data on detergent solubilized hOSC (Table 2) hOSC is monomeric in the crystal. This is in contradiction to the dimeric behavior of OSC from rat liver preparations observed in gelfiltration experiments (Kusano et al. (1991) Chem Pharm Bull 39, 239-241). The pairs of hOSC molecules that are created by applying the crystallographic twofold axes of space group C2221 have membrane portions that point into different directions. They can therefore not be biological dimers. OSC consists of two (α/α) barrel domains that are connected by loops and four smaller β-structures. Domain 1 is a (α/α)6 barrel whereas domain 2, that is inserted into domain 1, contains an (α/α) barrel that appears to be an evolved form of the (α/α)6 barrel of domain 1 with some helices missing (Wendt, K. U., Poralla, K., Schulz, G. E., Structure and function of a squalene cyclase, Science 277, 1811-1815(1997)). The amino ends of all inner helices of both barrel domains point to the center of the molecule. The loops connecting the helices and the N-terminal region with their β-structures fill the space between the barrel domains and enclose the large active site cavity that is located in the center of the hOSC molecule (
The five QW-sequence motifs, that are located C-terminal of some helices of the outer barrel ring (Poralla et al. (1994) Trends Biochem. Sci. 19, 157) assume a conformation with stacked side chains of Q and W that was also observed in the structure of the archeal homologue squalene hopen cyclase. They connect the outer helices with the inner helices by hydrogen bonds and are thought to contribute to thermodynamic stability of cyclases (Wendt, K. U., Poralla, K., Schulz, G. E. (1997), Structure and function of a squalene cyclase, Science 277, 1811-1815).
Substrate Binding Pocket
The large active site cavity is located between the two (α/α) barrel domains at the center of the OSC molecule. It is enclosed by loops and several β-sheets. It is lined mostly by hydrophobic and aromatic residues. The cavity extends from the catalytic Asp455 at the “top” down towards a channel that reaches the enzyme surface at the hydrophobic plateau. This channel is separated from the cavity by a constriction that is created by the side chains of residues Trp192, Cys233, Tyr237, Ile524 and M525 (
Inhibitor Binding
The co-crystallized inhibitor was completely defined in the initial 2.2 Å (Fo-Fc)-electron density map at the 3σ contour level. It binds in the active site cavity. The allyl-amino group of the inhibitor is hydrogen bound to the catalytic aspartate Asp455 that is responsible for initiating the cyclization reaction by protonating oxido-squalene. There is a charged hydrogen bond between the protonated amino nitrogen and the Asp455 carboxylate group at 2.9 Å distance. The amino group also interacts with several aromatic residues that are thought to initiate the cyclization reaction by stabilizing the positively charged early high-energy intermediates (
The alkyl spacer between the allyl-amino and the benzphenone groups is not fully extended showing a distance of only 6.3 Å from the amino-N-atom to the ether-O-atom. The distance between amine nitrogen and the benzophenone carbonyl has a influence on the potency of the inhibitor, with lowest IC50 values for a distance of 10.7 Å (Jolidon, S., Polak-Wyss, A., Hartmann, P. G., and Guerry, P. (1993). 2,3-Oxidosqualene-lanosterol cyclase: an attractive target for antifungal drug design. In: Recent Advances in the Chemistry of Anti-infective Agents, P. H. Bentley, ed. (Cambridge, U.K.: Royal Soc. Chemistry), pp.223-233). In the hOSC complex of inhibitor [4-[6-(allyl-methyl-amino)-hexyloxy]-2-fluoro-phenyl]-(4-bromo-phenyl)-methanone fumarate this distance is 12.0 Å, which compares well to the distance between the epoxide oxygen and the carbocation position of the protosterol cation.
The phenyl groups of the benzophenone portion of the inhibitor make several aromatic interactions to the protein. The terminal bromo phenyl group has edge-to-face on interactions with Trp192 (3.6 Å) and Trp230 (3.7 Å) and a face-to-face interaction with Phe521 (4.6 Å). The fluoro phenylgroup is stacked between the Phe696 (3.7 Å) and the His232 imidazole ring (3.1 Å) (
In contrast to hOSC the bacterial squalene hopene cyclase (SHC) is dimeric (Wendt, K. U., Poralla, K., Schulz, G. E. (1997), Structure and function of a squalene cyclase, Science, 277, 1811-1815). OSC and SHC have a common cyclase chain fold. The superposition of the structures yields 550 pairs of x-carbon atoms with a rmsd of 1.76 Å when a 4.5 Å cutoff was applied (pdb entry 2sqc). The rmsd-Cα is 0.85 Å, when only the 94 residues are superimposed that are conserved spatially and in sequence.
When compared to SHC, OSC has 70 additional N-terminal amino acid residues that form a small structural motif that folds into the region between the two (α/α) barrel domains opposite to the membrane attachment site. Together with the extended loop 427-431 this N-terminal structural motif could solidify the loops between the domains that form most of the ligand binding pocket. The relative orientation of the two (α/α) barrel domains in hOSC differs slightly from that in SHC.
The (α/α) barrel in domain 1 of hOSC is wider than that in SHC, with the Cα distance across the inner ring of helices increased by 1.2 Å to 15.8 Å (distance between A536 Cα to W714 Cα). This barrel widening might be a consequence of the more bulky OSC side chains that are pointing into the barrel center at the C-terminal side of the barrel (eg. F391, W590 and W714).
Method (Docking)
Docking calculations were performed with the docking software FRED (OpenEye Scientific Software). The first stage in the docking procedure is a shape fitting routine (docking algorithm), which takes a set of ligand conformers as input and tests them against a “bump map” (a Boolean grid with true values where ligand atoms can potentially be place). Orientations that clash with the protein or are distant from the active site are rejected. The crude docking solutions are further tested against a specified pharmacophore feature, and any poses that do not satisfy the pharmacophore are rejected. Poses surviving the shape fitting routine are then passed through a scoring function filter. In the docking procedure for OSC, docking was performed twice with two different scoring function filters, ChemScore and PLP. 5000 poses were returned by each of the two docking runs, and a consensus list of common compounds (˜500) from both runs was generated. Flags for optimization of hydroxyl group rotamers, rigid body optimization and torsion optimization were set to ‘true’ values in the scoring process. The number of compounds in the consensus list was further reduced by filtering out unwanted substructures (e.g. benzamidine) and by removing highly similar compounds (maximization of structural diversity). Finally 138 compounds (0.03% from virtually screened Roche compound library) were sent for screening.
Receptor Preparation
Water molecules were removed from the OSC X-ray structure and polar hydrogen atoms were added (Gerber P. R., Müller K. (1995), The MOLOC program with the MAB force field, J. Comput. Aid ed Mol. Design 9, 251-268) to the structure.
Binding Site Definition
The OSC inhibitor trans-Methyl-{4-[5-(methyl-propyl-amino)-pent-1-ynyl]-cyclohexyl}-carbamic acid 4-chloro-phenyl ester was used for the binding site definition in FRED. FRED builds a rectangular box around a given (x-ray, manually modeled) ligand and allows to increase the box size by the ‘-addbox’ flag. The box around trans-Methyl-{4-[5-(methyl-propyl-amino)-pent-1-ynyl]-cyclohexyl}-carbamic acid 4-chloro-phenyl ester was increased by 0.5 Angstrom.
Compound Library Preparation
For compounds from the Roche compound library multiconformer libraries in a binary format were generated by OMEGA (OpenEye Scientific Software). Modifications applied to the default settings of OMEGA were (i) rejection of conformers with an energy difference to the global minimum of >5.0 kcal/mol (GP_ENERGY_WINDOW), (ii) maximum number of output conformers 400 (GP_NUM_OUTPUT_CONFS) and (iii) low energy selection (no random selection) of conformers from the final ensemble (GP_SELECT_RANDOM false).
Results
20 compounds showed reasonable inhibition at 1 μM in the activity assay with liver microsomal preparations as described in Example 2 and were retested at 50 μM. 7 compounds showed >20% inhibition at 50 μM. 2 compounds showed good inhibition of 68% and 75% at 50 μM. The compounds represent a structurally new class of OSC inhibitors and disproved the assumption that a basic nitrogen atom is necessary for OSC inhibition. Further compounds showed 35%, 38%, and 57% inhibition at 50 μM.
OSC for Drug-Design (Active Site Differences to SHC)
Aromatic residues (indicated by an asterisk in
For olefin protonation in SHC catalysis a strong Brønsted acid is required. Based on crystallographic data it was proposed that acidity of catalytic Asp is increased by hydrogen bonding to a protonated His (
At the back of the hydrophobic tunnel the number of aromatic residues for both cyclases decreases, whereas sequence and structural differences between the cyclases increase. Comparison of the two complex structures with the inhibitor [4-[6-(allyl-methyl-amino)-hexyloxy]-2-fluoro-phenyl]-(4-bromo-phenyl)-methanone fumarate shows, that the fluorinated aromatic ring is located exactly between two aromatic side chains for SHC. Since residues for similar 1-interactions are lacking in OSC and because of the shift in the binding pocket caused by the side chain orientation of catalytic Asp the fluorinated aromatic ring of the inhibitor in OSC is located closer to the middle of the hydrophobic tunnel to pick up 7α-interactions with a close Phe side chain there. As a consequence for structure-based drug design, chain length and location of the 1-system of the inhibitor can not be optimized for OSC with structural information of SHC.
More differences between the active sites of the two cyclases are obvious at the end of the hydrophobic tunnel as well as in residues participating in the formation of the entrance to the hydrophobic tunnel. The binding site of OSC in the back part is shorter and accommodates water molecules. Thus, to avoid steric conflicts and to gain binding affinity for OSC, OSC inhibitors have to be shorter than comparable SHC inhibitors. Differences in aromatic residues and their location close to the entrance part of the binding site require different steric and electronic properties of OSC inhibitor substituents (p-C4H4—Cl in [4-[6-(allyl-methyl-amino)-hexyloxy]-2-fluoro-phenyl]-(4-bromo-phenyl)-methanone fumarate) to improve binding properties.
1Values in parentheses refer to the highest resolution bins.
2Rmerge = Σ|I−<I>|/ΣI where I is intensity.
3Rcryst = Σ|Fo−<Fc>|/ΣFo where Fo is the observed and Fc is the calculated structure factor amplitude.
4Rfree was calculated based on 5% of the total data omited during structure refinement.
5Calculated with PROCHECK (Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). PROCHECK: a program to check the stereochemical quality of protein structure. J. Appl. Crystallogr. 26, 283-291).
†= if not otherwise stated two times CMC
n.d.: not determined. Because of the high absorption of Triton X-100 At 280 nm the characterization performed with the interference optics did not allow a reliable evaluation of possible sedimentation losses
Column 2 lists a number for the atom in the structure.
Column 3 lists the element whose coordinates are measured. The first letter in the column defines the element.
Column 4 lists the type of amino acid.
Column 5 lists a number for the amino acid in the structure.
Columns 6-8 list the crystallographic coordinates X, Y, and Z respectively. The crystallographic coordinates define the atomic position of the element measured.
Column 9 lists an occupancy factor that refers to the fraction of the molecules in which each atom occupies the position specified by the coordinates. A value of “1” indicates that each atom has the same conformation, i.e., the same position, in all molecules of the crystal.
Column 10 lists a thermal factor “B” that measures movement of the atom around its atomic center.
| Number | Date | Country | Kind |
|---|---|---|---|
| 03014558.5 | Jul 2003 | EP | regional |
