US 2008/0293579 A1 · Crystal structure of polo-like kinase 3 (PLK3) and binding pockets thereof

Abstract

The invention relates to molecules or molecular complexes, which comprise binding pockets of PLK3 or its structural homologues. The invention relates to crystallizable compositions and crystals comprising PLK3. The present invention also relates to a data storage medium encoded with the structural coordinates of molecules and molecular complexes which comprise the PLK3 or PLK3-like ATP-binding pockets. The present invention also relates to a computer comprising such data storage material. The computer may generate a three-dimensional structure or graphical three-dimensional representation of such molecules or molecular complexes. This invention also relates to methods of using the structure coordinates to solve the structure of homologous proteins or protein complexes. In addition, this invention relates to methods of using the structure coordinates to screen for, identify and design compounds, including inhibitory compounds that bind to PLK3 or homologues thereof.

Claims20

Dependent claims

A crystal comprising an unphosphorylated Polo-Like Kinase 3 (PLK3) catalytic kinase domain complex.

A method of designing a compound which binds to a catalytic domain of a Polo-like Kinase 3 (PLK3) protein comprising a binding pocket, wherein said catalytic domain is characterized by:

(i) the atomic coordinates of amino acids 52-327 of SEQ ID NO:1 shown in FIG. 1 positioned within a rmsd of 1.2 Å or the atomic coordinates of amino acids 52-332 of SEQ ID NO:1 shown in FIG. 6 positioned within a rmsd of 1.2 Å;
(ii) the atomic coordinates of said binding pocket defined by amino acids L68, G69, K70, G71, G72, F73, A74, R75, C76, A89, K91, E110, H114, V123, L139, E140, L141, C142, S143, R144, K145, S146, H149, G189, N190, F192, D203 and F204 of FIG. 1 or FIG. 6 and which are within a rmsd of 1.2 Å;
(iii) the atomic coordinates of said binding pocket defined by amino acids R66, L67, L68, G69, K70, G71, G72, F73, A74, R75, C76, Y77, E78, Y88, A89, V90, K91, V92, I93, E110, H114, V123, R124, I137, L139, E140, L141, C142, S143, R144, K145, S146, L147, A148, H149, L188, G189, N190, F191, F192, I193, T194, E195, K200, V201, G202 and D203 of FIG. 1 or FIG. 6 and which are within a rmsd of 1.2 Å;
(iv) the atomic coordinates of said binding pocket defined by amino acids R66, L67, L68, G69, K70, G71, G72, F73, A74, R75, C76, Y77, E78, Y88, A89, V90, K91, V92, I93, Q103, K106, I107, E110, I111, H114, V123, R124, F125, I137, F138, L139, E140, L141, C142, S143, R144, K145, S146, L147, A148, H149, W151, K152, H183, D185, K187, L188, G189, N190, F191, F192, I193, T194, E195, K200, V201, G202, D203, F204, G205, L206, T223 and Y226 of FIG. 1 or FIG. 6 and which are within a rmsd of 1.0 Å;
or
(v) the atomic coordinates of said binding pocket defined by amino acids L68, H114, V123, L139, E140, C142, K145 and F192 of FIG. 1 or FIG. 6 and which are within a rmsd of 1.0 Å;
said method comprising the steps of:
(a) using the atomic coordinates of FIG. 1 or FIG. 6 to build a 3-D computer model of a compound interaction region of said protein comprising at least one of (i)-(v);
(b) assessing the stereochemical complementarity between a compound and said interaction region;
(c) optimizing said stereochemical complementarity in an iterative approach by observing changes in the protein or compound that affect the protein/compound associations;
and
(d) designing a compound which optimizes said protein/compound stereochemical complementarity.

9 more elements

A method of identifying a potential inhibitor of a Polo-like Kinase 3 (PLK3) protein comprising a binding pocket, wherein said method comprising the steps of:

(a) using the structure coordinates of FIG. 1 or FIG. 6 to generate a three-dimensional model;
(b) identifying said binding pocket residues, and using said residues to generate a specific three-dimensional (3-D) target;
(c) employing said 3-D target of (b) to design or select said potential inhibitor;
(d) obtaining said potential inhibitor;
and
(e) contacting said potential inhibitor with said Polo-like Kinase 3 (PLK3) protein in vitro to determine the ability of said potential inhibitor to interact with said Polo-like Kinase 3 (PLK3) protein;
whereby the ability to interact is an indication that said potential inhibitor of said Polo-like Kinase 3 (PLK3) protein is identified.

4 more elements

A method for identifying a candidate inhibitor of a molecule or molecular complex comprising a binding pocket or domain selected from the group consisting of:

(i) a set of amino acid residues that are identical to human Polo-like Kinase 3 (PLK3) amino acid residues of said binding pocket according to FIG. 1 or FIG. 6, wherein the root mean square deviation of the backbone atoms between said set of amino acid residues and said human Polo-like Kinase 3 (PLK3) amino acid residues is not greater than about 1.0 Å;
and
(ii) a set of amino acid residues that are identical to human Polo-like Kinase 3 (PLK3) amino acid residues according to FIG. 1 or FIG. 6, wherein the root mean square deviation between said set of amino acid residues and said human Polo-like Kinase 3 (PLK3) amino acid residues is not more than about 1.0 Å;
comprising the steps of:
(a) using a three-dimensional structure of the binding pocket or domain to design, select or optimize a plurality of chemical entities;
(b) contacting each chemical entity with the molecule or the molecular complex;
(c) monitoring the inhibition to the catalytic activity of the molecule or molecular complex by each chemical entity;
and
(d) selecting a chemical entity based on the inhibitory effect of the chemical entity on the catalytic activity of the molecule or molecular complex.

6 more elements

A method for identifying a candidate inhibitor that interacts with a binding site of a human Polo-Like Kinase 3 (PLK3) protein or a homologue thereof, comprising the steps of:

(a) obtaining a crystal comprising said human Polo-Like Kinase 3 (PLK3) protein, wherein the crystal is characterized with space group C2 and has unit cell parameters of a=146 Å, b=59 Å, c=47 Å;
β=95°;
(b) obtaining the structure coordinates of amino acids of the crystal of step (a);
(c) generating a three-dimensional model of said human Polo-Like Kinase 3 (PLK3) protein or said homologue thereof using the structure coordinates of the amino acids generated in step (b), a root mean square deviation from backbone atoms of said amino acids of not more than ±1.0 Å;
(d) determining a binding site of said human Polo-Like Kinase 3 (PLK3) protein or said homologue thereof from said three-dimensional model;
and
(e) performing computer fitting analysis to design or identify the candidate inhibitor which interacts with said binding site.
(f) contacting the designed or identified candidate inhibitor with said human Polo-Like Kinase 3 (PLK3) protein or said homologue thereof in vitro in order to determine the effect of the inhibitor on human Polo-Like Kinase 3 (PLK3) protein activity.

5 more elements

Dependencies are inferred from the claim text.

Crystal structure of polo-like kinase 3 (PLK3) and binding pockets thereof

Life of this patent

Crystal structure of polo-like kinase 3 (PLK3) and binding pockets thereof

Life of this patent

Abstract

Claims20