Protein kinase regulation

The method of any of the previous claims wherein the interaction is an interaction of the hydrophobic pocket of the said protein kinase with the polypeptide comprising the amino acid sequence Phe/Tyr-Xaa-Xaa-Phe/Tyr.

The method of any of the previous claims wherein the interacting polypeptide is part of the same polypeptide chain as the protein kinase.

The method of any of the preceding claims wherein the ability of the compound to inhibit, promote or mimic the interaction of the protein kinase with the interacting polypeptide is measured using surface plasmon resonance.

A method of selecting or designing a compound that modulates the activity of a hydrophobic pocket-containing protein kinase as defined in any of the preceding claims, the method comprising the step of using molecular modelling means to select or design a compound that is predicted to interact with the said hydrophobic pocket-containing protein kinase, wherein a three-dimensional structure of a compound is compared with a three-dimensional structure of the said hydrophobic pocket and/or with a three-dimensional structure of an interacting polypeptide as defined in any of the preceding claims, and a compound that is predicted to interact with the said hydrophobic pocket is selected.

A mutated protein kinase, wherein the protein kinase before mutation has a hydrophobic pocket in the position equivalent to the hydrophobic pocket of mouse Protein Kinase A (PKA) that is defined by residues including Lys76, Leu116, Val80 and/or Lys111 of full-length mouse PKA, and wherein one or more residues defining the hydrophobic pocket of the protein kinase is mutated.

A method of phosphorylating p70 S6 kinase on the residue equivalent to Thr412 of full length human p70 S6 kinase wherein the said p70 S6 kinase is exposed to recombinant PDK1.

A method of identifying a compound that modulates the activation and/or phosphorylation of p70 S6 kinase on the residue equivalent to Thr412 of full length human p70 S6 kinase by PDK1 wherein the activation and/or phosphorylation of p70 S6 kinase on the residue equivalent to Thr412 of full length human p70 S6 kinase by PDK1 is measured in the presence of more than one concentration of the compound.

A polypeptide comprising the amino acid sequence Phe/Tyr-Xaa-Xaa-Phe/Tyr, wherein said polypeptide does not comprise the amino acid sequence Phe/Tyr-Xaa-Xaa-Phe/Tyr-Zaa-Phe/Tyr or Phe/Tyr-Xaa-Xaa-Phe/Tyr-Ser/Thr-Phe/Tyr and is not full-length PKA.

A method of identifying a compound that modulates the protein kinase activity of a protein kinase having a hydrophobic pocket in the position equivalent to the hydrophobic pocket of mouse Protein Kinase A (PKA) that is defined by residues including Lys76, Leu116, Val80 and/or Lys111 of full-length mouse PKA comprising the steps of (1) determining the effect of a test compound on the protein kinase activity of the said protein kinase, and/or a mutant thereof, and (2) selecting a compound capable of modulating the protein kinase activity of the said protein kinase to different extents towards (i) a substrate that binds to the said hydrophobic pocket of the said protein kinase (hydrophobic pocket-dependent substrate) and (ii) a substrate (such as PKB) that does not bind, or binds to a lesser extent than the first said substrate (hydrophobic pocket-independent substrate), to the said hydrophobic pocket of the said protein kinase.

A method of identifying a compound that modulates the protein kinase activity of a protein kinase having a hydrophobic pocket in the position equivalent to the hydrophobic pocket of mouse Protein Kinase A (PKA) that is defined by residues including Lys76, Leu116, Val80 and/or Lys111 of full-length mouse PKA (for example PDK1), comprising the step of determining the effect of the compound on the protein kinase activity of, or ability of the compound to bind to (1) the said protein kinase mutated at a residue defining at least part of the said hydrophobic pocket of the protein kinase, for example the residue equivalent to lysine 76 of full-length mouse PKA.

The use of a compound capable of inhibiting to a different extents the rate or degree of phosphorylation by a protein kinase having a hydrophobic pocket in the position equivalent to the hydrophobic pocket of mouse Protein Kinase A (PKA) that is defined by residues including Lys76, Leu116, Val80 and/or Lys111 of full-length mouse PKA (for example PDK1), of (1) a hydrophobic pocket-dependent substrate and (2) a hydrophobic pocket-independent substrate of the protein kinase, in the manufacture of a medicament for the treatment of a patient in need of inhibition to different extents of (1) phosphorylation of a hydrophobic pocket-dependent substrate of the said protein kinase and (2) phosphorylation of a hydrophobic pocket-dependent substrate of the said protein kinase.