Factor IXa Crystals, Related Complexes and Methods
AssigneeSchering Corporation
InventorsBRIAN M. BEYER, ALAN W. HRUZA, RICHARD N. INGRAM, VINCENT S. MADISON, ANDREW J. PRONGAY, PAUL REICHERT
Life of this patent
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Abstract
The present invention relates to factor IXa complexes and crystals thereof as well as methods for identifying inhibitors of factor IXa.
Claims9
1-16. (canceled)
A method for determining the structure of a complex comprising a compound bound to factor IXa protein, said method comprising:
- (a) mixing the factor IXa protein with the compound;
- (b) crystallizing a factor IXa protein-compound complex;
- and (c) determining the structure of the complex by employing the data of any one of Tables 2-6 optionally varied by a root mean square deviation of conserved residue backbone atoms or of alpha carbon atoms of less than about 1.5 Å when superimposed on backbone atoms described in Table 2, 3, 4, 5 or 6.
A method for identifying a substance which inhibits blood clotting or binds to factor IXa comprising
- (a) mixing factor IXa protein with the substance;
- (b) crystallizing a factor IXa protein-substance complex;
- and
- (c) determining the structure of the complex by employing the data of any one of Tables 2-6 optionally varied by a root mean square deviation of conserved residue backbone atoms or of alpha carbon atoms of less than about 1.5 Å when superimposed on backbone atoms described in Table 2, 3, 4, 5 or 6;
- and, if said substance is observed to complex with factor IXa;
- optionally determining if the substance selectively inhibits factor IXa proteolytic activity but not factor Xa proteolytic activity;
- wherein the substance is identified as a blot clotting inhibitor or factor IXa binding substance if said complex and/or selective inhibition is observed.
A method for determining the structure of a complex comprising a second compound bound to factor IXa protein which is complexed with a first compound, said method comprising;
- (a) providing a crystal of factor IXa protein complexed with the first compound;
- (b) soaking the crystal comprising the first compound with a second compound to form a complex between said factor IXa protein and said second compound;
- and (c) determining the structure of the complex comprising the second compound by employing the structural data of any one of Tables 2-6 optionally varied by a root mean square deviation of conserved residue backbone atoms or of alpha carbon atoms of less than about 1.5 Å when superimposed on backbone atoms described in Table 2, 3, 4, 5 or 6.
A method for identifying a substance which inhibits blood clotting or binds to factor IXa comprising
- (a) providing a crystal of factor IXa protein complexed with a first substance;
- (b) soaking the crystal comprising the first substance with a second substance to form a complex between said factor IXa protein and said second substance;
- and (c) determining the structure of the complex comprising the second substance by employing the data of any one of Tables 2-6 optionally varied by a root mean square deviation of conserved residue backbone atoms or of alpha carbon atoms of less than about 1.5 Å when superimposed on backbone atoms described in Table 2, 3, 4, 5 or 6;
- and, if second said substance is observed to complex with factor IXa, optionally determining if the second substance selectively inhibits factor IXa proteolytic activity but not factor Xa proteolytic activity;
- wherein the second substance is identified as a blot clotting inhibitor or factor IXa binder if said complex and/or selective inhibition is observed.
23-27. (canceled)
A method for identifying a substance which binds to factor IXa or inhibits blood clotting comprising:
- determining the structure of a complex comprising a compound represented by structural formula A, B, C or D by employing the data of any one of Tables 2-6 optionally varied by a root mean square deviation of conserved residue backbone atoms or of alpha carbon atoms of less than about 1.5 Å when superimposed on backbone atoms or alpha carbon atoms described in Table 2, 3, 4, 5 or 6;
- and, employing a computational means to dock a candidate substance with the factor IXa serine protease domain to determine if said candidate substance binds to said serine protease domain;
- and, optionally, synthesizing said candidate substance;
- and, optionally, determining if said candidate substance binds to factor IXa or inhibits factor IXa proteolytic activity.
Dependencies are inferred from the claim text.