# Patent

## Title
Crystal structure of aurora-2 protein and binding pockets thereof

## Abstract

The present invention provides crystalline molecules or molecular complexes which comprise binding pockets of Aurora-2 or its homologues. The invention also provides crystals comprising Aurora-2. The present invention also relates to a computer comprising a data storage medium encoded with the structural coordinates of Aurora-2 binding pockets and methods of using a computer to evaluate the ability of a compound to bind to the molecule or molecular complex. This invention also provides methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention provides methods of using the structure coordinates to screen for and design compounds, including inhibitory compounds, that bind to Aurora-2 or homologues thereof.

## Background
This application is a divisional of U.S. patent application Ser. No. 10/979,375, filed Nov. 1, 2004; Confirmation No. 4847, and issued as U.S. Pat. No. 7,361,492, which is a continuation of PCT Application No. PCT/US03/13605, filed May 1, 2003, which claims benefit of U.S. Provisional Application No. 60/377,510, filed May 1, 2002


TECHNICAL FIELD OF THE INVENTION
The present invention provides crystalline molecules or molecular complexes which comprise binding pockets of Aurora-2 or its homologues. The present invention also provides crystals comprising Aurora-2. This invention also provides methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention provides methods of using the structure coordinates to design compounds, including inhibitory compounds and antibodies, that bind to Aurora-2 or homologues thereof.
BACKGROUND OF THE INVENTION
Protein kinases mediate intracellular signal transduction by causing a phosphoryl transfer from a nucleoside triphosphate to a protein acceptor involved in a signaling pathway. There are a number of kinases and pathways through which extracellular and other stimuli cause a variety of cellular responses to occur inside the cell. Examples of such stimuli include environmental and chemical stress signals (e.g., osmotic shock, heat shock, ultraviolet radiation, bacterial endotoxin, H2O2), cytokines (e.g., interleukin-1 (IL-1) and tumor necrosis factor-α (TNF-α)), growth factors (e.g., granulocyte macrophage-colony-stimulating factor (GM-CSF), and fibroblast growth factor (FGF). An extracellular stimulus may affect one or more cellular responses related to cell growth, migration, differentiation, secretion of hormones, activation of transcription factors, muscle contraction, glucose metabolism, control of protein synthesis and regulation of cell cycle.
Many disease states are associated with abnormal cellular responses triggered by protein kinase-mediated events. These diseases include autoimmune diseases, inflammatory diseases, neurological and neurodegenerative diseases, cancer, cardiovascular diseases, allergies and asthma, Alzheimer's disease and hormone-related diseases. Thus, an understanding of the structure, function, and inhibition of kinase activity could lead to useful human therapeutics.
Among medically important kinases are the serine/threonine kinases. The serine/threonine kinase family include the mammalian mitogen-activated protein (MAP) kinases. MAP kinases are activated by dual phosphorylation of threonine and tyrosine at the Thr-X-Tyr segment in the activation loop. Members of the MAP kinase family also share sequence similarity and conserved structural domains, and include the extracellular-signal regulated kinases (ERKs), Jun N-terminal kinases (JNKs) and p38 kinases. MAP kinases also phosphorylate various substrates including transcription factors, which in turn regulate the expression of specific sets of genes and mediate a specific response to the stimulus.
Another important group in the serine/threonine kinase family includes a subgroup of three closely related serine/threonine protein kinases, the Aurora kinases. The Aurora kinases play a key role in protein phosphorylation events that regulate the mitotic phase of the cell cycle. Aurora-2, for example, is up-regulated during the M phase of the cell cycle and localizes to the spindle pole during mitosis, suggesting a possible involvement in centrosomal functions. The Aurora kinases share a common structure, including a highly-conserved catalytic domain, and a very short N-terminal domain that varies in size (R. Giet and C. Prigent, J. Cell Sci., 112, pp. 3591-3601 (1999)). The N-terminal domains do not share any sequence similarity. The Aurora kinases are overexpressed in various types of cancer, such as colon, breast and other solid tumors (for a review see T. M. Goepfert and B. R. Brinkley, Curr. Top. Dev. Biol., 49, pp. 331-342 (2000)). Even more importantly, both the Aurora-1 and -2 genes are amplified in breast and colorectal cancers whereas the Aurora-3 gene is located in a region that is rearranged or deleted in several cancer cells. Overexpression of Aurora-2 in rodent fibroblasts induces transformation, indicating that Aurora-2 is oncogenic. Recently, Aurora-2 mRNA expression has been linked to chromosomal instability in human breast cancers (Y. Miyoshi et al., Int. J. Cancer, 92, pp. 370-373 (2001)).
Accordingly, there has been an interest in finding inhibitors of Aurora-1, Aurora-2 or Aurora-3 that are effective as therapeutic agents. A challenge has been to find protein kinase inhibitors that act in a selective manner for the Aurora family kinases. Since there are numerous protein kinases involved in a variety of cellular responses, non-selective inhibitors may lead to undesirable side effects. In this regard, the three-dimensional structure of the kinase would assist in the rational design of inhibitors. The determination of the amino acid residues in Aurora-2 binding pockets and the determination of the shape of those binding pockets would allow one to design selective inhibitors that bind favorably to this class of enzymes. The determination of the amino acid residues in Aurora-2 binding pockets and the determination of the shape of those binding pockets would also allow one to design inhibitors that can bind selectively to Aurora-1, Aurora-2 or Aurora-3, or any combination thereof.
Despite the fact that the genes for various Aurora-1, Aurora-2 and Aurora-3 have been isolated and the amino acid sequences of Aurora-1, Aurora-2 and Aurora-3 proteins are known, the X-ray crystal structural coordinate information of Aurora-1, Aurora-2 or Aurora-3 protein has not yet been described. Such information would be useful in identifying and designing therapeutic inhibitors of the Aurora kinases or homologues thereof.
SUMMARY OF THE INVENTION
Applicants have solved this problem by providing, for the first time, the crystal structures of Aurora-2-inhibitor complexes and the crystal structure of Aurora-2 bound to adenosine. The present invention provides crystalline molecules or molecular complexes comprising Aurora-2 binding pockets, or Aurora-2-like binding pockets that have similar three-dimensional shapes. In one embodiment, the molecules or molecular complexes are Aurora-2 proteins or homologues, or Aurora-2 protein complexes or homologues thereof. In another embodiment, the molecules or molecular complexes are Aurora-2 kinase domains or homologues thereof, or Aurora-2 kinase domain complexes or homologues thereof.
The invention also provides crystal compositions comprising Aurora-2 protein, Aurora-2 kinase domain or homologues thereof in the presence or absence of a chemical entity. The invention also provides a method of crystallizing Aurora-2 protein, Aurora-2 protein complex, or homologues thereof.
The invention further provides a computer comprising a data storage medium which comprises the structure coordinates of molecules and molecular complexes comprising all or part of the Aurora-2 binding pockets or Aurora-2-like binding pockets. Such storage medium, when read and utilized by a computer programmed with appropriate software, displays on a computer screen or similar viewing device, a three-dimensional graphical representation of a molecule or molecular complex comprising such binding pockets.
The invention provides methods for screening, designing, optimizing, evaluating and identifying compounds which bind to the molecules or molecular complexes or their binding pockets. Such compounds are potential inhibitors of Aurora-2 or its homologues. Such methods can be used to identify agonist or antagonist of Aurora-2 and its homologues.
The invention also provides a method for determining at least a portion of the three-dimensional structure of molecules or molecular complexes which contain at least some structurally similar features to Aurora-2, particularly Aurora-2 homologues. This is achieved by using at least some of the structure coordinates obtained from the Aurora-2 complexes.



BRIEF DESCRIPTION OF THE DRAWINGS
The following abbreviations are used in FIGS. 1-4:
“Atom type” refers to the element whose coordinates are measured. The first letter in the column defines the element.
“Resid” refers to the amino acid residue identity in the molecular model.
“X, Y, Z” define the atomic position of the element measured.
“B” is a thermal factor that measures movement of the atom around its atomic center.
“Occ” is 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 the molecules.
“Mol” refers to the molecule in the asymmetric unit.
FIG. 1A to 1HH lists the atomic structure coordinates for the Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine inhibitor complex as derived by X-ray diffraction from the crystal.
FIG. 2A to 2HH lists the atomic structure coordinates for the Aurora-2-(5-Methylthiazol-2-yl)-(2-phenyl-quinazolin-4-yl)-amine inhibitor complex as derived by X-ray diffraction from the crystal.
FIG. 3A to 3GG lists the atomic structure coordinates for the Aurora-2-(5-Methyl-2H-pyrazol-3-yl)-(2-(pyridin-3-ylmethylamino)-quinazolin-4-yl)-amine inhibitor complex as derived by X-ray diffraction from the crystal.
FIG. 4A to 4GG lists the atomic structure coordinates for the Aurora-2-adenosine complex as derived by X-ray diffraction from the crystal.
FIG. 5 depicts a ribbon diagram of the overall fold of Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex. The N-terminal lobe of the Aurora-2 catalytic domain corresponds to the β-strand sub-domain and encompasses amino acid residues 127 to 215. The α-helical sub-domain corresponds to amino acid residues 216 to 390. Key features of the kinase-fold such as the hinge (approximately amino acid residues 132 to 135), glycine rich loop (approximately amino acid residues 140 to 149) and activation loop or phosphorylation lip (approximately amino acid residues 272 to 289) are indicated. In each of the Aurora-2 crystal structures some of the amino acid residues at the N-terminus ( ̃107-126), C-terminus ( ̃391-403) and activation loop ( ̃279-289) were disordered. They exhibited only weak electron density and could not be fitted.
FIG. 6 shows a detailed representation of pockets in the catalytic active site of the Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex.
FIG. 7 shows a comparison between the activation loops of Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex in white, unphosphorylated GSK-3β in grey (ter Haar, E. et al., Nat. Struct. Biol. 8, 593-596 (2001)), and activated substrate-bound human CDK2 in black (PDB Accession number 1B38).
FIG. 8 shows that in each of the Aurora-2-inhibitor crystal structures, the Aurora-2 catalytic active site is partially occupied by the activation loop region (residues 275-279) which forms a unique hydrophobic pocket in the Aurora-2 catalytic active site. In comparison (see FIG. 7) the activation loops of other kinases adopt a more extended and “open” conformation. Residue W277 is conserved in the Aurora-1, Aurora-2 and Aurora-3 catalytic active sites and plays an important role in forming this unique hydrophobic pocket. FIGS. 8A, B, C and D represent the Aurora-2-adenosine, Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine, Aurora-2-(5-Methyl-2H-pyrazol-3-yl)-[2-(pyridin-3-ylmethylamino)-quinazolin-4-yl]-amine, Aurora-2-(5-Methylthiazol-2-yl)-(2-phenyl-quinazolin-4-yl)-amine complexes, respectively.
FIG. 9 shows a diagram of a system used to carry out the instructions encoded by the storage medium of FIGS. 10 and 11.
FIG. 10 shows a cross section of a magnetic storage medium.
FIG. 11 shows a cross section of an optically-readable data storage medium.



DETAILED DESCRIPTION OF THE INVENTION
In order that the invention described herein may be more fully understood, the following detailed description is set forth.
Throughout the specification, the word “comprise”, or variations such as “comprises” or “comprising” will be understood to imply the inclusion of a stated integer or groups of integers but not exclusion of any other integer or groups of integers.
The following abbreviations are used throughout the application:
















A = Ala = Alanine
T = Thr = Threonine



V = Val = Valine
C = Cys = Cysteine



L = Leu = Leucine
Y = Tyr = Tyrosine



I = Ile = Isoleucine
N = Asn = Asparagine



P = Pro = Proline
Q = Gln = Glutamine



F = Phe = Phenylalanine
D = Asp = Aspartic Acid



W = Trp = Tryptophan
E = Glu = Glutamic Acid



M = Met = Methionine
K = Lys = Lysine



G = Gly = Glycine
R = Arg = Arginine



S = Ser = Serine
H = His = Histidine










As used herein, the following definitions shall apply unless otherwise indicated.
The term “about” when used in the context of RMSD values takes into consideration the standard error of the RMSD value, which is ±0.1 Å.
The term “associating with” refers to a condition of proximity between a chemical entity or compound, or portions thereof, and a binding pocket or binding site on a protein. The association may be non-covalent—wherein the juxtaposition is energetically favored by hydrogen bonding or van der Waals or electrostatic interactions—or it may be covalent.
The term “ATP analogue” refers to a compound derived from adenosine-5′-triphosphate (ATP). The compound can be ADP, or a non-hydrolyzable analogue, such as, but not limited to adenylyl imidodiphosphate (AMPPNP). The analogue may be in complex with magnesium or manganese ions.
The term “Aurora protein” refers to kinases from the Aurora kinase family. Examples of this family of kinases include but are not limited to Aurora-1, Aurora-2, and Aurora-3.
The “Aurora-2 ATP-binding pocket” refers to a binding pocket of a molecule or molecular complex defined by the structure coordinates of a certain set of amino acid residues present in the Aurora-2 structure, as described below. In general, the ligand for the ATP-binding pocket is a nucleotide such as ATP. This binding pocket is in the catalytic active site of the kinase domain. In the protein kinase family, the ATP-binding pocket is generally located at the interface of the α-helical and β-strand sub-domains, and is bordered by the glycine rich loop and the hinge (See, Xie et al., Structure, 6, pp. 983-991 (1998), incorporated herein by reference).
The term “Aurora-2 kinase domain” or “Aurora-2-like kinase domain” refers to the catalytic domain of Aurora-2 or Aurora-2-like kinase, respectively. The kinase domain includes, for example, the catalytic active site which comprises the catalytic residues, the activation loop or phosphorylation lip, the DFGWSxxxxxxxRxTxCGTxDYLPPE or DFG motif, and the glycine-rich phosphate anchor or glycine-rich loop (See, Xie et al., Structure, 6, pp. 983-991 (1998); R. Giet and C. Prigent, J. Cell Sci., 112, pp. 3591-3601 (1999), incorporated herein by reference). The kinase domain in the Aurora-2 protein comprises amino acid residues selected from the group consisting of amino acids residues 107-403, 127-403, 107-387, and 127-387 according to SEQ ID NO: 1.
The term “Aurora-2-like” refers to all or a portion of a molecule or molecular complex that has a commonality of shape to all or a portion of the Aurora-2 protein. For example, in the Aurora-2-like ATP-binding pocket, the commonality of shape is defined by a root mean square deviation of the structure coordinates of the backbone atoms between the amino acids in the Aurora-2-like ATP-binding pocket and the amino acids in the Aurora-2 ATP-binding pocket (as set forth in FIG. 1, 2, 3 or 4). Compared to an amino acid in the Aurora-2 ATP-binding pocket, the corresponding amino acids in the Aurora-2-like ATP-binding pocket may or may not be identical. Depending on the Aurora-2 amino acid residues that define the Aurora-2-ATP binding pocket, one skilled in the art would be able to locate the corresponding amino acid residues that define an Aurora-2-like-ATP binding pocket in a protein based upon sequence and structural homology.
The term “Aurora-2 protein complex” or “Aurora-2 homologue complex” refers to a molecular complex formed by associating the Aurora-2 protein or Aurora-2 homologue with a chemical entity, for example, a ligand, a substrate, nucleotide triphosphate, nucleotide diphosphate, phosphate, an agonist or antagonist, inhibitor, antibody, drug or compound. In one embodiment, the chemical entity is selected from the group consisting of ATP, an ATP analogue, a nucleotide triphosphate and ATP-binding pocket inhibitor. In another embodiment, the inhibitor is an ATP analogue such as MgAMP-PNP (adenylyl imidodiphosphate), adenosine, (5-Methyl-2H-pyrazol-3-yl)-(2-(pyridin-3-ylmethylamino)-quinazolin-4-yl)-amine, (5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine or (5-methylthiazol-2-yl)-(2-phenyl-quinazolin-4-yl)-amine.
The term “binding pocket” refers to a region of a molecule or molecular complex, that, as a result of its shape and charge, favorably associates with another chemical entity or compound. The term “pocket” includes, but is not limited to, cleft, channel or site. Aurora-2 or Aurora-2-like molecules may have binding pockets which include, but are not limited to, peptide or substrate binding, ATP-binding and antibody binding sites.
The term “catalytic active site” or “active site” refers to the portion of the protein kinase to which nucleotide substrates bind. For example, the catalytic active site of Aurora-2 is at the interface between the N-terminal, β-strand sub-domain and the C-terminal, α-helical sub-domain, and is bordered by the glycine rich loop and the hinge (See, Xie et al., Structure, 6, pp. 983-991 (1998).
The term “chemical entity” refers to chemical compounds, complexes of at least two chemical compounds, and fragments of such compounds or complexes. The chemical entity may be, for example, a ligand, a substrate, a nucleotide triphosphate, a nucleotide diphosphate, phosphate, a nucleotide, an agonist, antagonist, inhibitor, antibody, drug, peptide, protein or compound.
“Conservative substitutions” refers to residues that are physically or functionally similar to the corresponding reference residues. That is, a conservative substitution and its reference residue have similar size, shape, electric charge, chemical properties including the ability to form covalent or hydrogen bonds, or the like. Preferred conservative substitutions are those fulfilling the criteria defined for an accepted point mutation in Dayhoff et al., Atlas of Protein Sequence and Structure, 5, pp. 345-352 (1978 & Supp.), which is incorporated herein by reference. Examples of conservative substitutions are substitutions including but not limited to the following groups: (a) valine, glycine; (b) glycine, alanine; (c) valine, isoleucine, leucine; (d) aspartic acid, glutamic acid; (e) asparagine, glutamine; (f) serine, threonine; (g) lysine, arginine, methionine; and (h) phenylalanine, tyrosine.
The term “corresponding amino acid” or “residue which corresponds to” refers to a particular amino acid or analogue thereof in an Aurora-2 protein or Aurora-2 homologue that is identical or functionally equivalent to an amino acid in Aurora-2 according to SEQ ID NO: 1.
Methods for identifying a corresponding amino acid are known in the art and are based upon sequence, structural alignment, its functional position or a combination thereof as compared to the Aurora-2 kinase. For example, corresponding amino acids may be identified by superimposing the backbone atoms of the amino acids in Aurora-2 and the Aurora-2 homologue using well known software applications, such as QUANTA (Accelrys, San Diego, Calif. ©2001, 2002). The corresponding amino acids may also be identified using sequence alignment programs such as the “bestfit” program available from the Genetics Computer Group which uses the local homology algorithm described by Smith and Waterman in Advances in Applied Mathematics 2, 482 (1981), which is incorporated herein by reference.
The term “crystallization solution” refers to a solution which promotes crystallization comprising at least one agent including a buffer, one or more salts, a precipitating agent, one or more detergents, sugars or organic compounds, lanthanide ions, a poly-ionic compound, and/or stabilizer.
The term “domain” refers to a portion of the Aurora-2 protein or homologue that can be separated based on its biological function, for example, catalysis. The domain may comprise a binding pocket, a sequence or a structural motif.
The term “fitting operation” refers to an operation that utilizes the structure coordinates of a chemical entity, binding pocket, molecule or molecular complex, or portion thereof, to associate the chemical entity with the binding pocket, molecule or molecular complex, or portion thereof. This may be achieved by positioning, rotating or translating the chemical entity in the binding pocket to match the shape and electrostatic complementarity of the binding pocket. Covalent interactions, non-covalent interactions such as hydrogen bond, electrostatic, hydrophobic, van der Waals interactions, and non-complementary electrostatic interactions such as repulsive charge-charge, dipole-dipole and charge-dipole interactions may be optimized. Alternatively, one may minimize the deformation energy of binding of the chemical entity to the binding pocket.
The term “generating a three-dimensional structure” or “generating a three-dimensional representation” refers to converting the lists of structure coordinates into structural models or graphical representation in three-dimensional space. This can be achieved through commercially or publicly available software. The three-dimensional structure may be displayed or used to perform computer modeling or fitting operations. In addition, the structure coordinates themselves may be used to perform computer modeling and fitting operations.
The term “homology model” refers to a structural model derived from known three-dimensional structure(s). Generation of the homology model, termed “homology modeling”, can include sequence alignment, residue replacement, residue conformation adjustment through energy minimization, or a combination thereof.
The term “homologue of Aurora-2” or “Aurora-2 homologue” refers to a molecule that is homologous to Aurora-2 by structure or sequence, but retains the kinase activity of an Aurora protein. Examples of homologues include but are not limited to human Aurora-2 and Aurora-2 from another species with conservative substitutions, additions, deletions or a combination thereof; or another member of the Aurora family of protein kinases including, but not limited to, Aurora-1 and Aurora-3, with conservative substitutions, additions, deletions or a combination thereof.
The term “homologue of Aurora-2 kinase domain” or “Aurora-2 kinase domain homologue” refers to a molecule having amino acids which correspond to the amino acids in the Aurora-2 kinase domain. Examples of homologues include but are not limited to the kinase domain of human Aurora-2 and Aurora-2 from another species with conservative substitutions; or the kinase domain of another member of the Aurora family of protein kinases including, but not limited to, Aurora-1 and Aurora-3, or with conservative substitutions.
The term “molecular complex” or “complex” refers to a molecule associated with at least one chemical entity.
The term “motif” refers to a portion of the Aurora-2 protein or homologue that defines a structural compartment or carries out a function in the protein, for example, catalysis, structural stabilization, or phosphorylation. The motif may be conserved in sequence, structure and function. The motif can be contiguous in primary sequence or three-dimensional space. Examples of a motif include but are not limited to the phosphorylation lip or activation loop, the glycine-rich phosphate anchor loop, the catalytic loop, the DFG or DFGWSxxxxxxxRxTxCGTxDYLPPE loop (See, Xie et al., Structure, 6, pp. 983-991 (1998); R. Giet and C. Prigent, J. Cell Sci., 112, pp. 3591-3601 (1999)), and the degradation box.
The term “part of a binding pocket” refers to less than all of the amino acid residues that define the binding pocket. For example, the structure coordinates of residues that constitute part of a binding pocket may be specific for defining the chemical environment of the binding pocket, or useful in designing fragments of an inhibitor that may interact with those residues. For example, the portion of residues may be key residues that play a role in ligand binding, or may be residues that are spatially related and define a three-dimensional compartment of the binding pocket. The residues may be contiguous or non-contiguous in primary sequence.
The term “part of an Aurora-2 kinase domain” or “part of an Aurora-2-like kinase domain” refers to less than all of the Aurora-2 or Aurora-2-like catalytic domain, respectively. The structure coordinates of residues that constitute part of an Aurora-2 or Aurora-2-like kinase domain may be specific for defining the chemical environment of the domain, or useful in designing fragments of an inhibitor that interact with those residues. For example, the portion of residues may be residues that play a role in ligand binding, or may be residues that are spatially related and define a three-dimensional compartment of the domain. The residues may be contiguous or non-contiguous in primary sequence. For example, part of an Aurora-2 kinase domain can be the active site, the DFG or DFGWSxxxxxxxRxTxCGTxDYLPPE motif, the glycine-rich loop, the activation loop, or the catalytic loop (see Xie et al., supra).
The term “part of an Aurora-2 protein” or “part of an Aurora-2 homologue” refers to less than all of the amino acid residues of an Aurora-2 protein or homologue. In one embodiment, part of an Aurora-2 protein or homologue defines the binding pockets, domains, sub-domains, and motifs of the protein or homologue. The structure coordinates of residues that constitute part of an Aurora-2 protein or homologue may be specific for defining the chemical environment of the protein, or useful in designing fragments of an inhibitor that may interact with those residues. The portion of residues may also be residues that are spatially related and define a three-dimensional compartment of a binding pocket, motif or domain. The residues may be contiguous or non-contiguous in primary sequence. For example, the portion of residues may be key residues that play a role in ligand or substrate binding, peptide binding, antibody binding, catalysis, structural stabilization or degradation.
The term “root mean square deviation” or “RMSD” means the square root of the arithmetic mean of the squares of the deviations from the mean. It is a way to express the deviation or variation from a trend or object. For purposes of this invention, the “root mean square deviation” defines the variation in the backbone of a protein from the backbone of Aurora-2, a binding pocket, a motif, a domain, or portion thereof, as defined by the structure coordinates of Aurora-2 described herein. It would be apparent to the skilled worker that the calculation of RMSD involves a standard error.
The term “soaked” refers to a process in which the crystal is transferred to a solution containing a compound of interest.
The term “structure coordinates” refers to Cartesian coordinates derived from mathematical equations related to the patterns obtained on diffraction of a monochromatic beam of X-rays by the atoms (scattering centers) of a protein or protein complex in crystal form. The diffraction data are used to calculate an electron density map of the repeating unit of the crystal. The electron density maps are then used to establish the positions of the individual atoms of the molecule or molecular complex.
The term “sub-domain” refers to a portion of the domain as defined above in the Aurora-2 protein or homologue. The catalytic kinase domain (amino acid residues selected from the group consisting of amino acids residues 107-403, 127-403, 107-387 and 127-387 according to SEQ ID NO: 1) of Aurora-2 is a bi-lobal structure consisting of an N-terminal, β-strand sub-domain (amino acid residues 127 to 215) and a C-terminal, α-helical sub-domain (amino acid residues 216 to 390).
The term “sufficiently homologous to Aurora-2” refers to a protein that has a sequence homology of at least 20% compared to Aurora-2 protein. In one embodiment, the sequence homology is at least 40%.
The term “three-dimensional structural information” refers to information obtained from the structure coordinates. Structural information generated can include the three-dimensional structure or graphical representation of the structure. Structural information can also be generated when subtracting distances between atoms in the structure coordinates, calculating chemical energies for an Aurora-2 molecule or molecular complex or homologues thereof, calculating or minimizing energies for an association of an Aurora-2 molecule or molecular complex or homologues thereof to a chemical entity.
Crystallizable Compositions and Crystals of Aurora-2 Protein and Protein Complexes
According to one embodiment, the invention provides a crystallizable composition or crystal comprising Aurora-2 kinase domain or Aurora-2 kinase domain homologue in the presence or absence of a chemical entity. The Aurora-2 kinase domain may be phosphorylated or unphosphorylated. Preferably, the chemical entity is an ATP analogue, nucleotide triphosphate, nucleotide diphosphate, phosphate, or an ATP-binding pocket inhibitor. More preferably, the chemical entity is MgAMP-PNP (adenylyl imidodiphosphate), adenosine, (5-Methyl-2H-pyrazol-3-yl)-(2-(pyridin-3-ylmethylamino)-quinazolin-4-yl)-amine, (5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine or (5-Methylthiazol-2-yl)-(2-phenyl-quinazolin-4-yl)-amine. In another embodiment, the crystal has a unit cell dimension of a=b=87 Å, c=76 Å, α=β=90°, γ=120° and belongs to space group P3221. It will be readily apparent to those skilled in the art that the unit cells of the crystal compositions may deviate ±1-2 Å from the above cell dimensions depending on the deviation in the unit cell calculations.
The Aurora-2 protein or its homologue may be produced by any well-known method, including synthetic methods, such as solid phase, liquid phase and combination solid phase/liquid phase syntheses; recombinant DNA methods, including cDNA cloning, optionally combined with site directed mutagenesis; and/or purification of the natural products. In a preferred embodiment, the protein is overexpressed in a baculovirus system or an E. coli system. In a more preferred embodiment, the protein is overexpressed in a baculovirus system.
The invention also provides a method of making crystals of Aurora-2 protein or a homologue thereof in the presence or absence of a chemical entity. Such methods comprise the steps of:
a. producing and purifying Aurora-2 protein;
b. combining said Aurora-2 protein, or a homologue thereof in the presence or absence of a chemical entity with a crystallization solution to produce a crystallizable composition; and
c. subjecting said crystallizable composition to conditions which promote crystallization.
The crystallization solution may include, but is not limited to, polyethylene glycol (PEG) at between about 10% to 30% v/v, 100-300 mM ammonium sulphate and a buffer that maintains pH at between about 4.0 and 8.0. In one embodiment, the crystallization solution comprises 25% PEG 3350, 50 mM 2-(N-morpholino) ethanesulfonic acid (MES) at pH 6.0 and 200 mM ammonium sulphate.
According to one embodiment, the crystallizable composition comprises Aurora-2 protein or a homologue thereof in the presence or absence of a chemical entity. In another embodiment, the crystallizable composition comprises Aurora-2 protein and a chemical entity. In one embodiment, the crystallizable composition further comprises a precipitant, polyethylene glycol (PEG) at between about 10 to 30% v/v, 100-300 mM ammonium sulphate and a buffer that maintains pH at between about 4.0 and 8.0, and optionally a reducing agent, such as dithiothreitol (DTT) at between about 1 to 20 mM. The Aurora-2 protein may be phosphorylated or unphosphorylated. The Aurora-2 protein or complex is preferably 85-100% pure prior to forming the composition. More preferably, the Aurora-2 protein or complex is 90-100% pure. Even more preferably, the Aurora-2 protein or complex is 95-100% pure.
In a preferred embodiment, the crystallizable composition comprises unphosphorylated Aurora-2 protein kinase domain, 25% PEG 3350, 50 mM 2-(N-morpholino)ethanesulfonic acid (MES) at pH 6.0, and 200 mM ammonium sulphate. In a more preferred embodiment, the crystallizable composition comprises unphosphorylated Aurora-2 protein kinase domain, 25% PEG 3350, 50 mM 2-(N-morpholino)ethanesulfonic acid (MES) at pH 6.0, 200 mM ammonium sulphate and a chemical entity selected from the group consisting of an inhibitor and substrate analogue.
In another embodiment, the method of making crystals of Aurora-2 proteins or a homologue thereof in the presence or absence of a chemical entity includes the use of a device for promoting crystallizations. Devices for promoting crystallization can include but are not limited to the hanging-drop, sitting-drop, sandwich-drop, dialysis, microbatch or microtube batch devices (U.S. Pat. Nos. 4,886,646, 5,096,676, 5,130,105, 5,221,410 and 5,400,741; Pav et al., Proteins: Structure, Function, and Genetics, 20, pp. 98-102 (1994); Chayen, Acta. Cryst., D54, pp. 8-15 (1998), Chayen, Structure, 5, pp. 1269-1274 (1997), D'Arcy et al., J. Cryst. Growth, 168, pp. 175-180 (1996) and Chayen, J. Appl. Cryst., 30, pp. 198-202 (1997), incorporated herein by reference). The hanging-drop, sitting-drop and some adaptations of the microbatch methods (D'Arcy et al., J. Cryst. Growth, 168, pp. 175-180 (1996) and Chayen, J. Appl. Cryst., 30, pp. 198-202 (1997)) produce crystals by vapor diffusion. The hanging drop and sitting drop containing the crystallizable composition is equilibrated against a reservoir containing a higher or lower concentration of precipitant. As the drop approaches equilibrium with the reservoir, the saturation of protein in the solution leads to the formation of crystals.
Microseeding may be used to increase the size and quality of crystals. In this instance, micro-crystals are crushed to yield a stock seed solution. The stock seed solution is diluted in series. Using a needle, glass rod or strand of hair, a small sample from each diluted solution is added to a set of equilibrated drops containing a protein concentration equal to or less than a concentration needed to create crystals without the presence of seeds. The aim is to end up with a single seed crystal that will act to nucleate crystal growth in the drop.
It would be readily apparent to one of skill in the art to vary the crystallization conditions disclosed above to identify other crystallization conditions that would produce crystals of Aurora-2 protein or a homologue thereof in the presence or absence of a chemical entity. Such variations include, but are not limited to, adjusting pH, protein concentration and/or crystallization temperature, changing the identity or concentration of salt and/or precipitant used, using a different method for crystallization, or introducing additives such as detergents (e.g., TWEEN 20 (monolaurate), LDOA, Brji 30 (4 lauryl ether)), sugars (e.g., glucose, maltose), organic compounds (e.g., dioxane, dimethylformamide), lanthanide ions, or poly-ionic compounds that aid in crystallizations. High throughput crystallization assays may also be used to assist in finding or optimizing the crystallization condition.
Binding Pockets of Aurora-2 Protein, Protein Complexes or Homologues Thereof.
As disclosed above, applicants have provided the three-dimensional X-ray crystal structures of three Aurora-2-inhibitor complexes and an Aurora-2-adenosine complex. The crystal structures of Aurora-2 presented here are the first reported within the Aurora subfamily. The invention will be useful for inhibitor design and to study the role of Aurora-1, Aurora-2 and Aurora-3 in cell signaling. The atomic coordinate data is presented in FIGS. 1-4.
In order to use the structure coordinates generated for Aurora-2, its complexes, one of its binding pockets, or an Aurora-2-like binding pocket thereof, it is often times necessary to convert the structure coordinates into a three-dimensional shape. This is achieved through the use of commercially available software that is capable of generating three-dimensional graphical representations of molecules or portions thereof from a set of structure coordinates.
Binding pockets, also referred to as binding sites in the present invention, are of significant utility in fields such as drug discovery. The association of natural ligands or substrates with the binding pockets of their corresponding receptors or enzymes is the basis of many biological mechanisms of action. Similarly, many drugs exert their biological effects through association with the binding pockets of receptors and enzymes. Such associations may occur with all or part of the binding pocket. An understanding of such associations will help lead to the design of drugs having more favorable associations with their target receptor or enzyme, and thus, improved biological effects. Therefore, this information is valuable in designing potential inhibitors of the binding pockets of biologically important targets. The ATP and substrate binding pockets of this invention will be important for drug design.
In one embodiment, part of binding pocket is at least two amino acid residues, preferably, E211 and A213. In another embodiment, the ATP-binding pocket comprises amino acids of L139, L194, L210, E211, A213, L263 and W277 according to any one of FIGS. 1-4. These were common residues found in the ATP-binding pockets of each of the protein complexes described in the present invention.
In another embodiment, the ATP-binding pocket comprises amino acids L139, G140, F144, V147, A160, K162, L194, L210, E211, Y212, A213, P214, L215, T217, R220, L263, A273, and W277 according to the structure of Aurora-2-(5-Methyl-2H-pyrazol-3-yl)-(2-(pyridin-3-ylmethylamino)-quinazolin-4-yl)-amine complex in FIG. 3. In another embodiment, the ATP-binding pocket comprises amino acids L139, G140, F144, V147, A160, K162, L194, L210, E211, Y212, A213, P214, L215, T217, R220, L263, A273, W277 and S278 according to the structure of Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex in FIG. 1, or Aurora-2-adenosine complex in FIG. 4. In yet another embodiment, the ATP-binding pocket comprises amino acids L139, G140, F144, V147, A160, K162, L194, L210, E211, Y212, A213, P214, L215, T217, R220, L263, A273, W277, S278, and V279 according to the structure of Aurora-2-(5-Methylthiazol-2-yl)-(2-phenyl-quinazolin-4-yl)-amine complex in FIG. 2. The above-identified amino acid residues were within 5 Å (“5 Å sphere amino acids”) of the inhibitor bound in the ATP-binding pockets. These residues were identified using the program QUANTA (Molecular Simulations, Inc., San Diego, Calif. ©1998, 2000), O (T. A. Jones et al., Acta Cryst., A47, pp. 110-119 (1991)) and RIBBONS (Carson, J. Appl. Cryst., 24, pp. 958-961 (1991)), which allow the display and output of all residues within 5 Å from the inhibitor.
In another embodiment, the ATP-binding pocket comprises amino acids R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, I158, L159, A160, L161, K162, L194, R195, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E260, N261, L262, L263, L264, K271, I272, A273, D274, F275 and W277 according to the structure of Aurora-2-(5-Methyl-2H-pyrazol-3-yl)-(2-(pyridin-3-ylmethylamino)-quinazolin-4-yl)-amine complex in FIG. 3. In another embodiment, the ATP-binding pocket comprises amino acids R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, I158, L159, A160, L161, K162, L194, R195, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E260, N261, L262, L263, L264, K271, I272, A273, D274, F275, W277, and S278 according to the structure of Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex in FIG. 1, or Aurora-2-adenosine complex in FIG. 4. In yet another embodiment, the ATP-binding pocket comprises amino acids R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, I158, L159, A160, L161, K162, L194, R195, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E260, N261, L262, L263, L264, K271, I272, A273, D274, F275, W277, S278, and V279 according to the structure of Aurora-2-(5-Methylthiazol-2-yl)-(2-phenyl-quinazolin-4-yl)-amine complex in FIG. 2. These amino acids residues were within 8 Å (“8 Å sphere amino acids”) of the inhibitor bound in the ATP-binding pockets. These residues were identified using the programs QUANTA, O and RIBBONS, supra.
Using a multiple alignment program to compare each Aurora-2 structure and structures of other members of the protein kinase family (Gerstein et al., J. Mol. Biol., 251, pp. 161-175 (1995), incorporated herein by reference), the above amino acids were identified as the ATP-binding pocket. For the comparison, first, a sequence alignment between members of the protein kinase family including GSK-3β (PDB Accession number 1IO9), p38 (K. P. Wilson et al., J. Biol. Chem., 271, pp. 27696-27700 (1996); Z. Wang et al., Proc. Natl. Acad. Sci. U.S.A., 94, pp. 2327-32 (1997)), cdk2 (PDB Accession number 1B38), SRC (Xu, W., et al., Cell 3, pp. 629-638 (1999); PDB Accession number 2SRC), MAPKAP2 (U.S. Provisional application 60/337,513), and ERK2 (Zhang et al., Nature, 367, pp. 704-711 (1994); PDB Accession number 1ERK) is performed. Second, a putative core is constructed by superimposing a series of corresponding structures in the protein kinase family. Third, residues of high spatial variation are discarded, and the core alignment is iteratively refined. The amino acids that make up the final core structure have low structural variance and have the same local and global conformation relative to the corresponding residues in the protein family.
Therefore, in another embodiment, the ATP-binding pocket comprises amino acids F133, I135, G136, R137, F144, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275 and W277 according to the structure of the Aurora-2-(5-Methyl-2H-pyrazol-3-yl)-(2-(pyridin-3-ylmethylamino)-quinazolin-4-yl)-amine complex in FIG. 3.
In another embodiment, the ATP-binding pocket comprises amino acids F133, I135, G136, R137, F144, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, W277 and S278 according to the structure of the Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex in FIG. 1 or Aurora-2-adenosine complex in FIG. 4.
In another embodiment, the ATP-binding pocket comprises amino acids F133, I135, G136, R137, F144, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, W277, S278 and V279 according to the structure of the Aurora-2-(5-Methylthiazol-2-yl)-(2-phenyl-quinazolin-4-yl)-amine complex in FIG. 2.
It will be readily apparent to those of skill in the art that the numbering of amino acids in other homologues of Aurora-2 may be different than that set forth for Aurora-2. Corresponding amino acids in homologues of Aurora-2 are easily identified by visual inspection of the amino acid sequences or by using commercially available sequence homology, structural homology or structure superimposition software programs.
Those of skill in the art understand that a set of structure coordinates for a molecule or a molecular-complex or a portion thereof, is a relative set of points that define a shape in three dimensions. Thus, it is possible that an entirely different set of coordinates could define a similar or identical shape. Moreover, slight variations in the individual coordinates will have little effect on overall shape. In terms of binding pockets, these variations would not be expected to significantly alter the nature of ligands that could associate with those pockets.
The variations in coordinates discussed above may be generated as a result of mathematical manipulations of the Aurora-2 structure coordinates. For example, the structure coordinates set forth in FIG. 1, 2, 3 or 4 could be manipulated by crystallographic permutations of the structure coordinates, fractionalization of the structure coordinates, integer additions or subtractions to sets of the structure coordinates, inversion of the structure coordinates or any combination of the above.
Alternatively, modifications in the crystal structure due to mutations, additions, substitutions, and/or deletions of amino acids, or other changes in any of the components that make up the crystal could also account for variations in structure coordinates. If such variations are within a certain root mean square deviation as compared to the original coordinates, the resulting three-dimensional shape is considered encompassed by this invention. Thus, for example, a ligand that binds to the binding pocket of Aurora-2 would also be expected to bind to another binding pocket whose structure coordinates define a shape that falls within the acceptable root mean square deviation.
Various computational analyses may be necessary to determine whether a binding pocket, motif, domain or portion thereof of a molecule or molecular complex is sufficiently similar to the binding pocket, motif, domain or portion thereof of Aurora-2. Such analyses may be carried out using well known software applications, such as ProFit (A. C. R. Martin, SciTech Software, ProFit version 1.8, University College London, http://www.bioinf.org.uk/software), Swiss-Pdb Viewer (Guex et al., Electrophoresis, 18, pp. 2714-2723 (1997)), the Molecular Similarity application of QUANTA (Molecular Simulations Inc., San Diego, Calif. © 1998, 2000) and as described in the accompanying User's Guide, which are incorporated herein by reference.
The above programs permit comparisons between different structures, different conformations of the same structure, and different parts of the same structure. The procedure used in QUANTA (Molecular Simulations, Inc., San Diego, Calif. ©1998, 2000) and Swiss-Pdb Viewer to compare structures is divided into four steps: 1) load the structures to be compared; 2) define the atom equivalences in these structures; 3) perform a fitting operation on the structures; and 4) analyze the results.
The procedure used in ProFit to compare structures includes the following steps: 1) load the structures to be compared; 2) specify selected residues of interest; 3) define the atom equivalences in the selected residues; 4) perform a fitting operation on the selected residues; and 5) analyze the results.
Each structure in the comparison is identified by a name. One structure is identified as the target (i.e., the fixed structure); all remaining structures are working structures (i.e., moving structures). Since atom equivalency within the above programs is defined by user input, for the purpose of this invention we will define equivalent atoms as protein backbone atoms (N, Cα, C and O) for Aurora-2 amino acids and corresponding amino acids in the structures being compared.
The corresponding amino acids may be identified by sequence alignment programs such as the “bestfit” program available from the Genetics Computer Group which uses the local homology algorithm described by Smith and Waterman in Advances in Applied Mathematics 2, 482 (1981), which is incorporated herein by reference. A suitable amino acid sequence alignment will require that the proteins being aligned share minimum percentage of identical amino acids. Generally, a first protein being aligned with a second protein should share in excess of about 35% identical amino acids [Hanks et al., Science, 241, 42 (1988); Hanks and Quinn, Methods in Enzymology, 200, 38 (1991)]. The identification of equivalent residues can also be assisted by secondary structure alignment, for example, aligning the α-helices, β-sheets in the structure. The program Swiss-Pdb Viewer has its own best fit algorithm that is based on secondary sequence alignment.
When a rigid fitting method is used, the working structure is translated and rotated to obtain an optimum fit with the target structure. The fitting operation uses an algorithm that computes the optimum translation and rotation to be applied to the moving structure, such that the root mean square difference of the fit over the specified pairs of equivalent atom is an absolute minimum. This number, given in angstroms, is reported by the above programs. The Swiss-Pdb Viewer program sets an RMSD cutoff for eliminating pairs of equivalent atoms that have high RMSD values. An RMSD cutoff value can be used to exclude pairs of equivalent atoms with extreme individual RMSD values. In the program ProFit, the RMSD cutoff value can be specified by the user.
The rigid fitting between structures was performed by QUANTA and then inputted into the program ProFit, from which the RMSD values were determined. For the 5 Å and 8 Å sphere amino acids, the RMSD values of the ATP-binding pocket between the Aurora-2-adenosine complex and the Aurora-2-inhibitor complexes are 0.61-0.77 Å and 0.58-0.64 Å, respectively. The comparison of the entire kinase domain between the Aurora-2 structures in the present invention yields RMSD values in the range of 0.61-0.77 Å using Aurora-2-adenosine as a reference. The RMSD values are averages of individual RMSD values calculated for the backbone atoms (C, O, N and Cα) of all residues in the kinase or ATP-binding pocket between the reference structure and the other Aurora-2-inhibitor complex structures.
For the purpose of this invention, any molecule, molecular complex, binding pocket, motif, domain thereof or portion thereof that is within a root mean square deviation for backbone atoms (N, Cα, C, O) when superimposed on the relevant backbone atoms described by structure coordinates listed in FIGS. 1-4 are encompassed by this invention.
Therefore, one embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues L139, L194, L210, E211, A213, L263, and W277 according to any one of FIGS. 1-4, wherein the root mean square deviation of the backbone atoms between said amino acids of said molecule or molecular complex and said Aurora-2 amino acids is not more than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues L139, G140, F144, V147, A160, K162, L194, L210, E211, Y212, A213, P214, L215, T217, R220, L263, A273, and W277 according to FIG. 3, wherein the root mean square deviation (RMSD) of the backbone atoms between said amino acid residues of said molecule or molecular complex and said Aurora-2 amino acids is not more than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues L139, G140, F144, V147, A160, K162, L194, L210, E211, Y212, A213, P214, L215, T217, R220, L263, A273, W277, and S278 according to FIG. 1 or 4, wherein the root mean square deviation (RMSD) of the backbone atoms between said amino acid residues of said molecule or molecular complex and said Aurora-2 amino acids is not more than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues L139, G140, F144, V147, A160, K162, L194, L210, E211, Y212, A213, P214, L215, T217, R220, L263, A273, W277, S278, and V279 according to FIG. 2, wherein the root mean square deviation (RMSD) of the backbone atoms between said amino acid residues of said molecule or molecular complex and said Aurora-2 amino acids is not more than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, I158, L159, A160, L161, K162, L194, R195, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E260, N261, L262, L263, L264, K271, I272, A273, D274, F275, and W277 according to FIG. 3, wherein the root mean square deviation of the backbone atoms between said amino acids of said molecule or molecular complex and said Aurora-2 amino acids is not greater than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, I158, L159, A160, L161, K162, L194, R195, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E260, N261, L262, L263, L264, K271, I272, A273, D274, F275, W277 and S278 according to FIG. 1 or 4, wherein the root mean square deviation of the backbone atoms between said amino acids of said molecule or molecular complex and said Aurora-2 amino acids is not greater than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, I158, L159, A160, L161, K162, L194, R195, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E260, N261, L262, L263, L264, K271, I272, A273, D274, F275, W277, S278, and V279 according to FIG. 2, wherein the root mean square deviation of the backbone atoms between said amino acids of said molecule or molecular complex and said Aurora-2 amino acids is not greater than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues F133, I135, G136, R137, F144, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, and W277 according to FIG. 3, wherein the root mean square deviation of the backbone atoms between said amino acids of said molecule or molecular complex and said Aurora-2 amino acids is not more than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues F133, I135, G136, R137, F144, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, W277, and S278 according to FIG. 1 or 4, wherein the root mean square deviation of the backbone atoms between said amino acids of said molecule or molecular complex and said Aurora-2 amino acids is not more than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising all or part of an Aurora-2 ATP-binding pocket defined by structure coordinates of a set of amino acid residues that correspond to Aurora-2 amino acid residues F133, I135, G136, R137, F144, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, W277, S278, and V279 according to FIG. 2, wherein the root mean square deviation of the backbone atoms between said amino acids of said molecule or molecular complex and said Aurora-2 amino acids is not more than about 3.0 Å. In one embodiment, the RMSD is not greater than about 2.0 Å. In one embodiment, the RMSD is not greater than about 1.0 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å. In one embodiment, the RMSD is not greater than about 0.3 Å. In one embodiment, the RMSD is not greater than about 0.2 Å.
Another embodiment of this invention provides a molecule or molecular complex comprising a protein defined by structure coordinates of a set of amino acid residues which correspond to Aurora-2 amino acid residues according to FIG. 1, 2, 3 or 4, wherein the root mean square deviation between said set of amino acid residues of said molecule or molecular complex and said Aurora-2 amino acid residues is not more than about 5 Å. In one embodiment, the RMSD is not greater than about 4 Å. In one embodiment, the RMSD is not greater than about 3 Å. In one embodiment, the RMSD is not greater than about 2 Å. In one embodiment, the RMSD is not greater than about 1.5 Å. In another embodiment, the RMSD is not greater than about 1 Å. In one embodiment, the RMSD is not greater than about 0.8 Å. In one embodiment, the RMSD is not greater than about 0.5 Å.
In one embodiment, the above molecules or molecular complexes are in crystalline form.
Computer Systems
According to another embodiment, this invention provided a machine-readable data storage medium, comprising a data storage material encoded with machine-readable data, wherein said data defines the above-mentioned molecules or molecular complexes. In one embodiment, the data defines the above-mentioned binding pockets by comprising the structure coordinates of said amino acid residues according to any one of FIG. 1-4. To use the structure coordinates generated for Aurora-2, homologues thereof, or one of its binding pockets, it is at times necessary to convert them into a three-dimensional shape. This is achieved through the use of commercially or publicly available software that is capable of generating a three-dimensional structure of molecules or potions thereof from a set of structure coordinates. The three-dimensional structure may be displayed as a graphical representation.
Therefore, according to another embodiment, this invention provides a machine-readable data storage medium comprising a data storage material encoded with machine readable data. In one embodiment, a machine programmed with instructions for using said data, is capable of generating a three-dimensional structure of any of the molecule or molecular complexes, or binding pockets thereof, that are described herein.
This invention also provides a computer comprising:

    
    
        (a) a machine-readable data storage medium comprising a data storage material encoded with machine-readable data, wherein said data defines any one of the above molecules or molecular complexes;
        (b) a working memory for storing instructions for processing said machine-readable data;
        (c) a central processing unit (CPU) coupled to said working memory and to said machine-readable data storage medium for processing said machine readable data and means for generating three-dimensional structural information of said molecule or molecular complex; and
        (d) output hardware coupled to said central processing unit for outputting three-dimensional structural information of said molecule or molecular complex, or information produced using said three-dimensional structural information of said molecule or molecular complex.
    
    


In one embodiment, the data defines the binding pocket or protein of the molecule or molecular complex.
Three-dimensional data generation may be provided by an instruction or set of instructions such as a computer program or commands for generating a three-dimensional structure or graphical representation from structure coordinates, or by subtracting distances between atoms, calculating chemical energies for an Aurora-2 molecule or molecular complex or homologues thereof, or calculating or minimizing energies for an association of an Aurora-2 molecule or molecular complex or homologues thereof to a chemical entity. The graphical representation can be generated or displayed by commercially available software programs. Examples of software programs include but are not limited to QUANTA [Accelrys ©2001, 2002], O [Jones et al., Acta Crystallogr. A47, pp. 110-119 (1991)] and RIBBONS [Carson, J. Appl. Crystallogr., 24, pp. 9589-961 (1991)], which are incorporated herein by reference. Certain software programs may imbue this representation with physico-chemical attributes which are known from the chemical composition of the molecule, such as residue charge, hydrophobicity, torsional and rotational degrees of freedom for the residue or segment, etc. Examples of software programs for calculating chemical energies are described in the Rational Drug Design section.
In one embodiment, the computer is executing an instruction such as a computer program for three dimensional data generation.
Information of said binding pocket or information produced by using said binding pocket can be outputted through display terminals, touchscreens, facsimile machines, modems, CD-ROMs printers or disk drives. The information can be in graphical or alphanumeric form.
FIG. 9 demonstrates one version of these embodiments. System (10) includes a computer (11) comprising a central processing unit (“CPU”) (20), a working memory (22) which may be, e.g., RAM (random-access memory) or “core” memory, mass storage memory (24) (such as one or more disk drives or CD-ROM drives), one or more cathode-ray tube (“CRT”) display terminals (26), one or more keyboards (28), one or more input lines (30), and one or more output lines (40), all of which are, interconnected by a conventional bi-directional system bus (50).
Input hardware (36), coupled to computer (11) by input lines (30), may be implemented in a variety of ways. Machine-readable data of this invention may be inputted via the use of a modem or modems (32) connected by a telephone line or dedicated data line (34). Alternatively or additionally, the input hardware (36) may comprise CD-ROM drives or disk drives (24). In conjunction with display terminal (26), keyboard (28) may also be used as an input device.
Output hardware (46), coupled to computer (11) by output lines (40), may similarly be implemented by conventional devices. By way of example, output hardware (46) may include CRT display terminal (26) for displaying a graphical representation of a binding pocket of this invention using a program such as QUANTA as described herein. Output hardware may also include a printer (42), so that hard copy output may be produced, or a disk drive (24), to store system output for later use. Output hardware may also include a CD or DVD recorder, ZIPTM or JAZTM drive, or other machine-readable data storage device.
In operation, CPU (20) coordinates the use of the various input and output devices (36), (46), coordinates data accesses from mass storage (24) and accesses to and from working memory (22), and determines the sequence of data processing steps. A number of programs may be used to process the machine-readable data of this invention. Such programs are discussed in reference to the computational methods of drug discovery as described herein. Specific references to components of the hardware system (10) are included as appropriate throughout the following description of the data storage medium.
FIG. 10 shows a cross section of a magnetic data storage medium (100) which can be encoded with a machine-readable data that can be carried out by a system such as system (10) of FIG. 9. Medium (100) can be a conventional floppy diskette or hard disk, having a suitable substrate (101), which may be conventional, and a suitable coating (102), which may be conventional, on one or both sides, containing magnetic domains (not visible) whose polarity or orientation can be altered magnetically. Medium (100) may also have an opening (not shown) for receiving the spindle of a disk drive or other data storage device (24).
The magnetic domains of coating (102) of medium (100) are polarized or oriented so as to encode in manner which may be conventional, machine readable data such as that described herein, for execution by a system such as system (10) of FIG. 9.
FIG. 11 shows a cross section of an optically-readable data storage medium (110) which also can be encoded with such a machine-readable data, or set of instructions, which can be carried out by a system such as system (10) of FIG. 9. Medium (110) can be a conventional compact disk read only memory (CD-ROM) or a rewritable medium such as a magneto-optical disk which is optically readable and magneto-optically writable. Medium (100) preferably has a suitable substrate (111), which may be conventional, and a suitable coating (112), which may be conventional, usually of one side of substrate (111).
In the case of CD-ROM, as is well known, coating (112) is reflective and is impressed with a plurality of pits (113) to encode the machine-readable data. The arrangement of pits is read by reflecting laser light off the surface of coating (112). A protective coating (114), which preferably is substantially transparent, is provided on top of coating (112).
In the case of a magneto-optical disk, as is well known, coating (112) has no pits (113), but has a plurality of magnetic domains whose polarity or orientation can be changed magnetically when heated above a certain temperature, as by a laser (not shown). The orientation of the domains can be read by measuring the polarization of laser light reflected from coating (112). The arrangement of the domains encodes the data as described above.
In one embodiment, the structure coordinates of said molecules or molecular complexes are produced by homology modeling of at least a portion of the structure coordinates of FIG. 1, 2, 3 or 4. Homology modeling can be used to generate structural models of Aurora-2 homologues or other homologous proteins based on the known structure of Aurora-2. This can be achieved by performing one or more of the following steps: performing sequence alignment between the amino acid sequence of an unknown molecule against the amino acid sequence of Aurora-2; identifying conserved and variable regions by sequence or structure; generating structure co-ordinates for structurally conserved residues of the unknown structure from those of Aurora-2; generating conformations for the structurally variable residues in the unknown structure; replacing the non-conserved residues of Aurora-2 with residues in the unknown structure; building side chain conformations; and refining and/or evaluating the unknown structure.
For example, since the protein sequence of the catalytic domains of Aurora-2 and Aurora-1 or Aurora-3 can be aligned relative to each other, it is possible to construct models of the structures of Aurora-1 or Aurora-3, particularly in the regions of the active site, using the Aurora-2 structure. Software programs that are useful in homology modeling include XALIGN [Wishart, D. S. et al., Comput. Appl. Biosci., 10, pp. 687-88 (1994)] and CLUSTAL W Alignment Tool [Higgins D. G. et al., Methods Enzymol., 266, pp. 383-402 (1996)]. See also, U.S. Pat. No. 5,884,230. These references are incorporated herein by reference.
To perform the sequence alignment, programs such as the “bestfit” program available from the Genetics Computer Group [Waterman in Advances in Applied Mathematics 2, 482 (1981), which is incorporated herein by reference] and CLUSTAL W Alignment Tool [Higgins D. G. et al., Methods Enzymol., 266, pp. 383-402 (1996), which is incorporated by reference] can be used. To model the amino acid side chains of Aurora-1 or Aurora-3, the amino acid residues in Aurora-2 can be replaced, using a computer graphics program such as “O” [Jones et al, (1991) Acta Cryst. Sect. A, 47: 110-119], by those of the homologous protein, where they differ. The same orientation or a different orientation of the amino acid can be used. Insertions and deletions of amino acid residues may be necessary where gaps occur in the sequence alignment. However, certain portions of the active site of Aurora-2 and its homologues are highly conserved with essentially no insertions and deletions.
Homology modeling can be performed using, for example, the computer programs SWISS-MODEL available through Glaxo Wellcome Experimental Research in Geneva, Switzerland; WHATIF available on EMBL servers; Schnare et al., J. Mol. Biol, 256: 701-719 (1996); Blundell et al., Nature 326: 347-352 (1987); Fetrow and Bryant, Bio/Technology 11:479-484 (1993); Greer, Methods in Enzymology 202: 239-252 (1991); and Johnson et al, Crit. Rev. Biochem. Mol Biol. 29:1-68 (1994). An example of homology modeling can be found, for example, in Szklarz G. D., Life Sci. 61: 2507-2520 (1997). These references are incorporated herein by reference.
Thus, in accordance with the present invention, data capable of generating the three dimensional structure of the above molecules or molecular complexes, or binding pockets thereof, can be stored in a machine-readable storage medium, which is capable of displaying a graphical three-dimensional representation of the structure.
Rational Drug Design
The Aurora-2 structure coordinates or the three-dimensional graphical representation generated from these coordinates may be used in conjunction with a computer for a variety of purposes, including drug discovery.
For example, the structure encoded by the data may be computationally evaluated for its ability to associate with chemical entities. Chemical entities that associate with Aurora-2 may inhibit Aurora-2 or its homologues, and are potential drug candidates. Alternatively, the structure encoded by the data may be displayed in a graphical three-dimensional representation on a computer screen. This allows visual inspection of the structure, as well as visual inspection of the structure's association with chemical entities.
Thus, according to another embodiment, the invention provides a method for designing, selecting and/or optimizing a chemical entity that binds to all or part of the molecule or molecular complex comprising the steps of:

    
    
        (a) providing the structure coordinates of said molecule or molecular complex on a computer comprising the means for generating three-dimensional structural information of all or part of said molecule or molecular complex from said structure coordinates; and
        (b) designing, selecting and/or optimizing said chemical entity by employing means for performing a fitting operation between said chemical entity and said three-dimensional structural information of all or part of said molecule or molecular complex.
    
    


In one embodiment, the method is for designing, selecting and or optimizing a chemical entity that binds with the binding pocket of a molecule or molecular complex. In one embodiment, the above method further comprises the following steps before step (a):

    
    
        (c) producing a crystal of a molecule or molecular complex comprising Aurora-2 or homologue thereof;
        (d) determining the three-dimensional structure coordinates of the molecule or molecular complex by X-ray diffraction of the crystal; and
        (e) identifying all or part of said binding pocket.
    
    


Three-dimensional structural information in step (a) may be generated by instructions such as a computer program or commands that can generate a three-dimensional structure or graphical representation; subtract distances between atoms; calculate chemical energies for an Aurora-2 molecule, molecular complex or homologues thereof; or calculate or minimize energies of an association of Aurora-2 molecule, molecular complex or homologues thereof to a chemical entity. These types of computer programs are known in the art. The graphical representation can be generated or displayed by commercially available software programs. Examples of software programs include but are not limited to QUANTA [Accelrys ©2001, 2002], O [Jones et al., Acta Crystallogr. A47, pp. 110-119 (1991)] and RIBBONS [Carson, J. Appl. Crystallogr., 24, pp. 9589-961 (1991)], which are incorporated herein by reference. Certain software programs may imbue this representation with physico-chemical attributes which are known from the chemical composition of the molecule, such as residue charge, hydrophobicity, torsional and rotational degrees of freedom for the residue or segment, etc. Examples of software programs for calculating chemical energies are described below.
Thus, according to another embodiment, the invention provides a method for evaluating the potential of a chemical entity to associate with all or part of a molecule or molecular complex as described previously in the different embodiments.
This method comprises the steps of: (a) employing computational means to perform a fitting operation between the chemical entity and all or part of the molecule or molecular complex described before; (b) analyzing the results of said fitting operation to quantify the association between the chemical entity and all or part of the molecule or molecular complex; and optionally (c) outputting said quantified association to a suitable output hardware, such as a CRT display terminal, a CD or DVD recorder, ZIPTM or JAZTM drive, a disk drive, or other machine-readable data storage device, as described previously. The method may further comprise generating a three-dimensional structure, graphical representation thereof, or both of all or part of the molecule or molecular complex prior to step (a). In one embodiment, the method is for evaluating the ability of a chemical entity to associate with all or part of the binding pocket of a molecule or molecular complex.
In another embodiment, the invention provides a method for screening a plurality of chemical entities to associate at a deformation energy of binding of less than −7 kcal/mol with said binding pocket:

    
    
        (a) employing computational means, which utilize said structure coordinates to perform a fitting operation between one of said chemical entities from the plurality of chemical entities and said binding pocket;
        (b) quantifying the deformation energy of binding between the chemical entity and the binding pocket;
        (c) repeating steps (a) and (b) for each remaining chemical entity; and
        (d) outputting a set of chemical entities that associate with the binding pocket at a deformation energy of binding of less than −7 kcal/mol to a suitable output hardware.
    
    


In another embodiment, the method comprises the steps of:

    
    
        (a) constructing a computer model of a binding pocket of the molecule or molecular complex;
        (b) selecting a chemical entity to be evaluated by a method selected from the group consisting of assembling said chemical entity; selecting a chemical entity from a small molecule database; de novo ligand design of said chemical entity; and modifying a known agonist or inhibitor, or a portion thereof, of an Aurora-2 protein or homologue thereof;
        (c) employing computational means to perform a fitting operation between computer models of said chemical entity to be evaluated and said binding pocket in order to provide an energy-minimized configuration of said chemical entity in the binding pocket; and
        (d) evaluating the results of said fitting operation to quantify the association between said chemical entity and the binding pocket model, whereby evaluating the ability of said chemical entity to associate with said binding pocket.
    
    


In another embodiment, the invention provides a method of using a computer for evaluating the ability of a chemical entity to associate with all or part of the molecule or molecular complex, wherein said computer comprises a machine-readable data storage medium comprising a data storage material encoded with said structure coordinates defining said binding pocket and means for generating a three-dimensional graphical representation of the binding pocket, and wherein said method comprises the steps of:

    
    
        (a) positioning a first chemical entity within all or part of said binding pocket using a graphical three-dimensional representation of the structure of the chemical entity and the binding pocket;
        (b) performing a fitting operation between said chemical entity and said binding pocket by employing computational means;
        (c) analyzing the results of said fitting operation to quantitate the association between said chemical entity and all or part of the binding pocket; and
        (d) outputting said quantitated association to a suitable output hardware.
    
    


The above method may further comprise the steps of:

    
    
        (e) repeating steps (a) through (d) with a second chemical entity; and
        (f) selecting at least one of said first or second chemical entity that associates with all or part of said binding pocket based on said quantitated association of said first or second chemical entity.
    
    


Alternatively, the structure coordinates of the Aurora-2 binding pockets may be utilized in a method for identifying an agonist or antagonist of a molecule comprising a binding pocket of Aurora-2. This method comprises the steps of:

    
    
        (a) using a three-dimensional structure of the molecule or molecular complex to design or select a chemical entity;
        (b) contacting the chemical entity with the molecule and molecular complex;
        (c) monitoring the activity of the molecule or molecular complex; and
        (d) classifying the chemical entity as an agonist or antagonist based on the effect of the chemical entity on the activity of the molecule or molecular complex.
    
    


In one embodiment, step (a) is using a three-dimensional structure of the binding pocket of the molecule or molecular complex. In another embodiment, the three-dimensional structure is displayed as a graphical representation.
In another embodiment, the method comprises the steps of:

    
    
        (a) constructing a computer model of a binding pocket of the molecule or molecular complex;
        (b) selecting a chemical entity to be evaluated by a method selected from the group consisting of assembling said chemical entity; selecting a chemical entity from a small molecule database; de novo ligand design of said chemical entity; and modifying a known agonist or inhibitor, or a portion thereof, of an Aurora-2 protein or homologue thereof;
        (c) employing computational means to perform a fitting operation between computer models of said chemical entity to be evaluated and said binding pocket in order to provide an energy-minimized configuration of said chemical entity in the binding pocket; and
        (d) evaluating the results of said fitting operation to quantify the association between said chemical entity and the binding pocket model, whereby evaluating the ability of said chemical entity to associate with said binding pocket;
        (e) synthesizing said chemical entity; and
        (f) contacting said chemical entity with said molecule or molecular complex to determine the ability of said compound to activate or inhibit said molecule.
    
    


In one embodiment, the invention provides a method of designing a compound or complex that associates with all or part of the binding pocket comprising the steps of:

    
    
        (a) providing the structure coordinates of said binding pocket or protein on a computer comprising the means for generating three-dimensional structural information from said structure coordinates; and
        (b) using the computer to perform a fitting operation to associate a first chemical entity with all or part of the binding pocket;
        (c) performing a fitting operation to associate at least a second chemical entity with all or part of the binding pocket;
        (d) quantifying the association between the first and second chemical entity and all or part of the binding pocket;
        (e) optionally repeating steps (b) to (d) with another first and second chemical entity, selecting a first and a second chemical entity based on said quantified association of all of said first and second chemical entity;
        (f) optionally, visually inspecting the relationship of the first and second chemical entity to each other in relation to the binding pocket on a computer screen using the three-dimensional graphical representation of the binding pocket and said first and second chemical entity; and
        (g) assembling the first and second chemical entity into a compound or complex that associates with all or part of said binding pocket by model building.
    
    


For the first time, the present invention permits the use of molecular design techniques to identify, select and design chemical entities, including inhibitory compounds, capable of binding to Aurora-2 or Aurora-2-like binding pockets, motifs and domains.
Applicants' elucidation of binding pockets on Aurora-2 provides the necessary information for designing new chemical entities and compounds that may interact with Aurora-2 substrate or ATP-binding pockets or Aurora-2-like substrate or ATP-binding pockets, in whole or in part. Due to the homology in the kinase core between Aurora-2, Aurora-1 and Aurora-3, compounds that inhibit Aurora-2 are also expected to inhibit Aurora-1 and Aurora-3, especially those compounds that bind the ATP-binding pocket.
Throughout this section, discussions about the ability of a chemical entity to bind to, associate with or inhibit Aurora-2 binding pockets refer to features of the entity alone. Assays to determine if a compound binds to Aurora-2 are well known in the art and are exemplified below.
The design of compounds that bind to or inhibit Aurora-2 binding pockets according to this invention generally involves consideration of two factors. First, the chemical entity must be capable of physically and structurally associating with parts or all of the Aurora-2 binding pockets. Non-covalent molecular interactions important in this association include hydrogen bonding, van der Waals interactions, hydrophobic interactions and electrostatic interactions.
Second, the chemical entity must be able to assume a conformation that allows it to associate with the Aurora-2 binding pockets directly. Although certain portions of the chemical entity will not directly participate in these associations, those portions of the chemical entity may still influence the overall conformation of the molecule. This, in turn, may have a significant impact on potency. Such conformational requirements include the overall three-dimensional structure and orientation of the chemical entity in relation to all or a portion of the binding pocket, or the spacing between functional groups of a chemical entity comprising several chemical entities that directly interact with the Aurora-2 or Aurora-2-like binding pockets.
The potential inhibitory or binding effect of a chemical entity on Aurora-2 binding pockets may be analyzed prior to its actual synthesis and testing by the use of computer modeling techniques. If the theoretical structure of the given entity suggests insufficient interaction and association between it and the Aurora-2 binding pockets, testing of the entity is obviated. However, if computer modeling indicates a strong interaction, the molecule may then be synthesized and tested for its ability to bind to an Aurora-2 binding pocket. This may be achieved by testing the ability of the molecule to inhibit Aurora-2 using the assays described in Example 8. In this manner, synthesis of inoperative compounds may be avoided.
A potential inhibitor of an Aurora-2 binding pocket may be computationally evaluated by means of a series of steps in which chemical entities or fragments are screened and selected for their ability to associate with the Aurora-2 binding pockets.
One skilled in the art may use one of several methods to screen chemical entities or fragments for their ability to associate with an Aurora-2 binding pocket. This process may begin by visual inspection of, for example, an Aurora-2 binding pocket on the computer screen based on the Aurora-2 structure coordinates in any of FIGS. 1-4 or other coordinates which define a similar shape generated from the machine-readable storage medium. Selected fragments or chemical entities may then be positioned in a variety of orientations, or docked, within that binding pocket as defined supra. Docking may be accomplished using software such as QUANTA (Molecular Simulations, Inc., San Diego, Calif. ©1998, 2000) and Sybyl (Tripos Associates, St. Louis, Mo.), followed by energy minimization and molecular dynamics with standard molecular mechanics force fields, such as CHARMM and AMBER.
Specialized computer programs may also assist in the process of selecting fragments or chemical entities. These include:
1. GRID (P. J. Goodford, “A Computational Procedure for Determining Energetically Favorable Binding Sites on Biologically Important Macromolecules”, J. Med. Chem., 28, pp. 849-857 (1985)). GRID is available from Oxford University, Oxford, UK.
2. MCSS (A. Miranker et al., “Functionality Maps of Binding Sites: A Multiple Copy Simultaneous Search Method.” Proteins: Structure, Function and Genetics, 11, pp. 29-34 (1991)). MCSS is available from Molecular Simulations, San Diego, Calif.
3. AUTODOCK (D. S. Goodsell et al., “Automated Docking of Substrates to Proteins by Simulated Annealing”, Proteins: Structure, Function, and Genetics, 8, pp. 195-202 (1990)). AUTODOCK is available from Scripps Research Institute, La Jolla, Calif.
4. DOCK (I. D. Kuntz et al., “A Geometric Approach to Macromolecule-Ligand Interactions”, J. Mol. Biol., 161, pp. 269-288 (1982)). DOCK is available from University of California, San Francisco, Calif.
Once suitable chemical entities or fragments have been selected, they can be assembled into a single compound or complex. Assembly may be preceded by visual inspection of the relationship of the fragments to each other on the three-dimensional image displayed on a computer screen in relation to the structure coordinates of Aurora-2. This would be followed by manual model building using software such as QUANTA (Molecular Simulations, Inc., San Diego, Calif. ©1998, 2000) or Sybyl (Tripos Associates, St. Louis, Mo.).
Useful programs to aid one of skill in the art in connecting the individual chemical entities or fragments include:
1. CAVEAT (P. A. Bartlett et al., “CAVEAT: A Program to Facilitate the Structure-Derived Design of Biologically Active Molecules”, in Molecular Recognition in Chemical and Biological Problems, Special Pub., Royal Chem. Soc., 78, pp. 182-196 (1989); G. Lauri and P. A. Bartlett, “CAVEAT: a Program to Facilitate the Design of Organic Molecules”, J. Comput. Aided Mol. Des., 8, pp. 51-66 (1994)). CAVEAT is available from the University of California, Berkeley, Calif.
2. 3D Database systems such as ISIS (MDL Information Systems, San Leandro, Calif.). This area is reviewed in Y. C. Martin, “3D Database Searching in Drug Design”, J. Med. Chem., 35, pp. 2145-2154 (1992).
3. HOOK (M. B. Eisen et al., “HOOK: A Program for Finding Novel Molecular Architectures that Satisfy the Chemical and Steric Requirements of a Macromolecule Binding Site”, Proteins: Struct., Funct., Genet., 19, pp. 199-221 (1994)). HOOK is available from Molecular Simulations, San Diego, Calif.
Instead of proceeding to build an inhibitor of an Aurora-2 binding pocket in a step-wise fashion one fragment or chemical entity at a time as described above, inhibitory or other Aurora-2 binding compounds may be designed as a whole or “de novo” using either an empty binding pocket or optionally including some portion(s) of a known inhibitor(s). There are many de novo ligand design methods including:
1. LUDI (H.-J. Bohm, “The Computer Program LUDI: A New Method for the De Novo Design of Enzyme Inhibitors”, J. Comp. Aid. Molec. Design, 6, pp. 61-78 (1992)). LUDI is available from Molecular Simulations Incorporated, San Diego, Calif.
2. LEGEND (Y. Nishibata et al., Tetrahedron, 47, p. 8985 (1991)). LEGEND is available from Molecular Simulations Incorporated, San Diego, Calif.
3. LeapFrog (available from Tripos Associates, St. Louis, Mo.).
4. SPROUT (V. Gillet et al., “SPROUT: A Program for Structure Generation)”, J. Comput. Aided Mol. Design, 7, pp. 127-153 (1993)). SPROUT is available from the University of Leeds, UK.
Other molecular modeling techniques may also be employed in accordance with this invention (see, e.g., N. C. Cohen et al., “Molecular Modeling Software and Methods for Medicinal Chemistry, J. Med. Chem., 33, pp. 883-894 (1990); see also, M. A. Navia and M. A. Murcko, “The Use of Structural Information in Drug Design”, Current Opinions in Structural Biology, 2, pp. 202-210 (1992); L. M. Balbes et al., “A Perspective of Modern Methods in Computer-Aided Drug Design”, Reviews in Computational Chemistry, Vol. 5, K. B. Lipkowitz and D. B. Boyd, Eds., VCH, New York, pp. 337-380 (1994); see also, W. C. Guida, “Software For Structure-Based Drug Design”, Curr. Opin. Struct. Biology, 4, pp. 777-781 (1994)).
Once a chemical entity has been designed or selected by the above methods, the efficiency with which that chemical entity may bind to an Aurora-2 binding pocket may be tested and optimized by computational evaluation. For example, an effective Aurora-2 binding pocket inhibitor must preferably demonstrate a relatively small difference in energy between its bound and free states (i.e., a small deformation energy of binding). Thus, the most efficient Aurora-2 binding pocket inhibitors should preferably be designed with a deformation energy of binding of not greater than about 10 kcal/mole, more preferably, not greater than 7 kcal/mole. Aurora-2 binding pocket inhibitors may interact with the binding pocket in more than one conformation that is similar in overall binding energy. In those cases, the deformation energy of binding is taken to be the difference between the energy of the free chemical entity and the average energy of the conformations observed when the inhibitor binds to the protein.
A chemical entity designed or selected as binding to an Aurora-2 binding pocket may be further computationally optimized so that in its bound state it would preferably lack repulsive electrostatic interaction with the target enzyme and with the surrounding water molecules. Such non-complementary electrostatic interactions include repulsive charge-charge, dipole-dipole and charge-dipole interactions.
Specific computer software is available in the art to evaluate compound deformation energy and electrostatic interactions. Examples of programs designed for such uses include: Gaussian 94, revision C (M. J. Frisch, Gaussian, Inc., Pittsburgh, Pa. ©1995); AMBER, version 4.1 (P. A. Kollman, University of California at San Francisco, ©1995); QUANTA/CHARMM (Molecular Simulations, Inc., San Diego, Calif. ©1998, 2000); Insight II/Discover (Molecular Simulations, Inc., San Diego, Calif. ©1998); DelPhi (Molecular Simulations, Inc., San Diego, Calif. ©1998); and AMSOL (Quantum Chemistry Program Exchange, Indiana University). These programs may be implemented, for instance, using a Silicon Graphics workstation such as an Indigo2 with “IMPACT” graphics. Other hardware systems and software packages will be known to those skilled in the art.
Another approach enabled by this invention, is the computational screening of small molecule databases for chemical entities or compounds that can bind in whole, or in part, to an Aurora-2 binding pocket. In this screening, the quality of fit of such entities to the binding pocket may be judged either by shape complementarity or by estimated interaction energy (E. C. Meng et al., J. Comp. Chem., 13, pp. 505-524 (1992)).
According to another embodiment, the invention provides compounds which associate with an Aurora-2 binding pocket produced or identified by the method set forth above.
Another particularly useful drug design technique enabled by this invention is iterative drug design. Iterative drug design is a method for optimizing associations between a protein and a compound by determining and evaluating the three-dimensional structures of successive sets of protein/compound complexes.
In iterative drug design, crystals of a series of protein or protein complexes are obtained and then the three-dimensional structures of each crystal is solved. Such an approach provides insight into the association between the proteins and compounds of each complex. This is accomplished by selecting compounds with inhibitory activity, obtaining crystals of this new protein/compound complex, solving the three-dimensional structure of the complex, and comparing the associations between the new protein/compound complex and previously solved protein/compound complexes. By observing how changes in the compound affected the protein/compound associations, these associations may be optimized.
In some cases, iterative drug design is carried out by forming successive protein-compound complexes and then crystallizing each new complex. High throughput crystallization assays may be used to find a new crystallization condition or to optimize the original protein or complex crystallization condition for the new complex. Alternatively, a pre-formed protein crystal may be soaked in the presence of an inhibitor, thereby forming a protein/compound complex and obviating the need to crystallize each individual protein/compound complex.
Structure Determination of Other Molecules
The structure coordinates set forth in FIGS. 1-4 can also be used to aid in obtaining structural information about other crystallized molecules or molecular complexes. This may be achieved by any of a number of well-known techniques, including molecular replacement.
According to an alternate embodiment, the machine-readable data storage medium comprises a data storage material encoded with a first set of machine readable data which comprises the Fourier transform of at least a portion of the structure coordinates set forth in FIGS. 1-4 or homology model thereof, and which, when using a machine programmed with instructions for using said data, can be combined with a second set of machine readable data comprising the X-ray diffraction pattern of a molecule or molecular complex to determine at least a portion of the structure coordinates corresponding to the second set of machine readable data.
In another embodiment, the invention provides a computer for determining at least a portion of the structure coordinates corresponding to X-ray diffraction data obtained from a molecule or molecular complex, wherein said computer comprises:

    
    
        (a) a machine-readable data storage medium comprising a data storage material encoded with machine-readable data, wherein said data comprises at least a portion of the structure coordinates of Aurora-2 according to any one of FIGS. 1-4 or homology model thereof;
        (b) a machine-readable data storage medium comprising a data storage material encoded with machine-readable data, wherein said data comprises X-ray diffraction data obtained from said molecule or molecular complex; and
        (c) instructions for performing a Fourier transform of the machine-readable data of (a) and for processing said machine-readable data of (b) into structure coordinates.
    
    


For example, the Fourier transform of at least a portion of the structure coordinates set forth in any one of FIGS. 1-4 or homology model thereof may be used to determine at least a portion of the structure coordinates of Aurora-2 homologues. In one embodiment, the molecule is an Aurora-2 homologue. In another embodiment, the molecular complex is selected from the group consisting of Aurora-2 complex and Aurora-2 homologue complex.
Therefore, in another embodiment this invention provides a method of utilizing molecular replacement to obtain structural information about a molecule or a molecular complex of unknown structure wherein the molecule or molecular complex is sufficiently homologous to Aurora-2, comprising the steps of:

    
    
        (a) crystallizing said molecule or molecular complex of unknown structure;
        (b) generating an X-ray diffraction pattern from said crystallized molecule or molecular complex;
        (c) applying at least a portion of the Aurora-2 structure coordinates set forth in one of FIGS. 1-4 or a homology model thereof to the X-ray diffraction pattern to generate a three-dimensional electron density map of at least a portion of the molecule or molecular complex whose structure is unknown; and
        (d) generating a structural model of the molecule or molecular complex from the three-dimensional electron density map.
    
    


In one embodiment, the method is performed using a computer. In another embodiment, the molecule is selected from the group consisting of Aurora-2 and Aurora-2 homologues. In another embodiment, the molecule is an Aurora molecular complex or homologue thereof.
By using molecular replacement, all or part of the structure coordinates of the Aurora-2 as provided by this invention or homology model thereof (and set forth in any one of FIGS. 1-4) can be used to determine the structure of a crystallized molecule or molecular complex whose structure is unknown more quickly and efficiently than attempting to determine such information ab initio.
Molecular replacement provides an accurate estimation of the phases for an unknown structure. Phases are a factor in equations used to solve crystal structures that can not be determined directly. Obtaining accurate values for the phases, by methods other than molecular replacement, is a time-consuming process that involves iterative cycles of approximations and refinements and greatly hinders the solution of crystal structures. However, when the crystal structure of a protein containing at least a homologous portion has been solved, the phases from the known structure may provide a satisfactory estimate of the phases for the unknown structure.
Thus, this method involves generating a preliminary model of a molecule or molecular complex whose structure coordinates are unknown, by orienting and positioning the relevant portion of the Aurora-2 according to any one of FIGS. 1-4 within the unit cell of the crystal of the unknown molecule or molecular complex so as best to account for the observed X-ray diffraction pattern of the crystal of the molecule or molecular complex whose structure is unknown. Phases can then be calculated from this model and combined with the observed X-ray diffraction pattern amplitudes to generate an electron density map of the structure whose coordinates are unknown. This, in turn, can be subjected to any well-known model building and structure refinement techniques to provide a final, accurate structure of the unknown crystallized molecule or molecular complex (E. Lattman, “Use of the Rotation and Translation Functions”, in Meth. Enzymol., 115, pp. 55-77 (1985); M. G. Rossmann, ed., “The Molecular Replacement Method”, Int. Sci. Rev. Ser., No. 13, Gordon & Breach, New York (1972)).
The structure of any portion of any crystallized molecule or molecular complex that is sufficiently homologous to any portion of the Aurora-2 can be resolved by this method.
In one embodiment, the method of molecular replacement is utilized to obtain structural information about an Aurora-2 homologue. The structure coordinates of Aurora-2 as provided by this invention are particularly useful in solving the structure of Aurora-2 complexes that are bound by ligands, substrates and inhibitors.
Furthermore, the structure coordinates of Aurora-2 as provided by this invention are useful in solving the structure of Aurora-2 proteins that have amino acid substitutions, additions and/or deletions (referred to collectively as “Aurora-2 mutants”, as compared to naturally occurring Aurora-2). These Aurora-2 mutants may optionally be crystallized in co-complex with a chemical entity, such as a non-hydrolyzable ATP analogue or a suicide substrate. The crystal structures of a series of such complexes may then be solved by molecular replacement and compared with that of wild-type Aurora-2. Potential sites for modification within the various binding pockets of the enzyme may thus be identified. This information provides an additional tool for determining the most efficient binding interactions, for example, increased hydrophobic interactions, between Aurora-2 and a chemical entity or compound.
The structure coordinates are also particularly useful in solving the structure of crystals of Aurora-2 or Aurora-2 homologues co-complexed with a variety of chemical entities. This approach enables the determination of the optimal sites for interaction between chemical entities, including candidate Aurora-2 inhibitors. For example, high resolution X-ray diffraction data collected from crystals exposed to different types of solvent allows the determination of where each type of solvent molecule resides. Small molecules that bind tightly to those sites can then be designed and synthesized and tested for their Aurora-2 inhibition activity.
All of the complexes referred to above may be studied using well-known X-ray diffraction techniques and may be refined using 1.5-3.4 Å resolution X-ray data to an R value of about 0.30 or less using computer software, such as X-PLOR (Yale University, ©1992, distributed by Molecular Simulations, Inc.; see, e.g., Blundell & Johnson, supra; Meth. Enzymol., vol. 114 & 115, H. W. Wyckoff et al., eds., Academic Press (1985)) or CNS (Brunger et al., Acta Cryst., D54, pp. 905-921, (1998)).
In order that this invention be more fully understood, the following examples are set forth. These examples are for the purpose of illustration only and are not to be construed as limiting the scope of the invention in any way.
Example 1
Expression and Purification of Aurora-2
The expression of Aurora-2 was carried out using standard procedures known in the art. A truncated Aurora-2 (amino acid residues 107-403) (full length sequence: GenBank AF011468; SEQ ID NO: 1) with an N-terminal hexa-histidine tag and a thrombin cleavage site was overexpressed in a baculovirus expression system.
Aurora-2 was purified using Ni/NTA agarose metal affinity chromatography (Qiagen, Hilden, Germany) followed by size-exclusion on a Superdex 200 column (Amersham Pharmacia Biotech, Uppsala, Sweden). The hexa-histidine tag was removed by incubation with thrombin (Calbiochem, La Jolla, Calif.). Incubation overnight incubation at 4° C. with 5 units/mg thrombin produced more than 90% Aurora-2 (amino acid residues 107-403), which was used for crystallographic studies. The reaction was quenched with PMSF (phenylmethylsulfonyl fluoride or α-toluenesulfonyl fluoride) and thrombin was removed with benzamidine sepharose (Pharmacia, Uppsala, Sweden). The protein was applied to a MonoS 10/10 column (Pharmacia, Uppsala, Sweden) equilibrated in 20 mM HEPES, pH 7.3, 10% Glycerol (v/v), 2 mM DTT, and eluted with a linear gradient from 0 to 500 mM NaCl in 80 column volumes. Unphosphorylated Aurora-2 (107-403) eluted at 148 mM NaCl. The protein was dialyzed against 25 mM Tris pH 8.0 containing 200 mM NaCl and 2 mM DTT at 4° C., concentrated to 15 mg/ml, and centrifuged at 100,000×g prior to crystallization. All protein molecular weights were confirmed by electrospray mass spectrometry.
Example 2
Formation of Aurora-2-Inhibitor Complex for Crystallization
Crystals of Aurora-2-inhibitor complex crystals were formed by co-crystallizing the protein with the inhibitors or with adenosine. The inhibitor was added to the Aurora-2 protein solution immediately after the final Mono-S purification step and prior to protein concentration (Example 1). Alternatively, inhibitor may be added to the concentrated Aurora-2 protein solution immediately before setting up the crystallization drop.
Example 3
Crystallization of Aurora-2 and Aurora-2-Inhibitor Complexes
Crystallization of Aurora-2 was carried out using the hanging drop vapor diffusion technique. The Aurora-2 formed diamond shaped or hexagonal plate-like crystals over a reservoir containing 25% PEG 3350, 50 mM MES pH 6.0, 200 mM ammonium sulphate. The crystallization droplet contained 1 μl of 15 mg ml−1 protein solution and 1 μl of reservoir solution. Crystals formed in less than 48 hours.
The formed crystals were transferred to a reservoir solution containing 15% glycerol. After soaking the crystals in 15% glycerol for less than 2 minutes, the crystals were scooped up with a cryo-loop, frozen in liquid nitrogen and stored for data collection.
Example 4
X-Ray Data Collection and Structure Determination
The Aurora-2-inhibitor complex structures and the Aurora-2-adenosine structure were solved by molecular replacement using X-ray diffraction data collected either (i) at beam line 5.0.2 of the Advanced Light Source Lawrence Berkeley Laboratory, Berkeley, Calif., USA, (ii) at beam line 14.2 of the CCLRC Synchrotron Radiation Source, Daresbury, Cheshire, UK, or (iii) at beamline X31, DESY, EMBL Outstation, Hamburg, Germany. The diffraction images were processed with the program MOSFLM (A. G. Leslie, Acta Cryst., D55, pp. 1696-1702 (1999)) and the data was scaled using SCALA (Collaborative Computational Project, N., Acta Cryst., D50, pp. 760-763 (1994)).
The data statistics, unit cell parameters and spacegroup of the Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine crystal structure is given in Table 1. The starting phases for the Aurora-2 complexes were obtained by molecular replacement using coordinates of GSK-3β (PDB Accession number 1I09) (E. ter Haar, et al., Nat. Struct. Biol., 8, pp. 593-596 (2001)) as a search model in the program AMoRe (J. Navaza, Acta. Cryst. A, 50, pp. 157-163 (1994)). The asymmetric unit contained a single Aurora-2 complex. Multiple rounds of rebuilding with QUANTA (Molecular Simulations, Inc., San Diego, Calif. ©1998, 2000) and refinement with CNX (Accelrys Inc., San Diego, Calif. ©2000) resulted in a final model that included residues 127 to 279 and residues 288 to 390. The refined model has a crystallographic R-factor of 26.3% and R-free of 33.2%.
The data statistics, unit cell parameters and spacegroup of the Aurora-2-(5-Methylthiazol-2-yl)-(2-phenyl-quinazolin-4-yl)-amine crystal structure is given in Table 2. The starting phases were obtained by molecular replacement using coordinates of the Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex as a search model in the program AMoRe. Multiple rounds of rebuilding with QUANTA (Molecular Simulations, Inc., San Diego, Calif. ©1998, 2000) and refinement with CNX (Accelrys Inc., San Diego, Calif. ©2000) resulted in a final model that included residues 120 to 279 and residues 287 to 388. The refined model has a crystallographic R-factor of 25.9% and R-free of 32.8%.
The data statistics, unit cell parameters and spacegroup of the Aurora-2-(5-Methyl-2H-pyrazol-3-yl)-(2-(pyridin-3-ylmethylamino)-quinazolin-4-yl)-amine crystal structure is given in Table 3. The starting phases were obtained by molecular replacement using coordinates of the Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex as a search model in the program AMoRe. Multiple rounds of rebuilding with QUANTA (Molecular Simulations, Inc., San Diego, Calif. ©1998, 2000) and refinement with CNX (Accelrys Inc., San Diego, Calif. ©2000) resulted in a final model that included residues 128 to 277 and residues 291 to 388. The refined model has a crystallographic R-factor of 23.6% and R-free of 29.1%.
The data statistics, unit cell parameters and spacegroup of the Aurora-2-adenosine crystal structure is given in Table 4. The starting phases were obtained by molecular replacement using coordinates of the Aurora-2-(5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex as a search model in the program AMoRe. Multiple rounds of rebuilding with QUANTA (Molecular Simulations, Inc., San Diego, Calif. ©1998, 2000) and refinement with CNX (Accelrys Inc., San Diego, Calif. ©2000) resulted in a final model that included residues 127 to 278 and residues 289 to 387. The refined model has a crystallographic R-factor of 26.4% and R-free of 31.7%.
In the above models, disordered residues were not included in the model. Alanine or glycine residues were used in the model if the side chains of certain residues could not be located in the electron density.
Example 5
Overall Structure of Aurora-2
Aurora-2 has the typical bi-lobal catalytic kinase fold or structural domain (S. K. Hanks, et al., Science, 241, pp. 42-52 (1988); Hanks, S. K. and A. M. Quinn, Meth. Enzymol., 200, pp. 38-62 (1991)) with a β-strand sub-domain (residues 127-215) at the N-terminal end and an α-helical sub-domain at the C-terminal end (residues 216-385) (FIG. 5). The ATP-binding pocket is at the interface of the α-helical and β-strand domains, and is bordered by the glycine rich loop and the hinge. The activation loop runs along the surface of the catalytic active site. The β-strand domain consists of five anti-parallel β-strands that form a β-barrel structure.
Comparison of the Aurora-2 Structure with Other Kinases
Comparison with other kinases such as GSK-3β, CDK2 and p38 revealed that the structure of Aurora-2 closely resembles the substrate-bound activated, form of a kinase. However, a unique feature that is present in all four Aurora-2 crystal structures is the unusual conformation of the activation loop (amino acid residues 273-292). Amino acid residues 275-290 act like a flexible flap that partially occludes the catalytic active site and creates a novel hydrophobic binding pocket in the catalytic active site (FIG. 6). This hydrophobic pocket is unique in that it partially overlaps with the tri-phosphate binding pocket of the catalytic active site. Comparison of the activation loops of GSK-3β (PDB Accession number 1IO9) (E. ter Haar, et al., Nat. Struct. Biol., 8, pp. 593-596 (2001)), P38 (PDB Accession number 1CM8) (Bellon, S., et al., Struct. Fold Des., 7, pp. 1057-65 (1999)) and substrate-bound activated CDK2 (PDB Accession number 1B38) (N. R. Brown et al., J. Biol. Chem., 274, pp. 8746-8756 (1999)) shows that in other closely related kinases, the activation loop adopts a more extended conformation, irrespective of whether activated protein was used in the crystal structure determination (FIG. 7).
Example 6
Catalytic Active Site of Aurora-2-Inhibitor Complexes
The inhibitor (5-Cyclopropyl-2H-pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine is bound in the deep cleft of the catalytic active site in the Aurora-2 structure (FIG. 6). The inhibitor forms three hydrogen bonds with the hinge portion of the ATP-binding pocket (dotted lines). The 1H pyrazole nitrogen shares a proton with the E211 backbone carbonyl. The other pyrazole nitrogen (position 2) accepts a proton from the A213 backbone nitrogen. Comparison with the adenosine-bound crystal structure reveals that the pyrazole mimics the binding of adenosine, a constituent of the natural ATP substrate.
The side chains of L210 and K162 are positioned inside the ATP-binding pocket. K162 is a catalytically important residue and is unable to make a salt bridge with D274 due to the formation of a unique hydrophobic binding pocket in the Aurora-2 catalytic active site. This lysine-glutamic acid salt bridge is seen in other kinase crystal structures.
FIG. 8 represents the binding pockets for each Aurora-2 complex in the present invention.
Example 7
The Use of Aurora-2 Coordinates for Inhibitor Design
The coordinates of any one of FIGS. 1-4 are used to design compounds, including inhibitory compounds, that associate with Aurora-1, Aurora-2, Aurora-3, or homologues of Aurora-1, Aurora-2 or Aurora-3. This process may be aided by using a computer comprising a machine-readable data storage medium encoded with a set of machine-executable instructions, wherein the recorded instructions are capable of displaying a three-dimensional representation of the Aurora-2 or a portion thereof. The graphical representation is used according to the methods described herein to design compounds. Such compounds associate with the Aurora-2 at the ATP-binding pocket or substrate binding pocket.
Example 8
Aurora-2 Activity Inhibition Assay
Compounds were screened for their ability to inhibit full length Aurora-2 (AA 1-403) activity using a standard coupled enzyme system (Fox et al., Protein Sci., 7, pp. 2249 (1998)). Reactions were carried out in a solution containing 100 mM HEPES (pH 7.5), 10 mM MgCl2, 25 mM NaCl, 300 μM NADH, 1 mM DTT and 3% DMSO. Final substrate concentrations in the assay were 200 μM ATP (Sigma Chemicals, St Louis, Mo.) and 800 μM peptide (LRRASLG, American Peptide, Sunnyvale, Calif.). Reactions were carried out at 30° C. and with 35 nM Aurora-2. Final concentrations of the components of the coupled enzyme system were 2.5 mM phosphoenolpyruvate, 200 μM NADH, 60 μg/ml pyruvate kinase and 20 μg/ml lactate dehydrogenase.
An assay stock buffer solution was prepared containing all of the reagents listed above with the exception of ATP and the test compound of interest. The assay stock buffer solution (60 μl) was incubated in a 96 well plate with 2 μl of the test compound of interest at final concentrations spanning 0.002 μM to 30 μM at 30° C. for 10 min. Typically, a 12 point titration was conducted by preparing serial dilutions (from 1 mM compound stocks) with DMSO of the test compounds in daughter plates. The reaction was initiated by the addition of 5 μl of ATP (final concentration 200 μM). Rates of reaction were obtained using a Molecular Devices Spectramax plate reader (Sunnyvale, Calif.) over 10 min at 30° C. The Ki values were determined from the rate data as a function of inhibitor concentration using computerized nonlinear regression (Prism 3.0, Graphpad Software, San Diego, Calif.).
Example 9
The Use of Aurora-2 Coordinates in the Design of Aurora-Specific Antibodies
The atomic coordinates in any one of FIGS. 1-4 also define, in great detail, the external solvent-accessible, hydrophilic, and mobile surface regions of the Aurora-2 catalytic kinase domain. Anti-peptide antibodies are known to react strongly against highly mobile regions but do not react with well-ordered regions of proteins. Mobility is therefore a major factor in the recognition of proteins by anti-peptide antibodies (J. A. Tainer et al., Nature, 312, pp. 127-134 (1984))
One skilled in the art would therefore be able to use the X-ray crystallography data to determine possible antigenic sites in the Aurora-2 kinase domain. Possible antigenic sites are exposed, small and mobile regions on the kinase surface which have atomic B-factors of greater than about 80 Å2 in FIGS. 1, 2, 3 and 4. This information can be used in conjunction with data from immunological studies to design and produce specific monoclonal or polyclonal antibodies.
This process may be aided by using a computer comprising a machine-readable data storage medium encoded with a set of machine-executable instructions, wherein the recorded instructions are capable of displaying a three-dimensional representation of the Aurora-2 or a portion thereof.







TABLE 1







Summary of data collection for Aurora-2 - (5-Cyclopropyl-2H-


pyrazol-3-yl)-(2-phenyl-quinazolin-4-yl)-amine complex










Source
ALS 5.0.2














Wavelength (Å)
1.1



Resolution (Å)
2.7



No. of Reflections
62,585/9,773



(measured/unique)



Completeness (%)
 99.4/99.4



(overall/outer shell)



I/σ(I)
23.1/1.9



(overall/outer shell)



Rmerge * (%)
 4.9/39



(overall/outer shell)



Molecules per asymmetric unit
1







Structure refinement










Resolution (Å)
30-2.7



No. of reflections
7381



R factor
26.3



Free R factor †
33.2



RMSD values
0.005/2.5° 



Bond lengths/angles







Space Group: P3221



Unit Cell: a = b = 87 Å, c = 76 Å; α = β = 90°, γ = 120°



* Rmerge = 100 × ΣhΣi @Ihi − <Ih> @/ΣhΣiIhi.



† The Free R factor was calculated with 7.9% of the data.













TABLE 2







Summary of data collection for Aurora-2 - (5-Methylthiazol-


2-yl)-(2-phenyl-quinazolin-4-yl)-amine complex










Source
Daresbury SRS 14.2














Wavelength (Å)
0.98



Resolution (Å)
2.5



No. of Reflections
113,308/12,094



(measured/unique)



Completeness (%)
 99.8/99.8



(overall/outer shell)



I/σ(I)
18.2/1.5



(overall/outer shell)



Rmerge * (%)
 8.2/46



(overall/outer shell)



Molecules per asymmetric unit
1







Structure refinement










Resolution (Å)
30-2.5



No. of reflections
9318



R factor
25.9



Free R factor ††
32.8



RMSD values
0.011/1.9° 



Bond lengths/angles







Space Group: P3221



Unit Cell: a = b = 87 Å, c = 76 Å; α = β = 90°, γ = 120°



* Rmerge = 100 × ΣhΣi @Ihi − <Ih> @/ΣhΣiIhi.



†† The Free R factor was calculated with 8.1% of the data.













TABLE 3







Summary of data collection for Aurora-2 - (5-Methyl-2H-pyrazol-


3-yl)-(2-(pyridin-3-ylmethylamino)-quinazolin-4-yl)-amine complex










Source
Daresbury SRS 14.2














Wavelength (Å)
0.98



Resolution (Å)
3.1



No. of Reflections
23,387/5,359



(measured/unique)



Completeness (%)
 99.8/99.8



(overall/outer shell)



I/σ(I)
15.9/2.5



(overall/outer shell)



Rmerge * (%)
 8.6/41



(overall/outer shell)



Molecules per asymmetric unit
1







Structure refinement










Resolution (Å)
30-3.3



No. of reflections
4409



R factor
23.6



Free R factor †††
29.1



RMSD values
 0.011/1.78°



Bond lengths/angles







Space Group: P3221



Unit Cell: a = b = 87 Å, c = 76 Å; α = β = 90°, γ = 120°



* Rmerge = 100 × ΣhΣi @Ihi − <Ih> @/ΣhΣiIhi.



††† The Free R factor was calculated with 4.3% of the data.













TABLE 4







Summary of data collection for Aurora-2 - adenosine complex










Source
EMBL Hamburg X31














Wavelength (Å)
0.8



Resolution (Å)
3.2



No. of Reflections
12,545/5,355



(measured/unique)



Completeness (%)
 96.5/96.5



(overall/outer shell)



I/σ(I)
14.5/1.2



(overall/outer shell)



Rmerge * (%)
 5.0/46.8



(overall/outer shell)



Molecules per asymmetric unit
1







Structure refinement










Resolution (Å)
20-3.2



No. of reflections
4016



R factor
26.4



Free R factor †††
31.7



RMSD values
 0.013/1.65°



Bond lengths/angles







Space Group: P3221



Unit Cell: a = b = 87 Å, c = 76 Å; α = β = 90°, γ =120°



* Rmerge = 100 × ΣhΣi @Ihi − <Ih> @/ΣhΣiIhi.



††† The Free R factor was calculated with 4.0% of the data.

## Claims

1. A method for designing, selecting and/or optimizing a chemical entity that binds to all or part of an Aurora-2 kinase binding pocket or protein comprising the steps of:
(a) employing the structural coordinates of said Aurora-2 kinase binding pocket or protein according to any one of FIGS. 1-4 to generate a three-dimensional model of said Aurora-2 kinase binding pocket or protein on a computer, wherein said computer comprises the means for generating said three-dimensional model;
(b) identifying a binding pocket for said chemical entity, wherein said binding pocket comprises: F133, I135, G136, R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, W277, S278, or V279 or combinations thereof; and
(c) employing the residues identified in (b) to design, select and/or optimize said chemical entity by performing a fitting operation between said chemical entity and said three-dimensional structural information of all or part of said binding pocket or protein.

2. A method for evaluating the ability of a chemical entity to associate with all or part of an Aurora-2 kinase binding pocket or protein comprising the steps of:
(a) employing the structural coordinates of said Aurora-2 kinase binding pocket or protein according to any one of FIGS. 1-4 to generate a three-dimensional model of said Aurora-2 kinase binding pocket or protein on a computer, wherein said computer comprises the means for generating said three-dimensional model;
(b) identifying a binding pocket for said chemical entity, wherein said binding pocket comprises: F133, I135, G136, R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, W277, S278, or V279 or combinations thereof;
(c) employing computational means to perform a fitting operation between the chemical entity and all or part of the binding pocket or protein identified in (b); and
(d) analyzing the results of said fitting operation to quantitate the association between the chemical entity and all or part of the binding pocket or protein.

3. A method of employing a computer for evaluating the ability of a chemical entity to associate with all or part of the binding pocket or protein of an Aurora-2 kinase, wherein said computer comprises a machine-readable data storage medium comprising a data storage material encoded with the structure coordinates of an Aurora-2 kinase binding pocket or protein according to any one of FIGS. 1-4 and means for generating a three-dimensional graphical representation of the binding pocket or protein, wherein said method comprises the steps of:
(a) employing the structural coordinates of said Aurora-2 kinase binding pocket or protein according to any one of FIGS. 1-4 to generate a three-dimensional model of said Aurora-2 kinase binding pocket or protein on said computer;
(b) identifying a binding pocket for said chemical entity, wherein said binding pocket comprises: F133, I135, G136, R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, W277, S278, or V279 or combinations thereof;
(c) employing computational means to perform a fitting operation between the chemical entity and all or part of the binding pocket or protein identified in (b); and
(d) analyzing the results of said fitting operation to quantitate the association between said chemical entity and all or part of the binding pocket or protein.

4. The method according to claim 3, further comprising the steps of:
(e) repeating steps (a) through (d) with a second chemical entity; and
(f) selecting at least one of said first or second chemical entity that associates with said all or part of said binding pocket or protein based on said quantitated association of said first or second chemical entity.

5. A method for identifying a potential agonist or antagonist of an Aurora-2 kinase or Aurora-2 kinase complex comprising the steps of:
(a) employing the structural coordinates of an Aurora-2 kinase binding pocket or protein according to any one of FIGS. 1-4 to generate a three-dimensional in silico model of said Aurora-2 kinase and to design or select a chemical entity,
wherein the binding pocket of said Aurora-2 kinase comprises: F133, I135, G136, R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, W277, S278, or V279 or combinations thereof;

(b) contacting the chemical entity with said Aurora-2 kinase or Aurora-2 kinase complex;
(c) monitoring the catalytic activity of said Aurora-2 kinase or Aurora-2 kinase complex; and
(d) classifying the chemical entity as an agonist or antagonist based on the effect of the chemical entity on the catalytic activity of said Aurora-2 kinase or Aurora-2 kinase complex.

6. A method of designing a compound or complex that associates with all or part of the binding pocket of an Aurora-2 kinase comprising the steps of:
(a) employing the structural coordinates of an Aurora-2 kinase binding pocket or protein according to any one of FIGS. 1-4 on a computer comprising the means for generating three-dimensional structural information from said structure coordinates;
(b) identifying a binding pocket for said chemical entity, wherein said binding pocket comprises: F133, I135, G136, R137, L139, G140, G142, F144, G145, N146, V147, Y148, L149, A150, R151, E152, I158, L159, A160, L161, K162, V163, V182, E183, Q185, H190, N192, I193, L194, R195, L196, Y197, G198, Y199, F200, V206, Y207, L208, I209, L210, E211, Y212, A213, P214, L215, T217, V218, Y219, R220, E221, D229, E230, Q231, R232, T233, A234, T235, Y236, I237, T238, E239, L240, A241, N242, A243, L244, S245, Y246, C247, H248, S249, K250, R251, V252, I253, H254, R255, D256, I257, K258, P259, E260, N261, L262, L263, L264, G265, S266, G268, E269, L270, K271, I272, A273, D274, F275, W277, S278, or V279 or combinations thereof;
(c) using the computer to perform a fitting operation to associate a first chemical entity with all or part of the binding pocket;
(d) performing a fitting operation to associate at least a second chemical entity with all or part of the binding pocket;
(e) quantifying the association between the first and second chemical entity and all or part of the binding pocket;
(f) optionally repeating steps (b) to (e) with another first and second chemical entity, selecting a first and a second chemical entity based on said quantified association of all of said first and second chemical entity;
(g) optionally, visually inspecting the relationship of the first and second chemical entity to each other in relation to the binding pocket on a computer screen using the three-dimensional graphical representation of the binding pocket and said first and second chemical entity; and
(h) assembling the first and second chemical entity into a compound or complex that associates with all or part of said binding pocket by model building.