US 7,065,452 B1Granted

Molecules comprising a calcineurin-like binding pocket and encoded data storage medium capable of graphically displaying them

AssigneeVertex Pharmaceuticals Incorporated

InventorsDavid M. Armistead, Matthew James Fitzgibbon, Mark Andrew Fleming, James P. Griffith, Eunice E. Kim, Joseph L. Kim, Michael D. Sintchak, John Allan Thomson, Keith P. Wilson

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Abstract

The present invention relates to crystallized molecules and molecular complexes which comprise the active site binding pocket or the FKBP12/FK506 binding pocket of calcineurin or close structural homologues to either binding pocket. This invention also relates to a data storage material encoded with the corresponding structure coordinates of those crystallized molecules or molecular complexes. Such data storage material is capable of displaying such molecules and molecular complexes as a graphical three-dimensional representation on a computer screen. In addition, this invention relates to methods of using the structure coordinates of those molecules or molecular complexes to solve the structure of homologous proteins. This invention also relates to methods of using the structure coordinates to screen and design compounds that bind to calcineurin or homologues thereof.

Claims8

Dependent claims

A method of using a computer for selecting at least one of a plurality of chemical entities based on its ability to associate with all or part of a molecule or molecular complex comprising a calcineurin A (CnA) binding pocket defined by structure coordinates of CnA amino acids 90, 91, 92, 118, 120, 121, 122, 150, 151, 156, 160, 199, 232, 253, 254, 256, 281, 282, 283, 284, 306, 311, 312, and 317 according to FIG. 1;

wherein said computer comprises a machine-readable data storage medium comprising a data storage material encoded with said structure coordinates and wherein said method comprises the steps of:
a) producing a crystal of a molecular complex comprising amino acids 17–392 of CnA and amino acids 1–169 of CnB;
intact FKBP12;
and FK506;
b) determining the three-dimensional structure coordinates of the molecular complex by X-ray diffraction of the crystal;
c) identifying the structural coordinates of a CnA binding pocket of said molecular complex of CnA amino acids 90, 91, 92, 118, 120, 121, 122, 150, 151, 156, 160, 199, 232, 253, 254, 256, 281, 282, 283, 284, 306, 311, 312, and 317, which coordinates fall within the range of those recited in FIG. 1±a root mean square deviation from the backbone atoms of said amino acids of 1.5 Å and encoding those coordinates on a data storage material;
d) utilizing said structure coordinates defining said CnA binding pocket and the structure coordinates of one of said plurality of chemical entities to position a chemical entity within all or part of the CnA binding pocket;
e) docking said chemical entity with all or part of the CnA binding pocket by employing computational means which utilize said structure coordinates defining said CnA binding pocket and the chemical entity, wherein said docking utilizes energy minimization;
f) analyzing the results of said docking to quantify the association between said chemical entity and all or part of the CnA binding pocket;
g) optionally repeating steps d) through f) with another of said plurality of chemical entities;
and
h) selecting at least one of said plurality of chemical entities that associates with all or part of the CnA binding pocket based on said quantified association of said chemical entity.

9 more elements

A method of using a computer for selecting at least one of a plurality of chemical entities based on its ability to associate with all or part of a molecule or molecular complex comprising a calcineurin A (CnA) binding pocket defined by structure coordinates of CnA amino acids 90, 91, 92, 118, 120, 121, 122, 150, 151, 156, 160, 199, 281, 282, 283, 306, 311, 232, and 254 according to FIG. 1;

wherein said computer comprises a machine-readable data storage medium comprising a data storage material encoded with said structure coordinates and wherein said method comprises the steps of:
a) producing a crystal of a molecular complex comprising amino acids 17–392 of CnA and amino acids 1–169 of CnB;
intact FKBP12;
and FK506;
b) determining the three-dimensional structure coordinates of the molecule or molecular complex by X-ray diffraction of the crystal;
c) identifying a CnA binding pocket of said molecule or molecular complex defined by structure coordinates of CnA amino acids 90, 91, 92, 118, 120, 121, 122, 150, 151, 156, 160, 199, 281, 282, 283, 306, 311, 232, and 254, which coordinates fall within the range of those recited in FIG. 1±a root mean square deviation from the backbone atoms of said amino acids of 1.5 Å and encoding those coordinates on a data storage material;
d) utilizing said structure coordinates defining said CnA binding pocket and the structure coordinates of one of said plurality of chemical entities to position a chemical entity within all or part of the CnA binding pocket;
e) docking said chemical entity with all or part of the CnA binding pocket by employing computational means which utilize said structure coordinates defining said CnA binding pocket and the chemical entity, wherein said docking utilizes energy minimization;
f) analyzing the results of said docking to quantify the association between said chemical entity and all or part of the CnA binding pocket;
g) optionally repeating steps d) through f) with another of said plurality of chemical entities;
and
h) selecting at least one of said plurality of chemical entities that associates with all or part of the CnA binding pocket based on said quantified association of said chemical entity.

9 more elements

A method of using a computer for selecting at least one of a plurality of chemical entities based on its ability to associate with all or part of a molecule or molecular complex comprising a CnA/CnB binding pocket defined by structure coordinates of CnA amino acids 122, 124, 159, 160, 310, 312, 313, 314, 339, 341, 343, 344, 345, 347, 351, 352, 353, 354, 355, 356, 359, 360, and 363;

and calcineurin B (CnB) amino acids 49, 50, 114, 115, 118, 119, 121, 122, 123, 124, 157, 158, 159, 161, and 162 according to FIG. 1;
wherein said computer comprises a machine-readable data storage medium comprising a data storage material encoded with said structure coordinates and wherein said method comprises the steps of:
a) producing a crystal of a molecular complex comprising amino acids 17–392 of CnA and amino acids 1–169 of CnB;
intact FKBP12;
and FK506;
b) determining the three-dimensional structure coordinates of the molecule or molecular complex by X-ray diffraction of the crystal;
c) identifying a CnA/CnB binding pocket of said molecule or molecular complex defined by structure coordinates of CnA amino acids 122, 124, 159, 160, 310, 312, 313, 314, 339, 341, 343, 344, 345, 347, 351, 352, 353, 354, 355, 356, 359, 360, and 363;
and calcineurin B (CnB) amino acids 49, 50, 114, 115, 118, 119, 121, 122, 123, 124, 157, 158, 159, 161, and 162, which coordinates fall within the range of those recited in FIG. 1±a root mean square deviation from the backbone atoms of said amino acids of 1.5 Å and encoding those coordinates on a data storage material;
d) utilizing said structure coordinates defining said CnA/CnB binding pocket and the structure coordinates of one of said plurality of chemical entities to position a chemical entity within all or part of the CnA/CnB binding pocket;
e) docking said chemical entity with all or part of the CnA/CnB binding pocket by employing computational means which utilize said structure coordinates defining said CnA/CnB binding pocket and the chemical entity, wherein said docking utilizes energy minimization;
f) analyzing the results of said docking to quantify the association between said chemical entity and all or part of the CnA/CnB binding pocket;
g) optionally repeating steps d) through f) with another of said plurality of chemical entities;
and
h) selecting at least one of said plurality of chemical entities that associates with all or part of the CnA/CnB binding pocket based on said quantified association of said chemical entity.

11 more elements

A method of using a computer for selecting at least one of a plurality of chemical entities based on its ability to associate with all or part of a molecule or molecular complex comprising a CnA/CnB binding pocket defined by structure coordinates of CnA amino acids 90, 91, 92, 118, 120, 121, 122, 124, 150, 151, 156, 159, 160, 199, 232, 253, 254, 256, 281, 282, 283, 284, 306, 310, 311, 312, 313, 314, 317, 339, 341, 343, 344, 345, 347, 351, 352, 353, 354, 355, 356, 359, 360, and 363;

and CnB amino acids 49, 50, 114, 115, 118, 119, 121, 122, 123, 124, 157, 158, 159, 161, and 162 according to Figure;
wherein said computer comprises a machine-readable data storage medium comprising a data storage material encoded with said structure coordinates and wherein said method comprises the steps of:
a) producing a crystal of a molecular complex comprising amino acids 17–392 of CnA and amino acids 1–169 of CnB;
intact FKBP12;
and FK506;
b) determining the three-dimensional structure coordinates of the molecule or molecular complex by X-ray diffraction of the crystal;
c) identifying a CnA/CnB binding pocket of said molecule or molecular complex defined by structure coordinates of CnA amino acids 90, 91, 92, 118, 120, 121, 122, 124, 150, 151, 156, 159, 160, 199, 232, 253, 254, 256, 281, 282, 283, 284, 306, 310, 311, 312, 313, 314, 317, 339, 341, 343, 344, 345, 347, 351, 352, 353, 354, 355, 356, 359, 360, and 363;
and CnB amino acids 49, 50, 114, 115, 118, 119, 121, 122, 123, 124, 157, 158, 159, 161, and 162, which coordinates fall within the range of those recited in FIG. 1±a root mean square deviation from the backbone atoms of said amino acids of 1.5 Å and encoding those coordinates on a data storage material;
d) utilizing said structure coordinates defining said CnA/CnB binding pocket and the structure coordinates of one of said plurality of chemical entities to position a chemical entity within all or part of the CnA/CnB binding pocket;
e) docking said chemical entity with all or part of the CnA/CnB binding pocket by employing computational means which utilize said structure coordinates defining said CnA/CnB binding pocket or structure coordinates of the chemical entity, wherein said docking utilizes energy minimization;
f) analyzing the results of said docking to quantify the association between said chemical entity and all or part of the CnA/CnB binding pocket;
g) optionally repeating steps d) through f) with another of said plurality of chemical entities;
and
h) selecting at least one of said plurality of chemical entities that associates with all or part of the CnA/CnB binding pocket based on said quantified association of said chemical entity.

11 more elements

Dependencies are inferred from the claim text.